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Shi Y, Tan Q, Gong T, Li QY, Zhu Y, Duan X, Yang C, Ding JW, Li S, Xie H, Li Y, Chen L. Cascaded signal amplification strategy for ultra-specific, ultra-sensitive, and visual detection of Shigella flexneri. Mikrochim Acta 2024; 191:271. [PMID: 38632191 DOI: 10.1007/s00604-024-06309-0] [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: 12/20/2023] [Accepted: 03/03/2024] [Indexed: 04/19/2024]
Abstract
Pathogen infections including Shigella flexneri have posed a significant threat to human health for numerous years. Although culturing and qPCR were the gold standards for pathogen detection, time-consuming and instrument-dependent restrict their application in rapid diagnosis and economically less-developed regions. Thus, it is urgently needed to develop rapid, simple, sensitive, accurate, and low-cost detection methods for pathogen detection. In this study, an immunomagnetic beads-recombinase polymerase amplification-CRISPR/Cas12a (IMB-RPA-CRISPR/Cas12a) method was built based on a cascaded signal amplification strategy for ultra-specific, ultra-sensitive, and visual detection of S. flexneri in the laboratory. Firstly, S. flexneri was specifically captured and enriched by IMB (Shigella antibody-coated magnetic beads), and the genomic DNA was released and used as the template in the RPA reaction. Then, the RPA products were mixed with the pre-loaded CRISPR/Cas12a for fluorescence visualization. The results were observed by naked eyes under LED blue light, with a sensitivity of 5 CFU/mL in a time of 70 min. With no specialized equipment or complicated technical requirements, the IMB-RPA-CRISPR/Cas12a diagnostic method can be used for visual, rapid, and simple detection of S. flexneri and can be easily adapted to monitoring other pathogens.
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Affiliation(s)
- Yaoqiang Shi
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Qi Tan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Tao Gong
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Qing-Yuan Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Ya Zhu
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Xiaoqiong Duan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Chunhui Yang
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Jia-Wei Ding
- Clinical Laboratory Department, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, China
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - He Xie
- The Hospital of Xidian Group, Xi'an, 710077, China
| | - Yujia Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China.
| | - Limin Chen
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China.
- The Joint Laboratory On Transfusion-Transmitted Diseases (TTDs) Between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Nanning, 530007, China.
- The Hospital of Xidian Group, Xi'an, 710077, China.
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Liu H, Chen P, Yang YL, Zhu KW, Wang T, Tang L, Liu YL, Cao S, Zhou G, Zeng H, Zhao XL, Zhang W, Chen XP. TBC1D16 predicts chemosensitivity and prognosis in adult acute myeloid leukemia (AML) patients. Eur J Pharmacol 2021; 895:173894. [PMID: 33476656 DOI: 10.1016/j.ejphar.2021.173894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
Acute myeloid leukemia (AML) is a hematopoietic disease with poor survival. Chemotherapy resistance is one of the determinant factors influencing AML prognosis. To identify genes possibly affecting the drug responses in AML, the Illumina Infinium MethylationEPIC (850K) was used to screen for differential DNA methylation loci between patients achieved complete remission (CR) or not (non-CR) after induction therapy in 37 AML patients. Then, 32 differentially methylated sites (DMS) were selected for replication in another 86 AML patients by next-generation sequencing. Nine sites including cg03988660, cg16804603, cg18166936, cg11308319, cg09095403, cg18493214, cg01443536, cg16030878 and cg10143426 were replicated. Analysis of the Gene Expression Omnibus (GEO) database showed that mRNA expression of TBC1D16 and HDAC4 was associated with AML prognosis. Methylation level of the cg16030878 in TBC1D16 3'-UTR correlated positively with TBC1D16 mRNA expression in samples both in the TCGA database and clinically collected in the study. Both higher cg16030878 methylation and higher TBC1D16 mRNA expression were associated with increased risk of non-CR and worse overall survival (OS) in AML patients. In AML cells, knockdown of TBC1D16 decreased cell proliferation and ERK phosphorylation levels, as well as increased sensitivity to mitoxantrone and decitabine indicated by IC50. In patients with combined use of decitabine, those patients with CR showed significantly lower TBC1D16 mRNA expression. On the contrary, knockdown of TBC1D16 resulted in decreased sensitivity to cytarabine in U937 cells. Our findings implicated that TBC1D16 is a potential predictor for chemosensitivity and prognosis in adult AML patients.
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Affiliation(s)
- Han Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Peng Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Yong-Long Yang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Ke-Wei Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Tao Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Ling Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Yan-Ling Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Shan Cao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Gan Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Hui Zeng
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China.
| | - Xie-Lan Zhao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China.
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China.
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, Hunan, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, PR China.
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3
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Wang Z, Zhang Y, Zhu S, Peng H, Chen Y, Cheng Z, Liu S, Luo Y, Li R, Deng M, Xu Y, Hu G, Chen L, Zhang G. A small molecular compound CC1007 induces cross-lineage differentiation by inhibiting HDAC7 expression and HDAC7/MEF2C interaction in BCR-ABL1 - pre-B-ALL. Cell Death Dis 2020; 11:738. [PMID: 32913188 PMCID: PMC7483467 DOI: 10.1038/s41419-020-02949-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
Histone deacetylase 7 (HDAC7), a member of class IIa HDACs, has been described to be an important regulator for B cell development and has a potential role in B cell acute lymphoblastic leukemia (B-ALL). CC1007, a BML-210 analog, is designed to indirectly inhibit class IIa HDACs by binding to myocyte enhancer factor-2 (MEF2) and blocking the recruitment of class IIa HDACs to MEF2-targeted genes to enhance the expression of these targets. In this study, we investigated the anticancer effects of CC1007 in breakpoint cluster region-Abelson 1 fusion gene-negative (BCR-ABL1−) pre-B-ALL cell lines and primary patient-derived BCR-ABL1− pre-B-ALL cells. CC1007 had obvious antileukemic activity toward pre-B-ALL cells in vitro and in vivo; it also significantly prolonged median survival time of pre-B-ALL-bearing mice. Interestingly, low dose of CC1007 could inhibit proliferation of BCR-ABL1− pre-B-ALL cells in a time-dependent manner not accompanied by significant cell apoptosis, but along with cross-lineage differentiation toward monocytic lineage. From a mechanistic angle, we showed that HDAC7 was overexpressed in BCR-ABL1− pre-B-ALL cells compared to normal bone marrow samples, and CC1007 could reduce the binding of HDAC7 at the promoters of monocyte–macrophage-specific genes via inhibition of HDAC7 expression and HDAC7:MEF2C interaction. These data indicated that CC1007 may be a promising agent for the treatment of BCR-ABL1− pre-B-ALL.
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Affiliation(s)
- Zhihua Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yang Zhang
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shicong Zhu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yongheng Chen
- Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Zhao Cheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Sufang Liu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yunya Luo
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Ruijuan Li
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Mingyang Deng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yunxiao Xu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Guoyu Hu
- Department of Hematology, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, Hunan, China
| | - Lin Chen
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Guangsen Zhang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China.
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4
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Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients. Sci Rep 2020; 10:2070. [PMID: 32034196 PMCID: PMC7005734 DOI: 10.1038/s41598-020-58819-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/29/2019] [Indexed: 02/05/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is featured with complex genomic alterations. Molecular profiling of large cohort of NSCLC patients is thus a prerequisite for precision medicine. We first validated the detection performance of a next-generation sequencing (NGS) cancer hotspot panel, OncoAim, on formalin-fixed paraffin-embedded (FFPE) samples. We then utilized OncoAim to delineate the genomic aberrations in Chinese NSCLC patients. Overall detection performance was powerful for mutations with allele frequency (MAF) ≥ 5% at >500 × coverage depth, with >99% sensitivity, high specificity (positive predictive value > 99%), 94% accuracy and 96% repeatability. Profiling 422 NSCLC FFPE samples revealed that patient characteristics, including gender, age, lymphatic spread, histologic grade and histologic subtype were significantly associated with the mutation incidence of EGFR and TP53. Moreover, RTK signaling pathway activation was enriched in adenocarcinoma, while PI(3)K pathway activation, oxidative stress pathway activation, and TP53 pathway inhibition were more prevalent in squamous cell carcinoma. Additionally, novel co-existence (e.g., variants in BRAF and PTEN) and mutual-exclusiveness (e.g., alterations in EGFR and NFE2L2) were found. Finally, we revealed distinct mutation spectrum in TP53, as well as a previously undervalued PTEN aberration. Our findings could aid in improving diagnosis, prognosis and personalized therapeutic decisions of Chinese NSCLC patients.
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Diness BR, Risom L, Frandsen TL, Hansen B, Andersen MK, Schmiegelow K, Wadt KAW. Putative new childhood leukemia cancer predisposition syndrome caused by germline bi-allelic missense mutations in DDX41. Genes Chromosomes Cancer 2018; 57:670-674. [PMID: 30144193 DOI: 10.1002/gcc.22680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 08/13/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
DDX41 has recently been identified as a new autosomal dominantly inherited cancer predisposition syndrome causing increased risk of adult onset acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). We report for the first time compound heterozygote germline missense DDX41 mutations located in the DEAD-box domain, identified in two siblings by exome sequencing. Both siblings have slight dysmorphic findings, psychomotor delays and intellectual disability, and one developed blastic plasmacytoid dendritic cell neoplasm (BPDCN) at age five. RNA-sequencing of bone marrow showed DDX41 expression including both mutations. However, the allele fraction of p.Pro321Leu accounted for 96% in the RNA-sequencing indicating this mutation to be the more significant variant. Exome sequencing of the leukemic blasts identified no additional known driver mutations. There is no pattern indicating autosomal dominantly inherited cancer predisposition in the family, but the father has sarcoidosis, which has been associated with heterozygous DDX41 mutation. We propose that bi-allelic mutations in DDX41 could potentially be a new cancer predisposition syndrome associated with delayed psychomotor development.
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Affiliation(s)
- Birgitte R Diness
- Department of Clinical Genetics, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lotte Risom
- Department of Clinical Genetics, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas L Frandsen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Bente Hansen
- Department of Pediatrics, Nordsjaellands Hospital, Hillerød, Denmark
| | - Mette K Andersen
- Department of Clinical Genetics, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Karin A W Wadt
- Department of Clinical Genetics, University Hospital Rigshospitalet, Copenhagen, Denmark
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Slattery ML, Pellatt AJ, Lee FY, Herrick JS, Samowitz WS, Stevens JR, Wolff RK, Mullany LE. Infrequently expressed miRNAs influence survival after diagnosis with colorectal cancer. Oncotarget 2017; 8:83845-83859. [PMID: 29137387 PMCID: PMC5663559 DOI: 10.18632/oncotarget.19863] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022] Open
Abstract
Half of miRNAs expressed in colorectal tissue are expressed < 50% of the population. Many infrequently expressed miRNAs have low levels of expression. We hypothesize that less frequently expressed miRNAs, when expressed at higher levels, influence both disease stage and survival after diagnosis with colorectal cancer (CRC); low levels of expression may be background noise. We examine 304 infrequently expressed miRNAs in 1893 population-based cases of CRC with paired carcinoma and normal mucosa miRNA profiles. We evaluate miRNAs with disease stage and survival after adjusting for age, study center, sex, MSI status, and AJCC stage. These miRNAs were further evaluated with RNA-Seq data to identify miRNA::mRNA associations that may provide insight into the functionality of miRNAs. Eleven miRNAs were associated with advanced disease stage among colon cancer patients (Q value = 0.10). Eight infrequently expressed miRNAs influenced survival if highly expressed in overall CRC. Of these, five increased likelihood of dying if they were highly expressed, i.e. miR-124-3p, miR-143-5p, miR-145-3p, miR31-5p, and miR-99b-5p, while three were associated with better survival if highly expressed, i.e. miR-362-5p, miR-374a-5p, and miR-590-5p. Thirteen miRNAs infrequently expressed in colon-specific carcinoma tissue were associated with CRC survival if highly expressed. Evaluation of miRNAs::mRNA associations showed that mRNA expression influenced by infrequently expressed miRNA contributed to networks and pathways shown to influence disease progression and prognosis. Our large study enabled us to examine the implications of infrequently expressed miRNAs after removal of background noise. These results require replication in other studies. Confirmation of our findings in other studies could lead to important markers for prognosis.
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Affiliation(s)
- Martha L Slattery
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | | | | | | | - Wade S Samowitz
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, Utah, USA
| | - Roger K Wolff
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Lila E Mullany
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
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Slattery ML, Lee FY, Pellatt AJ, Mullany LE, Stevens JR, Samowitz WS, Wolff RK, Herrick JS. Infrequently expressed miRNAs in colorectal cancer tissue and tumor molecular phenotype. Mod Pathol 2017; 30:1152-1169. [PMID: 28548123 PMCID: PMC5537006 DOI: 10.1038/modpathol.2017.38] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 12/16/2022]
Abstract
We have previously shown that commonly expressed miRNAs influenced tumor molecular phenotype in colorectal cancer. We hypothesize that infrequently expressed miRNAs, when showing higher levels of expression, help to define tumor molecular phenotype. In this study, we examine 304 miRNAs expressed in at least 30 individuals, but in <50% of the population and with a mean level of expression above 1.0 relative florescent unit. We examine associations in 1893 individuals who have the tumor molecular phenotype data as well as miRNA expression levels for both carcinoma and normal colorectal tissue. We compare miRNAs uniquely associated with tumor molecular phenotype to the RNAseq data to identify genes associated with these miRNAs. This information is used to further identify unique pathways associated with tumor molecular phenotypes of TP53-mutated, KRAS-mutated, CpG island methylator phenotype and microsatellite instability tumors. Thirty-seven miRNAs were uniquely associated with TP53-mutated tumors; 30 of these miRNAs had higher level of expression in TP53-mutated tumors, while seven had lower levels of expression. Of the 34 miRNAs associated with CpG island methylator phenotype-high tumors, 16 were more likely to have a CpG island methylator phenotype-high tumor and 19 were less likely to be CpG island methylator phenotype-high. For microsatellite instability, 13 of the 22 infrequently expressed miRNAs were significantly less likely to be expressed in microsatellite unstable tumors. KRAS-mutated tumors were not associated with any miRNAs after adjustment for multiple comparisons. Of the dysregulated miRNAs, 17 were more likely to be TP53-mutated tumors while simultaneously being less likely to be CpG island methylator phenotype-high and/or microsatellite instability tumors. Genes regulated by these miRNAs were involved in numerous functions and pathways that influence cancer risk and progression. In summary, some infrequently expressed miRNAs, when expressed at higher levels, appear to have significant biological meaning in terms of tumor molecular phenotype and gene expression profiles.
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Affiliation(s)
- Martha L Slattery
- Department of Medicine, University of Utah, Salt Lake City, UT, USA,Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, UT 84108, USA. E-mail:
| | | | | | - Lila E Mullany
- Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, UT, USA
| | - Wade S Samowitz
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Department of Medicine, University of Utah, Salt Lake City, UT, USA
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Dietary intake alters gene expression in colon tissue: possible underlying mechanism for the influence of diet on disease. Pharmacogenet Genomics 2017; 26:294-306. [PMID: 26959716 PMCID: PMC4853256 DOI: 10.1097/fpc.0000000000000217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Supplemental Digital Content is available in the text. Background Although the association between diet and disease is well documented, the biologic mechanisms involved have not been entirely elucidated. In this study, we evaluate how dietary intake influences gene expression to better understand the underlying mechanisms through which diet operates. Methods We used data from 144 individuals who had comprehensive dietary intake and gene expression data from RNAseq using normal colonic mucosa. Using the DESeq2 statistical package, we identified genes that showed statistically significant differences in expression between individuals in high-intake and low-intake categories for several dietary variables of interest adjusting for age and sex. We examined total calories, total fats, vegetable protein, animal protein, carbohydrates, trans-fatty acids, mutagen index, red meat, processed meat, whole grains, vegetables, fruits, fiber, folate, dairy products, calcium, and prudent and western dietary patterns. Results Using a false discovery rate of less than 0.1, meat-related foods were statistically associated with 68 dysregulated genes, calcium with three dysregulated genes, folate with four dysregulated genes, and nonmeat-related foods with 65 dysregulated genes. With a more stringent false discovery rate of less than 0.05, there were nine meat-related dysregulated genes and 23 nonmeat-related genes. Ingenuity pathway analysis identified three major networks among genes identified as dysregulated with respect to meat-related dietary variables and three networks among genes identified as dysregulated with respect to nonmeat-related variables. The top networks (Ingenuity Pathway Analysis network score >30) associated with meat-related genes were (i) cancer, organismal injury, and abnormalities, tumor morphology, and (ii) cellular function and maintenance, cellular movement, cell death, and survival. Among genes related to nonmeat consumption variables, the top networks were (i) hematological system development and function, nervous system development and function, tissue morphology and (ii) connective tissue disorders, organismal injury, and abnormalities. Conclusion Several dietary factors were associated with gene expression in our data. These findings provide insight into the possible mechanisms by which diet may influence disease processes.
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Performance Comparison of NextSeq and Ion Proton Platforms for Molecular Diagnosis of Clinical Oncology. TUMORI JOURNAL 2017; 103:223-230. [PMID: 28127742 DOI: 10.5301/tj.5000600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2016] [Indexed: 11/20/2022]
Abstract
Purpose Next-generation sequencing is a powerful approach to detect genetic mutations with which cancer diagnosis and treatment can be tailored to the individual patient in the era of personalized and precision medicine. Ion Torrent Systems Ion Proton and Illumina NextSeq are 2 major targeted sequencing platforms; however, not much work has been done to compare these platforms’ performance for mutation detection in formalin-fixed paraffin-embedded (FFPE) materials. Methods We benchmarked the performance by using a collection of FFPE samples from 23 patients with different cancers for NextSeq and Ion Proton platforms. We report analysis of sequencing in terms of average coverage depth, read length, and variant detection. Results Sequencing results by NextSeq and Ion Proton displayed near perfect coverage behavior (>99%) on target region. We analyzed the ability to call variants from each platform and found that Ion Proton sequencing can identify 89% of single nucleotide variants (SNVs) whose mutant allele frequency (MAF) is greater than or equal to 5% detected by the NextSeq pipeline in common analytical regions. The correlation coefficient of MAF for those common SNVs was 1.0046 (R2 = 0.973) between the 2 platforms. To call lower mutant frequency (5%-10%) mutations for NextSeq sequencing, coverage depth should be improved. The concordance of small insertions and deletions between these 2 pipelines was up to 100%. Conclusions The 2 sequencing pipelines evaluated were able to generate usable sequence and had high concordance. They are proper for mutation detection in clinical application.
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Tong KI, Ota K, Komuro A, Ueda T, Ito A, Anne Koch C, Okada H. Attenuated DNA damage repair delays therapy-related myeloid neoplasms in a mouse model. Cell Death Dis 2016; 7:e2401. [PMID: 27711078 PMCID: PMC5133969 DOI: 10.1038/cddis.2016.298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 07/31/2016] [Accepted: 08/22/2016] [Indexed: 12/18/2022]
Abstract
Therapy-related cancers are potentially fatal late life complications for patients who received radio- or chemotherapy. So far, the mouse model showing reduction or delay of these diseases has not been described. We found that the disruption of Aplf in mice moderately attenuated DNA damage repair and, unexpectedly, impeded myeloid neoplasms after exposure to ionizing radiation (IR). Irradiated mutant mice showed higher rates of p53-dependent cell death, fewer chromosomal translocations, and a delay in malignancy-induce;/– mice. Depletion of APLF in non-tumorigenic human cells also markedly reduced the risk of radiation-induced chromosomal aberrations. We therefore conclude that proficient DNA damage repair may promote chromosomal aberrations in normal tissues after irradiation and induce malignant evolution, thus illustrating the potential benefit in sensitizing p53 function by manipulating DNA repair efficiency in cancer patients undergoing genotoxic therapies.
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Affiliation(s)
- Kit I Tong
- The Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada M5G 2M9
| | - Kazushige Ota
- Department of Biochemistry, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan
| | - Akiyoshi Komuro
- Department of Biochemistry, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan
| | - Takeshi Ueda
- Department of Biochemistry, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan
| | - Akihiko Ito
- Department of Pathology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - C Anne Koch
- Radiation Medicine Program, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada M5G 2M9.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9
| | - Hitoshi Okada
- The Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada M5G 2M9.,Department of Biochemistry, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama 589-8511, Osaka, Japan.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9.,Anti-Aging Center, Kindai University, Higashi-Osaka, Osaka 577-8502, Japan
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11
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Ramli NS, Ismail P, Rahmat A. Red pitaya juice supplementation ameliorates energy balance homeostasis by modulating obesity-related genes in high-carbohydrate, high-fat diet-induced metabolic syndrome rats. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2016; 16:243. [PMID: 27456968 PMCID: PMC4960886 DOI: 10.1186/s12906-016-1200-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/07/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Red pitaya (Hylocereus polyrhizus) or known as buah naga merah in Malay belongs to the cactus family, Cactaceae. Red pitaya has been shown to give protection against liver damage and may reduce the stiffness of the heart. Besides, the beneficial effects of red pitaya against obesity have been reported; however, the mechanism of this protection is not clear. Therefore, in the present study, we have investigated the red pitaya-targeted genes in obesity using high-carbohydrate, high-fat diet-induced metabolic syndrome rat model. METHODS A total of four groups were tested: corn-starch (CS), corn-starch + red pitaya juice (CRP), high-carbohydrate, high-fat (HCHF) and high-carbohydrate, high-fat + red pitaya juice (HRP). The intervention with 5 % red pitaya juice was continued for 8 weeks after 8 weeks initiation of the diet. Retroperitoneal, epididymal and omental fat pads were collected and weighed. Plasma concentration of IL-6 and TNF-α were measured using commercial kits. Gene expression analysis was conducted using RNA extracted from liver samples. A total of eighty-four genes related to obesity were analyzed using PCR array. RESULTS The rats fed HCHF-diet for 16 weeks increased body weight, developed excess abdominal fat deposition and down-regulated the expression level of IL-1α, IL-1r1, and Cntfr as compared to the control group. Supplementation of red pitaya juice for 8 weeks increased omental and epididymal fat but no change in retroperitoneal fat was observed. Red pitaya juice reversed the changes in energy balance homeostasis in liver tissues by regulation of the expression levels of Pomc and Insr. The increased protein expression levels of IL-6 and TNF-α in HCHF group and red pitaya treated rats confirmed the results of gene expression. CONCLUSION Collectively, this study revealed the usefulness of this diet-induced rat model and the beneficial effects of red pitaya on energy balance homeostasis by modulating the anorectic, orexigenic and energy expenditure related genes.
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Affiliation(s)
- Nurul Shazini Ramli
- Department of Food Science, Universiti Putra Malaysia, Serdang, Selangor 43400 Malaysia
| | - Patimah Ismail
- Department of Biomedical Science, Universiti Putra Malaysia, Serdang, 43400 Malaysia
| | - Asmah Rahmat
- Department of Nutrition and Dietetics, Universiti Putra Malaysia, Serdang, 43400 Malaysia
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12
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Sandrim VC, Luizon MR, Palei AC, Tanus-Santos JE, Cavalli RC. Circulating microRNA expression profiles in pre-eclampsia: evidence of increased miR-885-5p levels. BJOG 2016; 123:2120-2128. [PMID: 26853698 DOI: 10.1111/1471-0528.13903] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To validate and to compare the circulating microRNA (miR) expression profiles between pre-eclampsia and healthy pregnant women, to perform correlation analysis of the differently expressed miRs with clinical and biochemical parameters, and to verify the extracellular localisation of miRs in apoptotic bodies, microvesicles, and exosomes. DESIGN A case-control study with a replication study. SETTING Pregnant women attending maternity hospitals in Southeastern Brazil. POPULATION Two obstetric white populations: a case-control study (19 pre-eclampsia and 14 healthy pregnant) and a replication study (eight pre-eclampsia and eight healthy pregnant). METHODS PCR-array with 84 different miRs was performed in plasma from five pre-eclampsia and four healthy pregnant women. In the case-control study, differently expressed miRs were validated using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), and correlated with clinical and biochemical parameters. The plasma was then fractioned to study the extracellular localisation of miRs. MAIN OUTCOME MEASURES Gene expression profiles of miRs. RESULTS From PCR-array, three miRs (miR-376c-3p, miR-19a-3p, and miR-19b-3p) were found to be down-regulated and the miR-885-5p was found to be up-regulated in pre-eclampsia compared with healthy pregnant women. In the validation step, miR-885-5p was the only significantly different miR (fold-change = 5.0, P < 0.05), which was confirmed in the replication study (fold-change = 4.5, P < 0.05). Moreover, miR-885-5p was significantly correlated with the hepatic enzyme aspartate transaminase (r = 0.66; P = 0.0034) and it was mostly associated with the exosomes (32-fold higher than apoptotic bodies). CONCLUSIONS miR-885-5p is increased in plasma from pre-eclampsia compared with healthy pregnant women, and it is released into circulation mainly inside exosomes. TWEETABLE ABSTRACT: miR-885-5p is increased in pre-eclampsia and is released into circulation mainly inside exosomes.
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Affiliation(s)
- V C Sandrim
- Department of Pharmacology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - M R Luizon
- Department of Pharmacology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - A C Palei
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA.,Cardiovascular-Renal Research Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - J E Tanus-Santos
- Department of Pharmacology, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - R C Cavalli
- Department of Gynaecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
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13
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Lu J, Tao YF, Li ZH, Cao L, Hu SY, Wang NN, Du XJ, Sun LC, Zhao WL, Xiao PF, Fang F, Xu LX, Li YH, Li G, Zhao H, Ni J, Wang J, Feng X, Pan J. Analyzing the gene expression profile of anaplastic histology Wilms' tumor with real-time polymerase chain reaction arrays. Cancer Cell Int 2015; 15:44. [PMID: 26136641 PMCID: PMC4486424 DOI: 10.1186/s12935-015-0197-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 04/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background Wilms’ tumor (WT) is one of the most common malignant neoplasms of the urinary tract in children. Anaplastic histology (unfavorable histology) accounts for about 10% of whole WTs, and it is the single most important histologic predictor of treatment response and survival in patients with WT; however, until now the molecular basis of this phenotype is not very clearly. Methods A real-time polymerase chain reaction (PCR) array was designed and tested. Next, the gene expression profile of pediatric anaplastic histology WT and normal adjacent tissues were analyzed. These expression data were anlyzed with Multi Experiment View (MEV) cluster software further. Datasets representing genes with altered expression profiles derived from cluster analyses were imported into the Ingenuity Pathway Analysis Tool (IPA). Results 88 real-time PCR primer pairs for quantitative gene expression analysis of key genes involved in pediatric anaplastic histology WT were designed and tested. The gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal controls; we identified 15 genes that are up-regulated and 16 genes that are down-regulated in the former. To investigate biological interactions of these differently regulated genes, datasets representing genes with altered expression profiles were imported into the IPA for further analysis, which revealed three significant networks: Cancer, Hematological Disease, and Gene Expression, which included 27 focus molecules and a significance score of 43. The IPA analysis also grouped the differentially expressed genes into biological mechanisms related to Cell Death and Survival 1.15E−12, Cellular Development 2.84E−11, Cellular Growth and Proliferation 2.84E-11, Gene Expression 4.43E−10, and DNA Replication, Recombination, and Repair 1.39E−07. The important upstream regulators of pediatric anaplastic histology WT were TP53 and TGFβ1 signaling (P = 1.15E−14 and 3.79E−13, respectively). Conclusions Our study demonstrates that the gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal tissues with real-time PCR array. We identified some genes that are dysregulated in pediatric anaplastic histology WT for the first time, such as HDAC7, and IPA analysis showed the most important pathways for pediatric anaplastic histology WT are TP53 and TGFβ1 signaling. This work may provide new clues into the molecular mechanisms behind pediatric anaplastic histology WT. Electronic supplementary material The online version of this article (doi:10.1186/s12935-015-0197-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Yan-Fang Tao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Zhi-Heng Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Lan Cao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Na-Na Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Xiao-Juan Du
- Department of Gastroenterology, the 5th Hospital of Chinese PLA, Yin chuan, China
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Pei-Fang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Fang Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Li-Xiao Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Yan-Hong Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Gang Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - He Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Jian Ni
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China
| | - Jian Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Xing Feng
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Jian Pan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
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Tao YF, Li ZH, Wang NN, Fang F, Xu LX, Pan J. tp53-dependent G2 arrest mediator candidate gene, Reprimo, is down-regulated by promoter hypermethylation in pediatric acute myeloid leukemia. Leuk Lymphoma 2015; 56:2931-44. [PMID: 25629980 DOI: 10.3109/10428194.2015.1011157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Reprimo (RPRM) is a novel tumor suppressor. However, the expression and molecular function of RPRM in pediatric acute myeloid leukemia (AML) is still unknown. We observed hypermethylation of the RPRM promoter in 8/11 leukemia cell lines and in 44.8% (47/105) of pediatric AML samples compared with 6.7% (2/30) of control samples. Bisulfite genomic sequencing analysis showed that the RPRM promoter was methylated in the majority of AML samples (66.2-83.1%), whereas RPRM was almost unmethylated in normal bone marrow samples (20.0-27.7%). Kaplan-Meier survival analysis revealed poor survival outcomes in samples with RPRM promoter methylation (p < 0.001). Proliferation of AML cells was inhibited in a dose-dependent manner (p < 0.05) after RPRM overexpression with lentivirus transfection. Apoptosis was up-regulated in RPRM-overexpressing AML cells. Real-time polymerase chain reaction array analysis revealed 50 dysregulated genes that might be implicated in apoptosis of RPRM-induced AML cells. RPRM may be a putative tumor suppressor in pediatric AML.
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Affiliation(s)
- Yan-Fang Tao
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Zhi-Heng Li
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Na-Na Wang
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Fang Fang
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Li-Xiao Xu
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Jian Pan
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
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15
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Barneda-Zahonero B, Collazo O, Azagra A, Fernández-Duran I, Serra-Musach J, Islam ABMMK, Vega-García N, Malatesta R, Camós M, Gómez A, Román-González L, Vidal A, López-Bigas N, Villanueva A, Esteller M, Parra M. The transcriptional repressor HDAC7 promotes apoptosis and c-Myc downregulation in particular types of leukemia and lymphoma. Cell Death Dis 2015; 6:e1635. [PMID: 25675295 PMCID: PMC4669785 DOI: 10.1038/cddis.2014.594] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 12/26/2022]
Abstract
The generation of B cells is a complex process requiring several cellular transitions, including cell commitment and differentiation. Proper transcriptional control to establish the genetic programs characteristic of each cellular stage is essential for the correct development of B lymphocytes. Deregulation of these particular transcriptional programs may result in a block in B-cell maturation, contributing to the development of hematological malignancies such as leukemia and lymphoma. However, very little is currently known about the role of transcriptional repressors in normal and aberrant B lymphopoiesis. Here we report that histone deacetylase 7 (HDAC7) is underexpressed in pro-B acute lymphoblastic leukemia (pro-B-ALL) and Burkitt lymphoma. Ectopic expression of HDAC7 induces apoptosis, leads to the downregulation of c-Myc and inhibits the oncogenic potential of cells in vivo, in a xenograft model. Most significantly, we have observed low levels of HDAC7 expression in B-ALL patient samples, which is correlated with the increased levels of c-Myc. From a mechanistic angle, we show that ectopically expressed HDAC7 localizes to the nucleus and interacts with the transcription factor myocyte enhancer factor C (MEF2C) and the corepressors HDAC3 and SMRT. Accordingly, both the HDAC7–MEF2C interaction domain as well as its catalytic domain are involved in the reduced cell viability induced by HDAC7. We conclude that HDAC7 has a potent anti-oncogenic effect on specific B-cell malignancies, indicating that its deregulation may contribute to the pathogenesis of the disease.
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Affiliation(s)
- B Barneda-Zahonero
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - O Collazo
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - A Azagra
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - I Fernández-Duran
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - J Serra-Musach
- Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Avenida Gran Via s/n km 2.7, 08907 L'Hospitalet, Barcelona, Spain
| | - A B M M K Islam
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - N Vega-García
- Department of Hematology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - R Malatesta
- Department of Hematology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - M Camós
- Department of Hematology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - A Gómez
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - L Román-González
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
| | - A Vidal
- Department of Pathology, University Hospital of Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - N López-Bigas
- 1] Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - A Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - M Esteller
- 1] Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain [3] Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
| | - M Parra
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research institute (IDIBELL), Avenida Gran Via 199, 08908 L'Hospitalet, Barcelona, Spain
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Tao YF, Xu LX, Lu J, Hu SY, Fang F, Cao L, Xiao PF, Du XJ, Sun LC, Li ZH, Wang NN, Su GH, Li YH, Li G, Zhao H, Li YP, Xu YY, Zhou HT, Wu Y, Jin MF, Liu L, Zhu XM, Ni J, Wang J, Xing F, Zhao WL, Pan J. Early B-cell factor 3 (EBF3) is a novel tumor suppressor gene with promoter hypermethylation in pediatric acute myeloid leukemia. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:4. [PMID: 25609158 PMCID: PMC4311429 DOI: 10.1186/s13046-014-0118-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/27/2014] [Indexed: 12/21/2022]
Abstract
Background Pediatric acute myeloid leukemia (AML) comprises up to 20% of all childhood leukemia. Recent research shows that aberrant DNA methylation patterning may play a role in leukemogenesis. The epigenetic silencing of the EBF3 locus is very frequent in glioblastoma. However, the expression profiles and molecular function of EBF3 in pediatric AML is still unclear. Methods Twelve human acute leukemia cell lines, 105 pediatric AML samples and 30 normal bone marrow/idiopathic thrombocytopenic purpura (NBM/ITP) control samples were analyzed. Transcriptional level of EBF3 was evaluated by semi-quantitative and real-time PCR. EBF3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS). The molecular mechanism of EBF3 was investigated by apoptosis assays and PCR array analysis. Results EBF3 promoter was hypermethylated in 10/12 leukemia cell lines. Aberrant EBF3 methylation was observed in 42.9% (45/105) of the pediatric AML samples using MSP analysis, and the BGS results confirmed promoter methylation. EBF3 expression was decreased in the AML samples compared with control. Methylated samples revealed similar survival outcomes by Kaplan-Meier survival analysis. EBF3 overexpression significantly inhibited cell proliferation and increased apoptosis. Real-time PCR array analysis revealed 93 dysregulated genes possibly implicated in the apoptosis of EBF3-induced AML cells. Conclusion In this study, we firstly identified epigenetic inactivation of EBF3 in both AML cell lines and pediatric AML samples for the first time. Our findings also showed for the first time that transcriptional overexpression of EBF3 could inhibit proliferation and induce apoptosis in AML cells. We identified 93 dysregulated apoptosis-related genes in EBF3-overexpressing, including DCC, AIFM2 and DAPK1. Most of these genes have never been related with EBF3 over expression. These results may provide new insights into the molecular mechanism of EBF3-induced apoptosis; however, further research will be required to determine the underlying details. Our findings suggest that EBF3 may act as a putative tumor suppressor gene in pediatric AML.
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Affiliation(s)
- Yan-Fang Tao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Li-Xiao Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Fang Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Lan Cao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Pei-Fang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Xiao-Juan Du
- Department of Gastroenterology, the 5th Hospital of Chinese PLA, Yin chuan, China.
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Zhi-Heng Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Na-Na Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Guang-Hao Su
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yan-Hong Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Gang Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - He Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yi-Ping Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yun-Yun Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Hui-Ting Zhou
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yi Wu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Mei-Fang Jin
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Lin Liu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Xue-Ming Zhu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jian Ni
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China.
| | - Jian Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Feng Xing
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jian Pan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
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Metallothionein III (MT3) is a putative tumor suppressor gene that is frequently inactivated in pediatric acute myeloid leukemia by promoter hypermethylation. J Transl Med 2014; 12:182. [PMID: 24962166 PMCID: PMC4082423 DOI: 10.1186/1479-5876-12-182] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/20/2014] [Indexed: 11/14/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is the second most common form of leukemia in children. Aberrant DNA methylation patterns are a characteristic feature in various tumors, including AML. Metallothionein III (MT3) is a tumor suppresser reported to show promoter hypermethylated in various cancers. However, the expression and molecular function of MT3 in pediatric AML is unclear. Methods Eleven human leukemia cell lines and 41 pediatric AML samples and 20 NBM/ITP (Norma bone marrow/Idiopathic thrombocytopenic purpura) control samples were analyzed. Transcription levels of MT3 were evaluated by semi-quantitative and real-time PCR. MT3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BSG). The molecular mechanism of MT3 was investigated by apoptosis assays and PCR array analysis. Results The MT3 promoter was hypermethylated in leukemia cell lines. More CpG’s methylated of MT3 was observed 39.0% pediatric AML samples compared to 10.0% NBM controls. Transcription of MT3 was also significantly decreased in AML samples compared to NBM/ITP controls (P < 0.001); patients with methylated MT3 exhibited lower levels of MT3 expression compared to those with unmethylated MT3 (P = 0.049). After transfection with MT3 lentivirus, proliferation was significantly inhibited in AML cells in a dose-dependent manner (P < 0.05). Annexin V assay showed that apoptosis was significantly upregulated MT3-overexpressing AML cells compared to controls. Real-time PCR array analysis revealed 34 dysregulated genes that may be implicated in MT3 overexpression and apoptosis in AML, including FOXO1. Conclusion MT3 may be a putative tumor suppressor gene in pediatric AML. Epigenetic inactivation of MT3 via promoter hypermethylation was observed in both AML cell lines and pediatric AML samples. Overexpression of MT3 may inhibit proliferation and induce apoptosis in AML cells. FOXO1 was dysregulated in MT3-overexpressing cells, offering an insight into the mechanism of MT3-induced apoptosis. However, further research is required to determine the underlying molecular details.
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Frejo MT, del Pino J, Lobo M, García J, Capo MA, Díaz MJ. Liver and kidney damage induced by 4-aminopyridine in a repeated dose (28 days) oral toxicity study in rats: Gene expression profile of hybrid cell death. Toxicol Lett 2014; 225:252-63. [DOI: 10.1016/j.toxlet.2013.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 10/25/2022]
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Petrini M, Felicetti F, Bottero L, Errico MC, Morsilli O, Boe A, De Feo A, Carè A. HOXB1 restored expression promotes apoptosis and differentiation in the HL60 leukemic cell line. Cancer Cell Int 2013; 13:101. [PMID: 24148231 PMCID: PMC3874656 DOI: 10.1186/1475-2867-13-101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/19/2013] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Homeobox (HOX) genes deregulation has been largely implicated in the development of human leukemia. Among the HOXB cluster, HOXB1 was silent in a number of analyzed acute myeloid leukemia (AML) primary cells and cell lines, whereas it was expressed in normal terminally differentiated peripheral blood cells. METHODS We evaluated the biological effects and the transcriptome changes determined by the retroviral transduction of HOXB1 in the human promyelocytic cell line HL60. RESULTS Our results suggest that the enforced expression of HOXB1 reduces cell growth proliferation, inducing apoptosis and cell differentiation along the monocytic and granulocytic lineages. Accordingly, gene expression analysis showed the HOXB1-dependent down-regulation of some tumor promoting genes, paralleled by the up-regulation of apoptosis- and differentiation-related genes, thus supporting a tumor suppressor role for HOXB1 in AML. Finally, we indicated HOXB1 promoter hypermethylation as a mechanism responsible for HOXB1 silencing. CONCLUSIONS We propose HOXB1 as an additional member of the HOX family with tumour suppressor properties suggesting a HOXB1/ATRA combination as a possible future therapeutic strategy in AML.
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Affiliation(s)
- Marina Petrini
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Federica Felicetti
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Lisabianca Bottero
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Maria Cristina Errico
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Ornella Morsilli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Alessandra Boe
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Alessandra De Feo
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
| | - Alessandra Carè
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore Sanità, Rome 00161, Italy
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Tao YF, Pang L, Du XJ, Sun LC, Hu SY, Lu J, Cao L, Zhao WL, Feng X, Wang J, Wu D, Wang N, Ni J, Pan J. Differential mRNA expression levels of human histone-modifying enzymes in normal karyotype B cell pediatric acute lymphoblastic leukemia. Int J Mol Sci 2013; 14:3376-94. [PMID: 23389039 PMCID: PMC3588049 DOI: 10.3390/ijms14023376] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/29/2013] [Accepted: 01/30/2013] [Indexed: 11/16/2022] Open
Abstract
Histone modification enzymes regulate gene expression by altering the accessibility of promoters to transcription factors. We sought to determine whether the genes encoding histone modification enzymes are dysregulated in pediatric acute lymphoblastic leukemia (ALL). A real-time PCR array was designed, tested and used to profile the expression of 85 genes encoding histone modification enzymes in bone marrow mononuclear cells from 30 pediatric ALL patients and 20 normal controls. The expression profile of histone-modifying genes was significantly different between normal karyotype B cell pediatric ALL and normal controls. Eleven genes were upregulated in pediatric ALL, including the histone deacetylases HDAC2 and PAK1, and seven genes were downregulated, including PRMT2 and the putative tumor suppressor EP300. Future studies will seek to determine whether these genes serve as biomarkers of pediatric ALL. Ingenuity Pathway Analysis revealed that Gene Expression and Organ Morphology was the highest rated network, with 13 focus molecules (significance score = 35). Ingenuity Pathway Analysis also indicated that curcumin and miR-34 are upstream regulators of histone-modifying enzymes; future studies will seek to validate these results and examine the role of curcumin and miR-34 in leukemia. This study provides new clues into the molecular mechanisms of pediatric ALL.
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Affiliation(s)
- Yan-Fang Tao
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Li Pang
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Xiao-Juan Du
- Department of Gastroenterology, the 5th Hospital of Chinese PLA, Yinchuan 750004, Ningxia, China; E-Mail:
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing100021, China; E-Mail:
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Jun Lu
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Lan Cao
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Xing Feng
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Jian Wang
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Dong Wu
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Na Wang
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
| | - Jian Ni
- Translational Research Center, The Second Clinical School, Nanjing Medical University, Nanjing 210011, Jiangsu, China; E-Mail:
| | - Jian Pan
- Department of Hematology and Oncology, Children’s Hospital of Soochow University, Suzhou 215003, Jiangsu, China; E-Mails: (Y.-F.T.); (L.P.); (S.-Y.H.); (J.L.); (L.C.); (W.-L.Z.); (X.F.); (J.W.); (D.W.); (N.W.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +86-512-6778-8216
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Souchelnytskyi S. INDIVIDUALIZATION OF CANCER TREATMENT: CONTRIBUTION OF OMICS TECHNOLOGIES TO CANCER DIAGNOSTIC. BIOTECHNOLOGIA ACTA 2013. [DOI: 10.15407/biotech6.04.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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