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Choi ES, Lee H, Lee CH, Goh SH. Overexpression of KLHL23 protein from read-through transcription of PHOSPHO2-KLHL23 in gastric cancer increases cell proliferation. FEBS Open Bio 2016; 6:1155-1164. [PMID: 27833855 PMCID: PMC5095152 DOI: 10.1002/2211-5463.12136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/20/2016] [Accepted: 09/28/2016] [Indexed: 01/05/2023] Open
Abstract
Gene fusion, as a prototypical pathognomonic mutation, contributes to genome complexity, and the cis‐transcription‐induced gene fusions generated by read‐through transcription of adjacent genes have been found to be important for tumor development. We screened read‐through transcription events from stomach adenocarcinoma RNA‐seq data and selected three candidates PHOSPHO2‐KLHL23, RPL17‐C18orf32, and PRR5‐ARHGAP8, to assess their biological role in gastric cancer. The expression of all three read‐through fusion transcripts was confirmed in gastric cancer cell lines and paired normal/tumor gastric cancer tissues by real‐time quantitative reverse transcription polymerase chain reaction and their expression was found to be significantly higher in the tumor (P < 0.05; n = 75). The correlation between the expression level and clinicopathological information was statistically analyzed. The level of the PHOSPHO2‐KLHL23 read‐through fusion transcript correlated with the Lauren classification and was significantly associated with the presence of perineural invasion. Overexpression of KLHL23 from PHOSPHO2‐KLHL23 read‐through transcript led to a significant increase in cell proliferation and resistance to anticancer drug treatment. Silencing of KLHL23 expression decreased cyclin D1 levels. The expression of KLHL23 from prevalent read‐through transcripts of PHOSPHO2‐KLHL23 in gastric cancer may undermine the efficacy of anticancer drug treatment.
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Affiliation(s)
- Eun-Seok Choi
- Precision Medicine Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea; Department of Environmental Medical Biology Institute of Tropical Medicine Yonsei University College of Medicine Seoul Korea
| | - Hanna Lee
- Precision Medicine Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea
| | - Chang-Hun Lee
- Cancer Cell and Molecular Biology Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea
| | - Sung-Ho Goh
- Precision Medicine Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea
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Hesson LB, Ng B, Zarzour P, Srivastava S, Kwok CT, Packham D, Nunez AC, Beck D, Ryan R, Dower A, Ford CE, Pimanda JE, Sloane MA, Hawkins NJ, Bourke MJ, Wong JWH, Ward RL. Integrated Genetic, Epigenetic, and Transcriptional Profiling Identifies Molecular Pathways in the Development of Laterally Spreading Tumors. Mol Cancer Res 2016; 14:1217-1228. [PMID: 27671336 DOI: 10.1158/1541-7786.mcr-16-0175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 11/16/2022]
Abstract
Laterally spreading tumors (LST) are colorectal adenomas that develop into extremely large lesions with predominantly slow progression to cancer, depending on lesion subtype. Comparing and contrasting the molecular profiles of LSTs and colorectal cancers offers an opportunity to delineate key molecular alterations that drive malignant transformation in the colorectum. In a discovery cohort of 11 LSTs and paired normal mucosa, we performed a comprehensive and unbiased screen of the genome, epigenome, and transcriptome followed by bioinformatics integration of these data and validation in an additional 84 large, benign colorectal lesions. Mutation rates in LSTs were comparable with microsatellite-stable colorectal cancers (2.4 vs. 2.6 mutations per megabase); however, copy number alterations were infrequent (averaging only 1.5 per LST). Frequent genetic, epigenetic, and transcriptional alterations were identified in genes not previously implicated in colorectal neoplasia (ANO5, MED12L, EPB41L4A, RGMB, SLITRK1, SLITRK5, NRXN1, ANK2). Alterations to pathways commonly mutated in colorectal cancers, namely, the p53, PI3K, and TGFβ pathways, were rare. Instead, LST-altered genes converged on axonal guidance, Wnt, and actin cytoskeleton signaling. These integrated omics data identify molecular features associated with noncancerous LSTs and highlight that mutation load, which is relatively high in LSTs, is a poor predictor of invasive potential. IMPLICATIONS The novel genetic, epigenetic, and transcriptional changes associated with LST development reveal important insights into why some adenomas do not progress to cancer. The finding that LSTs exhibit a mutational load similar to colorectal carcinomas has implications for the validity of molecular biomarkers for assessing cancer risk. Mol Cancer Res; 14(12); 1217-28. ©2016 AACR.
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Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia.
| | - Benedict Ng
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Peter Zarzour
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Sameer Srivastava
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia.,Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Chau-To Kwok
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Deborah Packham
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Dominik Beck
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Regina Ryan
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Ashraf Dower
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Caroline E Ford
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - John E Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Nicholas J Hawkins
- School of Medical Sciences, UNSW Australia, Kensington, Sydney, Australia
| | - Michael J Bourke
- Department of Gastroenterology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia. .,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland, Australia
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Srivastava S, Ludwig AK, Wong JWH, Hesson LB. An investigation of the potential for epigenetic inactivation by transcription read-through in a sporadic colorectal cancer. Gene 2016; 585:154-158. [PMID: 27016300 DOI: 10.1016/j.gene.2016.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/20/2016] [Indexed: 01/05/2023]
Abstract
Aberrant transcription read-through of a gene promoter as a result of genetic structural rearrangements can cause the epigenetic inactivation of a neighbouring gene. All reported cases have involved copy number alterations that remove the 3' poly(A) transcription terminator sequence of a gene leading to transcription read-through (TRT) and methylation of the gene promoter of a downstream gene. We aimed to determine whether deletion of poly (A) transcription terminator sequences was associated with the methylation of neighbouring genes in a CRC with extensive copy number alterations. We performed a high resolution CGH array and methylation analysis on a CRC specimen to identify such alterations. Analysis of the CRC using high-resolution CGH identified 6 genes with deletions in the 3' part of the gene that encompassed the poly(A) transcription terminator sequence. Bisulphite sequencing of the promoter region of neighbouring (affected) genes at these six regions showed all candidate genes were unmethylated. Considering the fact that six TRT affected genes in a CRC with multiple deletions show no signs of hypermethylated promoters, it would be fairly appropriate to suggest that epigenetic inactivation by TRT might be a rare phenomenon in sporadic CRCs.
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Affiliation(s)
- Sameer Srivastava
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia; Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India.
| | - Anne K Ludwig
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia; Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Bermúdez Brito M, Goulielmaki E, Papakonstanti EA. Focus on PTEN Regulation. Front Oncol 2015; 5:166. [PMID: 26284192 PMCID: PMC4515857 DOI: 10.3389/fonc.2015.00166] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022] Open
Abstract
The role of phosphatase and tensin homolog on chromosome 10 (PTEN) as a tumor suppressor has been for a long time attributed to its lipid phosphatase activity against PI(3,4,5)P3, the phospholipid product of the class I PI3Ks. Besides its traditional role as a lipid phosphatase at the plasma membrane, a wealth of data has shown that PTEN can function independently of its phosphatase activity and that PTEN also exists and plays a role in the nucleus, in cytoplasmic organelles, and extracellularly. Accumulating evidence has shed light on diverse physiological functions of PTEN, which are accompanied by a complex regulation of its expression and activity. PTEN levels and function are regulated transcriptionally, post-transcriptionally, and post-translationally. PTEN is also sensitive to regulation by its interacting proteins and its localization. Herein, we summarize the current knowledge on mechanisms that regulate the expression and enzymatic activity of PTEN and its role in human diseases.
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Affiliation(s)
- Miriam Bermúdez Brito
- Department of Biochemistry, School of Medicine, University of Crete , Heraklion , Greece
| | - Evangelia Goulielmaki
- Department of Biochemistry, School of Medicine, University of Crete , Heraklion , Greece
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Hesson LB, Sloane MA, Wong JW, Nunez AC, Srivastava S, Ng B, Hawkins NJ, Bourke MJ, Ward RL. Altered promoter nucleosome positioning is an early event in gene silencing. Epigenetics 2015; 9:1422-30. [PMID: 25437056 DOI: 10.4161/15592294.2014.970077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DNA methylation, and gene expression in the early stages of gene silencing. Genome-wide gene expression correlated with highly positioned nucleosomes upstream and downstream of a nucleosome-depleted transcription start site (TSS). Hypermethylated promoters displayed increased nucleosome occupancy, specifically at the TSS. We investigated 2 genes, CDH1 and CDKN2B, which were silenced in adenomas but lacked promoter hypermethylation. Instead, silencing correlated with loss of nucleosomes from the -2 position upstream of the TSS relative to normal mucosa. In contrast, permanent CDH1 silencing in carcinoma cells was characterized by promoter hypermethylation and dense nucleosome occupancy. Our findings suggest that silenced genes transition through an intermediary stage involving altered promoter nucleosome positioning, before permanent silencing by hypermethylation and dense nucleosome occupancy.
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Affiliation(s)
- Luke B Hesson
- a Adult Cancer Program; Lowy Cancer Research Center and Prince of Wales Clinical School; UNSW ; Sydney , Australia
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Hesson LB, Packham D, Kwok CT, Nunez AC, Ng B, Schmidt C, Fields M, Wong JWH, Sloane MA, Ward RL. Lynch syndrome associated with two MLH1 promoter variants and allelic imbalance of MLH1 expression. Hum Mutat 2015; 36:622-30. [PMID: 25762362 PMCID: PMC4682451 DOI: 10.1002/humu.22785] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/03/2015] [Indexed: 12/27/2022]
Abstract
Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A>G and c.-7C>T) within the MLH1 5′untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expression and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A>G and c.-7C>T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5′UTR in the pathogenesis of Lynch syndrome.
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Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Deborah Packham
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Chau-To Kwok
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Benedict Ng
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Christa Schmidt
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim
| | - Michael Fields
- Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia.,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland, Australia
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Hesson LB, Ward RL. The importance of distinguishing pseudogenes from parental genes. Clin Epigenetics 2015; 6:90. [PMID: 25553138 PMCID: PMC4280768 DOI: 10.1186/s13148-014-0033-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 11/28/2014] [Indexed: 12/03/2022] Open
Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW, Sydney, Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW, Sydney, Australia
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Sloane MA, Hesson LB, Nunez AC, Thompson BA, Ward RL. Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients. Clin Epigenetics 2014; 6:32. [PMID: 25530820 PMCID: PMC4272815 DOI: 10.1186/s13148-014-0032-6] [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: 07/04/2014] [Accepted: 11/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Splicing is more efficient when coupled with transcription and it has been proposed that nucleosomes enriched in exons are important for splice site recognition. Lynch syndrome is a familial cancer syndrome that can be caused by the autosomal dominant inheritance of splice site mutations in the MutL homolog 1 (MLH1) gene. To better understand the role of nucleosomes in splicing, we used MLH1 splice site mutations in Lynch syndrome cases as a model to investigate if abnormal splicing was associated with altered nucleosome positioning at exon-intron boundaries. FINDINGS Nucleosome Occupancy and Methylome sequencing (NOMe-seq) was used to determine the allele-specific positioning of nucleosomes around heterozygous splice site mutations in lymphoblastoid cells lines (LCLs) derived from six Lynch syndrome patients. These mutations were previously shown to cause exon skipping in five of the six patients. Allele-specific high-resolution nucleosome mapping across exons and exon-intron boundaries revealed high levels of nucleosomes across all regions examined. Alleles containing donor or acceptor splice site mutations showed no consistent alteration in nucleosome positioning or occupancy. CONCLUSION Nucleosomes were enriched at MLH1 exons in LCLs derived from Lynch syndrome patients, and in this model system the positioning of nucleosomes was unaltered at exon-intron boundaries containing splice site mutations. Thus, these splice site mutations alone do not significantly change the local organisation of nucleosomes.
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Affiliation(s)
- Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
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