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Swoboda RK, Somasundaram R, Caputo-Gross L, Marincola FM, Robbins P, Herlyn M, Herlyn D. Antimelanoma CTL recognizes peptides derived from an ORF transcribed from the antisense strand of the 3' untranslated region of TRIT1. Mol Ther Oncolytics 2015; 1:14009. [PMID: 27119099 PMCID: PMC4782943 DOI: 10.1038/mto.2014.9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 09/18/2014] [Indexed: 01/05/2023] Open
Abstract
Noncoding regions of the genome play an important role in tumorigenesis of cancer. Using expression cloning, we have identified a cytotoxic T lymphocyte (CTL)-defined antigen that recognizes a protein sequence derived from an open reading frame transcribed from the reverse strand in the 3' untranslated region of tRNA isopentenyltransferase 1 (TRIT1). A peptide derived from this open reading frame (ORF) sequence and predicted to bind to HLA-B57, sensitized HLA-B57(+) tumor cells to lysis by CTL793. The peptide also induced a CTL response in peripheral blood mononuclear cells (PBMC) of patient 793 and in two other melanoma patients. The CTL lysed peptide-pulsed HLA-B57(+) target cells and melanoma cells with endogenous antigen expression. The recognition of this antigen is not limited to HLA-B57-restricted CTLs. An HLA-A2 peptide derived from the ORF was able to induce CTLs in PBMC of 2 HLA-A2(+) patients. This study describes for the first time a CTL-defined melanoma antigen that is derived from an ORF on the reverse strand of the putative tumor suppressor gene TRIT1. This antigen has potential use as a vaccine or its ability to induce CTLs in vitro could be used as a predictive biomarker.
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Affiliation(s)
| | | | | | - Francesco M Marincola
- Department of Transfusion Medicine Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Know your limits: Assumptions, constraints and interpretation in systems biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1280-7. [DOI: 10.1016/j.bbapap.2009.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 05/04/2009] [Indexed: 12/20/2022]
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Yaragatti M, Wen Q. Analysis of functional genomic signals using the XOR gate. PLoS One 2009; 4:e5608. [PMID: 19440336 PMCID: PMC2680033 DOI: 10.1371/journal.pone.0005608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 04/17/2009] [Indexed: 11/24/2022] Open
Abstract
Modeling gene regulatory networks requires recognition of active transcriptional sites in the genome. For this reason, we present a novel approach for inferring active transcriptional regulatory modules in a genome using an established systems model of bit encoded DNA sequences. Our analysis showed variations in several properties between random and functional sequences. Cross correlation within random and functional groups uncovered a wave pattern associated with functional sequences. Using the exclusive-OR (XOR) logic gate, we formulated a scheme to threshold signals that may correlate to putative active transcriptional modules from a population of random genomic fragments. It is our intent to use this as a basis for identifying novel regulatory sites in the genome.
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Affiliation(s)
- Mahesh Yaragatti
- Biotechnology Program, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
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Seim I, Carter SL, Herington AC, Chopin LK. Complex organisation and structure of the ghrelin antisense strand gene GHRLOS, a candidate non-coding RNA gene. BMC Mol Biol 2008; 9:95. [PMID: 18954468 PMCID: PMC2621237 DOI: 10.1186/1471-2199-9-95] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 10/28/2008] [Indexed: 12/13/2022] Open
Abstract
Background The peptide hormone ghrelin has many important physiological and pathophysiological roles, including the stimulation of growth hormone (GH) release, appetite regulation, gut motility and proliferation of cancer cells. We previously identified a gene on the opposite strand of the ghrelin gene, ghrelinOS (GHRLOS), which spans the promoter and untranslated regions of the ghrelin gene (GHRL). Here we further characterise GHRLOS. Results We have described GHRLOS mRNA isoforms that extend over 1.4 kb of the promoter region and 106 nucleotides of exon 4 of the ghrelin gene, GHRL. These GHRLOS transcripts initiate 4.8 kb downstream of the terminal exon 4 of GHRL and are present in the 3' untranslated exon of the adjacent gene TATDN2 (TatD DNase domain containing 2). Interestingly, we have also identified a putative non-coding TATDN2-GHRLOS chimaeric transcript, indicating that GHRLOS RNA biogenesis is extremely complex. Moreover, we have discovered that the 3' region of GHRLOS is also antisense, in a tail-to-tail fashion to a novel terminal exon of the neighbouring SEC13 gene, which is important in protein transport. Sequence analyses revealed that GHRLOS is riddled with stop codons, and that there is little nucleotide and amino-acid sequence conservation of the GHRLOS gene between vertebrates. The gene spans 44 kb on 3p25.3, is extensively spliced and harbours multiple variable exons. We have also investigated the expression of GHRLOS and found evidence of differential tissue expression. It is highly expressed in tissues which are emerging as major sites of non-coding RNA expression (the thymus, brain, and testis), as well as in the ovary and uterus. In contrast, very low levels were found in the stomach where sense, GHRL derived RNAs are highly expressed. Conclusion GHRLOS RNA transcripts display several distinctive features of non-coding (ncRNA) genes, including 5' capping, polyadenylation, extensive splicing and short open reading frames. The gene is also non-conserved, with differential and tissue-restricted expression. The overlapping genomic arrangement of GHRLOS with the ghrelin gene indicates that it is likely to have interesting regulatory and functional roles in the ghrelin axis.
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Affiliation(s)
- Inge Seim
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia.
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Tanney A, Oliver GR, Farztdinov V, Kennedy RD, Mulligan JM, Fulton CE, Farragher SM, Field JK, Johnston PG, Harkin DP, Proutski V, Mulligan KA. Generation of a non-small cell lung cancer transcriptome microarray. BMC Med Genomics 2008; 1:20. [PMID: 18513400 PMCID: PMC2426710 DOI: 10.1186/1755-8794-1-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 05/30/2008] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality worldwide. At present no reliable biomarkers are available to guide the management of this condition. Microarray technology may allow appropriate biomarkers to be identified but present platforms are lacking disease focus and are thus likely to miss potentially vital information contained in patient tissue samples. METHODS A combination of large-scale in-house sequencing, gene expression profiling and public sequence and gene expression data mining were used to characterise the transcriptome of NSCLC and the data used to generate a disease-focused microarray - the Lung Cancer DSA research tool. RESULTS Built on the Affymetrix GeneChip platform, the Lung Cancer DSA research tool allows for interrogation of ~60,000 transcripts relevant to Lung Cancer, tens of thousands of which are unavailable on leading commercial microarrays. CONCLUSION We have developed the first high-density disease specific transcriptome microarray. We present the array design process and the results of experiments carried out to demonstrate the array's utility. This approach serves as a template for the development of other disease transcriptome microarrays, including non-neoplastic diseases.
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Affiliation(s)
- Austin Tanney
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Gavin R Oliver
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Vadim Farztdinov
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Richard D Kennedy
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Jude M Mulligan
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Ciaran E Fulton
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Susan M Farragher
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - John K Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool Cancer Research Centre, 200 London Road, Liverpool, L3 9TA, UK
| | - Patrick G Johnston
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - D Paul Harkin
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Vitali Proutski
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Karl A Mulligan
- Almac Diagnostics Ltd, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
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Barthelson RA, Lambert GM, Vanier C, Lynch RM, Galbraith DW. Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cells. BMC Genomics 2007; 8:340. [PMID: 17894886 PMCID: PMC2048942 DOI: 10.1186/1471-2164-8-340] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 09/25/2007] [Indexed: 11/10/2022] Open
Abstract
Background In the most general sense, studies involving global analysis of gene expression aim to provide a comprehensive catalog of the components involved in the production of recognizable cellular phenotypes. These studies are often limited by the available technologies. One technology, based on microarrays, categorizes gene expression in terms of the abundance of RNA transcripts, and typically employs RNA prepared from whole cells, where cytoplasmic RNA predominates. Results Using microarrays comprising oligonucleotide probes that represent either protein-coding transcripts or microRNAs (miRNA), we have studied global transcript accumulation patterns for the HepG2 (human hepatoma) cell line. Through subdividing the total pool of RNA transcripts into samples from nuclei, the cytoplasm, and whole cells, we determined the degree of correlation of these patterns across these different subcellular locations. The transcript and miRNA abundance patterns for the three RNA fractions were largely similar, but with some exceptions: nuclear RNA samples were enriched with respect to the cytoplasm in transcripts encoding proteins associated with specific nuclear functions, such as the cell cycle, mitosis, and transcription. The cytoplasmic RNA fraction also was enriched, when compared to the nucleus, in transcripts for proteins related to specific nuclear functions, including the cell cycle, DNA replication, and DNA repair. Some transcripts related to the ubiquitin cycle, and transcripts for various membrane proteins were sorted into either the nuclear or cytoplasmic fractions. Conclusion Enrichment or compartmentalization of cell cycle and ubiquitin cycle transcripts within the nucleus may be related to the regulation of their expression, by preventing their translation to proteins. In this way, these cellular functions may be tightly controlled by regulating the release of mRNA from the nucleus and thereby the expression of key rate limiting steps in these pathways. Many miRNA precursors were also enriched in the nuclear samples, with significantly fewer being enriched in the cytoplasm. Studies of mRNA localization will help to clarify the roles RNA processing and transport play in the regulation of cellular function.
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Affiliation(s)
- Roger A Barthelson
- Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Georgina M Lambert
- Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Cheryl Vanier
- Department of Biological Sciences, University of Nevada, Las Vegas, Nevada 89154, USA
| | - Ronald M Lynch
- Department of Physiology, University of Arizona, Tucson, Arizona 85721, USA
| | - David W Galbraith
- Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
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Abstract
The study of the profile of gene expression in a cell or tissue at a particular moment gives an insight into the plans of the cell for protein synthesis. Recent technological advances make it possible to analyze the expression of the entire genome in a single experiment. These "gene expression assays" complement or replace previous assays which measured the gene expression of only one gene, or a select group of genes. Within this chapter we outline the development of the gene expression assay and provide examples of the wide range of disciplines in which it is used. An overview of the current technologies is given, and includes an introduction to laser capture microdissection and linear amplification of RNA, both of which have extended the application of gene expression assays. Illustrative examples in the field of cancer and neuroscience highlight the scientific achievements. This technology has made in understanding the pathogenesis of diseases, including breast cancer, Huntington's disease, and schizophrenia. With recent advances including exon arrays to investigate alternative splicing, tiling arrays to investigate novel transcription start sites, and on-chip chromatin immunoprecipitation to investigate DNA-protein interactions, the future of gene expression assays is set to further our understanding of the complexities of gene expression.
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Affiliation(s)
- Janine Kirby
- Academic Neurology Unit, Section of Neuroscience, School of Medicine and Biomedical Sciences, University of Sheffield, Sheffield S10 2RX, United Kingdom
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Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan K, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res 2007; 17:828-38. [PMID: 17568001 PMCID: PMC1891342 DOI: 10.1101/gr.6018607] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. In addition to the characterization of a large number of differentially expressed alternative 5' and 3' transcript variants and novel transcriptional units, we identified 70 fusion transcript candidates in this study. One was validated as the product of a fusion gene between BCAS4 and BCAS3 resulting from an amplification followed by a translocation event between the two loci, chr20q13 and chr17q23. Through an examination of PETs that mapped to multiple genomic locations, we identified 4055 retrotransposed loci in the human genome, of which at least three were found to be transcriptionally active. The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes.
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Affiliation(s)
- Yijun Ruan
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
- Corresponding authors.E-mail ; fax 65-64789059.E-mail ; fax 65-64789059
| | - Hong Sain Ooi
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Siew Woh Choo
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Kuo Ping Chiu
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Xiao Dong Zhao
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - K.G. Srinivasan
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Fei Yao
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Chiou Yu Choo
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jun Liu
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Pramila Ariyaratne
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Wilson G.W. Bin
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Vladimir A. Kuznetsov
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Atif Shahab
- Bioinformatics Institute, Singapore 138671, Singapore
| | - Wing-Kin Sung
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
- School of Computing, National University of Singapore, Singapore 117543, Singapore
| | - Guillaume Bourque
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Chia-Lin Wei
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
- Corresponding authors.E-mail ; fax 65-64789059.E-mail ; fax 65-64789059
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Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 2007; 8:424-36. [PMID: 17486122 DOI: 10.1038/nrg2026] [Citation(s) in RCA: 367] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The identification and characterization of mammalian core promoters and transcription start sites is a prerequisite to understanding how RNA polymerase II transcription is controlled. New experimental technologies have enabled genome-wide discovery and characterization of core promoters, revealing that most mammalian genes do not conform to the simple model in which a TATA box directs transcription from a single defined nucleotide position. In fact, most genes have multiple promoters, within which there are multiple start sites, and alternative promoter usage generates diversity and complexity in the mammalian transcriptome and proteome. Promoters can be described by their start site usage distribution, which is coupled to the occurrence of cis-regulatory elements, gene function and evolutionary constraints. A comprehensive survey of mammalian promoters is a major step towards describing and understanding transcriptional control networks.
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Affiliation(s)
- Albin Sandelin
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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Willingham AT, Dike S, Cheng J, Manak JR, Bell I, Cheung E, Drenkow J, Dumais E, Duttagupta R, Ganesh M, Ghosh S, Helt G, Nix D, Piccolboni A, Sementchenko V, Tammana H, Kapranov P, Gingeras TR. Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2006; 71:101-10. [PMID: 17480199 DOI: 10.1101/sqb.2006.71.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Regions of the genome not coding for proteins or not involved in cis-acting regulatory activities are frequently viewed as lacking in functional value. However, a number of recent large-scale studies have revealed significant regulated transcription of unannotated portions of a variety of plant and animal genomes, allowing a new appreciation of the widespread transcription of large portions of the genome. High-resolution mapping of the sites of transcription of the human and fly genomes has provided an alternative picture of the extent and organization of transcription and has offered insights for biological functions of some of the newly identified unannotated transcripts. Considerable portions of the unannotated transcription observed are developmental or cell-type-specific parts of protein-coding transcripts, often serving as novel, alternative 5' transcriptional start sites. These distal 5' portions are often situated at significant distances from the annotated gene and alternatively join with or ignore portions of other intervening genes to comprise novel unannotated protein-coding transcripts. These data support an interlaced model of the genome in which many regions serve multifunctional purposes and are highly modular in their utilization. This model illustrates the underappreciated organizational complexity of the genome and one of the functional roles of transcription from unannotated portions of the genome.
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