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Wang L, Hu X, Wang P, Shao ZM. Integrative 3' Untranslated Region-Based Model to Identify Patients with Low Risk of Axillary Lymph Node Metastasis in Operable Triple-Negative Breast Cancer. Oncologist 2018; 24:22-30. [PMID: 30082491 DOI: 10.1634/theoncologist.2017-0609] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/09/2018] [Accepted: 05/16/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sentinel lymph node biopsy is the standard surgical staging approach for operable triple-negative breast cancer (TNBC) with clinically negative axillae. In this study, we sought to develop a model to predict TNBC patients with negative nodal involvement, who would benefit from the exemption of the axillary staging surgery. MATERIALS AND METHODS We evaluated 3' untranslated region (3'UTR) profiles using microarray data of TNBC from two Gene Expression Omnibus datasets. Samples from GSE31519 were divided into training set (n = 164) and validation set (n = 163), and GSE76275 was used to construct testing set (n = 164). We built a six-member 3'UTR panel (ADD2, COL1A1, APOL2, IL21R, PKP2, and EIF4G3) using an elastic net model to estimate the risk of lymph node metastasis (LNM). Receiver operating characteristic and logistic analyses were used to assess the association between the panel and LNM status. RESULTS The six-member 3'UTR-panel showed a high distinguishing power with an area under the curve of 0.712, 0.729, and 0.708 in the training, validation, and testing sets, respectively. After adjustment by tumor size, the 3'UTR panel retained significant predictive power in the training, validation, and testing sets (odds ratio = 4.93, 4.58, and 3.59, respectively; p < .05 for all). A combinatorial analysis of the 3'UTR panel and tumor size yielded an accuracy of 97.2%, 100%, and 100% in training, validation, and testing set, respectively. CONCLUSION This study established an integrative 3'UTR-based model as a promising predictor for nodal negativity in operable TNBC. Although a prospective study is needed to validate the model, our results may permit a no axillary surgery option for selected patients. IMPLICATIONS FOR PRACTICE Currently, sentinel lymph node biopsy is the standard approach for surgical staging in breast cancer patients with negative axillae. Prediction estimation for lymph node metastasis of breast cancer relies on clinicopathological characteristics, which is unreliable, especially in triple-negative breast cancer (TNBC)-a highly heterogeneous disease. The authors developed and validated an effective prediction model for the lymph node status of patients with TNBC, which integrates 3'UTR markers and tumor size. This is the first 3'UTR-based model that will help identify TNBC patients with low risk of nodal involvement who are most likely to benefit from exemption axillary surgery.
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Affiliation(s)
- Lei Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xin Hu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Peng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
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Bens M, Sahm A, Groth M, Jahn N, Morhart M, Holtze S, Hildebrandt TB, Platzer M, Szafranski K. FRAMA: from RNA-seq data to annotated mRNA assemblies. BMC Genomics 2016; 17:54. [PMID: 26763976 PMCID: PMC4712544 DOI: 10.1186/s12864-015-2349-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/22/2015] [Indexed: 11/25/2022] Open
Abstract
Background Advances in second-generation sequencing of RNA made a near-complete characterization of transcriptomes affordable. However, the reconstruction of full-length mRNAs via de novo RNA-seq assembly is still difficult due to the complexity of eukaryote transcriptomes with highly similar paralogs and multiple alternative splice variants. Here, we present FRAMA, a genome-independent annotation tool for de novo mRNA assemblies that addresses several post-assembly tasks, such as reduction of contig redundancy, ortholog assignment, correction of misassembled transcripts, scaffolding of fragmented transcripts and coding sequence identification. Results We applied FRAMA to assemble and annotate the transcriptome of the naked mole-rat and assess the quality of the obtained compilation of transcripts with the aid of publicy available naked mole-rat gene annotations. Based on a de novo transcriptome assembly (Trinity), FRAMA annotated 21,984 naked mole-rat mRNAs (12,100 full-length CDSs), corresponding to 16,887 genes. The scaffolding of 3488 genes increased the median sequence information 1.27-fold. In total, FRAMA detected and corrected 4774 misassembled genes, which were predominantly caused by fusion of genes. A comparison with three different sources of naked mole-rat transcripts reveals that FRAMA’s gene models are better supported by RNA-seq data than any other transcript set. Further, our results demonstrate the competitiveness of FRAMA to state of the art genome-based transcript reconstruction approaches. Conclusion FRAMA realizes the de novo construction of a low-redundant transcript catalog for eukaryotes, including the extension and refinement of transcripts. Thereby, results delivered by FRAMA provide the basis for comprehensive downstream analyses like gene expression studies or comparative transcriptomics. FRAMA is available at https://github.com/gengit/FRAMA. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2349-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Bens
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Arne Sahm
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Marco Groth
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Niels Jahn
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Michaela Morhart
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
| | - Susanne Holtze
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
| | - Matthias Platzer
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Karol Szafranski
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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Costessi L, Porro F, Iaconcig A, Muro AF. TDP-43 regulates β-adducin (Add2) transcript stability. RNA Biol 2015; 11:1280-90. [PMID: 25602706 DOI: 10.1080/15476286.2014.996081] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
TDP-43 is an RNA-binding protein involved in several steps of mRNA metabolism including transcription, splicing and stability. It is also involved in ALS and FTD, neurodegenerative diseases characterized by TDP-43 nuclear depletion. We previously identified TDP-43 as a binder of the downstream element (DSE) of the β-Adducin (Add2) brain-specific polyadenylation site (A4 PAS), suggesting its involvement in pre-mRNA 3' end processing. Here, by using chimeric minigenes, we showed that TDP-43 depletion in HeLa and HEK293 cells resulted in down-regulation of both the chimeric and endogenous Add2 transcripts. Despite having confirmed TDP-43-DSE in vitro interaction, we demonstrated that the in vivo effect was not mediated by the TDP-43-DSE interaction. In fact, substitution of the Add2 DSE with viral E-SV40 and L-SV40 DSEs, which are not TDP-43 targets, still resulted in decreased Add2 mRNA levels after TDP-43 downregulation. In addition, we failed to show interaction between TDP-43 and key polyadenylation factors, such as CstF-64 and CPSF160 and excluded TDP-43 involvement in pre-mRNA cleavage and regulation of polyA tail length. These evidences allowed us to exclude the pre-hypothesized role of TDP43 in modulating 3' end processing of Add2 pre-mRNA. Finally, we showed that TDP-43 regulates Add2 gene expression levels by increasing Add2 mRNA stability. Considering that Add2 in brain participates in synapse assembly, synaptic plasticity and their stability, and its genetic inactivation in mice leads to LTP, LTD, learning and motor-coordination deficits, we hypothesize that a possible loss of Add2 function by TDP-43 depletion may contribute to ALS and FTD disease states.
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Affiliation(s)
- Luisa Costessi
- a International Center for Genetic Engineering and Biotechnology (ICGEB) ; Trieste , Italy
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Wu X, Zeng Y, Guan J, Ji G, Huang R, Li QQ. Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. BMC Genomics 2015; 16:511. [PMID: 26155789 PMCID: PMC4568572 DOI: 10.1186/s12864-015-1691-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 06/05/2015] [Indexed: 12/22/2022] Open
Abstract
Background Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs. Accurate determination of poly(A) sites helps define the 3’-ends of genes, which is important for genome annotation and gene function research. Genomic studies have revealed the presence of poly(A) sites in intergenic regions, which may be attributed to 3’-UTR extensions and novel transcript units. However, there is no systematically evaluation of intergenic poly(A) sites in plants. Results Approximately 16,000 intergenic poly(A) site clusters (IPAC) in Arabidopsis thaliana were discovered and evaluated at the whole genome level. Based on the distributions of distance from IPACs to nearby sense and antisense genes, these IPACs were classified into three categories. About 70 % of them were from previously unannotated 3’-UTR extensions to known genes, which would extend 6985 transcripts of TAIR10 genome annotation beyond their 3’-ends, with a mean extension of 134 nucleotides. 1317 IPACs were originated from novel intergenic transcripts, 37 of which were likely to be associated with protein coding transcripts. 2957 IPACs corresponded to antisense transcripts for genes on the reverse strand, which might affect 2265 protein coding genes and 39 non-protein-coding genes, including long non-coding RNA genes. The rest of IPACs could be originated from transcriptional read-through or gene mis-annotations. Conclusions The identified IPACs corresponding to novel transcripts, 3’-UTR extensions, and antisense transcription should be incorporated into current Arabidopsis genome annotation. Comprehensive characterization of IPACs from this study provides insights of alternative polyadenylation and antisense transcription in plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1691-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Yong Zeng
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Jinting Guan
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, China. .,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, China.
| | - Rongting Huang
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China. .,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA. .,Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.
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Costessi L, Porro F, Iaconcig A, Nedeljkovic M, Muro AF. Characterization of the distal polyadenylation site of the ß-adducin (Add2) pre-mRNA. PLoS One 2013; 8:e58879. [PMID: 23554949 PMCID: PMC3598803 DOI: 10.1371/journal.pone.0058879] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/07/2013] [Indexed: 12/05/2022] Open
Abstract
Most genes have multiple polyadenylation sites (PAS), which are often selected in a tissue-specific manner, altering protein products and affecting mRNA stability, subcellular localization and/or translability. Here we studied the polyadenylation mechanisms associated to the beta-adducin gene (Add2). We have previously shown that the Add2 gene has a very tight regulation of alternative polyadenylation, using proximal PAS in erythroid tissues, and a distal one in brain. Using chimeric minigenes and cell transfections we identified the core elements responsible for polyadenylation at the distal PAS. Deletion of either the hexanucleotide motif (Hm) or the downstream element (DSE) resulted in reduction of mature mRNA levels and activation of cryptic PAS, suggesting an important role for the DSE in polyadenylation of the distal Add2 PAS. Point mutation of the UG repeats present in the DSE, located immediately after the cleavage site, resulted in a reduction of processed mRNA and in the activation of the same cryptic site. RNA-EMSA showed that this region is active in forming RNA-protein complexes. Competition experiments showed that RNA lacking the DSE was not able to compete the RNA-protein complexes, supporting the hypothesis of an essential important role for the DSE. Next, using a RNA-pull down approach we identified some of the proteins bound to the DSE. Among these proteins we found PTB, TDP-43, FBP1 and FBP2, nucleolin, RNA helicase A and vigilin. All these proteins have a role in RNA metabolism, but only PTB has a reported function in polyadenylation. Additional experiments are needed to determine the precise functional role of these proteins in Add2 polyadenylation.
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Affiliation(s)
- Luisa Costessi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Fabiola Porro
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Alessandra Iaconcig
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Mirjana Nedeljkovic
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Andrés Fernando Muro
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- * E-mail:
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