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Lysophosphatidylcholine in phospholipase A 2-modified LDL triggers secretion of angiopoietin 2. Atherosclerosis 2021; 327:87-99. [PMID: 34020784 DOI: 10.1016/j.atherosclerosis.2021.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND AND AIMS Secretory phospholipase A2 (PLA2) hydrolyzes LDL phospholipids generating modified LDL particles (PLA2-LDL) with increased atherogenic properties. Exocytosis of Weibel-Palade bodies (WPB) releases angiopoietin 2 (Ang2) and externalizes P-selectin, which both play important roles in vascular inflammation. Here, we investigated the effects of PLA2-LDL on exocytosis of WPBs. METHODS Human coronary artery endothelial cells (HCAECs) were stimulated with PLA2- LDL, and its uptake and effect on Ang2 release, leukocyte adhesion, and intracellular calcium levels were measured. The effects of PLA2-LDL on Ang2 release and WPB exocytosis were measured in and ex vivo in mice. RESULTS Exposure of HCAECs to PLA2-LDL triggered Ang2 secretion and promoted leukocyte-HCAEC interaction. Lysophosphatidylcholine was identified as a critical component of PLA2-LDL regulating the WPB exocytosis, which was mediated by cell-surface proteoglycans, phospholipase C, intracellular calcium, and cytoskeletal remodeling. PLA2-LDL also induced murine endothelial WPB exocytosis in blood vessels in and ex vivo, as evidenced by secretion of Ang2 in vivo, P-selectin translocation to plasma membrane in intact endothelial cells in thoracic artery and tracheal vessels, and reduced Ang2 staining in tracheal endothelial cells. Finally, in contrast to normal human coronary arteries, in which Ang2 was present only in the endothelial layer, at sites of advanced atherosclerotic lesions, Ang2 was detected also in the intima, media, and adventitia. CONCLUSIONS Our studies reveal PLA2-LDL as a potent agonist of endothelial WPB exocytosis, resulting in increased secretion of Ang2 and translocation of P-selectin. The results provide mechanistic insight into PLA2-LDL-dependent promotion of vascular inflammation and atherosclerosis.
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2
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Dapkunas A, Rantanen V, Gui Y, Lalowski M, Sainio K, Kuure S, Sariola H. Simple 3D culture of dissociated kidney mesenchyme mimics nephron progenitor niche and facilitates nephrogenesis Wnt-independently. Sci Rep 2019; 9:13433. [PMID: 31530822 PMCID: PMC6748995 DOI: 10.1038/s41598-019-49526-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023] Open
Abstract
Kidney mesenchyme (KM) and nephron progenitors (NPs) depend on WNT activity, and their culture in vitro requires extensive repertoire of recombinant proteins and chemicals. Here we established a robust, simple culture of mouse KM using a combination of 3D Matrigel and growth media supplemented with Fibroblast Growth Factor 2 (FGF2) and Src inhibitor PP2. This allows dissociated KM to spontaneously self-organize into spheres. To reassess the requirement of WNT activity in KM self-organization and NPs maintenance, cells were cultured with short pulse of high-dose GSK3β inhibitor BIO, on a constant low-dose or without BIO. Robust proliferation at 48 hours and differentiation at 1 week were observed in cultures with high BIO pulse. Importantly, dissociated KM cultured without BIO, similarly to that exposed to constant low dose of BIO, maintained NPs up to one week and spontaneously differentiated into nephron tubules at 3 weeks of culture. Our results show that KM is maintained and induced to differentiate in a simple culture system. They also imply that GSK3β/WNT-independent pathways contribute to the maintenance and induction of mouse KM. The robust and easy 3D culture enables further characterization of NPs, and may facilitate disease modeling when applied to human cells.
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Affiliation(s)
- Arvydas Dapkunas
- Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FI-00014, Helsinki, Finland. .,Meilahti Clinical Proteomics Core Facility, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Ville Rantanen
- Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FI-00014, Helsinki, Finland.,Genome-Scale Biology Research Program, Faculty of Medicine, University of Helsinki, FI-00014, Helsinki, Finland
| | - Yujuan Gui
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland
| | - Maciej Lalowski
- Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FI-00014, Helsinki, Finland.,Meilahti Clinical Proteomics Core Facility, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland
| | - Kirsi Sainio
- Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FI-00014, Helsinki, Finland
| | - Satu Kuure
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, FI-00014, Helsinki, Finland.,GM-unit, Laboratory Animal Centre, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland
| | - Hannu Sariola
- Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, FI-00014, Helsinki, Finland
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3
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Turunen SP, von Nandelstadh P, Öhman T, Gucciardo E, Seashore-Ludlow B, Martins B, Rantanen V, Li H, Höpfner K, Östling P, Varjosalo M, Lehti K. FGFR4 phosphorylates MST1 to confer breast cancer cells resistance to MST1/2-dependent apoptosis. Cell Death Differ 2019; 26:2577-2593. [PMID: 30903103 PMCID: PMC7224384 DOI: 10.1038/s41418-019-0321-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/18/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023] Open
Abstract
Cancer cells balance with the equilibrium of cell death and growth to expand and metastasize. The activity of mammalian sterile20-like kinases (MST1/2) has been linked to apoptosis and tumor suppression via YAP/Hippo pathway-independent and -dependent mechanisms. Using a kinase substrate screen, we identified here MST1 and MST2 among the top substrates for fibroblast growth factor receptor 4 (FGFR4). In COS-1 cells, MST1 was phosphorylated at Y433 residue in an FGFR4 kinase activity-dependent manner, as assessed by mass spectrometry. Blockade of this phosphorylation by Y433F mutation induced MST1 activation, as indicated by increased threonine phosphorylation of MST1/2, and the downstream substrate MOB1, in FGFR4-overexpressing T47D and MDA-MB-231 breast cancer cells. Importantly, the specific knockdown or short-term inhibition of FGFR4 in endogenous models of human HER2+ breast cancer cells likewise led to increased MST1/2 activation, in conjunction with enhanced MST1 nuclear localization and generation of N-terminal cleaved and autophosphorylated MST1. Unexpectedly, MST2 was also essential for this MST1/N activation and coincident apoptosis induction, although these two kinases, as well as YAP, were differentially regulated in the breast cancer models analyzed. Moreover, pharmacological FGFR4 inhibition specifically sensitized the HER2+ MDA-MB-453 breast cancer cells, not only to HER2/EGFR and AKT/mTOR inhibitors, but also to clinically relevant apoptosis modulators. In TCGA cohort, FGFR4 overexpression correlated with abysmal HER2+ breast carcinoma patient outcome. Therefore, our results uncover a clinically relevant, targetable mechanism of FGFR4 oncogenic activity via suppression of the stress-associated MST1/2-induced apoptosis machinery in tumor cells with prominent HER/ERBB and FGFR4 signaling-driven proliferation.
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Affiliation(s)
- S Pauliina Turunen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Pernilla von Nandelstadh
- Research Programs Unit, Genome-Scale Biology, Medicum, University of Helsinki and Helsinki University Hospital, Helsinki, FI-00014, Finland
| | - Tiina Öhman
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, FI-00014, Finland
| | - Erika Gucciardo
- Research Programs Unit, Genome-Scale Biology, Medicum, University of Helsinki and Helsinki University Hospital, Helsinki, FI-00014, Finland
| | - Brinton Seashore-Ludlow
- Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Beatriz Martins
- Research Programs Unit, Genome-Scale Biology, Medicum, University of Helsinki and Helsinki University Hospital, Helsinki, FI-00014, Finland
| | - Ville Rantanen
- Research Programs Unit, Genome-Scale Biology, Medicum, University of Helsinki and Helsinki University Hospital, Helsinki, FI-00014, Finland
| | - Huini Li
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Katrin Höpfner
- Research Programs Unit, Genome-Scale Biology, Medicum, University of Helsinki and Helsinki University Hospital, Helsinki, FI-00014, Finland
| | - Päivi Östling
- Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, SE-171 77, Sweden
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, FI-00014, Finland
| | - Kaisa Lehti
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, SE-171 77, Sweden. .,Research Programs Unit, Genome-Scale Biology, Medicum, University of Helsinki and Helsinki University Hospital, Helsinki, FI-00014, Finland.
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4
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Cervera A, Rantanen V, Ovaska K, Laakso M, Nuñez-Fontarnau J, Alkodsi A, Casado J, Facciotto C, Häkkinen A, Louhimo R, Karinen S, Zhang K, Lavikka K, Lyly L, Pal Singh M, Hautaniemi S. Anduril 2: upgraded large-scale data integration framework. Bioinformatics 2019; 35:3815-3817. [DOI: 10.1093/bioinformatics/btz133] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/28/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Abstract
Summary
Anduril is an analysis and integration framework that facilitates the design, use, parallelization and reproducibility of bioinformatics workflows. Anduril has been upgraded to use Scala for pipeline construction, which simplifies software maintenance, and facilitates design of complex pipelines. Additionally, Anduril’s bioinformatics repository has been expanded with multiple components, and tutorial pipelines, for next-generation sequencing data analysis.
Availabilityand implementation
Freely available at http://anduril.org.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alejandra Cervera
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Ville Rantanen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Kristian Ovaska
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Marko Laakso
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | | | - Amjad Alkodsi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Julia Casado
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Chiara Facciotto
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Antti Häkkinen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Riku Louhimo
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Sirkku Karinen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Kaiyang Zhang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Kari Lavikka
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Lauri Lyly
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Maninder Pal Singh
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki
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Abstract
The transcription factor PROX1 is essential for development and cell fate specification. Its function in cancer is context-dependent since PROX1 has been shown to play both oncogenic and tumour suppressive roles. Here, we show that PROX1 suppresses the transcription of MMP14, a metalloprotease involved in angiogenesis and cancer invasion, by binding and suppressing the activity of MMP14 promoter. Prox1 deletion in murine dermal lymphatic vessels in vivo and in human LECs increased MMP14 expression. In a hepatocellular carcinoma cell line expressing high endogenous levels of PROX1, its silencing increased both MMP14 expression and MMP14-dependent invasion in 3D. Moreover, PROX1 ectopic expression reduced the MMP14-dependent 3D invasiveness of breast cancer cells and angiogenic sprouting of blood endothelial cells in conjunction with MMP14 suppression. Our study uncovers a new transcriptional regulatory mechanism of cancer cell invasion and endothelial cell specification.
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Pezzini F, Bianchi M, Benfatto S, Griggio F, Doccini S, Carrozzo R, Dapkunas A, Delledonne M, Santorelli FM, Lalowski MM, Simonati A. The Networks of Genes Encoding Palmitoylated Proteins in Axonal and Synaptic Compartments Are Affected in PPT1 Overexpressing Neuronal-Like Cells. Front Mol Neurosci 2017; 10:266. [PMID: 28878621 PMCID: PMC5572227 DOI: 10.3389/fnmol.2017.00266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/07/2017] [Indexed: 12/13/2022] Open
Abstract
CLN1 disease (OMIM #256730) is an early childhood ceroid-lipofuscinosis associated with mutated CLN1, whose product Palmitoyl-Protein Thioesterase 1 (PPT1) is a lysosomal enzyme involved in the removal of palmitate residues from S-acylated proteins. In neurons, PPT1 expression is also linked to synaptic compartments. The aim of this study was to unravel molecular signatures connected to CLN1. We utilized SH-SY5Y neuroblastoma cells overexpressing wild type CLN1 (SH-p.wtCLN1) and five selected CLN1 patients’ mutations. The cellular distribution of wtPPT1 was consistent with regular processing of endogenous protein, partially detected inside Lysosomal Associated Membrane Protein 2 (LAMP2) positive vesicles, while the mutants displayed more diffuse cytoplasmic pattern. Transcriptomic profiling revealed 802 differentially expressed genes (DEGs) in SH-p.wtCLN1 (as compared to empty-vector transfected cells), whereas the number of DEGs detected in the two mutants (p.L222P and p.M57Nfs*45) was significantly lower. Bioinformatic scrutiny linked DEGs with neurite formation and neuronal transmission. Specifically, neuritogenesis and proliferation of neuronal processes were predicted to be hampered in the wtCLN1 overexpressing cell line, and these findings were corroborated by morphological investigations. Palmitoylation survey identified 113 palmitoylated protein-encoding genes in SH-p.wtCLN1, including 25 ones simultaneously assigned to axonal growth and synaptic compartments. A remarkable decrease in the expression of palmitoylated proteins, functionally related to axonal elongation (GAP43, CRMP1 and NEFM) and of the synaptic marker SNAP25, specifically in SH-p.wtCLN1 cells was confirmed by immunoblotting. Subsequent, bioinformatic network survey of DEGs assigned to the synaptic annotations linked 81 DEGs, including 23 ones encoding for palmitoylated proteins. Results obtained in this experimental setting outlined two affected functional modules (connected to the axonal and synaptic compartments), which can be associated with an altered gene dosage of wtCLN1. Moreover, these modules were interrelated with the pathological effects associated with loss of PPT1 function, similarly as observed in the Ppt1 knockout mice and patients with CLN1 disease.
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Affiliation(s)
- Francesco Pezzini
- Neurology (Neuropathology and Child Neurology), Department of Neuroscience, Biomedicine and Movement, University of VeronaVerona, Italy
| | - Marzia Bianchi
- Unit of Muscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Children's HospitalRome, Italy
| | - Salvatore Benfatto
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | - Francesca Griggio
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | - Stefano Doccini
- Molecular Medicine, IRCCS Stella MarisCalambrone-Pisa, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, IRCCS Bambino Gesù Children's HospitalRome, Italy
| | - Arvydas Dapkunas
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of HelsinkiHelsinki, Finland
| | - Massimo Delledonne
- Functional Genomics Center, Department of Biotechnology, University of VeronaVerona, Italy
| | | | - Maciej M Lalowski
- Medicum, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of HelsinkiHelsinki, Finland
| | - Alessandro Simonati
- Neurology (Neuropathology and Child Neurology), Department of Neuroscience, Biomedicine and Movement, University of VeronaVerona, Italy
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Ylivinkka I, Sihto H, Tynninen O, Hu Y, Laakso A, Kivisaari R, Laakkonen P, Keski-Oja J, Hyytiäinen M. Motility of glioblastoma cells is driven by netrin-1 induced gain of stemness. J Exp Clin Cancer Res 2017; 36:9. [PMID: 28069038 PMCID: PMC5223529 DOI: 10.1186/s13046-016-0482-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glioblastoma is an untreatable brain cancer. The tumors contain a population of stem-like cells which are highly invasive and resistant to therapies. These cells are the main reason for the lethality of glioblastoma. Extracellular guidance molecule netrin-1 promotes the invasiveness and survival of various cancer cell types. We have previously found that netrin-1 activates Notch signaling, and Notch signaling associates with cell stemness. Therefore, we have here investigated the effects of netrin-1 on glioblastoma pathogenesis and glioblastoma cell stemness. METHODS Glioma tissue microarrays were stained with immunohistochemistry and the results were used to evaluate the association between netrin-1 and survival of glioma patients. The localization of netrin-1 was analyzed utilizing fresh frozen glioblastoma tissues. The glioma cell invasion was investigated using ex vivo glioma tissue cultures and newly established primary cell cultures in 3D in vitro invasion assays. Intracranial mouse xenograft models were utilized to investigate the effects of netrin-1 on glioblastoma growth and invasion in vivo. RESULTS Netrin-1 expression associated with poor patient prognosis in grade II-III gliomas. In addition, its expression correlated with the stem-like cell marker nestin. Netrin-1 overexpression in cultured cells led to increased formation of stem-like cell spheroids. In glioblastoma tumor biopsies netrin-1 localized to hypoxic tumor areas known to be rich in the stem-like cells. In xenograft mouse models netrin-1 expression altered the phenotype of non-invasive glioblastoma cells into diffusively invading and increased the expression of glioma stem-like cell markers. Furthermore, a distinct invasion pattern where netrin-1 positive cells were following the invasive stem-like cells was detected both in mouse models and ex vivo human glioblastoma tissue cultures. Inhibition of netrin-1 signaling targeted especially the stem-like cells and inhibited their infiltrative growth. CONCLUSIONS Our findings describe netrin-1 as an important regulator of glioblastoma cell stemness and motility. Netrin-1 activates Notch signaling in glioblastoma cells resulting in subsequent gain of stemness and enhanced invasiveness of these cells. Moreover, inhibition of netrin-1 signaling may offer a way to target stem-like cells.
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Affiliation(s)
- Irene Ylivinkka
- Translational Cancer Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,The Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Harri Sihto
- Translational Cancer Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Tynninen
- Department of Pathology, Haartman Institute, University of Helsinki and HUSLAB, Helsinki, Finland
| | - Yizhou Hu
- Translational Cancer Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Aki Laakso
- Department of Neurosurgery, Helsinki University Hospital and Clinical Neurosciences, Neurosurgery, University of Helsinki, Helsinki, Finland
| | - Riku Kivisaari
- Department of Neurosurgery, Helsinki University Hospital and Clinical Neurosciences, Neurosurgery, University of Helsinki, Helsinki, Finland
| | - Pirjo Laakkonen
- Translational Cancer Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jorma Keski-Oja
- Translational Cancer Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,The Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Marko Hyytiäinen
- Translational Cancer Biology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Translational Cancer Biology Research Program, Biomedicum, University of Helsinki, B530b2, PL 63 (Haartmaninkatu 8), 00014, Helsinki, Finland.
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8
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Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S. SePIA: RNA and small RNA sequence processing, integration, and analysis. BioData Min 2016; 9:20. [PMID: 27213017 PMCID: PMC4875694 DOI: 10.1186/s13040-016-0099-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 05/08/2016] [Indexed: 02/07/2023] Open
Abstract
Background Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. Results We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow’s extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. Conclusion SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA’s modular design enables robust customization to a given experiment while maintaining overall workflow structure. It is available at http://anduril.org/sepia. Electronic supplementary material The online version of this article (doi:10.1186/s13040-016-0099-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine Icay
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Ping Chen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Alejandra Cervera
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Ville Rantanen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Rainer Lehtonen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
| | - Sampsa Hautaniemi
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland
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Seeing Is Believing: Quantifying Is Convincing: Computational Image Analysis in Biology. FOCUS ON BIO-IMAGE INFORMATICS 2016; 219:1-39. [DOI: 10.1007/978-3-319-28549-8_1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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