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Gagliardi S, Truffi M, Tinelli V, Garofalo M, Pandini C, Cotta Ramusino M, Perini G, Costa A, Negri S, Mazzucchelli S, Bonizzi A, Sitia L, Busacca M, Sevieri M, Mocchi M, Ricciardi A, Prosperi D, Corsi F, Cereda C, Morasso C. Bisdemethoxycurcumin (BDC)-Loaded H-Ferritin-Nanocages Mediate the Regulation of Inflammation in Alzheimer's Disease Patients. Int J Mol Sci 2022; 23:9237. [PMID: 36012501 PMCID: PMC9409287 DOI: 10.3390/ijms23169237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Bisdemethoxycurcumin (BDC) might be an inflammation inhibitor in Alzheimer's Disease (AD). However, BDC is almost insoluble in water, poorly absorbed by the organism, and degrades rapidly. We thus developed a new nanoformulation of BDC based on H-Ferritin nanocages (BDC-HFn). METHODS We tested the BDC-HFn solubility, stability, and ability to cross a blood-brain barrier (BBB) model. We tested the effect of BDC-HFn on AD and control (CTR) PBMCs to evaluate the transcriptomic profile by RNA-seq. RESULTS We developed a nanoformulation with a diameter of 12 nm to improve the solubility and stability. The comparison of the transcriptomics analyses between AD patients before and after BDC-HFn treatment showed a major number of DEG (2517). The pathway analysis showed that chemokines and macrophages activation differed between AD patients and controls after BDC-HFn treatment. BDC-HFn binds endothelial cells from the cerebral cortex and crosses through a BBB in vitro model. CONCLUSIONS Our data showed how BDC-Hfn could improve the stability of BDC. Significant differences in genes associated with inflammation between the same patients before and after BDC-Hfn treatment have been found. Inflammatory genes that are upregulated between AD and CTR after BDC-HFn treatment are converted and downregulated, suggesting a possible therapeutic approach.
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Affiliation(s)
| | - Marta Truffi
- Istituti Clinici Scientifici Maugeri IRCCS Spa SB, 27100 Pavia, Italy
| | - Veronica Tinelli
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, 20126 Milano, Italy
| | | | | | | | | | - Alfredo Costa
- IRCCS Mondino Foundation, 27100 Pavia, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Sara Negri
- Istituti Clinici Scientifici Maugeri IRCCS Spa SB, 27100 Pavia, Italy
| | - Serena Mazzucchelli
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, Via G. B. Grassi 74, 20157 Milano, Italy
| | - Arianna Bonizzi
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, Via G. B. Grassi 74, 20157 Milano, Italy
| | - Leopoldo Sitia
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, Via G. B. Grassi 74, 20157 Milano, Italy
| | | | - Marta Sevieri
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, Via G. B. Grassi 74, 20157 Milano, Italy
| | - Michela Mocchi
- Istituti Clinici Scientifici Maugeri IRCCS Spa SB, 27100 Pavia, Italy
| | | | - Davide Prosperi
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, 20126 Milano, Italy
| | - Fabio Corsi
- Istituti Clinici Scientifici Maugeri IRCCS Spa SB, 27100 Pavia, Italy
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, 20126 Milano, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, Via G. B. Grassi 74, 20157 Milano, Italy
| | | | - Carlo Morasso
- Istituti Clinici Scientifici Maugeri IRCCS Spa SB, 27100 Pavia, Italy
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Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth. Biomedicines 2021; 9:biomedicines9091120. [PMID: 34572306 PMCID: PMC8472193 DOI: 10.3390/biomedicines9091120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs show relevant implications in various biological and pathological processes. Thus, understanding the biological implications of these molecules in stem cell biology still represents a major challenge. The aim of this work is to study the transcriptional dysregulation of 357 non-coding genes, found through RNA-Seq approach, in murine neural precursor cells expanded inside the 3D micro-scaffold Nichoid versus standard culture conditions. Through weighted co-expression network analysis and functional enrichment, we highlight the role of non-coding RNAs in altering the expression of coding genes involved in mechanotransduction, stemness, and neural differentiation. Moreover, as non-coding RNAs are poorly conserved between species, we focus on those with human homologue sequences, performing further computational characterization. Lastly, we looked for isoform switching as possible mechanism in altering coding and non-coding gene expression. Our results provide a comprehensive dissection of the 3D scaffold Nichoid's influence on the biological and genetic response of neural precursor cells. These findings shed light on the possible role of non-coding RNAs in 3D cell growth, indicating that also non-coding RNAs are implicated in cellular response to mechanical stimuli.
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Nanoribbon-Based Electronic Detection of a Glioma-Associated Circular miRNA. BIOSENSORS-BASEL 2021; 11:bios11070237. [PMID: 34356707 PMCID: PMC8301916 DOI: 10.3390/bios11070237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022]
Abstract
Nanoribbon chips, based on “silicon-on-insulator” structures (SOI-NR chips), have been fabricated. These SOI-NR chips, whose surface was sensitized with covalently immobilized oligonucleotide molecular probes (oDNA probes), have been employed for the nanoribbon biosensor-based detection of a circular ribonucleic acid (circRNA) molecular marker of glioma in humans. The nucleotide sequence of the oDNA probes was complimentary to the sequence of the target oDNA. The latter represents a synthetic analogue of a glioma marker—NFIX circular RNA. In this way, the detection of target oDNA molecules in a pure buffer has been performed. The lowest concentration of the target biomolecules, detectable in our experiments, was of the order of ~10−17 M. The SOI-NR sensor chips proposed herein have allowed us to reveal an elevated level of the NFIX circular RNA in the blood of a glioma patient.
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Carelli S, Giallongo T, Rey F, Barzaghini B, Zandrini T, Pulcinelli A, Nardomarino R, Cerullo G, Osellame R, Cereda C, Zuccotti GV, Raimondi MT. Neural precursors cells expanded in a 3D micro-engineered niche present enhanced therapeutic efficacy in vivo. Nanotheranostics 2021; 5:8-26. [PMID: 33391972 PMCID: PMC7738947 DOI: 10.7150/ntno.50633] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Rationale: Stem Cells (SCs) show a great potential in therapeutics for restoring and regenerating native tissues. The clinical translation of SCs therapies is currently hindered by the inability to expand SCs in vitro in large therapeutic dosages, while maintaining their safety and potency. The use of biomaterials allows for the generation of active biophysical signals for directing SCs fate through 3D micro-scaffolds, such as the one named “Nichoid”, fabricated with two-photon laser polymerization with a spatial resolution of 100 nm. The aims of this study were: i) to investigate the proliferation, differentiation and stemness properties of neural precursor cells (NPCs) following their cultivation inside the Nichoid micro-scaffold; ii) to assess the therapeutic effect and safety in vivo of NPCs cultivated in the Nichoid in a preclinical experimental model of Parkinson's Disease (PD). Methods: Nichoids were fabricated by two photon laser polymerization onto circular glass coverslips using a home-made SZ2080 photoresist. NPCs were grown inside the Nichoid for 7 days, counted and characterized with RNA-Seq, Real Time PCR analysis, immunofluorescence and Western Blot. Then, NPCs were transplanted in a murine experimental model of PD, in which parkinsonism was induced by the intraperitoneal administration of the neurotoxin MPTP in C57/bl mice. The efficacy of engrafted Nichoid-expanded NPCs was evaluated by means of specific behavioral tests and, after animal sacrifice, with immunohistochemical studies in brain slices. Results: NPCs grown inside the Nichoid show a significantly higher cell viability and proliferation than in standard culture conditions in suspension. Furthermore, we report the mechanical conditioning of NPCs in 3D micro-scaffolds, showing a significant increase in the expression of pluripotency genes. We also report that such mechanical reprogramming of NPCs produces an enhanced therapeutic effect in the in vivo model of PD. Recovery of PD symptoms was significantly increased when animals were treated with Nichoid-grown NPCs, and this is accompanied by the recovery of dopaminergic markers expression in the striatum of PD affected mice. Conclusion: SCs demonstrated an increase in pluripotency potential when expanded inside the Nichoid, without the need of any genetic modification of cells, showing great promise for large-scale production of safe and functional cell therapies to be used in multiple clinical applications.
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Affiliation(s)
- Stephana Carelli
- Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", L. Sacco Department of Biomedical and Clinical Sciences, University of Milano, Milano, 20157, Italy
| | - Toniella Giallongo
- Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", L. Sacco Department of Biomedical and Clinical Sciences, University of Milano, Milano, 20157, Italy
| | - Federica Rey
- Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", L. Sacco Department of Biomedical and Clinical Sciences, University of Milano, Milano, 20157, Italy
| | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, 20133, Italy
| | - Tommaso Zandrini
- Istituto di Fotonica e Nanotecnologie (IFN)-CNR and Department of Physics, Politecnico di Milano, Milano, 20133, Italy
| | - Andrea Pulcinelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, 20133, Italy
| | - Riccardo Nardomarino
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, 20133, Italy
| | - Giulio Cerullo
- Istituto di Fotonica e Nanotecnologie (IFN)-CNR and Department of Physics, Politecnico di Milano, Milano, 20133, Italy
| | - Roberto Osellame
- Istituto di Fotonica e Nanotecnologie (IFN)-CNR and Department of Physics, Politecnico di Milano, Milano, 20133, Italy
| | - Cristina Cereda
- Genomic and Postgenomic Lab, IRCCS Mondino Foundation, Pavia, 27100, Italy
| | - Gian Vincenzo Zuccotti
- Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", L. Sacco Department of Biomedical and Clinical Sciences, University of Milano, Milano, 20157, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, 20133, Italy
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Garofalo M, Pandini C, Bordoni M, Pansarasa O, Rey F, Costa A, Minafra B, Diamanti L, Zucca S, Carelli S, Cereda C, Gagliardi S. Alzheimer's, Parkinson's Disease and Amyotrophic Lateral Sclerosis Gene Expression Patterns Divergence Reveals Different Grade of RNA Metabolism Involvement. Int J Mol Sci 2020; 21:ijms21249500. [PMID: 33327559 PMCID: PMC7765024 DOI: 10.3390/ijms21249500] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/27/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by a progressive degeneration of the central or peripheral nervous systems. A central role of the RNA metabolism has emerged in these diseases, concerning mRNAs processing and non-coding RNAs biogenesis. We aimed to identify possible common grounds or differences in the dysregulated pathways of AD, PD, and ALS. To do so, we performed RNA-seq analysis to investigate the deregulation of both coding and long non-coding RNAs (lncRNAs) in ALS, AD, and PD patients and controls (CTRL) in peripheral blood mononuclear cells (PBMCs). A total of 293 differentially expressed (DE) lncRNAs and 87 mRNAs were found in ALS patients. In AD patients a total of 23 DE genes emerged, 19 protein coding genes and four lncRNAs. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses, we found common affected pathways and biological processes in ALS and AD. In PD patients only five genes were found to be DE. Our data brought to light the importance of lncRNAs and mRNAs regulation in three principal neurodegenerative disorders, offering starting points for new investigations on deregulated pathogenic mechanisms.
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Affiliation(s)
- Maria Garofalo
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Cecilia Pandini
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
| | - Matteo Bordoni
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy;
| | - Orietta Pansarasa
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
| | - Federica Rey
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, University of Milan, Via G.B Grassi 74, 20157 Milan, Italy; (F.R.); (S.C.)
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, Via G.B. Grassi 74, 20157 Milano, Italy
| | - Alfredo Costa
- Unit of Behavioral Neurology, IRCCS Mondino Foundation, 27100 Pavia, Italy;
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Brigida Minafra
- Parkinson Unit and Movement disorders Mondino Foundation IRCCS, 27100 Pavia, Italy;
| | - Luca Diamanti
- Neuro-Oncology Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy;
| | - Susanna Zucca
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- enGenomesrl, 27100 Pavia, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, University of Milan, Via G.B Grassi 74, 20157 Milan, Italy; (F.R.); (S.C.)
- Pediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milano, Via G.B. Grassi 74, 20157 Milano, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
- Correspondence:
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (M.G.); (C.P.); (O.P.); (S.Z.); (S.G.)
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Dissecting the Effect of a 3D Microscaffold on the Transcriptome of Neural Stem Cells with Computational Approaches: A Focus on Mechanotransduction. Int J Mol Sci 2020; 21:ijms21186775. [PMID: 32942778 PMCID: PMC7555048 DOI: 10.3390/ijms21186775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022] Open
Abstract
3D cell cultures are becoming more and more important in the field of regenerative medicine due to their ability to mimic the cellular physiological microenvironment. Among the different types of 3D scaffolds, we focus on the Nichoid, a miniaturized scaffold with a structure inspired by the natural staminal niche. The Nichoid can activate cellular responses simply by subjecting the cells to mechanical stimuli. This kind of influence results in different cellular morphology and organization, but the molecular bases of these changes remain largely unknown. Through RNA-Seq approach on murine neural precursors stem cells expanded inside the Nichoid, we investigated the deregulated genes and pathways showing that the Nichoid causes alteration in genes strongly connected to mechanobiological functions. Moreover, we fully dissected this mechanism highlighting how the changes start at a membrane level, with subsequent alterations in the cytoskeleton, signaling pathways, and metabolism, all leading to a final alteration in gene expression. The results shown here demonstrate that the Nichoid influences the biological and genetic response of stem cells thorough specific alterations of cellular signaling. The characterization of these pathways elucidates the role of mechanical manipulation on stem cells, with possible implications in regenerative medicine applications.
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Dehghannasiri R, Szabo L, Salzman J. Ambiguous splice sites distinguish circRNA and linear splicing in the human genome. Bioinformatics 2020; 35:1263-1268. [PMID: 30192918 DOI: 10.1093/bioinformatics/bty785] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/04/2018] [Accepted: 09/04/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Identification of splice sites is critical to gene annotation and to determine which sequences control circRNA biogenesis. Full-length RNA transcripts could in principle complete annotations of introns and exons in genomes without external ontologies, i.e., ab initio. However, whether it is possible to reconstruct genomic positions where splicing occurs from full-length transcripts, even if sampled in the absence of noise, depends on the genome sequence composition. If it is not, there exist provable limits on the use of RNA-Seq to define splice locations (linear or circular) in the genome. RESULTS We provide a formal definition of splice site ambiguity due to the genomic sequence by introducing equivalent junction, which is the set of local genomic positions resulting in the same RNA sequence when joined through RNA splicing. We show that equivalent junctions are prevalent in diverse eukaryotic genomes and occur in 88.64% and 78.64% of annotated human splice sites in linear and circRNA junctions, respectively. The observed fractions of equivalent junctions and the frequency of many individual motifs are statistically significant when compared against the null distribution computed via simulation or closed-form. The frequency of equivalent junctions establishes a fundamental limit on the possibility of ab initio reconstruction of RNA transcripts without appealing to the ontology of "GT-AG" boundaries defining introns. Said differently, completely ab initio is impossible in the vast majority of splice sites in annotated circRNAs and linear transcripts. AVAILABILITY AND IMPLEMENTATION Two python scripts generating an equivalent junction sequence per junction are available at: https://github.com/salzmanlab/Equivalent-Junctions. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Linda Szabo
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University, Stanford, CA, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
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RNA-Seq profiling in peripheral blood mononuclear cells of amyotrophic lateral sclerosis patients and controls. Sci Data 2019; 6:190006. [PMID: 30720798 PMCID: PMC6362931 DOI: 10.1038/sdata.2019.6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/14/2018] [Indexed: 12/12/2022] Open
Abstract
Coding and long non-coding RNA (lncRNA) metabolism is now revealing its crucial role in Amyotrophic Lateral Sclerosis (ALS) pathogenesis. In this work, we present a dataset obtained via Illumina RNA-seq analysis on Peripheral Blood Mononuclear Cells (PBMCs) from sporadic and mutated ALS patients (mutations in FUS, TARDBP, SOD1 and VCP genes) and healthy controls. This dataset allows the whole-transcriptome characterization of PBMCs content, both in terms of coding and non-coding RNAs, in order to compare the disease state to the healthy controls, both for sporadic patients and for mutated patients. Our dataset is a starting point for the omni-comprehensive analysis of coding and lncRNAs, from an easy to withdraw, manage and store tissue that shows to be a suitable model for RNA profiling in ALS.
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von Reumont BM. Studying Smaller and Neglected Organisms in Modern Evolutionary Venomics Implementing RNASeq (Transcriptomics)-A Critical Guide. Toxins (Basel) 2018; 10:toxins10070292. [PMID: 30012955 PMCID: PMC6070909 DOI: 10.3390/toxins10070292] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/06/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022] Open
Abstract
Venoms are evolutionary key adaptations that species employ for defense, predation or competition. However, the processes and forces that drive the evolution of venoms and their toxin components remain in many aspects understudied. In particular, the venoms of many smaller, neglected (mostly invertebrate) organisms are not characterized in detail, especially with modern methods. For the majority of these taxa, even their biology is only vaguely known. Modern evolutionary venomics addresses the question of how venoms evolve by applying a plethora of -omics methods. These recently became so sensitive and enhanced that smaller, neglected organisms are now more easily accessible to comparatively study their venoms. More knowledge about these taxa is essential to better understand venom evolution in general. The methodological core pillars of integrative evolutionary venomics are genomics, transcriptomics and proteomics, which are complemented by functional morphology and the field of protein synthesis and activity tests. This manuscript focuses on transcriptomics (or RNASeq) as one toolbox to describe venom evolution in smaller, neglected taxa. It provides a hands-on guide that discusses a generalized RNASeq workflow, which can be adapted, accordingly, to respective projects. For neglected and small taxa, generalized recommendations are difficult to give and conclusions need to be made individually from case to case. In the context of evolutionary venomics, this overview highlights critical points, but also promises of RNASeq analyses. Methodologically, these concern the impact of read processing, possible improvements by perfoming multiple and merged assemblies, and adequate quantification of expressed transcripts. Readers are guided to reappraise their hypotheses on venom evolution in smaller organisms and how robustly these are testable with the current transcriptomics toolbox. The complementary approach that combines particular proteomics but also genomics with transcriptomics is discussed as well. As recently shown, comparative proteomics is, for example, most important in preventing false positive identifications of possible toxin transcripts. Finally, future directions in transcriptomics, such as applying 3rd generation sequencing strategies to overcome difficulties by short read assemblies, are briefly addressed.
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Affiliation(s)
- Björn Marcus von Reumont
- Justus Liebig University of Giessen, Institute for Insect Biotechnology, Heinrich Buff Ring 58, 35392 Giessen, Germany.
- Natural History Museum, Department of Life Sciences, Cromwell Rd, London SW75BD, UK.
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Long non-coding and coding RNAs characterization in Peripheral Blood Mononuclear Cells and Spinal Cord from Amyotrophic Lateral Sclerosis patients. Sci Rep 2018; 8:2378. [PMID: 29402919 PMCID: PMC5799454 DOI: 10.1038/s41598-018-20679-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/22/2018] [Indexed: 12/12/2022] Open
Abstract
Alteration in RNA metabolism, concerning both coding and long non-coding RNAs (lncRNAs), may play an important role in Amyotrophic Lateral Sclerosis (ALS) pathogenesis. In this work, we performed a whole transcriptome RNA-seq analysis to investigate the regulation of non-coding and coding RNAs in Sporadic ALS patients (SALS), mutated ALS patients (FUS, TARDBP and SOD1) and matched controls in Peripheral Blood Mononuclear Cells (PBMC). Selected transcripts were validated in spinal cord tissues. A total of 293 differentially expressed (DE) lncRNAs was found in SALS patients, whereas a limited amount of lncRNAs was deregulated in mutated patients. A total of 87 mRNAs was differentially expressed in SALS patients; affected genes showed an association with transcription regulation, immunity and apoptosis pathways. Taken together our data highlighted the importance of extending the knowledge on transcriptomic molecular alterations and on the significance of regulatory lncRNAs classes in the understanding of ALS disease. Our data brought the light on the importance of lncRNAs and mRNAs regulation in central and peripheral systems, offering starting points for new investigations about pathogenic mechanism involved in ALS disease.
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Abstract
The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases. We conclude with a discussion of the current experimental progress on the topic.
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12
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Sciarrillo R, Wojtuszkiewicz A, Kooi IE, Gómez VE, Boggi U, Jansen G, Kaspers GJ, Cloos J, Giovannetti E. Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models. J Vis Exp 2016:54714. [PMID: 28060337 PMCID: PMC5226372 DOI: 10.3791/54714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Drug resistance remains a major problem in the treatment of cancer for both hematological malignancies and solid tumors. Intrinsic or acquired resistance can be caused by a range of mechanisms, including increased drug elimination, decreased drug uptake, drug inactivation and alterations of drug targets. Recent data showed that other than by well-known genetic (mutation, amplification) and epigenetic (DNA hypermethylation, histone post-translational modification) modifications, drug resistance mechanisms might also be regulated by splicing aberrations. This is a rapidly growing field of investigation that deserves future attention in order to plan more effective therapeutic approaches. The protocol described in this paper is aimed at investigating the impact of aberrant splicing on drug resistance in solid tumors and hematological malignancies. To this goal, we analyzed the transcriptomic profiles of several in vitro models through RNA-seq and established a qRT-PCR based method to validate candidate genes. In particular, we evaluated the differential splicing of DDX5 and PKM transcripts. The aberrant splicing detected by the computational tool MATS was validated in leukemic cells, showing that different DDX5 splice variants are expressed in the parental vs. resistant cells. In these cells, we also observed a higher PKM2/PKM1 ratio, which was not detected in the Panc-1 gemcitabine-resistant counterpart compared to parental Panc-1 cells, suggesting a different mechanism of drug-resistance induced by gemcitabine exposure.
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Affiliation(s)
- Rocco Sciarrillo
- Department of Pediatric Oncology/Hematology, VU University Medical Center; Department of Hematology, VU University Medical Center; Department of Medical Oncology, VU University Medical Center
| | | | - Irsan E Kooi
- Department of Clinical Genetics, VU University Medical Center
| | | | - Ugo Boggi
- Division of General and Transplant Surgery, Azienda Ospedaliera Universitaria Pisana, Universita' di Pisa
| | - Gerrit Jansen
- Amsterdam Immunology and Rheumatology Center, VU University Medical Center
| | - Gert-Jan Kaspers
- Department of Pediatric Oncology/Hematology, VU University Medical Center; Princess Máxima Center for Pediatric Oncology
| | - Jacqueline Cloos
- Department of Pediatric Oncology/Hematology, VU University Medical Center
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center; Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa; Institute of Nanoscience and Nanotechnology, CNR-Nano;
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Yu W, Li Y, Wang Z, Liu L, Liu J, Ding F, Zhang X, Cheng Z, Chen P, Dou J. Transcriptomic changes in human renal proximal tubular cells revealed under hypoxic conditions by RNA sequencing. Int J Mol Med 2016; 38:894-902. [PMID: 27432315 DOI: 10.3892/ijmm.2016.2677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 07/07/2016] [Indexed: 11/05/2022] Open
Abstract
Chronic hypoxia often occurs among patients with chronic kidney disease (CKD). Renal proximal tubular cells may be the primary target of a hypoxic insult. However, the underlying transcriptional mechanisms remain undefined. In this study, we revealed the global changes in gene expression in HK‑2 human renal proximal tubular cells under hypoxic and normoxic conditions. We analyzed the transcriptome of HK‑2 cells exposed to hypoxia for 24 h using RNA sequencing. A total of 279 differentially expressed genes was examined, as these genes could potentially explain the differences in HK‑2 cells between hypoxic and normoxic conditions. Moreover, 17 genes were validated by qPCR, and the results were highly concordant with the RNA seqencing results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to better understand the functions of these differentially expressed genes. The upregulated genes appeared to be significantly enriched in the pathyway of extracellular matrix (ECM)-receptor interaction, and in paticular, the pathway of renal cell carcinoma was upregulated under hypoxic conditions. The downregulated genes were enriched in the signaling pathway related to antigen processing and presentation; however, the pathway of glutathione metabolism was downregulated. Our analysis revealed numerous novel transcripts and alternative splicing events. Simultaneously, we also identified a large number of single nucleotide polymorphisms, which will be a rich resource for future marker development. On the whole, our data indicate that transcriptome analysis provides valuable information for a more in depth understanding of the molecular mechanisms in CKD and renal cell carcinoma.
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Affiliation(s)
- Wenmin Yu
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yiping Li
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Zhi Wang
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Lei Liu
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Jing Liu
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Fengan Ding
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Xiaoyi Zhang
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Zhengyuan Cheng
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Pingsheng Chen
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Jun Dou
- Medical School of Southeast University, Nanjing, Jiangsu 210009, P.R. China
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14
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Song L, Sabunciyan S, Florea L. CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. Nucleic Acids Res 2016; 44:e98. [PMID: 26975657 PMCID: PMC4889935 DOI: 10.1093/nar/gkw158] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/28/2016] [Indexed: 11/29/2022] Open
Abstract
Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to accurately capture splicing variation has proven difficult. Current programs can find major isoforms of a gene but miss lower abundance variants, or are sensitive but imprecise. CLASS2 is a novel open source tool for accurate genome-guided transcriptome assembly from RNA-seq reads based on the model of splice graph. An extension of our program CLASS, CLASS2 jointly optimizes read patterns and the number of supporting reads to score and prioritize transcripts, implemented in a novel, scalable and efficient dynamic programming algorithm. When compared against reference programs, CLASS2 had the best overall accuracy and could detect up to twice as many splicing events with precision similar to the best reference program. Notably, it was the only tool to produce consistently reliable transcript models for a wide range of applications and sequencing strategies, including ribosomal RNA-depleted samples. Lightweight and multi-threaded, CLASS2 requires <3GB RAM and can analyze a 350 million read set within hours, and can be widely applied to transcriptomics studies ranging from clinical RNA sequencing, to alternative splicing analyses, and to the annotation of new genomes.
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Affiliation(s)
- Li Song
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Liliana Florea
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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15
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Facchiano A, Angelini C, Bosotti R, Guffanti A, Marabotti A, Marangoni R, Pascarella S, Romano P, Zanzoni A, Helmer-Citterich M. Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 2015; 16 Suppl 9:S1. [PMID: 26050789 PMCID: PMC4464032 DOI: 10.1186/1471-2105-16-s9-s1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014.
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16
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Han Y, Gao S, Muegge K, Zhang W, Zhou B. Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights 2015; 9:29-46. [PMID: 26609224 PMCID: PMC4648566 DOI: 10.4137/bbi.s28991] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing technologies have revolutionarily advanced sequence-based research with the advantages of high-throughput, high-sensitivity, and high-speed. RNA-seq is now being used widely for uncovering multiple facets of transcriptome to facilitate the biological applications. However, the large-scale data analyses associated with RNA-seq harbors challenges. In this study, we present a detailed overview of the applications of this technology and the challenges that need to be addressed, including data preprocessing, differential gene expression analysis, alternative splicing analysis, variants detection and allele-specific expression, pathway analysis, co-expression network analysis, and applications combining various experimental procedures beyond the achievements that have been made. Specifically, we discuss essential principles of computational methods that are required to meet the key challenges of the RNA-seq data analyses, development of various bioinformatics tools, challenges associated with the RNA-seq applications, and examples that represent the advances made so far in the characterization of the transcriptome.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Shouguo Gao
- Bioinformatics and Systems Biology Core, National Heart Lung Blood Institute, National Institutes of Health, Rockville Pike, Bethesda, MD, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA. ; Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, MD, USA
| | - Wei Zhang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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