1
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Sharma H, Valentine MNZ, Toki N, Sueki HN, Gustincich S, Takahashi H, Carninci P. Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nat Commun 2024; 15:1400. [PMID: 38383605 PMCID: PMC10881587 DOI: 10.1038/s41467-024-45517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
RNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA-RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
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Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiromi Nishiyori Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- Human Technopole, Milan, 20157, Italy.
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2
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Ao YQ, Gao J, Jiang JH, Wang HK, Wang S, Ding JY. Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village. Mol Ther 2023; 31:3389-3413. [PMID: 37740493 PMCID: PMC10727995 DOI: 10.1016/j.ymthe.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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3
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Pierattini B, D’Agostino S, Bon C, Peruzzo O, Alendar A, Codino A, Ros G, Persichetti F, Sanges R, Carninci P, Santoro C, Espinoza S, Valentini P, Pandolfini L, Gustincich S. SINEUP non-coding RNA activity depends on specific N6-methyladenosine nucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:402-414. [PMID: 37187707 PMCID: PMC10176434 DOI: 10.1016/j.omtn.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
SINEUPs are natural and synthetic antisense long non-coding RNAs (lncRNAs) selectively enhancing target mRNAs translation by increasing their association with polysomes. This activity requires two RNA domains: an embedded inverted SINEB2 element acting as effector domain, and an antisense region, the binding domain, conferring target selectivity. SINEUP technology presents several advantages to treat genetic (haploinsufficiencies) and complex diseases restoring the physiological activity of diseased genes and of compensatory pathways. To streamline these applications to the clinic, a better understanding of the mechanism of action is needed. Here we show that natural mouse SINEUP AS Uchl1 and synthetic human miniSINEUP-DJ-1 are N6-methyladenosine (m6A) modified by METTL3 enzyme. Then, we map m6A-modified sites along SINEUP sequence with Nanopore direct RNA sequencing and a reverse transcription assay. We report that m6A removal from SINEUP RNA causes the depletion of endogenous target mRNA from actively translating polysomes, without altering SINEUP enrichment in ribosomal subunit-associated fractions. These results prove that SINEUP activity requires an m6A-dependent step to enhance translation of target mRNAs, providing a new mechanism for m6A translation regulation and strengthening our knowledge of SINEUP-specific mode of action. Altogether these new findings pave the way to a more effective therapeutic application of this well-defined class of lncRNAs.
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Affiliation(s)
- Bianca Pierattini
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Sabrina D’Agostino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Carlotta Bon
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Omar Peruzzo
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Andrej Alendar
- The Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Azzurra Codino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Gloria Ros
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Francesca Persichetti
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Remo Sanges
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan
- Human Technopole, 20157 Milan, Italy
| | - Claudio Santoro
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Paola Valentini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Paola Valentini, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
| | - Luca Pandolfini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Luca Pandolfini, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Stefano Gustincich, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
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4
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Marušič M, Toplishek M, Plavec J. NMR of RNA - Structure and interactions. Curr Opin Struct Biol 2023; 79:102532. [PMID: 36746110 DOI: 10.1016/j.sbi.2023.102532] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/11/2022] [Accepted: 12/19/2022] [Indexed: 02/07/2023]
Abstract
RNA was shown to have a more substantial role in the regulation of diverse cellular processes than anticipated until recently. Answers to questions what is the structure of specific RNAs, how structure changes to accommodate different functional roles, and how RNA senses other biomolecules and changes its fold upon interaction create a complete representation of RNA involved in cellular processes. Nuclear magnetic resonance (NMR) spectroscopy encompasses a collection of methods and approaches that offer insight into several structural aspects of RNAs. We review the most recent advances in the field of viral, long non-coding, regulatory, and four-stranded RNAs, with an emphasis on the detection of dynamic sub-states and in view of chemical modifications that expand RNA's function.
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Affiliation(s)
- Maja Marušič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Maria Toplishek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia; University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Cesta OF 13, Ljubljana, Slovenia.
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5
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Bezzecchi E, Pagani G, Forte B, Percio S, Zaffaroni N, Dolfini D, Gandellini P. MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism. Front Cell Dev Biol 2022; 10:909097. [PMID: 35784469 PMCID: PMC9247157 DOI: 10.3389/fcell.2022.909097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/31/2022] [Indexed: 01/11/2023] Open
Abstract
Aside serving as host gene for miR-205, MIR205HG transcribes for a chromatin-associated long noncoding RNA (lncRNA) able to restrain the differentiation of prostate basal cells, thus being reannotated as LEADR (Long Epithelial Alu-interacting Differentiation-related RNA). We previously showed the presence of Alu sequences in the promoters of genes modulated upon MIR205HG/LEADR manipulation. Notably, an Alu element also spans the first and second exons of MIR205HG/LEADR, suggesting its possible involvement in target selection/binding. Here, we performed ChIRP-seq to map MIR205HG/LEADR chromatin occupancy at genome-wide level in prostate basal cells. Our results confirmed preferential binding to regions proximal to gene transcription start site (TSS). Moreover, enrichment of triplex-forming sequences was found upstream of MIR205HG/LEADR-bound genes, peaking at −1,500/−500 bp from TSS. Triplexes formed with one or two putative DNA binding sites within MIR205HG/LEADR sequence, located just upstream of the Alu element. Notably, triplex-forming regions of bound genes were themselves enriched in Alu elements. These data suggest, from one side, that triplex formation may be the prevalent mechanism by which MIR205HG/LEADR selects and physically interacts with target DNA, from the other that direct or protein-mediated Alu (RNA)/Alu (DNA) interaction may represent a further functional requirement. We also found that triplex-forming regions were enriched in specific histone modifications, including H3K4me1 in the absence of H3K27ac, H3K4me3 and H3K27me3, indicating that in prostate basal cells MIR205HG/LEADR may preferentially bind to primed proximal regulatory elements. This may underscore the need for basal cells to keep MIR205HG/LEADR target genes repressed but, at the same time, responsive to differentiation cues.
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Affiliation(s)
- Eugenia Bezzecchi
- Department of Biosciences, University of Milan, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Pagani
- Department of Biosciences, University of Milan, Milan, Italy
| | - Barbara Forte
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Percio
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, Milan, Italy
- *Correspondence: Paolo Gandellini,
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6
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Takase N, Otsu M, Hirakata S, Ishizu H, Siomi MC, Kawai G. T-hairpin structure found in the RNA element involved in piRNA biogenesis. RNA (NEW YORK, N.Y.) 2022; 28:541-550. [PMID: 34987083 PMCID: PMC8925976 DOI: 10.1261/rna.078967.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. In Drosophila, the Traffic jam (Tj) mRNA is consumed to produce piRNA in its 3'-UTR. A cis element located within the 3'-UTR, Tj-cis, is necessary for piRNA biogenesis. In this study, we analyzed the structure of the Tj-cis RNA, a 100-nt RNA corresponding to the Tj-cis element, by the SHAPE and NMR analyses and found that a stable hairpin structure formed in the 5' half of the Tj-cis RNA. The tertiary structure of the 16-nt stable hairpin was analyzed by NMR, and a novel stem-loop structure, the T-hairpin, was found. In the T-hairpin, four uridine residues are exposed to the solvent, suggesting that this stem-loop is the target of Yb protein, a Tudor domain-containing piRNA biogenesis factor. The piRNA biogenesis assay showed that both the T-hairpin and the 3' half are required for the function of the Tj-cis element, suggesting that both the T-hairpin and the 3' half are recognized by Yb protein.
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Affiliation(s)
- Naomi Takase
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Maina Otsu
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
| | - Shigeki Hirakata
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hirotsugu Ishizu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Gota Kawai
- Department of Life Science, Graduate School of Advanced Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan
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7
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Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A. NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res 2022; 50:4083-4099. [PMID: 35357505 PMCID: PMC9023295 DOI: 10.1093/nar/gkac212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 12/31/2022] Open
Abstract
Control of posttranscriptional mRNA decay is a crucial determinant of cell homeostasis and differentiation. mRNA lifetime is governed by cis-regulatory elements in their 3′ untranslated regions (UTR). Despite ongoing progress in the identification of cis elements we have little knowledge about the functional and structural integration of multiple elements in 3′UTR regulatory hubs and their recognition by mRNA-binding proteins (RBPs). Structural analyses are complicated by inconsistent mapping and prediction of RNA fold, by dynamics, and size. We here, for the first time, provide the secondary structure of a complete mRNA 3′UTR. We use NMR spectroscopy in a divide-and-conquer strategy complemented with SAXS, In-line probing and SHAPE-seq applied to the 3′UTR of Ox40 mRNA, which encodes a T-cell co-receptor repressed by the protein Roquin. We provide contributions of RNA elements to Roquin-binding. The protein uses its extended bi-modal ROQ domain to sequentially engage in a 2:1 stoichiometry with a 3′UTR core motif. We observe differential binding of Roquin to decay elements depending on their structural embedment. Our data underpins the importance of studying RNA regulation in a full sequence and structural context. This study serves as a paradigm for an approach in analysing structured RNA-regulatory hubs and their binding by RBPs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Lea Marie Becker
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - François McNicoll
- Goethe University Frankfurt, Institute for Molecular Biosciences, Max-von-Laue-Str. 13, 60438 Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Goethe University Frankfurt, Institute for Molecular Biosciences, Max-von-Laue-Str. 13, 60438 Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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8
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Towards SINEUP-based therapeutics: Design of an in vitro synthesized SINEUP RNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:1092-1102. [PMID: 35228902 PMCID: PMC8857549 DOI: 10.1016/j.omtn.2022.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/28/2022] [Indexed: 12/28/2022]
Abstract
SINEUPs are a novel class of natural and synthetic non-coding antisense RNA molecules able to increase the translation of a target mRNA. They present a modular organization comprising an unstructured antisense target-specific domain, which sets the specificity of each individual SINEUP, and a structured effector domain, which is responsible for the translation enhancement. In order to design a fully functional in vitro transcribed SINEUP for therapeutics applications, SINEUP RNAs were synthesized in vitro with a variety of chemical modifications and screened for their activity on endogenous target mRNA upon transfection. Three combinations of modified ribonucleotides-2'O methyl-ATP (Am), N6 methyl-ATP (m6A), and pseudo-UTP (ψ)-conferred SINEUP activity to naked RNA. The best combination tested in this study was fully modified with m6A and ψ. Aside from functionality, this combination conferred improved stability upon transfection and higher thermal stability. Common structural determinants of activity were identified by circular dichroisms, defining a core functional structure that is achieved with different combinations of modifications.
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9
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Zambrano N, Froechlich G, Lazarevic D, Passariello M, Nicosia A, De Lorenzo C, Morelli MJ, Sasso E. High-Throughput Monoclonal Antibody Discovery from Phage Libraries: Challenging the Current Preclinical Pipeline to Keep the Pace with the Increasing mAb Demand. Cancers (Basel) 2022; 14:cancers14051325. [PMID: 35267633 PMCID: PMC8909429 DOI: 10.3390/cancers14051325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Monoclonal antibodies are increasingly used for a broad range of diseases. Rising demand must face with time time-consuming and laborious processes to isolate novel monoclonal antibodies. Next-generation sequencing coupled to phage display provides timely and sustainable high throughput selection strategy to rapidly access novel target. Here, we describe the current NGS-guided strategies to identify potential binders from enriched sub-libraires by applying a user-friendly informatic pipeline to identify and discard false positive clones. Rescue step and strategies to boost mAb yield are also discussed to improve the limiting selection and screening steps. Abstract Monoclonal antibodies are among the most powerful therapeutics in modern medicine. Since the approval of the first therapeutic antibody in 1986, monoclonal antibodies keep holding great expectations for application in a range of clinical indications, highlighting the need to provide timely and sustainable access to powerful screening options. However, their application in the past has been limited by time-consuming and expensive steps of discovery and production. The screening of antibody repertoires is a laborious step; however, the implementation of next-generation sequencing-guided screening of single-chain antibody fragments has now largely overcome this issue. This review provides a detailed overview of the current strategies for the identification of monoclonal antibodies from phage display-based libraries. We also discuss the challenges and the possible solutions to improve the limiting selection and screening steps, in order to keep pace with the increasing demand for monoclonal antibodies.
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Affiliation(s)
- Nicola Zambrano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
- Correspondence: (N.Z.); (E.S.)
| | - Guendalina Froechlich
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences Ospedale San Raffaele, Via Olgettina 58, 20132 Milano, Italy; (D.L.); (M.J.M.)
| | - Margherita Passariello
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Alfredo Nicosia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Claudia De Lorenzo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Marco J. Morelli
- Center for Omics Sciences Ospedale San Raffaele, Via Olgettina 58, 20132 Milano, Italy; (D.L.); (M.J.M.)
| | - Emanuele Sasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Degli Studi di Napoli Federico II, Via Pansini 5, 80131 Napoli, Italy; (G.F.); (M.P.); (A.N.); (C.D.L.)
- CEINGE—Biotecnologie Avanzate s.c. a.r.l., Via Gaetano Salvatore 486, 80145 Naples, Italy
- Correspondence: (N.Z.); (E.S.)
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10
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Lin C, Li Y, Zhang E, Feillet F, Zhang S, Blau N. Importance of the long non-coding RNA (lncRNA) transcript HULC for the regulation of phenylalanine hydroxylase and treatment of phenylketonuria. Mol Genet Metab 2022; 135:171-178. [PMID: 35101330 DOI: 10.1016/j.ymgme.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
More than 1280 variants in the phenylalanine hydroxylase (PAH) gene are responsible for a broad spectrum of phenylketonuria (PKU) phenotypes. While the genotype-phenotype correlation is reaching 88%, for some inconsistent phenotypes with the same genotype additional factors like tetrahydrobiopterin (BH4), the PAH co-chaperone DNAJC12, phosphorylation of the PAH residues or epigenetic factors may play an important role. Very recently an additional player, the long non-coding RNA (lncRNA) transcript HULC, was described to regulate PAH activity and enhance residual enzyme activity of some PAH variants (e.g., the most common p.R408W) by using HULC mimics. In this review we present an overview of the lncRNA function and in particular the interplay of the HUCL transcript with the PAH and discuss potential applications for the future treatment of some PKU patients.
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Affiliation(s)
- Chunru Lin
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Yajuan Li
- Department of Molecular and Cellular Oncology, Division of Basic Science Research, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Eric Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - François Feillet
- INSERM, U1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy, France; Pediatric Department Reference Center for Inborn Errors of Metabolism Children University Hospital Nancy, Nancy, France
| | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital Zürich, Zurich, Switzerland.
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11
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Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids. Curr Biol 2022; 32:889-897.e9. [PMID: 35090588 PMCID: PMC8891063 DOI: 10.1016/j.cub.2021.12.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 12/30/2022]
Abstract
Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.
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12
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Arnoldi M, Zarantonello G, Espinoza S, Gustincich S, Di Leva F, Biagioli M. Design and Delivery of SINEUP: A New Modular Tool to Increase Protein Translation. Methods Mol Biol 2022; 2434:63-87. [PMID: 35213010 PMCID: PMC9703201 DOI: 10.1007/978-1-0716-2010-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SINEUP is a new class of long non-coding RNAs (lncRNAs) which contain an inverted Short Interspersed Nuclear Element (SINE) B2 element (invSINEB2) necessary to specifically upregulate target gene translation. Originally identified in the mouse AS-Uchl1 (antisense Ubiquitin carboxyl-terminal esterase L1) locus, natural SINEUP molecules are oriented head to head to their sense protein coding, target gene (Uchl1, in this example). Peculiarly, SINEUP is able to augment, in a specific and controlled way, the expression of the target protein, with no alteration of target mRNA levels. SINEUP is characterized by a modular structure with the Binding Domain (BD) providing specificity to the target transcript and an effector domain (ED)-containing the invSINEB2 element-able to promote the loading to the heavy polysomes of the target mRNA. Since the understanding of its modular structure in the endogenous AS-Uchl1 ncRNA, synthetic SINEUP molecules have been developed by creating a specific BD for the gene of interest and placing it upstream the invSINEB2 ED. Synthetic SINEUP is thus a novel molecular tool that potentially may be used for any industrial or biomedical application to enhance protein production, also as possible therapeutic strategy in haploinsufficiency-driven disorders.Here, we describe a detailed protocol to (1) design a specific BD directed to a gene of interest and (2) assemble and clone it with the ED to obtain a functional SINEUP molecule. Then, we provide guidelines to efficiently deliver SINEUP into mammalian cells and evaluate its ability to effectively upregulate target protein translation.
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Affiliation(s)
- Michele Arnoldi
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Zarantonello
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Francesca Di Leva
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
- Institute for Biomedicine, Eurac Research, Bolzano, Italy.
| | - Marta Biagioli
- Neuroepigenetics Laboratory, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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13
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Worpenberg L, Paolantoni C, Roignant JY. Functional interplay within the epitranscriptome: Reality or fiction? Bioessays 2021; 44:e2100174. [PMID: 34873719 DOI: 10.1002/bies.202100174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/11/2022]
Abstract
RNA modifications have recently emerged as an important regulatory layer of gene expression. The most prevalent and reversible modification on messenger RNA (mRNA), N6-methyladenosine, regulates most steps of RNA metabolism and its dysregulation has been associated with numerous diseases. Other modifications such as 5-methylcytosine and N1-methyladenosine have also been detected on mRNA but their abundance is lower and still debated. Adenosine to inosine RNA editing is widespread on coding and non-coding RNA and can alter mRNA decoding as well as protect against autoimmune diseases. 2'-O-methylation of the ribose and pseudouridine are widespread on ribosomal and transfer RNA and contribute to proper RNA folding and stability. While the understanding of the individual role of RNA modifications has now reached an unprecedented stage, still little is known about their interplay in the control of gene expression. In this review we discuss the examples where such interplay has been observed and speculate that with the progress of mapping technologies more of those will rapidly accumulate.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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SINEUPs: a novel toolbox for RNA therapeutics. Essays Biochem 2021; 65:775-789. [PMID: 34623427 PMCID: PMC8564737 DOI: 10.1042/ebc20200114] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022]
Abstract
RNA molecules have emerged as a new class of promising therapeutics to expand the range of druggable targets in the genome. In addition to ‘canonical’ protein-coding mRNAs, the emerging richness of sense and antisense long non-coding RNAs (lncRNAs) provides a new reservoir of molecular tools for RNA-based drugs. LncRNAs are composed of modular structural domains with specific activities involving the recruitment of protein cofactors or directly interacting with nucleic acids. A single therapeutic RNA transcript can then be assembled combining domains with defined secondary structures and functions, and antisense sequences specific for the RNA/DNA target of interest. As the first representative molecules of this new pharmacology, we have identified SINEUPs, a new functional class of natural antisense lncRNAs that increase the translation of partially overlapping mRNAs. Their activity is based on the combination of two domains: an embedded mouse inverted SINEB2 element that enhances mRNA translation (effector domain) and an overlapping antisense region that provides specificity for the target sense transcript (binding domain). By genetic engineering, synthetic SINEUPs can potentially target any mRNA of interest increasing translation and therefore the endogenous level of the encoded protein. In this review, we describe the state-of-the-art knowledge of SINEUPs and discuss recent publications showing their potential application in diseases where a physiological increase of endogenous protein expression can be therapeutic.
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15
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Korn SM, Ulshöfer CJ, Schneider T, Schlundt A. Structures and target RNA preferences of the RNA-binding protein family of IGF2BPs: An overview. Structure 2021; 29:787-803. [PMID: 34022128 DOI: 10.1016/j.str.2021.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 02/08/2023]
Abstract
Insulin-like growth factor 2 mRNA-binding proteins (IMPs, IGF2BPs) act in mRNA transport and translational control but are oncofetal tumor marker proteins. The IMP protein family represents a number of bona fide multi-domain RNA-binding proteins with up to six RNA-binding domains, resulting in a high complexity of possible modes of interactions with target mRNAs. Their exact mechanism in stability control of oncogenic mRNAs is only partially understood. Our and other laboratories' recent work has significantly pushed the understanding of IMP protein specificities both toward RNA engagement and between each other from NMR and crystal structures serving the basis for systematic biochemical and functional investigations. We here summarize the known structural and biochemical information about IMP RNA-binding domains and their RNA preferences. The article also touches on the respective roles of RNA secondary and protein tertiary structures for specific RNA-protein complexes, including the limited knowledge about IMPs' protein-protein interactions, which are often RNA mediated.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Corinna Jessica Ulshöfer
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Tim Schneider
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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Chemo-enzymatic synthesis of 13C- and 19F-labeled uridine-5′-triphosphate for RNA NMR probing. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02757-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Generation of a Novel Mesothelin-Targeted Oncolytic Herpes Virus and Implemented Strategies for Manufacturing. Int J Mol Sci 2021; 22:ijms22020477. [PMID: 33418877 PMCID: PMC7825047 DOI: 10.3390/ijms22020477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 01/19/2023] Open
Abstract
Background: HER2-based retargeted viruses are in advanced phases of preclinical development of breast cancer models. Mesothelin (MSLN) is a cell-surface tumor antigen expressed in different subtypes of breast and non-breast cancer. Its recent identification as a marker of some triple-negative breast tumors renders it an attractive target, presently investigated in clinical trials employing antibody drug conjugates and CAR-T cells. The availability of MSLN-retargeted oncolytic viruses may complement the current immunotherapeutic panel of biological drugs against HER2-negative breast and non-breast tumors. Methods: A fully virulent, tumor-targeted oncolytic Herpes simplex virus-1 (MSLN-THV) with a selectivity for mesothelin-expressing cancer cells was generated. Recombineering technology was used to replace an essential moiety of the viral glycoprotein D with antibody fragments derived from clinically validated MSLN monoclonal antibodies, and to allow IL12 cargo expression in infected cells. Panels of breast and female reproductive system cell lines were used to verify the oncolytic potential of the viral constructs. A platform for production of the retargeted viruses was developed in HEK 293 cells, providing stable expression of a suitable chimeric receptor. Results: We demonstrated the selectivity of viral infection and cytotoxicity by MSLN-retargeted viruses in a panel of mesothelin-positive cancer cells, originating from breast and female reproductive system tumors. We also developed a second-generation oncolytic MSLN-THV, encoding IL12, to enhance the immunotherapeutic potential of the viral backbone. A non-tumor cell line expressing a chimeric MSLN/Nectin-1 receptor, de-sensitized from antiviral responses by genetic inactivation of the Stimulator of Interferon Genes (STING)-dependent pathway was engineered, to optimize viral yields. Conclusions: Our proof-of-concept study proposes MSLN-retargeted herpesviruses as potential cancer immunotherapeutics for assessments in preclinical models of MSLN-positive tumors, complementing the available panel of oncolytic viruses to HER2-negative breast tumors.
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