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Li L, Ding X, Sheft AP, Schimenti JC. A high throughput CRISPR perturbation screen identifies epigenetic regulators impacting primordial germ cell development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582097. [PMID: 38463983 PMCID: PMC10925113 DOI: 10.1101/2024.02.26.582097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Certain environmental factors can impact fertility and reproductive parameters such as the number and quality of sperm and eggs. One possible mechanism is the perturbation of epigenetic landscapes in the germline. To explore this possibility, we conducted a CRISPRi screen of epigenetic-related genes to identify those that specifically perturb the differentiation of embryonic stem cells (ESCs) into primordial germ cell-like cells (PGCLCs), exploiting a highly scalable cytokine-free platform. Of the 701 genes screened, inhibition of 53 decreased the efficiency of PGCLC formation. NCOR2, a transcriptional repressor that acts via recruitment of Class I and Class IIa histone deacetylases (HDACs) to gene targets, was particularly potent in suppressing PGCLC differentiation. Consistent with evidence that histone deacetylation is crucial for germline differentiation, we found that the HDAC inhibitors (HDACi) valproic acid (VPA; an anti-convulsant) and sodium butyrate (SB; a widely-used dietary supplement) also suppressed ESC>PGCLC differentiation. Furthermore, exposure of developing mouse embryos to SB or VPA caused hypospermatogenesis. Transcriptome analyses of HDACi-treated, differentiating ESC>PGCLC cultures revealed suppression of germline-associated pathways and enhancement of somatic pathways. This work demonstrates the feasibility of conducting large-scale functional screens of genes, chemicals, or other agents that may impact germline development.
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Rocca R, Grillone K, Citriniti EL, Gualtieri G, Artese A, Tagliaferri P, Tassone P, Alcaro S. Targeting non-coding RNAs: Perspectives and challenges of in-silico approaches. Eur J Med Chem 2023; 261:115850. [PMID: 37839343 DOI: 10.1016/j.ejmech.2023.115850] [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: 07/25/2023] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
The growing information currently available on the central role of non-coding RNAs (ncRNAs) including microRNAs (miRNAS) and long non-coding RNAs (lncRNAs) for chronic and degenerative human diseases makes them attractive therapeutic targets. RNAs carry out different functional roles in human biology and are deeply deregulated in several diseases. So far, different attempts to therapeutically target the 3D RNA structures with small molecules have been reported. In this scenario, the development of computational tools suitable for describing RNA structures and their potential interactions with small molecules is gaining more and more interest. Here, we describe the most suitable strategies to study ncRNAs through computational tools. We focus on methods capable of predicting 2D and 3D ncRNA structures. Furthermore, we describe computational tools to identify, design and optimize small molecule ncRNA binders. This review aims to outline the state of the art and perspectives of computational methods for ncRNAs over the past decade.
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Affiliation(s)
- Roberta Rocca
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | | | | | - Anna Artese
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy.
| | | | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
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Lou K, Wassarman DR, Yang T, Paung Y, Zhang Z, O’Loughlin TA, Moore MK, Egan RK, Greninger P, Benes CH, Seeliger MA, Taunton J, Gilbert LA, Shokat KM. IFITM proteins assist cellular uptake of diverse linked chemotypes. Science 2022; 378:1097-1104. [PMID: 36480603 PMCID: PMC9924227 DOI: 10.1126/science.abl5829] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The search for cell-permeable drugs has conventionally focused on low-molecular weight (MW), nonpolar, rigid chemical structures. However, emerging therapeutic strategies break traditional drug design rules by employing flexibly linked chemical entities composed of more than one ligand. Using complementary genome-scale chemical-genetic approaches we identified an endogenous chemical uptake pathway involving interferon-induced transmembrane proteins (IFITMs) that modulates the cell permeability of a prototypical biopic inhibitor of MTOR (RapaLink-1, MW: 1784 g/mol). We devised additional linked inhibitors targeting BCR-ABL1 (DasatiLink-1, MW: 1518 g/mol) and EIF4A1 (BisRoc-1, MW: 1466 g/mol), uptake of which was facilitated by IFITMs. We also found that IFITMs moderately assisted some proteolysis-targeting chimeras and examined the physicochemical requirements for involvement of this uptake pathway.
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Affiliation(s)
- Kevin Lou
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
| | - Douglas R. Wassarman
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
| | - Tangpo Yang
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook
University, Stony Brook, New York 11794-8651, United States
| | - Ziyang Zhang
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
- Department of Chemistry, University of California,
Berkeley, Berkeley, 94720, CA, United States
| | - Thomas A. O’Loughlin
- Helen Diller Family Comprehensive Cancer Center, University
of California, San Francisco, San Francisco, CA 94158, United States
- Department of Urology, University of California, San
Francisco, San Francisco, CA 94158, United States
| | - Megan K. Moore
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
| | - Regina K. Egan
- Center for Cancer Research, Massachusetts General Hospital
Cancer Center, Charlestown, MA 02129, United States
| | - Patricia Greninger
- Center for Cancer Research, Massachusetts General Hospital
Cancer Center, Charlestown, MA 02129, United States
| | - Cyril H. Benes
- Center for Cancer Research, Massachusetts General Hospital
Cancer Center, Charlestown, MA 02129, United States
- Department of Medicine, Harvard Medical School, Boston, MA
02115, United States
| | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook
University, Stony Brook, New York 11794-8651, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
| | - Luke A. Gilbert
- Helen Diller Family Comprehensive Cancer Center, University
of California, San Francisco, San Francisco, CA 94158, United States
- Department of Urology, University of California, San
Francisco, San Francisco, CA 94158, United States
- Innovative Genomics Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
- Arc Institute, Palo Alto, CA, 94304, United States
| | - Kevan M. Shokat
- Department of Cellular and Molecular Pharmacology,
University of California, San Francisco, San Francisco, CA 94158, United
States
- Howard Hughes Medical Institute, University of California,
San Francisco, San Francisco, CA 94158, United States
- Department of Chemistry, University of California,
Berkeley, Berkeley, 94720, CA, United States
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Decoding the Roles of Long Noncoding RNAs in Hepatocellular Carcinoma. Int J Mol Sci 2021; 22:ijms22063137. [PMID: 33808647 PMCID: PMC8003515 DOI: 10.3390/ijms22063137] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies worldwide. HCC is associated with several etiological factors, including HBV/HCV infections, cirrhosis, and fatty liver diseases. However, the molecular mechanism underlying HCC development remains largely elusive. The advent of high-throughput sequencing has unveiled an unprecedented discovery of a plethora of long noncoding RNAs (lncRNAs). Despite the lack of coding capacity, lncRNAs have key roles in gene regulation through interacting with various biomolecules. It is increasingly evident that the dysregulation of lncRNAs is inextricably linked to HCC cancer phenotypes, suggesting that lncRNAs are potential prognostic markers and therapeutic targets. In light of the emerging research in the study of the regulatory roles of lncRNAs in HCC, we discuss the association of lncRNAs with HCC. We link the biological processes influenced by lncRNAs to cancer hallmarks in HCC and describe the associated functional mechanisms. This review sheds light on future research directions, including the potential therapeutic applications of lncRNAs.
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