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Androsavich JR. Frameworks for transformational breakthroughs in RNA-based medicines. Nat Rev Drug Discov 2024; 23:421-444. [PMID: 38740953 DOI: 10.1038/s41573-024-00943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA has sparked a revolution in modern medicine, with the potential to transform the way we treat diseases. Recent regulatory approvals, hundreds of new clinical trials, the emergence of CRISPR gene editing, and the effectiveness of mRNA vaccines in dramatic response to the COVID-19 pandemic have converged to create tremendous momentum and expectation. However, challenges with this relatively new class of drugs persist and require specialized knowledge and expertise to overcome. This Review explores shared strategies for developing RNA drug platforms, including layering technologies, addressing common biases and identifying gaps in understanding. It discusses the potential of RNA-based therapeutics to transform medicine, as well as the challenges associated with improving applicability, efficacy and safety profiles. Insights gained from RNA modalities such as antisense oligonucleotides (ASOs) and small interfering RNAs are used to identify important next steps for mRNA and gene editing technologies.
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Affiliation(s)
- John R Androsavich
- RNA Accelerator, Pfizer Inc, Cambridge, MA, USA.
- Ginkgo Bioworks, Boston, MA, USA.
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2
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Beliakova-Bethell N. Targeting noncoding RNAs to reactivate or eliminate latent HIV reservoirs. Curr Opin HIV AIDS 2024; 19:47-55. [PMID: 38169367 PMCID: PMC10872953 DOI: 10.1097/coh.0000000000000838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW Expression of noncoding RNAs (ncRNAs) is more tissue and cell type-specific than expression of protein-coding genes. Understanding the mechanisms of action of ncRNAs and their roles in HIV replication and latency may inform targets for the latent HIV reservoir reactivation or elimination with high specificity to CD4 + T cells latently infected with HIV. RECENT FINDINGS While the number of studies in the field of ncRNAs and HIV is limited, evidence points to complex interactions between different ncRNAs, protein-coding RNAs, and proteins. Latency-reversing agents modulate the expression of ncRNAs, with some effects being inhibitory for HIV reactivation. An important limitation of basic research on the ncRNA mechanisms of action is the reliance on cell lines. Because of cell type specificity, it is uncertain whether the ncRNAs function similarly in primary cells. SUMMARY Comprehensive functional screens to uncover all ncRNAs that regulate HIV expression and the detailed exploration of their mechanisms of action in relevant cell types are needed to identify promising targets for HIV reservoir clearance. Classes of ncRNAs as a whole rather than individual ncRNAs might represent an attractive target for reservoir elimination. Compound screens for latency reversal should factor in the complexity of their effects on ncRNAs.
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Affiliation(s)
- Nadejda Beliakova-Bethell
- Department of Medicine, University of California at San Diego, CA, USA
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
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3
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Paudel B, Jeong SY, Martinez CP, Rickman A, Haluck-Kangas A, Bartom ET, Fredriksen K, Affaneh A, Kessler JA, Mazzulli JR, Murmann AE, Rogalski E, Geula C, Ferreira A, Heckmann BL, Green DR, Sadleir KR, Vassar R, Peter ME. Death Induced by Survival gene Elimination (DISE) correlates with neurotoxicity in Alzheimer's disease and aging. Nat Commun 2024; 15:264. [PMID: 38238311 PMCID: PMC10796375 DOI: 10.1038/s41467-023-44465-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by progressive neurodegeneration, but the specific events that cause cell death remain poorly understood. Death Induced by Survival gene Elimination (DISE) is a cell death mechanism mediated by short (s) RNAs acting through the RNA-induced silencing complex (RISC). DISE is thus a form of RNA interference, in which G-rich 6mer seed sequences in the sRNAs (position 2-7) target hundreds of C-rich 6mer seed matches in genes essential for cell survival, resulting in the activation of cell death pathways. Here, using Argonaute precipitation and RNAseq (Ago-RP-Seq), we analyze RISC-bound sRNAs to quantify 6mer seed toxicity in several model systems. In mouse AD models and aging brain, in induced pluripotent stem cell-derived neurons from AD patients, and in cells exposed to Aβ42 oligomers, RISC-bound sRNAs show a shift to more toxic 6mer seeds compared to controls. In contrast, in brains of "SuperAgers", humans over age 80 who have superior memory performance, RISC-bound sRNAs are shifted to more nontoxic 6mer seeds. Cells depleted of nontoxic sRNAs are sensitized to Aβ42-induced cell death, and reintroducing nontoxic RNAs is protective. Altogether, the correlation between DISE and Aβ42 toxicity suggests that increasing the levels of nontoxic miRNAs in the brain or blocking the activity of toxic RISC-bound sRNAs could ameliorate neurodegeneration.
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Affiliation(s)
- Bidur Paudel
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Si-Yeon Jeong
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Ministry of Food and Drug Safety, Pharmaceutical Safety Bureau, Pharmaceutical Policy Division 187, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | - Carolina Pena Martinez
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Alexis Rickman
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Ashley Haluck-Kangas
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Kristina Fredriksen
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Amira Affaneh
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - John A Kessler
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Joseph R Mazzulli
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Andrea E Murmann
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emily Rogalski
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Healthy Aging & Alzheimer's Research Care (HAARC) Center, Department of Neurology, The University of Chicago, Chicago, IL, 60637, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Adriana Ferreira
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Bradlee L Heckmann
- USF Health Byrd Alzheimer's Center and Neuroscience Institute; Department of Molecular Medicine, Morsani College of Medicine, Tampa, FL, 33613, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine R Sadleir
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Robert Vassar
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Marcus E Peter
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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4
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Haymour L, Jean M, Smulski C, Legembre P. CD95 (Fas) and CD95L (FasL)-mediated non-canonical signaling pathways. Biochim Biophys Acta Rev Cancer 2023; 1878:189004. [PMID: 37865305 DOI: 10.1016/j.bbcan.2023.189004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Although the interaction of CD95L (also known as FasL) with its so-called death receptor CD95 (Fas) induces an apoptotic signal responsible for the elimination of infected and cancer cells and maintenance of tissue homeostasis, this receptor can also implement non apoptotic signaling pathways. This latter signaling is involved in metastatic dissemination in certain cancers and the severity of auto-immune disorders. The signaling complexity of this pair is increased by the fact that CD95 expression itself seems to contribute to oncogenesis via a CD95L-independent manner and, that both ligand and receptor might interact with other partners modulating their pathophysiological functions. Finally, CD95L itself can trigger cell signaling in immune cells rendering complex the interpretation of mouse models in which CD95 or CD95L are knocked out. Herein, we discuss these non-canonical responses and their biological functions.
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Affiliation(s)
- Layla Haymour
- UMR CNRS 7276, INSERM U1262, CRIBL, Université Limoges, Limoges, France
| | - Mickael Jean
- Université de Rennes, Institut des Sciences Chimiques de Rennes - UMR CNRS 6226 Equipe COrInt, Rennes F-35000, France
| | - Cristian Smulski
- Medical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Negro, Argentina
| | - Patrick Legembre
- UMR CNRS 7276, INSERM U1262, CRIBL, Université Limoges, Limoges, France.
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5
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Czarnek M, Kochan J, Wawro M, Myrczek R, Bereta J. Construction of a Set of Novel Transposon Vectors for Efficient Silencing of Protein and lncRNA Genes via CRISPR Interference. Mol Biotechnol 2023; 65:1598-1607. [PMID: 36707469 PMCID: PMC10471651 DOI: 10.1007/s12033-023-00675-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/16/2023] [Indexed: 01/29/2023]
Abstract
In recent years, CRISPR interference (CRISPRi) technology of gene silencing has emerged as a promising alternative to RNA interference (RNAi) surpassing the latter in terms of efficiency and accuracy. Here, we describe the construction of a set of transposon vectors suitable for constitutive or tetracycline (doxycycline)-inducible silencing of genes of interest via CRISPRi method and conferring three different antibiotic resistances, using vectors available via Addgene repository. We have analyzed the performance of the new vectors in the silencing of mouse Adam10 and human lncRNA, NORAD. The empty vector variants can be used to efficiently silence any genes of interest.
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Affiliation(s)
- Maria Czarnek
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Rafał Myrczek
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Joanna Bereta
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland.
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Patel M, Peter ME. DISE, an ancient anti-cancer mechanism that senses mutational load in cancerous cells? Oncotarget 2023; 14:839-841. [PMID: 37747368 PMCID: PMC10519245 DOI: 10.18632/oncotarget.28466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Indexed: 09/26/2023] Open
Affiliation(s)
| | - Marcus E. Peter
- Correspondence to:Marcus E. Peter, Department of Medicine, Division of Hematology and Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60616, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60616, USA email
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7
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Corbin JM, Georgescu C, Wang L, Wren JD, Bieniasz M, Xu C, Asch AS, Ruiz Echevarría MJ. An unbiased seed-based RNAi selection screen identifies small RNAs that inhibit androgen signaling and prostate cancer cell growth. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:257-272. [PMID: 37554515 PMCID: PMC10404560 DOI: 10.1016/j.omtn.2023.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/26/2023] [Indexed: 08/10/2023]
Abstract
Blocking androgen receptor signaling is the mainstay of therapy for advanced prostate cancer (PCa). However, acquired resistance to single agents targeting this pathway results in the development of lethal castration-resistant PCa. Combination therapy approaches represent a promising strategy for the treatment of advanced disease. Here, we explore a therapeutic strategy for PCa based on the ability of shRNAs/siRNAs to function essentially as miRNAs and, via seed sequence complementarity, induce RNA interference of numerous targets simultaneously. We developed a library that contained shRNAs with all possible seed sequence combinations to identify those ones that most potently reduce cell growth and viability when expressed in PCa cells. Validation of some of these RNAi sequences indicated that the toxic effect is associated with seed sequence complementarity to the 3' UTR of AR coregulatory and essential genes. In fact, expression of siRNAs containing the identified toxic seed sequences led to global inhibition of AR-mediated gene expression and reduced expression of cell-cycle genes. When tested in mice, the toxic shRNAs also inhibited castration-resistant PCa and exhibited therapeutic efficacy in pre-established tumors. Our findings highlight RNAi of androgen signaling networks as a promising therapeutic strategy for PCa.
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Affiliation(s)
- Joshua M. Corbin
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Pathology, Biomedical Sciences Building, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK 73104, USA
| | - Constantin Georgescu
- Genes and Human Disease Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Lin Wang
- Aging and Metabolism Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Genes and Human Disease Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Magdalena Bieniasz
- Aging and Metabolism Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Chao Xu
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Biostatistics and Epidemiology, Hudson College of Public Health, University of Oklahoma Health Sciences Center, 801 N.E. 13 Street, Oklahoma City, OK 73104, USA
| | - Adam S. Asch
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Maria J. Ruiz Echevarría
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Pathology, Biomedical Sciences Building, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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8
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Vaidyanathan A, Taylor HE, Hope TJ, D'Aquila RT, Bartom ET, Hultquist JF, Peter ME. Analysis of the Contribution of 6-mer Seed Toxicity to HIV-1-Induced Cytopathicity. J Virol 2023; 97:e0065223. [PMID: 37310263 PMCID: PMC10373551 DOI: 10.1128/jvi.00652-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 06/14/2023] Open
Abstract
HIV-1 (HIV) infects CD4+ T cells, the gradual depletion of which can lead to AIDS in the absence of antiretroviral therapy (ART). Some cells, however, survive HIV infection and persist as part of the latently infected reservoir that causes recurrent viremia after ART cessation. Improved understanding of the mechanisms of HIV-mediated cell death could lead to a way to clear the latent reservoir. Death induced by survival gene elimination (DISE), an RNA interference (RNAi)-based mechanism, kills cells through short RNAs (sRNAs) with toxic 6-mer seeds (positions 2 to 7 of sRNA). These toxic seeds target the 3' untranslated region (UTR) of mRNAs, decreasing the expression of hundreds of genes critical for cell survival. In most cells under normal conditions, highly expressed cell-encoded nontoxic microRNAs (miRNAs) block access of toxic sRNAs to the RNA-induced silencing complex (RISC) that mediates RNAi, promoting cell survival. HIV has been shown to inhibit the biogenesis of host miRNAs in multiple ways. We now report that HIV infection of cells deficient in miRNA expression or function results in enhanced RISC loading of an HIV-encoded miRNA HIV-miR-TAR-3p, which can kill cells by DISE through a noncanonical (positions 3 to 8) 6-mer seed. In addition, cellular RISC-bound sRNAs shift to lower seed viability. This also occurs after latent HIV provirus reactivation in J-Lat cells, suggesting independence of permissiveness of cells to viral infection. More precise targeting of the balance between protective and cytotoxic sRNAs could provide new avenues to explore novel cell death mechanisms that could be used to kill latent HIV. IMPORTANCE Several mechanisms by which initial HIV infection is cytotoxic to infected cells have been reported and involve various forms of cell death. Characterizing the mechanisms underlying the long-term survival of certain T cells that become persistent provirus reservoirs is critical to developing a cure. We recently discovered death induced by survival gene elimination (DISE), an RNAi-based mechanism of cell death whereby toxic short RNAs (sRNAs) containing 6-mer seed sequences (exerting 6-mer seed toxicity) targeting essential survival genes are loaded into RNA-induced silencing complex (RISC) complexes, resulting in inescapable cell death. We now report that HIV infection in cells with low miRNA expression causes a shift of mostly cellular RISC-bound sRNAs to more toxic seeds. This could prime cells to DISE and is further enhanced by the viral microRNA (miRNA) HIV-miR-TAR-3p, which carries a toxic noncanonical 6-mer seed. Our data provide multiple new avenues to explore novel cell death mechanisms that could be used to kill latent HIV.
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Affiliation(s)
- Aparajitha Vaidyanathan
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Harry E. Taylor
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Preventive Medicine, Division of Biostatistics, Northwestern University, Chicago, Illinois, USA
| | - Thomas J. Hope
- Department of Cell & Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Richard T. D'Aquila
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Preventive Medicine, Division of Biostatistics, Northwestern University, Chicago, Illinois, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Marcus E. Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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Haluck-Kangas A, Fink M, Bartom ET, Peter ME. CD95/Fas ligand mRNA is toxic to cells through more than one mechanism. MOLECULAR BIOMEDICINE 2023; 4:11. [PMID: 37059938 PMCID: PMC10105004 DOI: 10.1186/s43556-023-00119-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/03/2023] [Indexed: 04/16/2023] Open
Abstract
CD95/Fas ligand (CD95L) induces apoptosis through protein binding to the CD95 receptor. However, CD95L mRNA also induces toxicity in the absence of CD95 through induction of DISE (Death Induced by Survival Gene Elimination), a form of cell death mediated by RNA interference (RNAi). We now report that CD95L mRNA processing generates a short (s)RNA nearly identical to shL3, a commercial CD95L-targeting shRNA that led to the discovery of DISE. Neither of the miRNA biogenesis proteins Drosha nor Dicer are required for this processing. Interestingly, CD95L toxicity depends on the core component of the RISC, Ago2, in some cell lines, but not in others. In the HCT116 colon cancer cell line, Ago 1-4 appear to function redundantly in RNAi. In fact, Ago 1/2/3 knockout cells retain sensitivity to CD95L mRNA toxicity. Toxicity was only blocked by mutation of all in-frame start codons in the CD95L ORF. Dying cells exhibited an enrichment of RISC bound (R)-sRNAs with toxic 6mer seed sequences, while expression of the non-toxic CD95L mutant enriched for loading of R-sRNAs with nontoxic 6mer seeds. However, CD95L is not the only source of these R-sRNAs. We find that CD95L mRNA may induce DISE directly and indirectly, and that alternate mechanisms may underlie CD95L mRNA processing and toxicity.
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Affiliation(s)
- Ashley Haluck-Kangas
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Chicago, IL, USA
| | - Madelaine Fink
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Chicago, IL, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Chicago, IL, USA
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marcus E Peter
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, Chicago, IL, USA.
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10
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CD95/Fas ligand induced toxicity. Biochem Soc Trans 2023; 51:21-29. [PMID: 36629505 PMCID: PMC10149114 DOI: 10.1042/bst20211187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
The role of CD95/Fas ligand (CD95L/FasL) in the induction of CD95-mediated extrinsic apoptosis is well characterized. Trimerized, membrane-bound CD95L ligates the CD95 receptor activating downstream signaling resulting in the execution of cells by caspase proteins. However, the expression of CD95L has been reported to induce cell death in contexts in which this pathway is unlikely to be activated, such as in cell autonomous activation induced cell death (AICD) and in CD95-resistant cancer cell lines. Recent data suggests that the CD95L mRNA exerts toxicity through death induced by survival gene elimination (DISE). DISE results from the targeting of networks of survival genes by toxic short RNA (sRNA)s in the RNA-induced silencing complex (RISC). CD95L mRNA contributes to this death directly, through the processing of its mRNA into toxic sRNAs that are loaded into the RISC, and indirectly, by promoting the loading of other toxic sRNAs. Interestingly, CD95L is not the only mRNA that is processed and loaded into the RISC. Protein-coding mRNAs involved in protein translation are also selectively loaded. We propose a model in which networks of mRNA-derived sRNAs modulate DISE, with networks of genes providing non-toxic RISC substrate sRNAs that protect against DISE, and opposing networks of stress-activated genes that produce toxic RISC substrate sRNAs that promote DISE.
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11
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The length of uninterrupted CAG repeats in stem regions of repeat disease associated hairpins determines the amount of short CAG oligonucleotides that are toxic to cells through RNA interference. Cell Death Dis 2022; 13:1078. [PMID: 36585400 PMCID: PMC9803637 DOI: 10.1038/s41419-022-05494-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/31/2022]
Abstract
Extended CAG trinucleotide repeats (TNR) in the genes huntingtin (HTT) and androgen receptor (AR) are the cause of two progressive neurodegenerative disorders: Huntington's disease (HD) and Spinal and Bulbar Muscular Atrophy (SBMA), respectively. Anyone who inherits the mutant gene in the complete penetrance range (>39 repeats for HD and 44 for SBMA) will develop the disease. An inverse correlation exists between the length of the CAG repeat and the severity and age of onset of the diseases. Growing evidence suggests that it is the length of uninterrupted CAG repeats in the mRNA rather than the length of poly glutamine (polyQ) in mutant (m)HTT protein that determines disease progression. One variant of mHTT (loss of inhibition; LOI) causes a 25 year earlier onset of HD when compared to a reference sequence, despite both coding for a protein that contains an identical number of glutamines. Short 21-22 nt CAG repeat (sCAGs)-containing RNAs can cause disease through RNA interference (RNAi). RNA hairpins (HPs) forming at the CAG TNRs are stabilized by adjacent CCG (in HD) or CUG repeats (in SBMA) making them better substrates for Dicer, the enzyme that processes CAG HPs into sCAGs. We now show that cells deficient in Dicer or unable to mediate RNAi are resistant to the toxicity of the HTT and AR derived HPs. Expression of a small HP that mimics the HD LOI variant is more stable and more toxic than a reference HP. We report that the LOI HP is processed by Dicer, loaded into the RISC more efficiently, and gives rise to a higher quantity of RISC-bound 22 nt sCAGs. Our data support the notion that RNAi contributes to the cell death seen in HD and SBMA and provide an explanation for the dramatically reduced onset of disease in HD patients that carry the LOI variant.
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12
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Wang F, Calvo-Roitberg E, Rembetsy-Brown JM, Fang M, Sousa J, Kartje Z, Krishnamurthy PM, Lee J, Green M, Pai A, Watts J. G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects. Nucleic Acids Res 2022; 50:12657-12673. [PMID: 36511872 PMCID: PMC9825156 DOI: 10.1093/nar/gkac1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/11/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Friedreich's ataxia is an incurable disease caused by frataxin (FXN) protein deficiency, which is mostly induced by GAA repeat expansion in intron 1 of the FXN gene. Here, we identified antisense oligonucleotides (ASOs), complementary to two regions within the first intron of FXN pre-mRNA, which could increase FXN mRNA by ∼2-fold in patient fibroblasts. The increase in FXN mRNA was confirmed by the identification of multiple overlapping FXN-activating ASOs at each region, two independent RNA quantification assays, and normalization by multiple housekeeping genes. Experiments on cells with the ASO-binding sites deleted indicate that the ASO-induced FXN activation was driven by indirect effects. RNA sequencing analyses showed that the two ASOs induced similar transcriptome-wide changes, which did not resemble the transcriptome of wild-type cells. This RNA-seq analysis did not identify directly base-paired off-target genes shared across ASOs. Mismatch studies identified two guanosine-rich motifs (CCGG and G4) within the ASOs that were required for FXN activation. The phosphorodiamidate morpholino oligomer analogs of our ASOs did not activate FXN, pointing to a PS-backbone-mediated effect. Our study demonstrates the importance of multiple, detailed control experiments and target validation in oligonucleotide studies employing novel mechanisms such as gene activation.
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Affiliation(s)
- Feng Wang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ezequiel Calvo-Roitberg
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Julia M Rembetsy-Brown
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Minggang Fang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Zachary J Kartje
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
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13
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Zhang Y, Jin T, Dou Z, Wei B, Zhang B, Sun C. The dual role of the CD95 and CD95L signaling pathway in glioblastoma. Front Immunol 2022; 13:1029737. [PMID: 36505426 PMCID: PMC9730406 DOI: 10.3389/fimmu.2022.1029737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022] Open
Abstract
Binding of CD95, a cell surface death receptor, to its homologous ligand CD95L, transduces a cascade of downstream signals leading to apoptosis crucial for immune homeostasis and immune surveillance. Although CD95 and CD95L binding classically induces programmed cell death, most tumor cells show resistance to CD95L-induced apoptosis. In some cancers, such as glioblastoma, CD95-CD95L binding can exhibit paradoxical functions that promote tumor growth by inducing inflammation, regulating immune cell homeostasis, and/or promoting cell survival, proliferation, migration, and maintenance of the stemness of cancer cells. In this review, potential mechanisms such as the expression of apoptotic inhibitor proteins, decreased activity of downstream elements, production of nonapoptotic soluble CD95L, and non-apoptotic signals that replace apoptotic signals in cancer cells are summarized. CD95L is also expressed by other types of cells, such as endothelial cells, polymorphonuclear myeloid-derived suppressor cells, cancer-associated fibroblasts, and tumor-associated microglia, and macrophages, which are educated by the tumor microenvironment and can induce apoptosis of tumor-infiltrating lymphocytes, which recognize and kill cancer cells. The dual role of the CD95-CD95L system makes targeted therapy strategies against CD95 or CD95L in glioblastoma difficult and controversial. In this review, we also discuss the current status and perspective of clinical trials on glioblastoma based on the CD95-CD95L signaling pathway.
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Affiliation(s)
- Yanrui Zhang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Taian Jin
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhangqi Dou
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Boxing Wei
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Buyi Zhang
- Department of Pathology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,*Correspondence: Buyi Zhang, ; Chongran Sun,
| | - Chongran Sun
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, Zhejiang, China,Clinical Research Center for Neurological Diseases of Zhejiang Province, Hangzhou, Zhejiang, China,*Correspondence: Buyi Zhang, ; Chongran Sun,
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14
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Nedorezova DD, Dubovichenko MV, Belyaeva EP, Grigorieva ED, Peresadina AV, Kolpashchikov DM. Specificity of oligonucleotide gene therapy (OGT) agents. Theranostics 2022; 12:7132-7157. [PMID: 36276652 PMCID: PMC9576606 DOI: 10.7150/thno.77830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotide gene therapy (OGT) agents (e. g. antisense, deoxyribozymes, siRNA and CRISPR/Cas) are promising therapeutic tools. Despite extensive efforts, only few OGT drugs have been approved for clinical use. Besides the problem of efficient delivery to targeted cells, hybridization specificity is a potential limitation of OGT agents. To ensure tight binding, a typical OGT agent hybridizes to the stretch of 15-25 nucleotides of a unique targeted sequence. However, hybrids of such lengths tolerate one or more mismatches under physiological conditions, the problem known as the affinity/specificity dilemma. Here, we assess the scale of this problem by analyzing OGT hybridization-dependent off-target effects (HD OTE) in vitro, in animal models and clinical studies. All OGT agents except deoxyribozymes exhibit HD OTE in vitro, with most thorough evidence of poor specificity reported for siRNA and CRISPR/Cas9. Notably, siRNA suppress non-targeted genes due to (1) the partial complementarity to mRNA 3'-untranslated regions (3'-UTR), and (2) the antisense activity of the sense strand. CRISPR/Cas9 system can cause hundreds of non-intended dsDNA breaks due to low specificity of the guide RNA, which can limit therapeutic applications of CRISPR/Cas9 by ex-vivo formats. Contribution of this effects to the observed in vivo toxicity of OGT agents is unclear and requires further investigation. Locked or peptide nucleic acids improve OGT nuclease resistance but not specificity. Approaches that use RNA marker dependent (conditional) activation of OGT agents may improve specificity but require additional validation in cell culture and in vivo.
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Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Mikhail V. Dubovichenko
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina P. Belyaeva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina D. Grigorieva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Arina V. Peresadina
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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15
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Feng Z, Hom ME, Bearrood TE, Rosenthal ZC, Fernández D, Ondrus AE, Gu Y, McCormick AK, Tomaske MG, Marshall CR, Kline T, Chen CH, Mochly-Rosen D, Kuo CJ, Chen JK. Targeting colorectal cancer with small-molecule inhibitors of ALDH1B1. Nat Chem Biol 2022; 18:1065-1075. [PMID: 35788181 PMCID: PMC9529790 DOI: 10.1038/s41589-022-01048-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 04/26/2022] [Indexed: 12/21/2022]
Abstract
Aldehyde dehydrogenases (ALDHs) are promising cancer drug targets, as certain isoforms are required for the survival of stem-like tumor cells. We have discovered selective inhibitors of ALDH1B1, a mitochondrial enzyme that promotes colorectal and pancreatic cancer. We describe bicyclic imidazoliums and guanidines that target the ALDH1B1 active site with comparable molecular interactions and potencies. Both pharmacophores abrogate ALDH1B1 function in cells; however, the guanidines circumvent an off-target mitochondrial toxicity exhibited by the imidazoliums. Our lead isoform-selective guanidinyl antagonists of ALDHs exhibit proteome-wide target specificity, and they selectively block the growth of colon cancer spheroids and organoids. Finally, we have used genetic and chemical perturbations to elucidate the ALDH1B1-dependent transcriptome, which includes genes that regulate mitochondrial metabolism and ribosomal function. Our findings support an essential role for ALDH1B1 in colorectal cancer, provide molecular probes for studying ALDH1B1 functions and yield leads for developing ALDH1B1-targeting therapies.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Marisa E Hom
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas E Bearrood
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Zachary C Rosenthal
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Daniel Fernández
- Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Alison E Ondrus
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Yuchao Gu
- Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | | | | | - Cody R Marshall
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Toni Kline
- SPARK at Stanford, Stanford University, Stanford, CA, USA
| | - Che-Hong Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Calvin J Kuo
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
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16
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Bartom ET, Kocherginsky M, Paudel B, Vaidyanathan A, Haluck-Kangas A, Patel M, O’Shea KL, Murmann AE, Peter ME. SPOROS: A pipeline to analyze DISE/6mer seed toxicity. PLoS Comput Biol 2022; 18:e1010022. [PMID: 35358200 PMCID: PMC9004739 DOI: 10.1371/journal.pcbi.1010022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/12/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
microRNAs (miRNAs) are (18-22nt long) noncoding short (s)RNAs that suppress gene expression by targeting the 3’ untranslated region of target mRNAs. This occurs through the seed sequence located in position 2-7/8 of the miRNA guide strand, once it is loaded into the RNA induced silencing complex (RISC). G-rich 6mer seed sequences can kill cells by targeting C-rich 6mer seed matches located in genes that are critical for cell survival. This results in induction of Death Induced by Survival gene Elimination (DISE), through a mechanism we have called 6mer seed toxicity. miRNAs are often quantified in cells by aligning the reads from small (sm)RNA sequencing to the genome. However, the analysis of any smRNA Seq data set for predicted 6mer seed toxicity requires an alternative workflow, solely based on the exact position 2–7 of any short (s)RNA that can enter the RISC. Therefore, we developed SPOROS, a semi-automated pipeline that produces multiple useful outputs to predict and compare 6mer seed toxicity of cellular sRNAs, regardless of their nature, between different samples. We provide two examples to illustrate the capabilities of SPOROS: Example one involves the analysis of RISC-bound sRNAs in a cancer cell line (either wild-type or two mutant lines unable to produce most miRNAs). Example two is based on a publicly available smRNA Seq data set from postmortem brains (either from normal or Alzheimer’s patients). Our methods (found at https://github.com/ebartom/SPOROS and at Code Ocean: https://doi.org/10.24433/CO.1732496.v1) are designed to be used to analyze a variety of smRNA Seq data in various normal and disease settings. We recently discovered a kill code embedded in the genome with powerful anti-cancer activity. It is based on only 6 nucleotides (comprised of A, G, C, or U) that when present in the sequence of a small double stranded RNA allows it to act like a microRNA (miRNA). miRNAs are important regulators of many cell functions. The ~2,300 known miRNAs in the human genome function through their business end, the seed sequence. When this seed sequence is 6 nucleotides long (6mer seed) and is comprised of mostly Gs, then these small RNAs can kill all cancer cells. Hence, this code is found in a number of miRNAs that have anti-cancer activities. However, the code is not limited to miRNAs and may also affect normal tissue under certain conditions. We have now developed SPOROS, a semi-automated bioinformatics pipeline that allows one to analyze any data set of sequenced small RNAs with a focus on their 6mer seed content and their potential to kill cells. We present two examples of such an analysis: the first example is a data set we generated on the expression of all small RNAs in a human colon cancer cell line compared to matching mutant cell lines that cannot produce most miRNAs; the second example is a publicly available data set of small RNAs isolated from normal brains and from brains of patients with Alzheimer’s disease.
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Affiliation(s)
- Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (MEP); (ETB)
| | - Masha Kocherginsky
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Bidur Paudel
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Aparajitha Vaidyanathan
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Ashley Haluck-Kangas
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Monal Patel
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Kaitlyn L. O’Shea
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Andrea E. Murmann
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Marcus E. Peter
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (MEP); (ETB)
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17
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Patel M, Bartom ET, Paudel B, Kocherginsky M, O'Shea KL, Murmann AE, Peter ME. Identification of the toxic 6mer seed consensus for human cancer cells. Sci Rep 2022; 12:5130. [PMID: 35332222 PMCID: PMC8948288 DOI: 10.1038/s41598-022-09051-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/16/2022] [Indexed: 12/13/2022] Open
Abstract
6mer seed toxicity is a novel cell death mechanism that kills cancer cells by triggering death induced by survival gene elimination (DISE). It is based on si- or shRNAs with a specific G-rich nucleotide composition in position 2–7 of their guide strand. An arrayed screen of 4096 6mer seeds on two human and two mouse cell lines identified G-rich 6mers as the most toxic seeds. We have now tested two additional cell lines, one human and one mouse, identifying the GGGGGC consensus as the most toxic average 6mer seed for human cancer cells while slightly less significant for mouse cancer cells. RNA Seq and bioinformatics analyses suggested that an siRNA containing the GGGGGC seed (siGGGGGC) is toxic to cancer cells by targeting GCCCCC seed matches located predominantly in the 3′ UTR of a set of genes critical for cell survival. We have identified several genes targeted by this seed and demonstrate direct and specific targeting of GCCCCC seed matches, which is attenuated upon mutation of the GCCCCC seed matches in these 3′ UTRs. Our data show that siGGGGGC kills cancer cells through its miRNA-like activity and points at artificial miRNAs, si- or shRNAs containing this seed as a potential new cancer therapeutics.
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Affiliation(s)
- Monal Patel
- Department of Medicine/Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bidur Paudel
- Department of Medicine/Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Masha Kocherginsky
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kaitlyn L O'Shea
- Department of Preventive Medicine/Division of Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Andrea E Murmann
- Department of Medicine/Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marcus E Peter
- Department of Medicine/Division of Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. .,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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18
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Haluck-Kangas A, Patel M, Paudel B, Vaidyanathan A, Murmann AE, Peter ME. DISE/6mer seed toxicity-a powerful anti-cancer mechanism with implications for other diseases. J Exp Clin Cancer Res 2021; 40:389. [PMID: 34893072 PMCID: PMC8662895 DOI: 10.1186/s13046-021-02177-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023] Open
Abstract
micro(mi)RNAs are short noncoding RNAs that through their seed sequence (pos. 2-7/8 of the guide strand) regulate cell function by targeting complementary sequences (seed matches) located mostly in the 3' untranslated region (3' UTR) of mRNAs. Any short RNA that enters the RNA induced silencing complex (RISC) can kill cells through miRNA-like RNA interference when its 6mer seed sequence (pos. 2-7 of the guide strand) has a G-rich nucleotide composition. G-rich seeds mediate 6mer Seed Toxicity by targeting C-rich seed matches in the 3' UTR of genes critical for cell survival. The resulting Death Induced by Survival gene Elimination (DISE) predominantly affects cancer cells but may contribute to cell death in other disease contexts. This review summarizes recent findings on the role of DISE/6mer Seed Tox in cancer; its therapeutic potential; its contribution to therapy resistance; its selectivity, and why normal cells are protected. In addition, we explore the connection between 6mer Seed Toxicity and aging in relation to cancer and certain neurodegenerative diseases.
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Affiliation(s)
- Ashley Haluck-Kangas
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Monal Patel
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Bidur Paudel
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Aparajitha Vaidyanathan
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Andrea E. Murmann
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Marcus E. Peter
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
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19
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Czarnek M, Sarad K, Karaś A, Kochan J, Bereta J. Non-targeting control for MISSION shRNA library silences SNRPD3 leading to cell death or permanent growth arrest. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:711-731. [PMID: 34703654 PMCID: PMC8517100 DOI: 10.1016/j.omtn.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 09/03/2021] [Indexed: 12/15/2022]
Abstract
In parallel with the expansion of RNA interference (RNAi) techniques, accumulating evidence indicates that RNAi analyses might be seriously biased due to the off-target effects of gene-specific short hairpin RNAs (shRNAs). Our findings indicated that off-target effects of non-targeting shRNA comprise another source of misinterpreted shRNA-based data. We found that SHC016, which is one of two non-targeting shRNA controls for the MISSION (commercialized TRC) library, exerts deleterious effects that lead to elimination of the shRNA-coding cassette from the genomes of cultured murine and human cells. Here, we used a lentiviral vector with inducible SHC016 expression to confirm that this shRNA induces apoptosis in murine cells and senescence or mitotic catastrophe depending on the p53 status in human tumor cells. We identified the core spliceosomal protein, small nuclear ribonucleoprotein Sm D3 (SNRPD3), as a major SHC016 target in several cell lines and confirmed that CRISPRi knockdown of SNRPD3 mimics the effects of SHC016 expression in A549 and U251 cells. The overexpression of SNRPD3 rescued U251 cells from SHC016-induced mitotic catastrophe. Our findings disqualified non-targeting SHC016 shRNA and added a new premise to the discussion about the sources of uncertainty in RNAi results.
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Affiliation(s)
- Maria Czarnek
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Katarzyna Sarad
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Agnieszka Karaś
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Joanna Bereta
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
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20
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Qadir AS, Guégan JP, Ginestier C, Chaibi A, Bessede A, Charafe-Jauffret E, Macario M, Lavoué V, Rouge TDLM, Law C, Vilker J, Wang H, Stroup E, Schipma MJ, Bridgeman B, Murmann AE, Ji Z, Legembre P, Peter ME. CD95/Fas protects triple negative breast cancer from anti-tumor activity of NK cells. iScience 2021; 24:103348. [PMID: 34816102 PMCID: PMC8593563 DOI: 10.1016/j.isci.2021.103348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/12/2021] [Accepted: 10/22/2021] [Indexed: 11/04/2022] Open
Abstract
The apoptosis inducing receptor CD95/Fas has multiple tumorigenic activities. In different genetically engineered mouse models tumor-expressed CD95 was shown to be critical for cell growth. Using a combination of immune-deficient and immune-competent mouse models, we now establish that loss of CD95 in metastatic triple negative breast cancer (TNBC) cells prevents tumor growth by modulating the immune landscape. CD95-deficient, but not wild-type, tumors barely grow in an immune-competent environment and show an increase in immune infiltrates into the tumor. This growth reduction is caused by infiltrating NK cells and does not involve T cells or macrophages. In contrast, in immune compromised mice CD95 k.o. cells are not growth inhibited, but they fail to form metastases. In summary, we demonstrate that in addition to its tumor and metastasis promoting activities, CD95 expression by tumor cells can exert immune suppressive activities on NK cells, providing a new target for immune therapy.
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Affiliation(s)
- Abdul S. Qadir
- Division Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Christophe Ginestier
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Univ, Epithelial Stem Cells and Cancer Lab, Equipe labellisée LIGUE contre le cancer, Marseille, France
| | - Assia Chaibi
- Explicyte, Cours de l’Argonne, 33000 Bordeaux, France
| | - Alban Bessede
- Explicyte, Cours de l’Argonne, 33000 Bordeaux, France
| | - Emmanuelle Charafe-Jauffret
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Univ, Epithelial Stem Cells and Cancer Lab, Equipe labellisée LIGUE contre le cancer, Marseille, France
| | - Manon Macario
- CRCM, Inserm, CNRS, Institut Paoli-Calmettes, Aix-Marseille Univ, Epithelial Stem Cells and Cancer Lab, Equipe labellisée LIGUE contre le cancer, Marseille, France
| | - Vincent Lavoué
- Department of Gynecology, University Hospital of Rennes, Rennes, France
| | | | - Calvin Law
- Division Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jacob Vilker
- Division Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hongbin Wang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew J. Schipma
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bryan Bridgeman
- Division Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Andrea E. Murmann
- Division Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, USA
| | | | - Marcus E. Peter
- Division Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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21
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Ahn SH, Gu D, Koh Y, Lee HS, Chi SW. AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity. Sci Rep 2021; 11:19161. [PMID: 34580386 PMCID: PMC8476540 DOI: 10.1038/s41598-021-98708-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/13/2021] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is associated with fatal pulmonary fibrosis. Small interfering RNAs (siRNAs) can be developed to induce RNA interference against SARS-CoV-2, and their susceptible target sites can be inferred by Argonaute crosslinking immunoprecipitation sequencing (AGO CLIP). Here, by reanalysing AGO CLIP data in RNA viruses, we delineated putative AGO binding in the conserved non-structural protein 12 (nsp12) region encoding RNA-dependent RNA polymerase (RdRP) in SARS-CoV-2. We utilised the inferred AGO binding to optimise the local RNA folding parameter to calculate target accessibility and predict all potent siRNA target sites in the SARS-CoV-2 genome, avoiding sequence variants. siRNAs loaded onto AGO also repressed seed (positions 2–8)-matched transcripts by acting as microRNAs (miRNAs). To utilise this, we further screened 13 potential siRNAs whose seed sequences were matched to known antifibrotic miRNAs and confirmed their miRNA-like activity. A miR-27-mimicking siRNA designed to target the nsp12 region (27/RdRP) was validated to silence a synthesised nsp12 RNA mimic in lung cell lines and function as an antifibrotic miR-27 in regulating target transcriptomes related to TGF-β signalling. siRNA sequences with an antifibrotic miRNA-like activity that could synergistically treat COVID-19 are available online (http://clip.korea.ac.kr/covid19).
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Affiliation(s)
- Seung Hyun Ahn
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Dowoon Gu
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Yongjun Koh
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Hye-Sook Lee
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Sung Wook Chi
- Department of Life Sciences, Korea University, Seoul, Korea.
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22
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Programmable RNA targeting with the single-protein CRISPR effector Cas7-11. Nature 2021; 597:720-725. [PMID: 34489594 DOI: 10.1038/s41586-021-03886-5] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/09/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-Cas interference is mediated by Cas effector nucleases that are either components of multisubunit complexes-in class 1 CRISPR-Cas systems-or domains of a single protein-in class 2 systems1-3. Here we show that the subtype III-E effector Cas7-11 is a single-protein effector in the class 1 CRISPR-Cas systems originating from the fusion of a putative Cas11 domain and multiple Cas7 subunits that are derived from subtype III-D. Cas7-11 from Desulfonema ishimotonii (DiCas7-11), when expressed in Escherichia coli, has substantial RNA interference effectivity against mRNAs and bacteriophages. Similar to many class 2 effectors-and unique among class 1 systems-DiCas7-11 processes pre-CRISPR RNA into mature CRISPR RNA (crRNA) and cleaves RNA at positions defined by the target:spacer duplex, without detectable non-specific activity. We engineered Cas7-11 for RNA knockdown and editing in mammalian cells. We show that Cas7-11 has no effects on cell viability, whereas other RNA-targeting tools (such as short hairpin RNAs and Cas13) show substantial cell toxicity4,5. This study illustrates the evolution of a single-protein effector from multisubunit class 1 effector complexes, expanding our understanding of the diversity of CRISPR systems. Cas7-11 provides the basis for new programmable RNA-targeting tools that are free of collateral activity and cell toxicity.
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23
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Patel M, Wang Y, Bartom ET, Dhir R, Nephew KP, Matei D, Murmann AE, Lengyel E, Peter ME. The Ratio of Toxic-to-Nontoxic miRNAs Predicts Platinum Sensitivity in Ovarian Cancer. Cancer Res 2021; 81:3985-4000. [PMID: 34224372 PMCID: PMC8338879 DOI: 10.1158/0008-5472.can-21-0953] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 01/09/2023]
Abstract
Ovarian cancer remains one of the deadliest gynecologic malignancies affecting women, and development of resistance to platinum remains a major barrier to achieving a cure. Multiple mechanisms have been identified to confer platinum resistance. Numerous miRNAs have been linked to platinum sensitivity and resistance in ovarian cancer. miRNA activity occurs mainly when the guide strand of the miRNA, with its seed sequence at position 2-7/8, is loaded into the RNA-induced silencing complex (RISC) and targets complementary short seed matches in the 3' untranslated region of mRNAs. Toxic 6mer seeds, which target genes critical for cancer cell survival, have been found in tumor-suppressive miRNAs. Many siRNAs and short hairpin RNAs (shRNA) can also kill cancer cells via toxic seeds, the most toxic of which carry G-rich 6mer seed sequences. We showed here that treatment of ovarian cancer cells with platinum led to increased RISC-bound miRNAs carrying toxic 6mer seeds and decreased miRNAs with nontoxic seeds. Platinum-tolerant cells did not exhibit this toxicity shift but retained sensitivity to cell death mediated by siRNAs carrying toxic 6mer seeds. Analysis of RISC-bound miRNAs in tumors from patients with ovarian cancer revealed that the ratio between miRNAs with toxic versus nontoxic seeds was predictive of treatment outcome. Application of the 6mer seed toxicity concept to cancer relevant miRNAs provides a new framework for understanding and predicting cancer therapy responses. SIGNIFICANCE: These findings demonstrate that the balance of miRNAs that carry toxic and nontoxic 6mer seeds contributes to platinum resistance in ovarian cancer.
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Affiliation(s)
- Monal Patel
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Yinu Wang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Rohin Dhir
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois
| | - Kenneth P Nephew
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
| | - Andrea E Murmann
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois
| | - Marcus E Peter
- Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
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24
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Serine-Threonine Kinase Receptor-Associated Protein (STRAP) Knockout Decreases the Malignant Phenotype in Neuroblastoma Cell Lines. Cancers (Basel) 2021; 13:cancers13133201. [PMID: 34206917 PMCID: PMC8268080 DOI: 10.3390/cancers13133201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Serine-threonine kinase receptor-associated protein (STRAP) plays an important role in neural development but also in tumor growth. Neuroblastoma, a tumor of neural crest origin, is the most common extracranial solid malignancy of childhood and it continues to carry a poor prognosis. The recent discovery of the role of STRAP in another pediatric solid tumor, osteosarcoma, and the known function of STRAP in neural development, led us to investigate the role of STRAP in neuroblastoma tumorigenesis. Methods: STRAP protein expression was abrogated in two human neuroblastoma cell lines, SK-N-AS and SK-N-BE(2), using transient knockdown with siRNA, stable knockdown with shRNA lentiviral transfection, and CRISPR-Cas9 genetic knockout. STRAP knockdown and knockout cells were examined for phenotypic alterations in vitro and tumor growth in vivo. Results: Cell proliferation, motility, and growth were significantly decreased in STRAP knockout compared to wild-type cells. Indicators of stemness, including mRNA abundance of common stem cell markers Oct4, Nanog, and Nestin, the percentage of cells expressing CD133 on their surface, and the ability to form tumorspheres were significantly decreased in the STRAP KO cells. In vivo, STRAP knockout cells formed tumors less readily than wild-type tumor cells. Conclusion: These novel findings demonstrated that STRAP plays a role in tumorigenesis and maintenance of neuroblastoma stemness.
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25
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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26
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Corbin JM, Georgescu C, Wren JD, Xu C, Asch AS, Ruiz-Echevarría MJ. Seed-mediated RNA interference of androgen signaling and survival networks induces cell death in prostate cancer cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:337-351. [PMID: 33850637 PMCID: PMC8022159 DOI: 10.1016/j.omtn.2021.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
Resistance to anti-androgen therapy in prostate cancer (PCa) is often driven by genetic and epigenetic aberrations in the androgen receptor (AR) and coregulators that maintain androgen signaling activity. We show that specific small RNAs downregulate expression of multiple essential and androgen receptor-coregulatory genes, leading to potent androgen signaling inhibition and PCa cell death. Expression of different short hairpin/small interfering RNAs (sh-/siRNAs) designed to target TMEFF2 preferentially reduce viability of PCa but not benign cells, and growth of murine xenografts. Surprisingly, this effect is independent of TMEFF2 expression. Transcriptomic and sh/siRNA seed sequence studies indicate that expression of these toxic shRNAs lead to downregulation of androgen receptor-coregulatory and essential genes through mRNA 3′ UTR sequence complementarity to the seed sequence of the toxic shRNAs. These findings reveal a form of the “death induced by survival gene elimination” mechanism in PCa cells that mainly targets AR signaling, and that we have termed androgen network death induced by survival gene elimination (AN-DISE). Our data suggest that AN-DISE may be a novel therapeutic strategy for PCa.
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Affiliation(s)
- Joshua M Corbin
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, Oklahoma City, OK, USA.,Department of Pathology, Biomedical Sciences building, Oklahoma University Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK 73104, USA
| | - Constantin Georgescu
- Genes and Human Disease Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Jonathan D Wren
- Genes and Human Disease Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Chao Xu
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, Oklahoma City, OK, USA.,Department of Biostatistics and Epidemiology, Hudson College of Public Health, Oklahoma University Health Sciences Center, 801 N.E. 13 Street, Oklahoma City, OK, USA
| | - Adam S Asch
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, Oklahoma City, OK, USA.,Department of Medicine, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Maria J Ruiz-Echevarría
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, Oklahoma City, OK, USA.,Department of Pathology, Biomedical Sciences building, Oklahoma University Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK 73104, USA.,Department of Medicine, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
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27
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Gu D, Ahn SH, Eom S, Lee HS, Ham J, Lee DH, Cho YK, Koh Y, Ignatova E, Jang ES, Chi SW. AGO-accessible anticancer siRNAs designed with synergistic miRNA-like activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:1172-1190. [PMID: 33664996 PMCID: PMC7900643 DOI: 10.1016/j.omtn.2021.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023]
Abstract
Small interfering RNAs (siRNAs) therapeutically induce RNA interference (RNAi) of disease-causing genes, but they also silence hundreds of seed-matched off-targets as behaving similar to microRNAs (miRNAs). miRNAs control the pathophysiology of tumors, wherein their accessible binding sites can be sequenced by Argonaute crosslinking immunoprecipitation (AGO CLIP). Herein, based on AGO CLIP, we develop potent anticancer siRNAs utilizing miRNA-like activity (mi/siRNAs). The mi/siRNAs contain seed sequences (positions 2-7) of tumor-suppressive miRNAs while maintaining perfect sequence complementarity to the AGO-accessible tumor target sites. Initially, host miRNA interactions with human papillomavirus 18 (HPV18) were identified in cervical cancer by AGO CLIP, revealing tumor-suppressive activity of miR-1/206 and miR-218. Based on the AGO-miRNA binding sites, mi/siRNAs were designed to target E6 and E7 (E6/E7) transcript with seed sequences of miR-1/206 (206/E7) and miR-218 (218/E7). Synergistic anticancer activity of 206/E7 and 218/E7 was functionally validated and confirmed via RNA sequencing and in vivo xenograft models (206/E7). Other mi/siRNA sequences were additionally designed for cervical, ovarian, and breast cancer, and available as an online tool (http://ago.korea.ac.kr/misiRNA); some of the mi/siRNAs were validated for their augmented anticancer activity (206/EphA2 and 206/Her2). mi/siRNAs could coordinate miRNA-like activity with robust siRNA function, demonstrating the potential of AGO CLIP analysis for RNAi therapeutics.
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Affiliation(s)
- Dowoon Gu
- Department of Life Sciences, Korea University, Seoul 02481, Korea
| | - Seung Hyun Ahn
- Department of Life Sciences, Korea University, Seoul 02481, Korea
| | - Sangkyeong Eom
- Department of Life Sciences, Korea University, Seoul 02481, Korea
| | - Hye-Sook Lee
- Department of Life Sciences, Korea University, Seoul 02481, Korea.,EncodeGEN, Co., Ltd., Seoul 06329, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Juyoung Ham
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Dong Ha Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - You Kyung Cho
- Department of Life Sciences, Korea University, Seoul 02481, Korea
| | - Yongjun Koh
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02481, Korea
| | | | - Eun-Sook Jang
- Department of Life Sciences, Korea University, Seoul 02481, Korea.,EncodeGEN, Co., Ltd., Seoul 06329, Korea
| | - Sung Wook Chi
- Department of Life Sciences, Korea University, Seoul 02481, Korea
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28
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Zhan H, Li A, Cai Z, Huang W, Liu Y. Improving transgene expression and CRISPR-Cas9 efficiency with molecular engineering-based molecules. Clin Transl Med 2020; 10:e194. [PMID: 33135339 PMCID: PMC7533053 DOI: 10.1002/ctm2.194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/08/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023] Open
Abstract
As a novel and robust gene‐editing tool, the Clustered Regularly Interspaced Short Palindromic Repeats CRISPR‐associated protein 9 (CRISPR‐Cas9) system has revolutionized gene therapy. Plasmid vector delivery is the most commonly used method for integrating the CRISPR‐Cas9 system into cells. However, such foreign cytosolic DNAs trigger an innate immune response (IIR) within cells, which can hinder gene editing by inhibiting transgene expression. Although some small molecules have been shown to avoid the action of IIR on plasmids, they only work on a single target and may also affect cell viability. A genetic approach that works at a comprehensive level for manipulating IIR is still lacking. Here, we designed and constructed several artificial nucleic acid molecules (ANAMs), which are combinations of aptamers binding to two key players of IIR (β‐catenin and NF‐κB). ANAMs strongly inhibited the IIR in cells, thus improving transgene expression. We also used ANAMs to improve the gene‐editing efficiency of the CRISPR‐Cas9 system and its derivatives, thus enhancing the apoptosis of cancer cells induced by CRISPR‐Cas9. ANAMs can be valuable tools for improving transgene expression and gene editing in mammalian cells.
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Affiliation(s)
- Hengji Zhan
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Aolin Li
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhiming Cai
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Weiren Huang
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
| | - Yuchen Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, China
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29
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Ariss MM, Terry AR, Islam ABMMK, Hay N, Frolov MV. Amalgam regulates the receptor tyrosine kinase pathway through Sprouty in glial cell development in the Drosophila larval brain. J Cell Sci 2020; 133:jcs.250837. [PMID: 32878945 DOI: 10.1242/jcs.250837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/24/2020] [Indexed: 01/04/2023] Open
Abstract
The receptor tyrosine kinase (RTK) pathway plays an essential role in development and disease by controlling cell proliferation and differentiation. Here, we profile the Drosophila larval brain by single-cell RNA-sequencing and identify Amalgam (Ama), which encodes a cell adhesion protein of the immunoglobulin IgLON family, as regulating the RTK pathway activity during glial cell development. Depletion of Ama reduces cell proliferation, affects glial cell type composition and disrupts the blood-brain barrier (BBB), which leads to hemocyte infiltration and neuronal death. We show that Ama depletion lowers RTK activity by upregulating Sprouty (Sty), a negative regulator of the RTK pathway. Knockdown of Ama blocks oncogenic RTK signaling activation in the Drosophila glioma model and halts malignant transformation. Finally, knockdown of a human ortholog of Ama, LSAMP, results in upregulation of SPROUTY2 in glioblastoma cell lines, suggesting that the relationship between Ama and Sty is conserved.
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Affiliation(s)
- Majd M Ariss
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander R Terry
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Abul B M M K Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Nissim Hay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA
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30
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Lin A, Giuliano CJ, Palladino A, John KM, Abramowicz C, Yuan ML, Sausville EL, Lukow DA, Liu L, Chait AR, Galluzzo ZC, Tucker C, Sheltzer JM. Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. Sci Transl Med 2020; 11:11/509/eaaw8412. [PMID: 31511426 DOI: 10.1126/scitranslmed.aaw8412] [Citation(s) in RCA: 345] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/19/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022]
Abstract
Ninety-seven percent of drug-indication pairs that are tested in clinical trials in oncology never advance to receive U.S. Food and Drug Administration approval. While lack of efficacy and dose-limiting toxicities are the most common causes of trial failure, the reason(s) why so many new drugs encounter these problems is not well understood. Using CRISPR-Cas9 mutagenesis, we investigated a set of cancer drugs and drug targets in various stages of clinical testing. We show that-contrary to previous reports obtained predominantly with RNA interference and small-molecule inhibitors-the proteins ostensibly targeted by these drugs are nonessential for cancer cell proliferation. Moreover, the efficacy of each drug that we tested was unaffected by the loss of its putative target, indicating that these compounds kill cells via off-target effects. By applying a genetic target-deconvolution strategy, we found that the mischaracterized anticancer agent OTS964 is actually a potent inhibitor of the cyclin-dependent kinase CDK11 and that multiple cancer types are addicted to CDK11 expression. We suggest that stringent genetic validation of the mechanism of action of cancer drugs in the preclinical setting may decrease the number of therapies tested in human patients that fail to provide any clinical benefit.
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Affiliation(s)
- Ann Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Stony Brook University, Stony Brook, NY 11794, USA
| | - Christopher J Giuliano
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Stony Brook University, Stony Brook, NY 11794, USA
| | - Ann Palladino
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kristen M John
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Hofstra University, Hempstead, NY 11549, USA
| | - Connor Abramowicz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,New York Institute of Technology, Glen Head, NY 11545, USA
| | - Monet Lou Yuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Syosset High School, Syosset, NY 11791, USA
| | - Erin L Sausville
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Devon A Lukow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Stony Brook University, Stony Brook, NY 11794, USA
| | - Luwei Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Stony Brook University, Stony Brook, NY 11794, USA
| | | | | | - Clara Tucker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,Stony Brook University, Stony Brook, NY 11794, USA
| | - Jason M Sheltzer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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31
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Lin A, Sheltzer JM. Discovering and validating cancer genetic dependencies: approaches and pitfalls. Nat Rev Genet 2020; 21:671-682. [DOI: 10.1038/s41576-020-0247-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 12/21/2022]
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32
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Jordan B. [Significant target misidentification]. Med Sci (Paris) 2020; 36:87-89. [PMID: 32014106 DOI: 10.1051/medsci/2019258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bertrand Jordan
- UMR 7268 ADÉS, Aix-Marseille, Université /EFS/CNRS ; CoReBio PACA, case 901, Parc scientifique de Luminy, 13288 Marseille Cedex 09, France
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33
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The mechanism of how CD95/Fas activates the Type I IFN/STAT1 axis, driving cancer stemness in breast cancer. Sci Rep 2020; 10:1310. [PMID: 31992798 PMCID: PMC6987111 DOI: 10.1038/s41598-020-58211-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/09/2020] [Indexed: 01/18/2023] Open
Abstract
CD95/Fas is an apoptosis inducing death receptor. However, it also has multiple nonapoptotic activities that are tumorigenic. Chronic stimulation of CD95 on breast cancer cells can increase their cancer initiating capacity through activation of a type I interferon (IFN-I)/STAT1 pathway when caspases are inhibited. We now show that this activity relies on the canonical components of the CD95 death-inducing signaling complex, FADD and caspase-8, and on the activation of NF-κB. We identified caspase-2 as the antagonistic caspase that downregulates IFN-I production. Once produced, IFN-Is bind to their receptors activating both STAT1 and STAT2 resulting in upregulation of the double stranded (ds)RNA sensor proteins RIG-I and MDA5, and a release of a subset of endogenous retroviruses. Thus, CD95 is part of a complex cell autonomous regulatory network that involves activation of innate immune components that drive cancer stemness and contribute to therapy resistance.
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Murmann AE, Bartom ET, Schipma MJ, Vilker J, Chen S, Peter ME. 6mer Seed Toxicity in Viral microRNAs. iScience 2019; 23:100737. [PMID: 31838022 PMCID: PMC7033618 DOI: 10.1016/j.isci.2019.11.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are short double-stranded noncoding RNAs (19-23 nucleotides) that regulate gene expression by suppressing mRNAs through RNA interference. Targeting is determined by the seed sequence (position 2-7/8) of the mature miRNA. A minimal G-rich seed of just six nucleotides is highly toxic to cells by targeting genes essential for cell survival. A screen of 215 miRNAs encoded by 17 human pathogenic viruses (v-miRNAs) now suggests that a number of v-miRNAs can kill cells through a G-rich 6mer sequence embedded in their seed. Specifically, we demonstrate that miR-K12-6-5p, an oncoviral mimic of the tumor suppressive miR-15/16 family encoded by human Kaposi sarcoma-associated herpes virus, harbors a noncanonical toxic 6mer seed (position 3-8) and that v-miRNAs are more likely than cellular miRNAs to utilize a noncanonical 6mer seed. Our data suggest that during evolution viruses evolved to use 6mer seed toxicity to kill cells. Tumor suppressive miR-15/16-5p with a toxic 6mer seed targets survival genes kshv-miR-K12-6-5p, a paralog of hsa-miR-15/16-5p carries an offset toxic 6mer seed A screen of 215 viral miRNAs identifies miRNAs that contain a toxic 6mer seed Many human viral miRNAs have the capacity to kill through 6mer seed toxicity
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Affiliation(s)
- Andrea E Murmann
- Division Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Matthew J Schipma
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jacob Vilker
- Division Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Marcus E Peter
- Division Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA.
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35
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Nalbantoglu S, Karadag A. Introductory Chapter: Insight into the OMICS Technologies and Molecular Medicine. Mol Med 2019. [DOI: 10.5772/intechopen.86450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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36
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Giuliano CJ, Lin A, Girish V, Sheltzer JM. Generating Single Cell-Derived Knockout Clones in Mammalian Cells with CRISPR/Cas9. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 128:e100. [PMID: 31503414 PMCID: PMC6741428 DOI: 10.1002/cpmb.100] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 technology enables the rapid generation of loss-of-function mutations in a targeted gene in mammalian cells. A single cell harboring those mutations can be used to establish a new cell line, thereby creating a CRISPR-induced knockout clone. These clonal cell lines serve as crucial tools for exploring protein function, analyzing the consequences of gene loss, and investigating the specificity of biological reagents. However, the successful derivation of knockout clones can be technically challenging and may be complicated by multiple factors, including incomplete target ablation and interclonal heterogeneity. Here, we describe optimized protocols and plasmids for generating clonal knockouts in mammalian cell lines. We provide strategies for guide RNA design, CRISPR delivery, and knockout validation that facilitate the derivation of true knockout clones and are amenable to multiplexed gene targeting. These protocols will be broadly useful for researchers seeking to apply CRISPR to study gene function in mammalian cells. © 2019 The Authors.
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Affiliation(s)
- Christopher J. Giuliano
- Cold Spring Harbor LaboratoryCold Spring HarborNew York
- Stony Brook UniversityStony BrookNew York
- Massachusetts Institute of TechnologyCambridgeMassachusetts
| | - Ann Lin
- Cold Spring Harbor LaboratoryCold Spring HarborNew York
- Stony Brook UniversityStony BrookNew York
| | - Vishruth Girish
- Cold Spring Harbor LaboratoryCold Spring HarborNew York
- Stony Brook UniversityStony BrookNew York
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37
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Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs. Genes (Basel) 2018; 9:genes9110531. [PMID: 30400232 PMCID: PMC6266926 DOI: 10.3390/genes9110531] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/26/2018] [Indexed: 12/25/2022] Open
Abstract
Short nuclear regulatory RNAs play a key role in the main stages of maturation of the precursors of the major RNA species. Small nuclear RNAs (snRNAs) form the core of the spliceosome and are responsible for the splicing of pre-mRNA molecules. Small nucleolar RNAs (snoRNAs) direct post-transcriptional modification of pre-rRNAs. A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. We have created a set of snoRNAs and snRNA analogs and studied the effect of base modifications, specifically, pseudouridine (Ψ) and 5-methylcytidine (m⁵C), on the immune-stimulating and cytotoxic properties of these RNAs. Here, we performed a whole-transcriptome study of the influence of synthetic snoRNA analogs with various modifications on gene expression in human cells. Moreover, we confirmed the role of PKR in the recognition of snoRNA and snRNA analogs using the short hairpin RNA (shRNA) technique. We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs.
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38
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Gao QQ, Putzbach WE, Murmann AE, Chen S, Sarshad AA, Peter JM, Bartom ET, Hafner M, Peter ME. 6mer seed toxicity in tumor suppressive microRNAs. Nat Commun 2018; 9:4504. [PMID: 30374110 PMCID: PMC6206098 DOI: 10.1038/s41467-018-06526-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022] Open
Abstract
Many small-interfering (si)RNAs are toxic to cancer cells through a 6mer seed sequence (positions 2–7 of the guide strand). Here we performed an siRNA screen with all 4096 6mer seeds revealing a preference for guanine in positions 1 and 2 and a high overall G or C content in the seed of the most toxic siRNAs for four tested human and mouse cell lines. Toxicity of these siRNAs stems from targeting survival genes with C-rich 3′UTRs. The master tumor suppressor miRNA miR-34a-5p is toxic through such a G-rich 6mer seed and is upregulated in cells subjected to genotoxic stress. An analysis of all mature miRNAs suggests that during evolution most miRNAs evolved to avoid guanine at the 5′ end of the 6mer seed sequence of the guide strand. In contrast, for certain tumor-suppressive miRNAs the guide strand contains a G-rich toxic 6mer seed, presumably to eliminate cancer cells. Small interfering (siRNAs) can be toxic to cancer cells. Here the authors investigate the toxicity of microRNA in cancer cells by performing a siRNA screen that tests the miRNA activities of an extensive list of miRNAs with different 6mer seed sequences.
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Affiliation(s)
- Quan Q Gao
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA
| | - William E Putzbach
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA
| | - Andrea E Murmann
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, NIH, Bethesda, MD, 20892, USA
| | | | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, NIH, Bethesda, MD, 20892, USA
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Northwestern University, Chicago, IL, 60611, USA. .,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA.
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Putzbach W, Haluck-Kangas A, Gao QQ, Sarshad AA, Bartom ET, Stults A, Qadir AS, Hafner M, Peter ME. CD95/Fas ligand mRNA is toxic to cells. eLife 2018; 7:38621. [PMID: 30324908 PMCID: PMC6191286 DOI: 10.7554/elife.38621] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/15/2018] [Indexed: 12/21/2022] Open
Abstract
CD95/Fas ligand binds to the death receptor CD95 to induce apoptosis in sensitive cells. We previously reported that CD95L mRNA is enriched in sequences that, when converted to si/shRNAs, kill all cancer cells by targeting critical survival genes (Putzbach et al., 2017). We now report expression of full-length CD95L mRNA itself is highly toxic to cells and induces a similar form of cell death. We demonstrate that small (s)RNAs derived from CD95L are loaded into the RNA induced silencing complex (RISC) which is required for the toxicity and processing of CD95L mRNA into sRNAs is independent of both Dicer and Drosha. We provide evidence that in addition to the CD95L transgene a number of endogenous protein coding genes involved in regulating protein translation, particularly under low miRNA conditions, can be processed to sRNAs and loaded into the RISC suggesting a new level of cell fate regulation involving RNAi.
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Affiliation(s)
- Will Putzbach
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Ashley Haluck-Kangas
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Quan Q Gao
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Austin Stults
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Abdul S Qadir
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, United States.,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
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Murmann AE, Yu J, Opal P, Peter ME. Trinucleotide Repeat Expansion Diseases, RNAi, and Cancer. Trends Cancer 2018; 4:684-700. [PMID: 30292352 DOI: 10.1016/j.trecan.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 01/12/2023]
Abstract
Many neurodegenerative diseases are caused by unstable trinucleotide repeat (TNR) expansions located in disease-associated genes. siRNAs based on CAG repeat expansions effectively kill cancer cell lines in vitro through RNAi. They also cause significant reduction in tumor growth in a human ovarian cancer mouse model with no toxicity to the treated mice. This suggests that cancer cells are particularly sensitive to CAG TNR-derived siRNAs, and explains a reported inverse correlation between the length of CAG TNRs and reduced global cancer incidences in some CAG TNR diseases. This review discusses both mutant proteins and mutant RNAs as a cause of TNR diseases, with a focus on RNAi and its role in contributing to disease pathology and in suppressing cancer.
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Affiliation(s)
- Andrea E Murmann
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jindan Yu
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Puneet Opal
- Davee Department of Neurology, Northwestern University, Chicago, IL 60611, USA
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA.
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41
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Tawara K, Bolin C, Koncinsky J, Kadaba S, Covert H, Sutherland C, Bond L, Kronz J, Garbow JR, Jorcyk CL. OSM potentiates preintravasation events, increases CTC counts, and promotes breast cancer metastasis to the lung. Breast Cancer Res 2018; 20:53. [PMID: 29898744 PMCID: PMC6001163 DOI: 10.1186/s13058-018-0971-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/21/2018] [Indexed: 02/08/2023] Open
Abstract
Background Systemic and chronic inflammatory conditions in patients with breast cancer have been associated with reduced patient survival and increased breast cancer aggressiveness. This paper characterizes the role of an inflammatory cytokine, oncostatin M (OSM), in the preintravasation aspects of breast cancer metastasis. Methods OSM expression levels in human breast cancer tissue samples were assessed using tissue microarrays, and expression patterns based on clinical stage were assessed. To determine the in vivo role of OSM in breast cancer metastasis to the lung, we used three orthotopic breast cancer mouse models, including a syngeneic 4T1.2 mouse mammary cancer model, the MDA-MB-231 human breast cancer xenograft model, and an OSM-knockout (OSM-KO) mouse model. Progression of metastatic disease was tracked by magnetic resonance imaging and bioluminescence imaging. Endpoint analysis included circulating tumor cell (CTC) counts, lung metastatic burden analysis by qPCR, and ex vivo bioluminescence imaging. Results Using tissue microarrays, we found that tumor cell OSM was expressed at the highest levels in ductal carcinoma in situ. This finding suggests that OSM may function during the earlier steps of breast cancer metastasis. In mice bearing MDA-MB-231-Luc2 xenograft tumors, peritumoral injection of recombinant human OSM not only increased metastases to the lung and decreased survival but also increased CTC numbers. To our knowledge, this is the first time that a gp130 family inflammatory cytokine has been shown to directly affect CTC numbers. Using a 4T1.2 syngeneic mouse model of breast cancer, we found that mice bearing 4T1.2-shOSM tumors with knocked down tumor expression of OSM had reduced CTCs, decreased lung metastatic burden, and increased survival compared with mice bearing control tumors. CTC numbers were further reduced in OSM-KO mice bearing the same tumors, demonstrating the importance of both paracrine- and autocrine-produced OSM in this process. In vitro studies further supported the hypothesis that OSM promotes preintravasation aspects of cancer metastasis, because OSM induced both 4T1.2 tumor cell detachment and migration. Conclusions Collectively, our findings suggest that OSM plays a crucial role in the early steps of metastatic breast cancer progression, resulting in increased CTCs and lung metastases as well as reduced survival. Therefore, early therapeutic inhibition of OSM in patients with breast cancer may prevent breast cancer metastasis. Electronic supplementary material The online version of this article (10.1186/s13058-018-0971-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ken Tawara
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Celeste Bolin
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Jordan Koncinsky
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Sujatha Kadaba
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Hunter Covert
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Caleb Sutherland
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Laura Bond
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | | | - Joel R Garbow
- Mallinckrodt Institute of Radiology, Washington University, St. Louis, MO, 63110, USA
| | - Cheryl L Jorcyk
- Department of Biological Sciences, Biomolecular Sciences Program, Boise State University, 1910 University Drive, Boise, ID, 83725, USA.
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42
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Chang KW, Tseng YT, Chen YC, Yu CY, Liao HF, Chen YC, Tu YFE, Wu SC, Liu IH, Pinskaya M, Morillon A, Pain B, Lin SP. Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. BMC Genomics 2018; 19:425. [PMID: 29859049 PMCID: PMC5984780 DOI: 10.1186/s12864-018-4820-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
Background The PIWI/piRNA pathway is a conserved machinery important for germ cell development and fertility. This piRNA-guided molecular machinery is best known for repressing derepressed transposable elements (TE) during epigenomic reprogramming. The extent to which piRNAs are involved in modulating transcripts beyond TEs still need to be clarified, and it may be a stage-dependent event. We chose chicken germline as a study model because of the significantly lower TE complexity in the chicken genome compared to mammalian species. Results We generated high-confidence piRNA candidates in various stages across chicken germline development by 3′-end-methylation-enriched small RNA sequencing and in-house bioinformatics analysis. We observed a significant developmental stage-dependent loss of TE association and a shifting of the ping-pong cycle signatures. Moreover, the stage-dependent reciprocal abundance of LINE retrotransposons, CR1-C, and its associated piRNAs implicated the developmental stage-dependent role of piRNA machinery. The stage dependency of piRNA expression and its potential functions can be better addressed by analyzing the piRNA precursors/clusters. Interestingly, the new piRNA clusters identified from embryonic chicken testes revealed evolutionary conservation between chickens and mammals, which was previously thought to not exist. Conclusions In this report, we provided an original chicken RNA resource and proposed an analytical methodology that can be used to investigate stage-dependent changes in piRNA compositions and their potential roles in TE regulation and beyond, and also revealed possible conserved functions of piRNAs in developing germ cells. Electronic supplementary material The online version of this article (10.1186/s12864-018-4820-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kai-Wei Chang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.,Present Address: Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Yen-Tzu Tseng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chen Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan.,Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Chih-Yun Yu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chun Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Fan Evan Tu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Shinn-Chih Wu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - I-Hsuan Liu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Shau-Ping Lin
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan. .,Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106, Taiwan. .,Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, 106, Taiwan. .,Center for Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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43
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Abstract
Off-target effects (OTE) are an undesired side effect of RNA interference (RNAi) caused by partial complementarity between the targeting siRNA and mRNAs other than the gene to be silenced. The death receptor CD95 and its ligand CD95L contain multiple sequences that when expressed as either si- or shRNAs kill cancer cells through a defined OTE that targets critical survival genes. Death induced by survival gene elimination (DISE) is characterized by specific morphological changes such as elongated cell shapes, senescence-like enlarged cells, appearance of large intracellular vesicles, release of mitochondrial ROS followed by activation of caspase-2, and induction of a necrotic form of mitotic catastrophe. Using genome-wide shRNA lethality screens with eight different cancer cell lines, we recently identified 651 genes as critical for the survival of cancer cells. To determine whether the toxic shRNAs targeting these 651 genes contained shRNAs that kill cancer cell through DISE rather than by silencing their respective target genes, we tested all shRNAs in the TRC library derived from a subset of these genes targeting tumor suppressors (TS). We now report that only by monitoring the responses of cancer cells following expression of shRNAs derived from these putative TS it was possible to identify DISE-inducing shRNAs in five of the genes. These data indicate that DISE in general is not an undefined toxic response of cells caused by a random OTE but rather a specific cellular response with shared features that points at a specific biological function involving multiple genes in the genome.
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Affiliation(s)
- Monal Patel
- a Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine , Northwestern University , Chicago , IL 60611 , USA
| | - Marcus E Peter
- a Department of Medicine/Division Hematology/Oncology, Feinberg School of Medicine , Northwestern University , Chicago , IL 60611 , USA.,b Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine , Northwestern University , Chicago , IL 60611 , USA
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44
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Murmann AE, Gao QQ, Putzbach WE, Patel M, Bartom ET, Law CY, Bridgeman B, Chen S, McMahon KM, Thaxton CS, Peter ME. Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells. EMBO Rep 2018; 19:embr.201745336. [PMID: 29440125 DOI: 10.15252/embr.201745336] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 12/13/2022] Open
Abstract
Trinucleotide repeat (TNR) expansions in the genome cause a number of degenerative diseases. A prominent TNR expansion involves the triplet CAG in the huntingtin (HTT) gene responsible for Huntington's disease (HD). Pathology is caused by protein and RNA generated from the TNR regions including small siRNA-sized repeat fragments. An inverse correlation between the length of the repeats in HTT and cancer incidence has been reported for HD patients. We now show that siRNAs based on the CAG TNR are toxic to cancer cells by targeting genes that contain long reverse complementary TNRs in their open reading frames. Of the 60 siRNAs based on the different TNRs, the six members in the CAG/CUG family of related TNRs are the most toxic to both human and mouse cancer cells. siCAG/CUG TNR-based siRNAs induce cell death in vitro in all tested cancer cell lines and slow down tumor growth in a preclinical mouse model of ovarian cancer with no signs of toxicity to the mice. We propose to explore TNR-based siRNAs as a novel form of anticancer reagents.
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Affiliation(s)
- Andrea E Murmann
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Quan Q Gao
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - William E Putzbach
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Monal Patel
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
| | - Calvin Y Law
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Bryan Bridgeman
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Kaylin M McMahon
- Department of Urology, Northwestern University, Chicago, IL, USA.,Simpson Querrey Institute (SQI) for BioNanotechnology, Chicago, IL, USA
| | - C Shad Thaxton
- Department of Urology, Northwestern University, Chicago, IL, USA.,Simpson Querrey Institute (SQI) for BioNanotechnology, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.,International Institute for Nanotechnology, Evanston, IL, USA
| | - Marcus E Peter
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA .,Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA
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45
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Zealy RW, Fomin M, Davila S, Makowsky D, Thigpen H, McDowell CH, Cummings JC, Lee ES, Kwon SH, Min KW, Yoon JH. Long noncoding RNA complementarity and target transcripts abundance. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:224-234. [PMID: 29421307 DOI: 10.1016/j.bbagrm.2018.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 01/05/2023]
Abstract
Eukaryotic mRNA metabolism regulates its stability, localization, and translation using complementarity with counter-part RNAs. To modulate their stability, small and long noncoding RNAs can establish complementarity with their target mRNAs. Although complementarity of small interfering RNAs and microRNAs with target mRNAs has been studied thoroughly, partial complementarity of long noncoding RNAs (lncRNAs) with their target mRNAs has not been investigated clearly. To address that research gap, our lab investigated whether the sequence complementarity of two lncRNAs, lincRNA-p21 and OIP5-AS1, influenced the quantity of target RNA expression. We predicted a positive correlation between lncRNA complementarity and target mRNA quantity. We confirmed this prediction using RNA affinity pull down, microarray, and RNA-sequencing analysis. In addition, we utilized the information from this analysis to compare the quantity of target mRNAs when two lncRNAs, lincRNA-p21 and OIP5-AS1, are depleted by siRNAs. We observed that human and mouse lincRNA-p21 regulated target mRNA abundance in complementarity-dependent and independent manners. In contrast, affinity pull down of OIP5-AS1 revealed that changes in OIP5-AS1 expression influenced the amount of some OIP5-AS1 target mRNAs and miRNAs, as we predicted from our sequence complementarity assay. Altogether, the current study demonstrates that partial complementarity of lncRNAs and mRNAs (even miRNAs) assist in determining target RNA expression and quantity.
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Affiliation(s)
- Richard W Zealy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Mikhail Fomin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sylvia Davila
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Daniel Makowsky
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Haley Thigpen
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Catherine H McDowell
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - James C Cummings
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Edward S Lee
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sang-Ho Kwon
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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46
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Putzbach W, Gao QQ, Patel M, Haluck-Kangas A, Murmann AE, Peter ME. DISE: A Seed-Dependent RNAi Off-Target Effect That Kills Cancer Cells. Trends Cancer 2018; 4:10-19. [PMID: 29413418 DOI: 10.1016/j.trecan.2017.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 01/23/2023]
Abstract
Off-target effects (OTEs) represent a significant caveat for RNAi caused by substantial complementarity between siRNAs and unintended mRNAs. We now discuss the existence of three types of seed-dependent OTEs (sOTEs). Type I involves unintended targeting through the guide strand seed of an siRNA. Type II is caused by the activity of the seed on the designated siRNA passenger strand when loaded into the RNA-induced silencing complex (RISC). Both type I and II sOTEs will elicit unpredictable cellular responses. By contrast, in sOTE type III the guide strand seed preferentially targets essential survival genes resulting in death induced by survival gene elimination (DISE). In this Opinion article, we discuss DISE as a consequence of RNAi that may preferentially affect cancer cells.
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Affiliation(s)
- William Putzbach
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Quan Q Gao
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Monal Patel
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ashley Haluck-Kangas
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Andrea E Murmann
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marcus E Peter
- Department of Medicine, Division Hematology/Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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