1
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Singh A, Xue A, Tai J, Mbadugha F, Obi P, Mascarenhas R, Tyagi A, Siena A, Chen YG. A scalable and cost-efficient rRNA depletion approach to enrich RNAs for molecular biology investigations. RNA (NEW YORK, N.Y.) 2024; 30:728-738. [PMID: 38485192 PMCID: PMC11098455 DOI: 10.1261/rna.079761.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
Transcriptomics analyses play pivotal roles in understanding the complex regulatory networks that govern cellular processes. The abundance of rRNAs, which account for 80%-90% of total RNA in eukaryotes, limits the detection and investigation of other transcripts. While mRNAs and long noncoding RNAs have poly(A) tails that are often used for positive selection, investigations of poly(A)- RNAs, such as circular RNAs, histone mRNAs, and small RNAs, typically require the removal of the abundant rRNAs for enrichment. Current approaches to deplete rRNAs for downstream molecular biology investigations are hampered by restrictive RNA input masses and high costs. To address these challenges, we developed rRNA Removal by RNaseH (rRRR), a method to efficiently deplete rRNAs from a wide range of human, mouse, and rat RNA inputs and of varying qualities at a cost 10- to 20-fold cheaper than other approaches. We used probe-based hybridization and enzymatic digestion to selectively target and remove rRNA molecules while preserving the integrity of non-rRNA transcripts. Comparison of rRRR to two commercially available approaches showed similar rRNA depletion efficiencies and comparable off-target effects. Our developed method provides researchers with a valuable tool for investigating gene expression and regulatory mechanisms across a wide range of biological systems at an affordable price that increases the accessibility for researchers to enter the field, ultimately advancing our understanding of cellular processes.
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Affiliation(s)
- Amrita Singh
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Amy Xue
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Justin Tai
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Faith Mbadugha
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Prisca Obi
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Romario Mascarenhas
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Antariksh Tyagi
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Adamo Siena
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06519, USA
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2
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Goraichuk IV, Harden M, Spackman E, Suarez DL. The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing. Front Microbiol 2024; 15:1328987. [PMID: 38351914 PMCID: PMC10864109 DOI: 10.3389/fmicb.2024.1328987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.
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Affiliation(s)
- Iryna V. Goraichuk
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Mark Harden
- College of Veterinary Medicine, Tuskegee University, Tuskegee, AL, United States
| | - Erica Spackman
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - David L. Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
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3
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Huang L, Zhang J, Deng Y, Wang H, Zhao P, Zhao G, Zeng W, Wang Y, Chen C, Wagstaff W, Haydon RC, Reid RR, He TC, Shen L, Luu HH, Zhao L. Niclosamide (NA) overcomes cisplatin resistance in human ovarian cancer. Genes Dis 2023; 10:1687-1701. [PMID: 37397523 PMCID: PMC10311098 DOI: 10.1016/j.gendis.2022.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/08/2022] [Accepted: 12/04/2022] [Indexed: 01/03/2023] Open
Abstract
Ovarian cancer (OC) is one of the most lethal malignancies of the female reproductive system. OC patients are usually diagnosed at advanced stages due to the lack of early diagnosis. The standard treatment for OC includes a combination of debulking surgery and platinum-taxane chemotherapy, while several targeted therapies have recently been approved for maintenance treatment. The vast majority of OC patients relapse with chemoresistant tumors after an initial response. Thus, there is an unmet clinical need to develop new therapeutic agents to overcome the chemoresistance of OC. The anti-parasite agent niclosamide (NA) has been repurposed as an anti-cancer agent and exerts potent anti-cancer activities in human cancers including OC. Here, we investigated whether NA could be repurposed as a therapeutic agent to overcome cisplatin-resistant (CR) in human OC cells. To this end, we first established two CR lines SKOV3CR and OVCAR8CR that exhibit the essential biological characteristics of cisplatin resistance in human cancer. We showed that NA inhibited cell proliferation, suppressed cell migration, and induced cell apoptosis in both CR lines at a low micromole range. Mechanistically, NA inhibited multiple cancer-related pathways including AP1, ELK/SRF, HIF1, and TCF/LEF, in SKOV3CR and OVCAR8CR cells. NA was further shown to effectively inhibit xenograft tumor growth of SKOV3CR cells. Collectively, our findings strongly suggest that NA may be repurposed as an efficacious agent to combat cisplatin resistance in chemoresistant human OC, and further clinical trials are highly warranted.
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Affiliation(s)
- Linjuan Huang
- Departments of Obstetrics and Gynecology, Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400046, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jing Zhang
- Departments of Obstetrics and Gynecology, Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400046, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Youling Deng
- Departments of Obstetrics and Gynecology, Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400046, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and Department of Clinical Biochemistry, The School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Piao Zhao
- Departments of Obstetrics and Gynecology, Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400046, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Guozhi Zhao
- Departments of Obstetrics and Gynecology, Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400046, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Wei Zeng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Neurology, The Second Affiliated Hospital of Jianghan University, Wuhan, Hubei 430050, China
| | - Yonghui Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Clinical Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Suture Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Ling Zhao
- Departments of Obstetrics and Gynecology, Orthopaedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400046, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
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4
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Butt SL, Kariithi HM, Volkening JD, Taylor TL, Leyson C, Pantin-Jackwood M, Suarez DL, Stanton JB, Afonso CL. Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples. Front Vet Sci 2022; 9:1073919. [PMID: 36532355 PMCID: PMC9751482 DOI: 10.3389/fvets.2022.1073919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/14/2022] [Indexed: 01/10/2024] Open
Abstract
Co-infections of avian species with different RNA viruses and pathogenic bacteria are often misdiagnosed or incompletely characterized using targeted diagnostic methods, which could affect the accurate management of clinical disease. A non-targeted sequencing approach with rapid and precise characterization of pathogens should help respiratory disease management by providing a comprehensive view of the causes of disease. Long-read portable sequencers have significant potential advantages over established short-read sequencers due to portability, speed, and lower cost. The applicability of short reads random sequencing for direct detection of pathogens in clinical poultry samples has been previously demonstrated. Here we demonstrate the feasibility of long read random sequencing approaches to identify disease agents in clinical samples. Experimental oropharyngeal swab samples (n = 12) from chickens infected with infectious bronchitis virus (IBV), avian influenza virus (AIV) and Mycoplasma synoviae (MS) and field-collected clinical oropharyngeal swab samples (n = 11) from Kenyan live bird markets previously testing positive for Newcastle disease virus (NDV) were randomly sequenced on the MinION platform and results validated by comparing to real time PCR and short read random sequencing in the Illumina MiSeq platform. In the swabs from experimental infections, each of three agents in every RT-qPCR-positive sample (Ct range 19-34) was detectable within 1 h on the MinION platform, except for AIV one agent in one sample (Ct = 36.21). Nine of 12 IBV-positive samples were assigned genotypes within 1 h, as were five of 11 AIV-positive samples. MinION relative abundances of the test agent (AIV, IBV and MS) were highly correlated with RT-qPCR Ct values (R range-0.82 to-0.98). In field-collected clinical swab samples, NDV (Ct range 12-37) was detected in all eleven samples within 1 h of MinION sequencing, with 10 of 11 samples accurately genotyped within 1 h. All NDV-positive field samples were found to be co-infected with one or more additional respiratory agents. These results demonstrate that MinION sequencing can provide rapid, and sensitive non-targeted detection and genetic characterization of co-existing respiratory pathogens in clinical samples with similar performance to the Illumina MiSeq.
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Affiliation(s)
- Salman L. Butt
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - Henry M. Kariithi
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
- Biotechnology Research Institute, Kenyan Agricultural and Livestock Research Organization, Nairobi, Kenya
| | | | - Tonya L. Taylor
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - Christina Leyson
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - Mary Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - David L. Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, United States
| | - James B. Stanton
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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5
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Parris DJ, Kariithi H, Suarez DL. Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry. J Vet Diagn Invest 2022; 34:638-645. [PMID: 35791437 PMCID: PMC9266509 DOI: 10.1177/10406387221102430] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023] Open
Abstract
PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7-12 per sample) compared to commercial kits (US$30-50 per sample).
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Affiliation(s)
| | | | - David L. Suarez
- David L. Suarez, Southeast
Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural
Research Service, USDA, 934 College Station Rd, Athens, GA 30605,
USA.
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6
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Hu X, Zhang Y, Du M, Yang E. Efficient and specific DNA oligonucleotide rRNA probe-based rRNA removal in Talaromyces marneffei. Mycology 2022; 13:106-118. [PMID: 35711330 PMCID: PMC9196791 DOI: 10.1080/21501203.2021.2017045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Emerging evidence showed that lncRNAs play important roles in a wide range of biological processes of fungi such as Saccharomyces cerevisiae. However, systemic identification of lncRNAs in non-model fungi is a challenging task as the efficiency of rRNA removal has been proved to be affected by mismatches of universal rRNA-targeting probes of commercial kits, which forces deeper sequencing depth and increases costs. Here, we developed a low-cost and simple rRNA depletion method (rProbe) that could efficiently remove more than 99% rRNA in both yeast and mycelium samples of Talaromyces marneffei. The efficiency and robustness of rProbe were demonstrated to outperform the Illumina Ribo-Zero kit. Using rProbe RNA-seq, we identified 115 differentially expressed lncRNAs and constructed lncRNA-mRNA co-expression network related to dimorphic switch of T. marneffei. Our rRNA removal method has the potential to be a useful tool to explore non-coding transcriptomes of non-model fungi by adjusting rRNA probe sequences species specifically.
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Affiliation(s)
- Xueyan Hu
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yun Zhang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Minghao Du
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ence Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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7
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Wang X, Feng Y, Zhou S, Yang X, Liu Y, Peng Q, Kong X, Zhou L, Zeng Z. Long transcripts minus touchdown qPCR (LTMT-qPCR): a simplified and convenient method for the screening and quantification of microRNA profiles. J Transl Med 2021; 101:1618-1626. [PMID: 34376779 DOI: 10.1038/s41374-021-00648-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/17/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Due to the short length and differences in abundance of microRNAs, microRNA profile screening and quantification is challenging. In this study, we found that size selection magnetic beads could be employed to easily and efficiently remove long RNA transcripts. After removing the long transcripts, the remaining small RNAs could be concentrated and then reverse-transcribed using universal stem-loop primers (USLP), with six randomized nucleotides at the 3' end region. The efficiency of reverse transcription decreased when the number of randomized nucleotides was reduced. In addition, we found that touchdown qPCR improved microRNA profile detection, with lower CT values and better detection efficiency than the regular qPCR protocol, especially for those low-abundance microRNAs. Finally, we incorporated these observations to create a new protocol we named long transcripts minus touchdown qPCR (LTMT-qPCR). We performed a side-by-side comparison of LTMT with USLP and traditional stem-loop primer (TSLP) protocols. We found that LTMT has higher detection efficiency than USLP, especially for the detection of low-abundance microRNAs. Although LTMT was equivalent to TSLP in terms of microRNA profile detection, LTMT is more convenient, user-friendly, and cost-effective. Taken together, the present data indicate that LTMT is a simple, rapid, and user-friendly approach that has higher precision, accuracy, and sensitivity than the previously described methods, making it more suitable for microRNA profile screening and quantification.
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Affiliation(s)
- Xi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yixiao Feng
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shixian Zhou
- Department of Pathology, Central Hospital of Jiangjin District, Chongqing, China
| | - Xiaorong Yang
- Chongqing Institute for Food and Drug Control, Chongqing, China
| | - Yan Liu
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Qi Peng
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xuehua Kong
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Lan Zhou
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Zongyue Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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8
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He F, Ni N, Wang H, Zeng Z, Zhao P, Shi D, Xia Y, Chen C, Hu D, Qin K, Wagstaff W, Qin D, Hendren-Santiago B, Ho S, Haydon R, Luu H, Reid R, Shen L, Gan H, Fan J, He TC. OUHP: an optimized universal hairpin primer system for cost-effective and high-throughput RT-qPCR-based quantification of microRNA (miRNA) expression. Nucleic Acids Res 2021; 50:e22. [PMID: 34850128 PMCID: PMC8887422 DOI: 10.1093/nar/gkab1153] [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: 05/16/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are single-stranded, ∼22-nucleotide noncoding RNAs that regulate many cellular processes. While numerous miRNA quantification technologies are available, a recent analysis of 12 commercial platforms revealed high variations in reproducibility, sensitivity, accuracy, specificity and concordance within and/or between platforms. Here, we developed a universal hairpin primer (UHP) system that negates the use of miRNA-specific hairpin primers (MsHPs) for quantitative reverse transcription PCR (RT-qPCR)-based miRNA quantification. Specifically, we analyzed four UHPs that share the same hairpin structure but are anchored with two, three, four and six degenerate nucleotides at 3'-ends (namely UHP2, UHP3, UHP4 and UHP6), and found that the four UHPs yielded robust RT products and quantified miRNAs with high efficiency. UHP-based RT-qPCR miRNA quantification was not affected by long transcripts. By analyzing 14 miRNAs, we demonstrated that UHP4 closely mimicked MsHPs in miRNA quantification. Fine-tuning experiments identified an optimized UHP (OUHP) mix with a molar composition of UHP2:UHP4:UHP6 = 8:1:1, which closely recapitulated MsHPs in miRNA quantification. Using synthetic LET7 isomiRs, we demonstrated that the OUHP-based qPCR system exhibited high specificity and sensitivity. Collectively, our results demonstrate that the OUHP system can serve as a reliable and cost-effective surrogate of MsHPs for RT-qPCR-based miRNA quantification for basic research and precision medicine.
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Affiliation(s)
| | | | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zongyue Zeng
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Piao Zhao
- Departments of Nephrology, Gastroenterology, Laboratory Diagnostic Medicine, and Orthopaedic Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China,Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Department of Orthopaedic Surgery, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Daniel A Hu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Kevin H Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - David Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bryce Hendren-Santiago
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Sherwin H Ho
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Section of Plastic Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA,Section of Plastic Surgery, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hua Gan
- Correspondence may also be addressed to Hua Gan. Tel: +86 23 8901 2019; Fax: +86 23 8901 2019;
| | - Jiaming Fan
- Correspondence may also be addressed to Jiaming Fan. Tel: +86 23 6848 5240;
| | - Tong-Chuan He
- To whom correspondence should be addressed. Tel: +1 773 702 7169; Fax: +1 773 834 4598;
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9
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Mao Y, Ni N, Huang L, Fan J, Wang H, He F, Liu Q, Shi D, Fu K, Pakvasa M, Wagstaff W, Tucker AB, Chen C, Reid RR, Haydon RC, Ho SH, Lee MJ, He TC, Yang J, Shen L, Cai L, Luu HH. Argonaute (AGO) proteins play an essential role in mediating BMP9-induced osteogenic signaling in mesenchymal stem cells (MSCs). Genes Dis 2021; 8:918-930. [PMID: 34522718 PMCID: PMC8427325 DOI: 10.1016/j.gendis.2021.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/04/2021] [Accepted: 04/16/2021] [Indexed: 01/03/2023] Open
Abstract
As multipotent progenitor cells, mesenchymal stem cells (MSCs) can renew themselves and give rise to multiple lineages including osteoblastic, chondrogenic and adipogenic lineages. It's previously shown that BMP9 is the most potent BMP and induces osteogenic and adipogenic differentiation of MSCs. However, the molecular mechanism through which BMP9 regulates MSC differentiation remains poorly understood. Emerging evidence indicates that noncoding RNAs, especially microRNAs, may play important roles in regulating MSC differentiation and bone formation. As highly conserved RNA binding proteins, Argonaute (AGO) proteins are essential components of the multi-protein RNA-induced silencing complexes (RISCs), which are critical for small RNA biogenesis. Here, we investigate possible roles of AGO proteins in BMP9-induced lineage-specific differentiation of MSCs. We first found that BMP9 up-regulated the expression of Ago1, Ago2 and Ago3 in MSCs. By engineering multiplex siRNA vectors that express multiple siRNAs targeting individual Ago genes or all four Ago genes, we found that silencing individual Ago expression led to a decrease in BMP9-induced early osteogenic marker alkaline phosphatase (ALP) activity in MSCs. Furthermore, we demonstrated that simultaneously silencing all four Ago genes significantly diminished BMP9-induced osteogenic and adipogenic differentiation of MSCs and matrix mineralization, and ectopic bone formation. Collectively, our findings strongly indicate that AGO proteins and associated small RNA biogenesis pathway play an essential role in mediating BMP9-induced osteogenic differentiation of MSCs.
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Affiliation(s)
- Yukun Mao
- Departments of Spine Surgery and Musculoskeletal Tumor, and Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Na Ni
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Linjuan Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Departments of Nephrology, and Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Spine Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, 410011, PR China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430022, PR China
| | - Kai Fu
- Departments of Spine Surgery and Musculoskeletal Tumor, and Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Andrew Blake Tucker
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Sherwin H. Ho
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Michael J. Lee
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jian Yang
- Department of Biomedical Engineering, Materials Research Institute, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Lin Cai
- Departments of Spine Surgery and Musculoskeletal Tumor, and Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
- Corresponding author. Department of Spine Surgery and Musculoskeletal Tumor, Zhongnan Hospital, Wuhan University, Wuhan, Hubei Province, 430071, China.
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Corresponding author. Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, 5841 South Maryland Avenue, MC3079, Chicago, IL 60637, USA. Fax: +(773) 834 4598.
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Chen R, Wang X, Zhou S, Zeng Z. LncRNA HOXA-AS2 Promotes Tumor Progression by Suppressing miR-567 Expression in Oral Squamous Cell Carcinoma. Cancer Manag Res 2021; 13:5443-5455. [PMID: 34267554 PMCID: PMC8275166 DOI: 10.2147/cmar.s305946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/13/2021] [Indexed: 12/13/2022] Open
Abstract
Introduction Growing evidence suggests that long non-coding RNAs (lncRNAs), such as lncRNA HOXA-AS2, are critical regulators involved in human cancer. However, the biological functions and detailed mechanisms underlying how lncRNA HOXA-AS2 affects oral squamous cell carcinoma (OSCC) remain unexplored. Methods The expression of lncRNA HOXA-AS2 and miR-567 was determined in OSCC cell lines and clinical tissues by quantitative real-time PCR (qRT-PCR). Target site prediction and luciferase report assays were used to explore their potential interaction and binding sites between lncRNA HOXA-AS2 and miR-567. Overexpression or silencing expression of lncRNA HOXA-AS2 was performed to confirm that miR-567 was suppressed by lncRNA HOXA-AS2. WST-1 assay, crystal staining assay, and cell cycle analysis were used to assess the cell viability and proliferation ability. The target gene of miR-567 was predicted by Targetscan and validated by luciferase report assay as well as qRT-PCR and Western Blot. Xenograft nude mice model was done to demonstrate that lncRNA HOXA-AS2 promoted cell proliferation via targeting miR-567/CDK8 in vivo. Results LncRNA HOXA-AS2 was up-regulated in OSCC cells and tissues with the expression of miR-567 decreased. The tissue lncRNA HOXA-AS2 expression was found to positively correlate with the TNM stage and lymph node metastasis of OSCC patients. In terms of the mechanism, we found that lncRNA HOXA-AS2 negatively regulates miR-567 expression via a direct interaction. Functionally, overexpression of lncRNA HOXA-AS2 significantly promoted OSCC cell proliferation, while knockdown of lncRNA HOXA-AS2 significantly inhibited it. We also observed that miR-567 directly targets the 3' UTR of CDK8. Moreover, silencing lncRNA HOXA-AS2 inhibited tumor growth with the expression of miR-567 increased and CDK8 decreased in vivo. Conclusion LncRNA HOXA-AS2 was up-regulated in OSCC, and its up-regulation correlated with poor clinical outcomes. The lncRNA also promoted OSCC cell proliferation by directly binding to miR-567, leading to an increase in CDK8 expression. The potential prognostic value of lncRNA HOXA-AS2 should be explored in future studies.
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Affiliation(s)
- Rui Chen
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Xi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.,Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Shixian Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.,Department of Pathology, Central Hospital of Jiangjin District, Chongqing, 402260, People's Republic of China
| | - Zongyue Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
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11
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Zhao X, Huang B, Wang H, Ni N, He F, Liu Q, Shi D, Chen C, Zhao P, Wang X, Wagstaff W, Pakvasa M, Tucker AB, Lee MJ, Wolf JM, Reid RR, Hynes K, Strelzow J, Ho SH, Yu T, Yang J, Shen L, He TC, Zhang Y. A functional autophagy pathway is essential for BMP9-induced osteogenic differentiation of mesenchymal stem cells (MSCs). Am J Transl Res 2021; 13:4233-4250. [PMID: 34150011 PMCID: PMC8205769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Mesenchymal stem cells (MSCs) are capable of differentiating into bone, cartilage and adipose tissues. We identified BMP9 as the most potent osteoinductive BMP although detailed mechanism underlying BMP9-regulated osteogenesis of MSCs is indeterminate. Emerging evidence indicates that autophagy plays a critical role in regulating bone homeostasis. We investigated the possible role of autophagy in osteogenic differentiation induced by BMP9. We showed that BMP9 upregulated the expression of multiple autophagy-related genes in MSCs. Autophagy inhibitor chloroquine (CQ) inhibited the osteogenic activity induced by BMP9 in MSCs. While overexpression of ATG5 or ATG7 did not enhance osteogenic activity induced by BMP9, silencing Atg5 expression in MSCs effectively diminished BMP9 osteogenic signaling activity and blocked the expression of the osteogenic regulator Runx2 and the late marker osteopontin induced by BMP9. Stem cell implantation study revealed that silencing Atg5 in MSCs profoundly inhibited ectopic bone regeneration and bone matrix mineralization induced by BMP9. Collectively, our results strongly suggest a functional autophagy pathway may play an essential role in regulating osteogenic differentiation induced by BMP9 in MSCs. Thus, restoration of dysregulated autophagic activity in MSCs may be exploited to treat fracture healing, bone defects or osteoporosis.
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Affiliation(s)
- Xia Zhao
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266061, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Bo Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang UniversityNanchang 330031, China
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and School of Laboratory and Diagnostic Medicine, Chongqing Medical UniversityChongqing 400016, China
| | - Na Ni
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and School of Laboratory and Diagnostic Medicine, Chongqing Medical UniversityChongqing 400016, China
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Departments of Medicine/Gastroenterology, Orthopaedic Surgery, The First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016, China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Departments of Orthopaedic Surgery and Spine Surgery, Second Xiangya Hospital, Central South UniversityChangsha, China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Department of Orthopaedics, Union Hospital of Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Piao Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Departments of Medicine/Gastroenterology, Orthopaedic Surgery, The First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016, China
| | - Xi Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and School of Laboratory and Diagnostic Medicine, Chongqing Medical UniversityChongqing 400016, China
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Andrew Blake Tucker
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Michael J Lee
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Jennifer Moriatis Wolf
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Section of Plastic Surgery and Laboratory of Craniofacial Biology and Development, and Section of Surgical Research, Department of Surgery, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Kelly Hynes
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Jason Strelzow
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Sherwin H Ho
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Tengbo Yu
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266061, China
| | - Jian Yang
- Department of Biomedical Engineering, Materials Research Institute, The Huck Institutes of The Life Sciences, The Pennsylvania State UniversityUniversity Park, PA 16802, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Section of Surgical Research, Department of Surgery, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
- Section of Surgical Research, Department of Surgery, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Yongtao Zhang
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266061, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL 60637, USA
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12
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Wang X, Zhao L, Wu X, Luo H, Wu D, Zhang M, Zhang J, Pakvasa M, Wagstaff W, He F, Mao Y, Zhang Y, Niu C, Wu M, Zhao X, Wang H, Huang L, Shi D, Liu Q, Ni N, Fu K, Hynes K, Strelzow J, El Dafrawy M, He TC, Qi H, Zeng Z. Development of a simplified and inexpensive RNA depletion method for plasmid DNA purification using size selection magnetic beads (SSMBs). Genes Dis 2021; 8:298-306. [PMID: 33997177 PMCID: PMC8093646 DOI: 10.1016/j.gendis.2020.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/03/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
Plasmid DNA (pDNA) isolation from bacterial cells is one of the most common and critical steps in molecular cloning and biomedical research. Almost all pDNA purification involves disruption of bacteria, removal of membrane lipids, proteins and genomic DNA, purification of pDNA from bulk lysate, and concentration of pDNA for downstream applications. While many liquid-phase and solid-phase pDNA purification methods are used, the final pDNA preparations are usually contaminated with varied degrees of host RNA, which cannot be completely digested by RNase A. To develop a simple, cost-effective, and yet effective method for RNA depletion, we investigated whether commercially available size selection magnetic beads (SSMBs), such as Mag-Bind® TotalPure NGS Kit (or Mag-Bind), can completely deplete bacterial RNA in pDNA preparations. In this proof-of-principle study, we demonstrated that, compared with RNase A digestion and two commercial plasmid affinity purification kits, the SSMB method was highly efficient in depleting contaminating RNA from pDNA minipreps. Gene transfection and bacterial colony formation assays revealed that pDNA purified from SSMB method had superior quality and integrity to pDNA samples cleaned up by RNase A digestion and/or commercial plasmid purification kits. We further demonstrated that the SSMB method completely depleted contaminating RNA in large-scale pDNA samples. Furthermore, the Mag-bind-based SSMB method costs only 5-10% of most commercial plasmid purification kits on a per sample basis. Thus, the reported SSMB method can be a valuable and inexpensive tool for the removal of bacterial RNA for routine pDNA preparations.
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Affiliation(s)
- Xi Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Ling Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaoxing Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Huaxiu Luo
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Di Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Meng Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510405, PR China
| | - Jing Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yukun Mao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Orthopaedic Surgery and Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
| | - Yongtao Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, 266061, PR China
| | - Changchun Niu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Laboratory Diagnostic Medicine, Chongqing General Hospital, Chongqing, 400021, PR China
| | - Meng Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Institute of Bone and Joint Research, The departments of Orthopaedic Surgery and Obstetrics and Gynecology, The First and Second Hospitals of Lanzhou University, Lanzhou, Gansu Province, 730030, PR China
| | - Xia Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, 266061, PR China
| | - Hao Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Linjuan Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430022, PR China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Spine Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, 410011, PR China
| | - Na Ni
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Kai Fu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Orthopaedic Surgery and Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
| | - Kelly Hynes
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Jason Strelzow
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Mostafa El Dafrawy
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Hongbo Qi
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Zongyue Zeng
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
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13
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Zhao L, Huang L, Zhang J, Fan J, He F, Zhao X, Wang H, Liu Q, Shi D, Ni N, Wagstaff W, Pakvasa M, Fu K, Tucker AB, Chen C, Reid RR, Haydon RC, Luu HH, Shen L, Qi H, He TC. The inhibition of BRAF activity sensitizes chemoresistant human ovarian cancer cells to paclitaxel-induced cytotoxicity and tumor growth inhibition. Am J Transl Res 2020; 12:8084-8098. [PMID: 33437383 PMCID: PMC7791515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/13/2020] [Indexed: 06/12/2023]
Abstract
Ovarian cancer is one of the most common cancers in women and the second most common cause of gynecologic cancer death in women worldwide. While ovarian cancer is highly heterogeneous in histological subtypes and molecular genetic makeup, epithelial ovarian cancer is the most common subtype. The clinical outcomes of ovarian cancer largely depend on early detection and access to appropriate surgery and systemic therapy. While combination therapy with platinum-based drugs and paclitaxel (PTX) remains the first-line systemic therapy for ovarian cancer, many patients experience recurrence and die of progressive chemoresistance. Thus, there is an unmet clinical need to overcome recurrent disease due to resistance to chemotherapies of ovarian cancer. Here, we investigated whether BRAF inhibitors (BRAFi) could sensitize PTX-resistant ovarian cancer cells to PTX, and thus would overcome the resistance to chemotherapies. We found that BRAF and several members of the RAS/MAPK pathways were upregulated upon PTX treatment in ovarian cancer cells, and that BRAF expression was significantly elevated in the PTX-resistant ovarian cancer cells. While the BRAFi vemurafenib (VEM) alone did not cause any significant cytotoxicity in PTX-resistant ovarian cancer cells, VEM significantly enhanced PTX-induced growth inhibition and apoptosis in a dose-dependent manner. Furthermore, VEM and PTX were shown to synergistically inhibit tumor growth and cell proliferation of PTX-resistant human ovarian cancer cells in vivo. Collectively, these findings strongly suggest that BRAFi may be exploited as synergistic sensitizers of paclitaxel in treating chemoresistant ovarian cancer.
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Affiliation(s)
- Ling Zhao
- Departments of Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Linjuan Huang
- Departments of Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Jing Zhang
- Departments of Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and The School of Laboratory Diagnostic Medicine, Chongqing Medical UniversityChongqing, China
| | - Fang He
- Departments of Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and The School of Laboratory Diagnostic Medicine, Chongqing Medical UniversityChongqing, China
| | - Xia Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao UniversityQingdao 266061, China
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and The School of Laboratory Diagnostic Medicine, Chongqing Medical UniversityChongqing, China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Spine Surgery, Second Xiangya Hospital, Central South UniversityChangsha 410011, China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Orthopaedic Surgery, Union Hospital of Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Na Ni
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and The School of Laboratory Diagnostic Medicine, Chongqing Medical UniversityChongqing, China
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Kai Fu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan UniversityWuhan 430072, China
| | - Andrew B Tucker
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Surgery Section of Plastic Surgery, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Surgery, The University of Chicago Medical CenterChicago, IL 60637, USA
| | - Hongbo Qi
- Departments of Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Surgery, The University of Chicago Medical CenterChicago, IL 60637, USA
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14
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Cao D, Lei Y, Ye Z, Zhao L, Wang H, Zhang J, He F, Huang L, Shi D, Liu Q, Ni N, Pakvasa M, Wagstaff W, Zhao X, Fu K, Tucker AB, Chen C, Reid RR, Haydon RC, Luu HH, He TC, Liao Z. Blockade of IGF/IGF-1R signaling axis with soluble IGF-1R mutants suppresses the cell proliferation and tumor growth of human osteosarcoma. Am J Cancer Res 2020; 10:3248-3266. [PMID: 33163268 PMCID: PMC7642656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023] Open
Abstract
Primary bone tumor, also known as osteosarcoma (OS), is the most common primary malignancy of bone in children and young adults. Current treatment protocols yield a 5-year survival rate of near 70% although approximately 80% of patients have metastatic disease at the time of diagnosis. However, long-term survival rates have remained virtually unchanged for nearly four decades, largely due to our limited understanding of the disease process. One major signaling pathway that has been implicated in human OS tumorigenesis is the insulin-like growth factor (IGF)/insulin-like growth factor-1 receptor (IGF1R) signaling axis. IGF1R is a heterotetrameric α2β2 receptor, in which the α subunits comprise the ligand binding site, whereas the β subunits are transmembrane proteins containing intracellular tyrosine kinase domains. Although numerous strategies have been devised to target IGF/IGF1R axis, most of them have failed in clinical trials due to the lack of specificity and/or limited efficacy. Here, we investigated whether a more effective and specific blockade of IGF1R activity in human OS cells can be accomplished by employing dominant-negative IGF1R (dnIGF1R) mutants. We engineered the recombinant adenoviruses expressing two IGF1R mutants derived from the α (aa 1-524) and β (aa 741-936) subunits, and found that either dnIGF1Rα and/or dnIGF1Rβ effectively inhibited cell migration, colony formation, and cell cycle progression of human OS cells, which could be reversed by exogenous IGF1. Furthermore, dnIGF1Rα and/or dnIGF1Rβ inhibited OS xenograft tumor growth in vivo, with the greatest inhibition of tumor growth shown by dnIGF1Rα. Mechanistically, the dnIGF1R mutants down-regulated the expression of PI3K/AKT and RAS/RAF/MAPK, BCL2, Cyclin D1 and most EMT regulators, while up-regulating pro-apoptotic genes in human OS cells. Collectively, these findings strongly suggest that the dnIGF1R mutants, especially dnIGF1Rα, may be further developed as novel anticancer agents that target IGF signaling axis with high specificity and efficacy.
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Affiliation(s)
- Daigui Cao
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Chongqing Medical UniversityChongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Orthopaedic Surgery, Chongqing General Hospital Affiliated with The University of Chinese Academy of SciencesChongqing, China
| | - Yan Lei
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Otolaryngology, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
| | - Zhenyu Ye
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of General Surgery, The Second Affiliated Hospital of Soochow UniversitySuzhou, China
| | - Ling Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Otolaryngology, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
| | - Hao Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and The School of Laboratory and Diagnostic Medicine, Chongqing Medical UniversityChongqing, China
| | - Jing Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Otolaryngology, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Otolaryngology, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
| | - Linjuan Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Otolaryngology, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical UniversityChongqing, China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Orthopaedics, Union Hospital of Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Spine Surgery, Second Xiangya Hospital, Central South UniversityChangsha, China
| | - Na Ni
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, and The School of Laboratory and Diagnostic Medicine, Chongqing Medical UniversityChongqing, China
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Xia Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao UniversityQingdao, China
| | - Kai Fu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan UniversityWuhan, China
| | - Andrew B Tucker
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Connie Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Surgery Section of Plastic and Reconstructive Surgery, The University of Chicago Medical CenterChicago, IL, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
| | - Zhan Liao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical CenterChicago, IL, USA
- Department of Orthopaedic Surgery, Xiangya Hospital of Central South UniversityChangsha, China
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