1
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Rao J, Wang X, Chen X, Liu Y, Jiang J, Wang Z. Multi-omics analysis reveals that Cas13d contributes to PI3K-AKT signaling and facilitates cell proliferation via PFKFB4 upregulation. Gene 2024; 927:148760. [PMID: 38992762 DOI: 10.1016/j.gene.2024.148760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/30/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
The CRISPR-Cas system is a powerful gene editing technology, the clinical application of which is currently constrained due to safety concerns. A substantial body of safety research concerning Cas9 exists; however, scant attention has been directed toward investigating the safety profile of the emergent Cas13 system, which confers RNA editing capabilities. In particular, uncertainties persist regarding the potential cellular impacts of Cas13d in the absence of reliance on a cleavage effect. In this study, we conducted an initial exploration of the effects of Cas13d on HeLa cells. Total RNA and protein samples were extracted after transfection with a Cas13d-expressing plasmid construct, followed by transcriptomic and proteomic sequencing. Differential gene expression analysis identified 94 upregulated and 847 downregulated genes, while differential protein expression analysis identified 185 upregulated and 231 downregulated proteins. Subsequently, enrichment analysis was conducted on the transcriptome and proteome sequencing data, revealing that the PI3K-Akt signaling pathway is a common term. After intersecting the differentially expressed genes enriched in the PI3K-Akt signaling pathway with all the differentially expressed proteins, it was found that the expression of the related regulatory gene PFKFB4 was upregulated. Moreover, western blot analysis demonstrated that Cas13d can mediate PI3K-Akt signaling upregulation through overexpression of PFKFB4. CCK-8 assay, colony formation, and EdU experiments showed that Cas13d can promote cell proliferation. Our data demonstrate, for the first time, that Cas13d significantly impacts the transcriptomic and proteomic profiles, and proliferation phenotype, of HeLa cells, thus offering novel insights into safety considerations regarding gene editing systems.
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Affiliation(s)
- Jin Rao
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xuefu Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiangyu Chen
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yudi Liu
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Junfeng Jiang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China; Histology and Embryology Department, Naval Medical University, Shanghai, China.
| | - Zhinong Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China.
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2
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Bohrer C, Varon E, Peretz E, Reinitz G, Kinor N, Halle D, Nissan A, Shav-Tal Y. CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced. Histochem Cell Biol 2024; 162:91-107. [PMID: 38763947 PMCID: PMC11227459 DOI: 10.1007/s00418-024-02294-w] [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] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Super-enhancers are unique gene expression regulators widely involved in cancer development. Spread over large DNA segments, they tend to be found next to oncogenes. The super-enhancer c-MYC locus forms long-range chromatin looping with nearby genes, which brings the enhancer and the genes into proximity, to promote gene activation. The colon cancer-associated transcript 1 (CCAT1) gene, which is part of the MYC locus, transcribes a lncRNA that is overexpressed in colon cancer cells through activation by MYC. Comparing different types of cancer cell lines using RNA fluorescence in situ hybridization (RNA FISH), we detected very prominent CCAT1 expression in HeLa cells, observed as several large CCAT1 nuclear foci. We found that dozens of CCAT1 transcripts accumulate on the gene locus, in addition to active transcription occurring from the gene. The accumulating transcripts are released from the chromatin during cell division. Examination of CCAT1 lncRNA expression patterns on the single-RNA level showed that unspliced CCAT1 transcripts are released from the gene into the nucleoplasm. Most of these unspliced transcripts were observed in proximity to the active gene but were not associated with nuclear speckles in which unspliced RNAs usually accumulate. At larger distances from the gene, the CCAT1 transcripts appeared spliced, implying that most CCAT1 transcripts undergo post-transcriptional splicing in the zone of the active gene. Finally, we show that unspliced CCAT1 transcripts can be detected in the cytoplasm during splicing inhibition, which suggests that there are several CCAT1 variants, spliced and unspliced, that the cell can recognize as suitable for export.
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Affiliation(s)
- Chaya Bohrer
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Varon
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eldar Peretz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Gita Reinitz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Kinor
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - David Halle
- Biochemistry Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Aviram Nissan
- Ziv Medical Center, Safed, Israel
- Surgical Innovation Laboratory, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel.
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3
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Moldovan JB, Kopera HC, Liu Y, Garcia-Canadas M, Catalina P, Leone PE, Sanchez L, Kitzman JO, Kidd JM, Garcia-Perez JL, Moran JV. Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes. Nucleic Acids Res 2024:gkae448. [PMID: 38850156 DOI: 10.1093/nar/gkae448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/10/2024] Open
Abstract
Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1) ORF2-encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 (Alu-permissive) strains, but not in HeLa-JVM or HeLa-H1 (Alu-nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA-derived SINEs and tRNA-derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR-Alu (SVA) element, and an L1 ORF1-containing mRNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu-permissive and Alu-nonpermissive HeLa strains, suggesting that 7SL- and tRNA-derived SINEs use strategies to 'hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1-containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu-permissive and Alu-nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu-nonpermissive HeLa strains.
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Affiliation(s)
- John B Moldovan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C Kopera
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ying Liu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marta Garcia-Canadas
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | | | - Paola E Leone
- Genetics and Genomics Laboratory, SOLCA Hospital, Quito, Ecuador
| | - Laura Sanchez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jose Luis Garcia-Perez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | - John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Yu L, Majerciak V, Lobanov A, Mirza S, Band V, Liu H, Cam M, Hughes SH, Lowy DR, Zheng ZM. HPV oncogenes expressed from only one of multiple integrated HPV DNA copies drive clonal cell expansion in cervical cancer. mBio 2024; 15:e0072924. [PMID: 38624210 PMCID: PMC11077993 DOI: 10.1128/mbio.00729-24] [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: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
The integration of HPV DNA into human chromosomes plays a pivotal role in the onset of papillomavirus-related cancers. HPV DNA integration often occurs by linearizing the viral DNA in the E1/E2 region, resulting in the loss of a critical viral early polyadenylation signal (PAS), which is essential for the polyadenylation of the E6E7 bicistronic transcripts and for the expression of the viral E6 and E7 oncogenes. Here, we provide compelling evidence that, despite the presence of numerous integrated viral DNA copies, virus-host fusion transcripts originate from only a single integrated HPV DNA in HPV16 and HPV18 cervical cancers and cervical cancer-derived cell lines. The host genomic elements neighboring the integrated HPV DNA are critical for the efficient expression of the viral oncogenes that leads to clonal cell expansion. The fusion RNAs that are produced use a host RNA polyadenylation signal downstream of the integration site, and almost all involve splicing to host sequences. In cell culture, siRNAs specifically targeting the host portion of the virus-host fusion transcripts effectively silenced viral E6 and E7 expression. This, in turn, inhibited cell growth and promoted cell senescence in HPV16+ CaSki and HPV18+ HeLa cells. Showing that HPV E6 and E7 expression from a single integration site is instrumental in clonal cell expansion sheds new light on the mechanisms of HPV-induced carcinogenesis and could be used for the development of precision medicine tailored to combat HPV-related malignancies. IMPORTANCE Persistent oncogenic HPV infections lead to viral DNA integration into the human genome and the development of cervical, anogenital, and oropharyngeal cancers. The expression of the viral E6 and E7 oncogenes plays a key role in cell transformation and tumorigenesis. However, how E6 and E7 could be expressed from the integrated viral DNA which often lacks a viral polyadenylation signal in the cancer cells remains unknown. By analyzing the integrated HPV DNA sites and expressed HPV RNAs in cervical cancer tissues and cell lines, we show that HPV oncogenes are expressed from only one of multiple chromosomal HPV DNA integrated copies. A host polyadenylation signal downstream of the integrated viral DNA is used for polyadenylation and stabilization of the virus-host chimeric RNAs, making the oncogenic transcripts targetable by siRNAs. This observation provides further understanding of the tumorigenic mechanism of HPV integration and suggests possible therapeutic strategies for the development of precision medicine for HPV cancers.
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Affiliation(s)
- Lulu Yu
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, Bethesda, Maryland, USA
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Haibin Liu
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Douglas R. Lowy
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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5
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Moldovan JB, Kopera HC, Liu Y, Garcia-Canadas M, Catalina P, Leone PE, Sanchez L, Kitzman JO, Kidd JM, Garcia-Perez JL, Moran JV. Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592410. [PMID: 38746229 PMCID: PMC11092746 DOI: 10.1101/2024.05.03.592410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1 or L1) ORF2 -encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 ( Alu -permissive) strains, but not in HeLa-JVM or HeLa-H1 ( Alu -nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA -derived SINEs and tRNA -derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR - Alu ( SVA ) element, and an L1 ORF1 -containing messenger RNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu -permissive and Alu -nonpermissive HeLa strains, suggesting that 7SL - and tRNA -derived SINE RNAs use strategies to 'hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1 -containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu -permissive and Alu -nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu -nonpermissive HeLa strains.
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6
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Bailly R, Malfante M, Allier C, Paviolo C, Ghenim L, Padmanabhan K, Bardin S, Mars J. Detecting abnormal cell behaviors from dry mass time series. Sci Rep 2024; 14:7053. [PMID: 38528035 DOI: 10.1038/s41598-024-57684-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/20/2024] [Indexed: 03/27/2024] Open
Abstract
The prediction of pathological changes on single cell behaviour is a challenging task for deep learning models. Indeed, in self-supervised learning methods, no prior labels are used for the training and all of the information for event predictions are extracted from the data themselves. We present here a novel self-supervised learning model for the detection of anomalies in a given cell population, StArDusTS. Cells are monitored over time, and analysed to extract time-series of dry mass values. We assessed its performances on different cell lines, showing a precision of 96% in the automatic detection of anomalies. Additionally, anomaly detection was also associated with cell measurement errors inherent to the acquisition or analysis pipelines, leading to an improvement of the upstream methods for feature extraction. Our results pave the way to novel architectures for the continuous monitoring of cell cultures in applied research or bioproduction applications, and for the prediction of pathological cellular changes.
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Affiliation(s)
- Romain Bailly
- Univ. Grenoble Alpes, CEA, List, F-38000, Grenoble, France
- Univ. Grenoble Alpes, CNRS, Grenoble-INP, GIPSA-Lab, 38000, Grenoble, France
| | | | - Cédric Allier
- Univ. Grenoble Alpes, CEA, Leti, F-38000, Grenoble, France
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Chiara Paviolo
- Univ. Grenoble Alpes, CEA, Leti, F-38000, Grenoble, France
| | - Lamya Ghenim
- Univ. Grenoble Alpes, INSERM, CEA-IRIG, BGE, Biomics, F-38000, Grenoble, France
| | - Kiran Padmanabhan
- Institut de Génomique Fonctionnelle de Lyon, Univ. Lyon, CNRS/ENS, UMR 5242, Lyon, France
| | - Sabine Bardin
- Institut Curie, PSL Research University, CNRS, UMR 144, Molecular Mechanisms of Intracellular Transport, F-75005, Paris, France
| | - Jérôme Mars
- Univ. Grenoble Alpes, CNRS, Grenoble-INP, GIPSA-Lab, 38000, Grenoble, France
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7
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Eskandari E, Negri GL, Tan S, MacAldaz ME, Ding S, Long J, Nielsen K, Spencer SE, Morin GB, Eaves CJ. Dependence of human cell survival and proliferation on the CASP3 prodomain. Cell Death Discov 2024; 10:63. [PMID: 38321033 PMCID: PMC10847432 DOI: 10.1038/s41420-024-01826-6] [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: 11/03/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/08/2024] Open
Abstract
Mechanisms that regulate cell survival and proliferation are important for both the development and homeostasis of normal tissue, and as well as for the emergence and expansion of malignant cell populations. Caspase-3 (CASP3) has long been recognized for its proteolytic role in orchestrating cell death-initiated pathways and related processes; however, whether CASP3 has other functions in mammalian cells that do not depend on its known catalytic activity have remained unknown. To investigate this possibility, we examined the biological and molecular consequences of reducing CASP3 levels in normal and transformed human cells using lentiviral-mediated short hairpin-based knockdown experiments in combination with approaches designed to test the potential rescue capability of different components of the CASP3 protein. The results showed that a ≥50% reduction in CASP3 levels rapidly and consistently arrested cell cycle progression and survival in all cell types tested. Mass spectrometry-based proteomic analyses and more specific flow cytometric measurements strongly implicated CASP3 as playing an essential role in regulating intracellular protein aggregate clearance. Intriguingly, the rescue experiments utilizing different forms of the CASP3 protein showed its prosurvival function and effective removal of protein aggregates did not require its well-known catalytic capability, and pinpointed the N-terminal prodomain of CASP3 as the exclusive component needed in a diversity of human cell types. These findings identify a new mechanism that regulates human cell survival and proliferation and thus expands the complexity of how these processes can be controlled. The graphical abstract illustrates the critical role of CASP3 for sustained proliferation and survival of human cells through the clearance of protein aggregates.
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Affiliation(s)
- Ebrahim Eskandari
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Susanna Tan
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Margarita E MacAldaz
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Shengsen Ding
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Justin Long
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Karina Nielsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sandra E Spencer
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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8
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Mezher N, Mroweh O, Karam L, Ibrahim JN, Kobeissy PH. Experimental models in Familial Mediterranean Fever (FMF): Insights into pathophysiology and therapeutic strategies. Exp Mol Pathol 2024; 135:104883. [PMID: 38266955 DOI: 10.1016/j.yexmp.2024.104883] [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: 07/19/2023] [Revised: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Familial Mediterranean Fever (FMF) is a recurrent polyserositis characterized by self-limiting episodes or attacks of fever along with serosal inflammation. It mainly impacts people of the Mediterranean and Middle Eastern basin. FMF is a recessive autoinflammatory condition caused by mutation in the MEFV gene located on chromosome 16p13. MEFV mutations lead to the activation of the pyrin inflammasome resulting in an uncontrolled release of IL-1β. Various in vitro, in vivo and ex vivo experimental models have been developed to further comprehend the etiology and pathogenesis of FMF. These models have been proven to be clinically relevant to human FMF and can provide significant information about biological systems with respect to this condition. Additionally, these models have provided pertinent contributions to the development of potent therapeutic strategies against FMF. In this review, we describe the different experimental models utilized in FMF and we focus primarily on the most widely used models that have produced prominent insights into the pathophysiology of the disease.
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Affiliation(s)
- Nawal Mezher
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon
| | - Ola Mroweh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon
| | - Louna Karam
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon
| | - José-Noel Ibrahim
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon.
| | - Philippe Hussein Kobeissy
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University (LAU), Beirut, Lebanon.
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9
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Kraszewska I, Sarad K, Andrysiak K, Kopacz A, Schmidt L, Krüger M, Dulak J, Jaźwa-Kusior A. Casein kinase 2 activity is a host restriction factor for AAV transduction. Mol Ther 2024; 32:84-102. [PMID: 37952087 PMCID: PMC10787142 DOI: 10.1016/j.ymthe.2023.11.010] [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: 03/17/2023] [Revised: 09/29/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
So far, the mechanisms that impede AAV transduction, especially in the human heart, are poorly understood, hampering the introduction of new, effective gene therapy strategies. Therefore, the aim of this study was to identify and overcome the main cellular barriers to successful transduction in the heart, using induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iPSC-CMs), iPSC-derived cardiac fibroblasts (iPSC-CFs), and primary endothelial cells to model vector-host interactions. Through phosphoproteome analysis we established that casein kinase 2 (CK2) signaling is one of the most significantly affected pathways upon AAV exposure. Transient inhibition of CK2 activity substantially enhanced the transduction rate of AAV2, AAV6, and AAV9 in all tested cell types. In particular, CK2 inhibition improved the trafficking of AAVs through the cytoplasm, impaired DNA damage response through destabilization of MRE11, and altered the RNA processing pathways, which were also highly responsive to AAV transduction. Also, it augmented transgene expression in already transduced iPSC-CFs, which retain AAV genomes in a functional, but probably silent form. In summary, the present study provides new insights into the current understanding of the host-AAV vector interaction, identifying CK2 activity as a key barrier to efficient transduction and transgene expression, which may translate to improving the outcome of AAV-based therapies in the future.
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Affiliation(s)
- Izabela Kraszewska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Katarzyna Sarad
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Kalina Andrysiak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Kopacz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Luisa Schmidt
- CECAD Research Center, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Marcus Krüger
- CECAD Research Center, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agnieszka Jaźwa-Kusior
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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10
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Cao F, Sun H, Yang Z, Bai Y, Hu X, Hou Y, Bian X, Liu Y. Multiple approaches revealed MGc80-3 as a somatic hybrid with HeLa cells rather than a gastric cancer cell line. Int J Cancer 2024; 154:155-168. [PMID: 37543987 DOI: 10.1002/ijc.34677] [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: 02/11/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/08/2023]
Abstract
The short-tandem-repeats (STR) profiles of MGc80-3 and HeLa partially overlap, raising suspicion of contamination in the MGc80-3 cell line. However, there has not been any relevant study demonstrating whether MGc80-3 was fully replaced by HeLa cells, just mixed with HeLa cells (co-existing), or was a somatic hybrid with HeLa cells. In addition to STR profiling, various approaches, including single nucleotide polymorphisms genotyping, polymerase chain reaction, screening for human papillomaviruses type 18 (HPV-18) fragment, chromosome karyotyping, pathological examination of xenografts, tissue-specific-90-gene expression signature and high-throughput RNA sequencing were used to determine the nature of MGc80-3. Our study found that the abnormal STR profile, partially overlapping with that of HeLa cells (64.62% to 71.64%), could not verify MGc80-3 as a HeLa cell line. However, the STR 13.3 repeat allele in the D13S317 locus that seemed to be unique to HeLa cells was detected in MGc80-3. Almost all the MGc80-3 cells exhibited HPV-18 fragments in the genome as well as certain HeLa marker chromosomes, such as M7 and M12. The molecular assay of the 90-gene expression signature still considered MGc80-3 as a stomach cancer using an algorithmic analysis. The expression pattern of multiple genes in MGc80-3 was quite different from that in HeLa cells, which showed that certain characteristics belonged to gastric cancer cell lines. High throughput RNA sequencing showed the distinct patterns of gene expression in MGc80-3. In conclusion, MGc80-3 cell line is a somatic hybrid with HeLa cells rather than a pure gastric cancer cell line.
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Affiliation(s)
- Fang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital &Institute, Beijing, China
| | - Hao Sun
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhenli Yang
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yanhua Bai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital &Institute, Beijing, China
| | - Xiao Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital &Institute, Beijing, China
| | - Yuhong Hou
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaocui Bian
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yuqin Liu
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
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11
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Sinitcyn P, Richards AL, Weatheritt RJ, Brademan DR, Marx H, Shishkova E, Meyer JG, Hebert AS, Westphall MS, Blencowe BJ, Cox J, Coon JJ. Global detection of human variants and isoforms by deep proteome sequencing. Nat Biotechnol 2023; 41:1776-1786. [PMID: 36959352 PMCID: PMC10713452 DOI: 10.1038/s41587-023-01714-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/15/2023] [Indexed: 03/25/2023]
Abstract
An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically identified by peptide sequences representing a small fraction of their total amino acids. Hence, an average shotgun experiment fails to distinguish different protein variants and isoforms. Deeper proteome sequencing is therefore required for the global discovery of protein isoforms. Using six different human cell lines, six proteases, deep fractionation and three tandem mass spectrometry fragmentation methods, we identify a million unique peptides from 17,717 protein groups, with a median sequence coverage of approximately 80%. Direct comparison with RNA expression data provides evidence for the translation of most nonsynonymous variants. We have also hypothesized that undetected variants likely arise from mutation-induced protein instability. We further observe comparable detection rates for exon-exon junction peptides representing constitutive and alternative splicing events. Our dataset represents a resource for proteoform discovery and provides direct evidence that most frame-preserving alternatively spliced isoforms are translated.
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Affiliation(s)
- Pavel Sinitcyn
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
- Morgridge Institute for Research, Madison, WI, USA
| | - Alicia L Richards
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Dain R Brademan
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Harald Marx
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesse G Meyer
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander S Hebert
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael S Westphall
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Benjamin J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, USA.
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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12
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Cero C, Shu W, Reese AL, Douglas D, Maddox M, Singh AP, Ali SL, Zhu AR, Katz JM, Pierce AE, Long KT, Nilubol N, Cypess RH, Jacobs JL, Tian F, Cypess AM. Standardized In Vitro Models of Human Adipose Tissue Reveal Metabolic Flexibility in Brown Adipocyte Thermogenesis. Endocrinology 2023; 164:bqad161. [PMID: 37944134 PMCID: PMC11032247 DOI: 10.1210/endocr/bqad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/10/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Functional human brown and white adipose tissue (BAT and WAT) are vital for thermoregulation and nutritional homeostasis, while obesity and other stressors lead, respectively, to cold intolerance and metabolic disease. Understanding BAT and WAT physiology and dysfunction necessitates clinical trials complemented by mechanistic experiments at the cellular level. These require standardized in vitro models, currently lacking, that establish references for gene expression and function. We generated and characterized a pair of immortalized, clonal human brown (hBA) and white (hWA) preadipocytes derived from the perirenal and subcutaneous depots, respectively, of a 40-year-old male individual. Cells were immortalized with hTERT and confirmed to be of a mesenchymal, nonhematopoietic lineage based on fluorescence-activated cell sorting and DNA barcoding. Functional assessments showed that the hWA and hBA phenocopied primary adipocytes in terms of adrenergic signaling, lipolysis, and thermogenesis. Compared to hWA, hBA were metabolically distinct, with higher rates of glucose uptake and lactate metabolism, and greater basal, maximal, and nonmitochondrial respiration, providing a mechanistic explanation for the association between obesity and BAT dysfunction. The hBA also responded to the stress of maximal respiration by using both endogenous and exogenous fatty acids. In contrast to certain mouse models, hBA adrenergic thermogenesis was mediated by several mechanisms, not principally via uncoupling protein 1 (UCP1). Transcriptomics via RNA-seq were consistent with the functional studies and established a molecular signature for each cell type before and after differentiation. These standardized cells are anticipated to become a common resource for future physiological, pharmacological, and genetic studies of human adipocytes.
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Affiliation(s)
- Cheryl Cero
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Weiguo Shu
- American Type Culture Collection, Cell Biology R&D, 217 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Amy L Reese
- American Type Culture Collection, Sequencing and Bioinformatics Center, 10801 University Blvd, Manassas, VA 20110, USA
| | - Diana Douglas
- American Type Culture Collection, Cell Biology R&D, 217 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Michael Maddox
- American Type Culture Collection, Cell Biology R&D, 217 Perry Parkway, Gaithersburg, MD 20877, USA
- Current Affiliation: Vita Therapeutics, 801 W. Baltimore Street, Suite 301, Baltimore, MD 21201, USA
| | - Ajeet P Singh
- American Type Culture Collection, Sequencing and Bioinformatics Center, 10801 University Blvd, Manassas, VA 20110, USA
| | - Sahara L Ali
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander R Zhu
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacqueline M Katz
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anne E Pierce
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kelly T Long
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naris Nilubol
- Surgical Oncology Program, Center for Cancer Research, NCI, NIH, 10 Center Drive, Room 4-5952, Bethesda, MD 20892, USA
| | - Raymond H Cypess
- American Type Culture Collection, 10801 University Blvd, Manassas, VA 20110, USA
| | - Jonathan L Jacobs
- American Type Culture Collection, Sequencing and Bioinformatics Center, 10801 University Blvd, Manassas, VA 20110, USA
| | - Fang Tian
- American Type Culture Collection, Cell Biology R&D, 217 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Aaron M Cypess
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Kowalewicz-Kulbat M, Krawczyk KT, Szulc-Kielbik I, Rykowski S, Denel-Bobrowska M, Olejniczak AB, Locht C, Klink M. Cytotoxic effects of halophilic archaea metabolites on ovarian cancer cell lines. Microb Cell Fact 2023; 22:197. [PMID: 37759261 PMCID: PMC10537157 DOI: 10.1186/s12934-023-02206-y] [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: 07/19/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Ovarian cancer is one of the most frequent and deadly gynaecological cancers, often resistant to platinum-based chemotherapy, the current standard of care. Halophilic microorganisms have been shown to produce a large variety of metabolites, some of which show toxicity to various cancer cell lines. However, none have yet been shown to be active against ovarian cancer cells. Here, we examined the effects of metabolites secreted by the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae on various cancer cell lines, including ovarian cancer cell lines. RESULTS 1H NMR analyses of Hrd. rudnickae and Nnm. salaciae culture supernatants contain a complex mixture of metabolites that differ between species, and even between two different strains of the same species, such as Hrd. rudnickae strains 64T and 66. By using the MTT and the xCELLigence RTCA assays, we found that the secreted metabolites of all three halophilic strains expressed cytotoxicity to the ovarian cancer cell lines, especially A2780, as well as its cisplatin-resistant derivative A2780cis, in a dose-dependent manner. The other tested cell lines A549, HepG2, SK-OV-3 and HeLa were only minimally, or not at all affected by the archaeal metabolites, and this was only seen with the MTT assay. CONCLUSIONS The halophilic archaea Hrd. rudnickae and Nnm. salaciae, isolated from a Polish salt mine and Lake Medee in the Mediterranean Sea, respectively, secrete metabolites that are active against ovarian cancer cells, including those that are resistant to cisplatin. This opens potential new possibilities for the treatment of these frequent and deadly gynaecological cancers.
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Affiliation(s)
- Magdalena Kowalewicz-Kulbat
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
| | - Krzysztof T Krawczyk
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | | | | | | | - Camille Locht
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Magdalena Klink
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
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14
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Katz L, Kiyota T, Woolman M, Wu M, Pires L, Fiorante A, Ye LA, Leong W, Berman HK, Ghazarian D, Ginsberg HJ, Das S, Aman A, Zarrine-Afsar A. Metabolic Lipids in Melanoma Enable Rapid Determination of Actionable BRAF-V600E Mutation with Picosecond Infrared Laser Mass Spectrometry in 10 s. Anal Chem 2023; 95:14430-14439. [PMID: 37695851 DOI: 10.1021/acs.analchem.3c02901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Rapid molecular profiling of biological tissues with picosecond infrared laser mass spectrometry (PIRL-MS) has enabled the detection of clinically important histologic types and molecular subtypes of human cancers in as little as 10 s of data collection and analysis time. Utilizing an engineered cell line model of actionable BRAF-V600E mutation, we observed statistically significant differences in 10 s PIRL-MS molecular profiles between BRAF-V600E and BRAF-wt cells. Multivariate statistical analyses revealed a list of mass-to-charge (m/z) values most significantly responsible for the identification of BRAF-V600E mutation status in this engineered cell line that provided a highly controlled testbed for this observation. These metabolites predicted BRAF-V600E expression in human melanoma cell lines with greater than 98% accuracy. Through chromatography and tandem mass spectrometry analysis of cell line extracts, a 30-member "metabolite array" was characterized for determination of BRAF-V600E expression levels in subcutaneous melanoma xenografts with an average sensitivity and specificity of 95.6% with 10 s PIRL-MS analysis. This proof-of-principle work warrants a future large-scale study to identify a metabolite array for 10 s determination of actionable BRAF-V600E mutation in human tissue to guide patient care.
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Affiliation(s)
- Lauren Katz
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Taira Kiyota
- Ontario Institute for Cancer Research (OICR), 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
| | - Michael Woolman
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Megan Wu
- Peter Gilgan Centre for Research and Learning & Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Layla Pires
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Alexa Fiorante
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Lan Anna Ye
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Wey Leong
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | - Hal K Berman
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto and the Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON M5G 2C4, Canada
| | - Danny Ghazarian
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
| | - Howard J Ginsberg
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Sixth Floor, Toronto, ON M5S 1A8, Canada
| | - Sunit Das
- Peter Gilgan Centre for Research and Learning & Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | - Ahmed Aman
- Ontario Institute for Cancer Research (OICR), 661 University Avenue, Suite 510, Toronto, ON M5G 0A3, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St, Toronto, ON M5S 3M2, Canada
| | - Arash Zarrine-Afsar
- Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
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15
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Fu Q, Polanco A, Lee YS, Yoon S. Critical challenges and advances in recombinant adeno-associated virus (rAAV) biomanufacturing. Biotechnol Bioeng 2023; 120:2601-2621. [PMID: 37126355 DOI: 10.1002/bit.28412] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/27/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
Gene therapy is a promising therapeutic approach for genetic and acquired diseases nowadays. Among DNA delivery vectors, recombinant adeno-associated virus (rAAV) is one of the most effective and safest vectors used in commercial drugs and clinical trials. However, the current yield of rAAV biomanufacturing lags behind the necessary dosages for clinical and commercial use, which embodies a concentrated reflection of low productivity of rAAV from host cells, difficult scalability of the rAAV-producing bioprocess, and high levels of impurities materialized during production. Those issues directly impact the price of gene therapy medicine in the market, limiting most patients' access to gene therapy. In this context, the current practices and several critical challenges associated with rAAV gene therapy bioprocesses are reviewed, followed by a discussion of recent advances in rAAV-mediated gene therapy and other therapeutic biological fields that could improve biomanufacturing if these advances are integrated effectively into the current systems. This review aims to provide the current state-of-the-art technology and perspectives to enhance the productivity of rAAV while reducing impurities during production of rAAV.
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Affiliation(s)
- Qiang Fu
- Department of Biomedical Engineering and Biotechnology, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Ashli Polanco
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
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16
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Kamentseva RS, Kharchenko MV, Gabdrahmanova GV, Kotov MA, Kosheverova VV, Kornilova ES. EGF, TGF- α and Amphiregulin Differently Regulate Endometrium-Derived Mesenchymal Stromal/Stem Cells. Int J Mol Sci 2023; 24:13408. [PMID: 37686213 PMCID: PMC10487484 DOI: 10.3390/ijms241713408] [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: 06/29/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
The prototypical receptor tyrosine kinase epidermal growth factor receptor (EGFR) is regulated by a set of its ligands, which determines the specificity of signaling and intracellular fate of the receptor. The EGFR signaling system is well characterized in immortalized cell lines such as HeLa derived from tumor tissues, but much less is known about EGFR function in untransformed multipotent stromal/stem cells (MSCs). We compared the effect of epidermal growth factor (EGF), transforming growth factor-α (TGF-α) and amphiregulin (AREG) on physiological responses in endometrial MSCs (enMSC) and HeLa cells. In addition, using Western blotting and confocal microscopy, we studied the internalization and degradation of EGFR stimulated by the three ligands in these cell lines. We demonstrated that unlike HeLa, EGF and TGF-α, but not AREG, stimulated enMSC proliferation and prevented decidual differentiation in an EGFR-dependent manner. In HeLa cells, EGF targeted EGFR for degradation, while TGF-α stimulated its recycling. Surprisingly, in enMSC, both ligands caused EGFR degradation. In both cell lines, AREG-EGFR internalization was not registered. In HeLa cells, EGFR was degraded within 2 h, restoring its level in 24 h, while in enMSC, degradation took more than 4-8 h, and the low EGFR level persisted for several days. This indicates that EGFR homeostasis in MSCs may differ significantly from that in immortalized cell lines.
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Affiliation(s)
- Rimma Sergeevna Kamentseva
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia; (M.V.K.); (V.V.K.); (E.S.K.)
| | - Marianna Viktorovna Kharchenko
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia; (M.V.K.); (V.V.K.); (E.S.K.)
| | - Gulnara Vladikovna Gabdrahmanova
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia; (M.V.K.); (V.V.K.); (E.S.K.)
| | - Michael Alexandrovich Kotov
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia; (M.V.K.); (V.V.K.); (E.S.K.)
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, Hlopina St. 11, St. Petersburg 195251, Russia
| | - Vera Vladislavovna Kosheverova
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia; (M.V.K.); (V.V.K.); (E.S.K.)
| | - Elena Sergeevna Kornilova
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia; (M.V.K.); (V.V.K.); (E.S.K.)
- Faculty of Biology, St. Petersburg State University, 7-9 Universitetskaya Embankment, St. Petersburg 199034, Russia
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17
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Bhosle VK, Tan JM, Li T, Hua R, Kwon H, Li Z, Patel S, Tessier-Lavigne M, Robinson LA, Kim PK, Brumell JH. SLIT2/ROBO1 signaling suppresses mTORC1 for organelle control and bacterial killing. Life Sci Alliance 2023; 6:e202301964. [PMID: 37311584 PMCID: PMC10264968 DOI: 10.26508/lsa.202301964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
SLIT/ROBO signaling impacts many aspects of tissue development and homeostasis, in part, through the regulation of cell growth and proliferation. Recent studies have also linked SLIT/ROBO signaling to the regulation of diverse phagocyte functions. However, the mechanisms by which SLIT/ROBO signaling acts at the nexus of cellular growth control and innate immunity remain enigmatic. Here, we show that SLIT2-mediated activation of ROBO1 leads to inhibition of mTORC1 kinase activity in macrophages, leading to dephosphorylation of its downstream targets, including transcription factor EB and ULK1. Consequently, SLIT2 augments lysosome biogenesis, potently induces autophagy, and robustly promotes the killing of bacteria within phagosomes. Concordant with these results, we demonstrate decreased lysosomal content and accumulated peroxisomes in the spinal cords of embryos from Robo1 -/- , Robo2 -/- double knockout mice. We also show that impediment of auto/paracrine SLIT-ROBO signaling axis in cancer cells leads to hyperactivation of mTORC1 and inhibition of autophagy. Together, these findings elucidate a central role of chemorepellent SLIT2 in the regulation of mTORC1 activity with important implications for innate immunity and cancer cell survival.
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Affiliation(s)
- Vikrant K Bhosle
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Joel Mj Tan
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Taoyingnan Li
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Rong Hua
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Hyunwoo Kwon
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Zhubing Li
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Sajedabanu Patel
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Marc Tessier-Lavigne
- Laboratory of Brain Development and Repair, Rockefeller University, New York, NY, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Lisa A Robinson
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Division of Nephrology, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Peter K Kim
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - John H Brumell
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- SickKids IBD Centre, Hospital for Sick Children, Toronto, Canada
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18
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Zhao Z, Khurana A, Antony F, Young JW, Hewton KG, Brough Z, Zhong T, Parker SJ, Duong van Hoa F. A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell. Mol Cell Proteomics 2023; 22:100588. [PMID: 37295717 PMCID: PMC10416069 DOI: 10.1016/j.mcpro.2023.100588] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Membrane proteins play critical roles at the cell surface and their misfunction is a hallmark of many human diseases. A precise evaluation of the plasma membrane proteome is therefore essential for cell biology and for discovering novel biomarkers and therapeutic targets. However, the low abundance of this proteome relative to soluble proteins makes it difficult to characterize, even with the most advanced proteomics technologies. Here, we apply the peptidisc membrane mimetic to purify the cell membrane proteome. Using the HeLa cell line as a reference, we capture 500 different integral membrane proteins, with half annotated to the plasma membrane. Notably, the peptidisc library is enriched with several ABC, SLC, GPCR, CD, and cell adhesion molecules that generally exist at low to very low copy numbers in the cell. We extend the method to compare two pancreatic cell lines, Panc-1 and hPSC. Here we observe a striking difference in the relative abundance of the cell surface cancer markers L1CAM, ANPEP, ITGB4, and CD70. We also identify two novel SLC transporters, SLC30A1 and SLC12A7, that are highly present in the Panc-1 cell only. The peptidisc library thus emerges as an effective way to survey and compare the membrane proteome of mammalian cells. Furthermore, since the method stabilizes membrane proteins in a water-soluble state, members of the library, here SLC12A7, can be specifically isolated.
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Affiliation(s)
- Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arshdeep Khurana
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Frank Antony
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - John W Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Keeley G Hewton
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Zora Brough
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tianshuang Zhong
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seth J Parker
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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19
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McClure RS, Rericha Y, Waters KM, Tanguay RL. 3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. FRONTIERS IN BIOINFORMATICS 2023; 3:1234218. [PMID: 37576716 PMCID: PMC10414111 DOI: 10.3389/fbinf.2023.1234218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Methods and results: Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. Conclusions: These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.
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Affiliation(s)
- Ryan S. McClure
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
| | - Yvonne Rericha
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
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20
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Kim S, Seo YA. In vitro studies of manganese transport and homeostasis. Methods Enzymol 2023; 687:185-206. [PMID: 37666632 DOI: 10.1016/bs.mie.2023.04.023] [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: 09/06/2023]
Abstract
Manganese (Mn) is an essential micronutrient required for fundamental cell functions and vital physiological processes. More than a dozen putative Mn transporters have been described over the last two decades, but few have been thoroughly evaluated. Recent genetic studies have revealed vital roles for solute carrier family 39, member 8 (SLC39A8) in Mn homeostasis. SLC39A8 can mediate the cellular uptake of the essential metals zinc, iron, and Mn, as well as the non-essential metal cadmium. However, loss-of-function mutations in SLC39A8 have been found in patients with severe Mn deficiency in the blood without affecting other metals. An in vitro study from our laboratory showed that SLC39A8 is a cell-surface transporter that strongly stimulates 54Mn incorporation into cells (Choi, Nguyen, Gupta, Iwase, & Seo, 2018). By contrast, the disease-associated mutations completely abrogated the cellular uptake of 54Mn (Choi et al., 2018), thereby providing a causal link between SLC39A8 deficiency and Mn deficiency. The importance of SLC39A8 is now increasingly recognized in multiple disease processes, and SLC39A8 has emerged as a critical regulator of Mn homeostasis. Thus, exploring the function of SLC39A8 in cellular Mn homeostasis is of significant research interest. This chapter describes the advanced methods used in our laboratory to examine Mn homeostasis and transport. Specifically, genetic and molecular approaches are described in HeLa cells overexpressing SLC39A8 and disease-associated SLC39A8 mutants. These methods are useful for characterizing the roles of Mn in diverse cellular events.
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Affiliation(s)
- Sangnam Kim
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Young Ah Seo
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States.
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21
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Gelléri M, Chen SY, Hübner B, Neumann J, Kröger O, Sadlo F, Imhoff J, Hendzel MJ, Cremer M, Cremer T, Strickfaden H, Cremer C. True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin. Cell Rep 2023; 42:112567. [PMID: 37243597 DOI: 10.1016/j.celrep.2023.112567] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggest only modest compaction differences (∼2-10×) between the active nuclear compartment (ANC) and inactive nuclear compartment (INC). Here, we present maps of nuclear landscapes with true-to-scale DNA densities, ranging from <5 to >300 Mbp/μm3. Maps are generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial optical resolution and are supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription into nuclei of living cells demonstrates their localization and movements within the ANC and exclusion from the INC.
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Affiliation(s)
- Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Shih-Ya Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Jan Neumann
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Ole Kröger
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Filip Sadlo
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Jorg Imhoff
- Neuroconsult GmbH, 69120 Heidelberg, Germany
| | - Michael J Hendzel
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Hilmar Strickfaden
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany; Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University Heidelberg, 69120 Heidelberg, Germany.
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22
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Joo J, Cho S, Hong S, Min S, Kim K, Kumar R, Choi JM, Shin Y, Jung I. Probabilistic establishment of speckle-associated inter-chromosomal interactions. Nucleic Acids Res 2023; 51:5377-5395. [PMID: 37013988 PMCID: PMC10287923 DOI: 10.1093/nar/gkad211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 03/08/2023] [Accepted: 03/25/2023] [Indexed: 04/05/2023] Open
Abstract
Inter-chromosomal interactions play a crucial role in genome organization, yet the organizational principles remain elusive. Here, we introduce a novel computational method to systematically characterize inter-chromosomal interactions using in situ Hi-C results from various cell types. Our method successfully identifies two apparently hub-like inter-chromosomal contacts associated with nuclear speckles and nucleoli, respectively. Interestingly, we discover that nuclear speckle-associated inter-chromosomal interactions are highly cell-type invariant with a marked enrichment of cell-type common super-enhancers (CSEs). Validation using DNA Oligopaint fluorescence in situ hybridization (FISH) shows a strong but probabilistic interaction behavior between nuclear speckles and CSE-harboring genomic regions. Strikingly, we find that the likelihood of speckle-CSE associations can accurately predict two experimentally measured inter-chromosomal contacts from Hi-C and Oligopaint DNA FISH. Our probabilistic establishment model well describes the hub-like structure observed at the population level as a cumulative effect of summing individual stochastic chromatin-speckle interactions. Lastly, we observe that CSEs are highly co-occupied by MAZ binding and MAZ depletion leads to significant disorganization of speckle-associated inter-chromosomal contacts. Taken together, our results propose a simple organizational principle of inter-chromosomal interactions mediated by MAZ-occupied CSEs.
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Affiliation(s)
- Jaegeon Joo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sunghyun Cho
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sukbum Hong
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunwoo Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kyukwang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Rajeev Kumar
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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23
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Akyüz K, Goisauf M, Chassang G, Kozera Ł, Mežinska S, Tzortzatou-Nanopoulou O, Mayrhofer MT. Post-identifiability in changing sociotechnological genomic data environments. BIOSOCIETIES 2023:1-28. [PMID: 37359141 PMCID: PMC10042674 DOI: 10.1057/s41292-023-00299-7] [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] [Accepted: 01/13/2023] [Indexed: 03/30/2023]
Abstract
Data practices in biomedical research often rely on standards that build on normative assumptions regarding privacy and involve 'ethics work.' In an increasingly datafied research environment, identifiability gains a new temporal and spatial dimension, especially in regard to genomic data. In this paper, we analyze how genomic identifiability is considered as a specific data issue in a recent controversial case: publication of the genome sequence of the HeLa cell line. Considering developments in the sociotechnological and data environment, such as big data, biomedical, recreational, and research uses of genomics, our analysis highlights what it means to be (re-)identifiable in the postgenomic era. By showing how the risk of genomic identifiability is not a specificity of the HeLa controversy, but rather a systematic data issue, we argue that a new conceptualization is needed. With the notion of post-identifiability as a sociotechnological situation, we show how past assumptions and ideas about future possibilities come together in the case of genomic identifiability. We conclude by discussing how kinship, temporality, and openness are subject to renewed negotiations along with the changing understandings and expectations of identifiability and status of genomic data.
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Affiliation(s)
- Kaya Akyüz
- Department of Science and Technology Studies, University of Vienna, Universitätsstraße 7/Stiege II/6, Stock (NIG), 1010 Vienna, Austria
- BBMRI-ERIC, Graz, Austria
| | - Melanie Goisauf
- Department of Science and Technology Studies, University of Vienna, Universitätsstraße 7/Stiege II/6, Stock (NIG), 1010 Vienna, Austria
- BBMRI-ERIC, Graz, Austria
| | - Gauthier Chassang
- CERPOP, Université de Toulouse, Inserm, Université Paul Sabatier, Toulouse, France
- Plateforme GenoToul Societal “Ethique et Biosciences”, Toulouse, France
| | | | - Signe Mežinska
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- BBMRI.LV, Riga, Latvia
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24
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Samant RS, Batista S, Larance M, Ozer B, Milton CI, Bludau I, Wu E, Biggins L, Andrews S, Hervieu A, Johnston HE, Al-Lazikhani B, Lamond AI, Clarke PA, Workman P. Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes. Mol Cell Proteomics 2023; 22:100485. [PMID: 36549590 PMCID: PMC9898794 DOI: 10.1016/j.mcpro.2022.100485] [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: 06/27/2022] [Revised: 11/16/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
The molecular chaperone heat shock protein 90 (HSP90) works in concert with co-chaperones to stabilize its client proteins, which include multiple drivers of oncogenesis and malignant progression. Pharmacologic inhibitors of HSP90 have been observed to exert a wide range of effects on the proteome, including depletion of client proteins, induction of heat shock proteins, dissociation of co-chaperones from HSP90, disruption of client protein signaling networks, and recruitment of the protein ubiquitylation and degradation machinery-suggesting widespread remodeling of cellular protein complexes. However, proteomics studies to date have focused on inhibitor-induced changes in total protein levels, often overlooking protein complex alterations. Here, we use size-exclusion chromatography in combination with mass spectrometry (SEC-MS) to characterize the early changes in native protein complexes following treatment with the HSP90 inhibitor tanespimycin (17-AAG) for 8 h in the HT29 colon adenocarcinoma cell line. After confirming the signature cellular response to HSP90 inhibition (e.g., induction of heat shock proteins, decreased total levels of client proteins), we were surprised to find only modest perturbations to the global distribution of protein elution profiles in inhibitor-treated HT29 cells at this relatively early time-point. Similarly, co-chaperones that co-eluted with HSP90 displayed no clear difference between control and treated conditions. However, two distinct analysis strategies identified multiple inhibitor-induced changes, including known and unknown components of the HSP90-dependent proteome. We validate two of these-the actin-binding protein Anillin and the mitochondrial isocitrate dehydrogenase 3 complex-as novel HSP90 inhibitor-modulated proteins. We present this dataset as a resource for the HSP90, proteostasis, and cancer communities (https://www.bioinformatics.babraham.ac.uk/shiny/HSP90/SEC-MS/), laying the groundwork for future mechanistic and therapeutic studies related to HSP90 pharmacology. Data are available via ProteomeXchange with identifier PXD033459.
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Affiliation(s)
- Rahul S Samant
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom; Signalling Programme, The Babraham Institute, Cambridge, United Kingdom.
| | - Silvia Batista
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Mark Larance
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, United Kingdom
| | - Bugra Ozer
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Christopher I Milton
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Estelle Wu
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Laura Biggins
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Alexia Hervieu
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Harvey E Johnston
- Signalling Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Bissan Al-Lazikhani
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Angus I Lamond
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, United Kingdom
| | - Paul A Clarke
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom
| | - Paul Workman
- Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, United Kingdom.
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25
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Beelen NA, Ehlers FAI, Kooreman LFS, Bos GMJ, Wieten L. An in vitro model to monitor natural killer cell effector functions against breast cancer cells derived from human tumor tissue. Methods Cell Biol 2023; 173:133-153. [PMID: 36653080 DOI: 10.1016/bs.mcb.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Adoptive natural killer (NK) cell-based immunotherapy poses a promising treatment approach in cancer. Despite minimal toxicities associated with NK cell infusion, the potential of NK cell therapy is inhibited by the immunosuppressive tumor microenvironment (TME). Multiple approaches to improve anti-cancer NK cell effector functions are being investigated. While much of this preclinical research is currently performed with commercially available tumor cell lines, this approach lacks the influence of the TME and heterogeneity of the primary tumor in patients. Here, we describe a comprehensive protocol for NK cell cytotoxicity- and degranulation assays against tumor cells derived from primary breast cancer tissue. Treatments to boost NK cell anti-tumor effector functions can be implemented in this model. Moreover, by using culture supernatants in follow up assays or by including additional cell types in the co-culture system, other NK cell effector mechanisms that further orchestrate innate and adaptive immunity could be studied.
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Affiliation(s)
- Nicky A Beelen
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center, Maastricht, The Netherlands; GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands; Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Femke A I Ehlers
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center, Maastricht, The Netherlands; GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands; Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Loes F S Kooreman
- GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands; Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Gerard M J Bos
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center, Maastricht, The Netherlands; GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Lotte Wieten
- GROW-School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands; Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands.
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26
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Łaska G, Sieniawska E, Maciejewska-Turska M, Świątek Ł, Pasco DS, Balachandran P. Pulsatilla vulgaris Inhibits Cancer Proliferation in Signaling Pathways of 12 Reporter Genes. Int J Mol Sci 2023; 24:ijms24021139. [PMID: 36674653 PMCID: PMC9860614 DOI: 10.3390/ijms24021139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
This study aimed to examine if methanolic extracts of Pulsatilla vulgaris Mill. can inhibit HeLa cell proliferation through the modulation of cancer-related signaling pathways. The cytotoxicity and chemical composition of P. vulgaris leaves and root extracts were also determined. Research showed that root extract of P. vulgaris inhibited 12 signaling pathways in a cervical cancer cell line and the most potent activation inhibition was observed for MYC, Notch, Wnt, E2F, Ets, Stat3, Smad, Hdghog, AP-1, and NF-κB, at a concentration of 40 µg/mL. The methanolic extracts of P. vulgaris enhanced apoptotic death and deregulated cellular proliferation, differentiation, and progression toward the neoplastic phenotype by altering key signaling molecules required for cell cycle progression. This is the first study to report the influence of P. vulgaris on cancer signaling pathways. Additionally, our detailed phytochemical analysis of the methanolic extracts of P. vulgaris gives a conclusion that compounds, which strongly suppressed the growth and proliferation of HeLa cancer cells were mainly triterpenoid saponins accompanied by phenolic acids.
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Affiliation(s)
- Grażyna Łaska
- Department of Agri-Food Engineering and Environmental Management, Bialystok University of Technology, 15-351 Bialystok, Poland
| | - Elwira Sieniawska
- Department of Natural Products Chemistry, Medical University of Lublin, 20-093 Lublin, Poland
- Correspondence:
| | - Magdalena Maciejewska-Turska
- Department of Pharmacognosy with the Medicinal Plant Garden, Medical University of Lublin, 20-093 Lublin, Poland
| | - Łukasz Świątek
- Department of Virology with SARS Laboratory, Medical University of Lublin, 20-093 Lublin, Poland
| | - David S. Pasco
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA
| | - Premalatha Balachandran
- National Center for Natural Products Research, Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA
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27
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Tutty MA, Holmes S, Prina-Mello A. Cancer Cell Culture: The Basics and Two-Dimensional Cultures. Methods Mol Biol 2023; 2645:3-40. [PMID: 37202610 DOI: 10.1007/978-1-0716-3056-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite significant advances in investigative and therapeutic methodologies for cancer, 2D cell culture remains an essential and evolving competency in this fast-paced industry. From basic monolayer cultures and functional assays to more recent and ever-advancing cell-based cancer interventions, 2D cell culture plays a crucial role in cancer diagnosis, prognosis, and treatment. Research and development in this field call for a great deal of optimization, while the heterogenous nature of cancer itself demands personalized precision for its intervention. In this way, 2D cell culture is ideal, providing a highly adaptive and responsive platform, where skills can be honed and techniques modified. Furthermore, it is arguably the most efficient, economical, and sustainable methodology available to researchers and clinicians alike.In this chapter, we discuss the history of cell culture and the varying types of cell and cell lines used today, the techniques used to characterize and authenticate them, the applications of 2D cell culture in cancer diagnosis and prognosis, and more recent developments in the area of cell-based cancer interventions and vaccines.
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Affiliation(s)
- Melissa Anne Tutty
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Sarah Holmes
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland.
| | - Adriele Prina-Mello
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
- Nanomedicine and Molecular Imaging Group, Trinity Translational Medicine Institute (TTMI), School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity St. James's Cancer Institute, St. James's Hospital, Trinity College Dublin, Dublin, Ireland
- Advanced Materials and Bioengineering Research (AMBER) Centre, CRANN Institute, Trinity College Dublin, Dublin, Ireland
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28
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Otsuka S, Tempkin JOB, Zhang W, Politi AZ, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Morero NR, Sali A, Ellenberg J. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature 2023; 613:575-581. [PMID: 36599981 PMCID: PMC9849139 DOI: 10.1038/s41586-022-05528-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/04/2022] [Indexed: 01/05/2023]
Abstract
Understanding how the nuclear pore complex (NPC) is assembled is of fundamental importance to grasp the mechanisms behind its essential function and understand its role during the evolution of eukaryotes1-4. There are at least two NPC assembly pathways-one during the exit from mitosis and one during nuclear growth in interphase-but we currently lack a quantitative map of these events. Here we use fluorescence correlation spectroscopy calibrated live imaging of endogenously fluorescently tagged nucleoporins to map the changes in the composition and stoichiometry of seven major modules of the human NPC during its assembly in single dividing cells. This systematic quantitative map reveals that the two assembly pathways have distinct molecular mechanisms, in which the order of addition of two large structural components, the central ring complex and nuclear filaments are inverted. The dynamic stoichiometry data was integrated to create a spatiotemporal model of the NPC assembly pathway and predict the structures of postmitotic NPC assembly intermediates.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Max Perutz Labs, University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
| | - Jeremy O B Tempkin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Wanlu Zhang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Z Politi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Arina Rybina
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrea Callegari
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Koch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Natalia Rosalia Morero
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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Yu S, Guo M, Zhang Y, Bo C, Liang H, Wang H, Yang X. Comparative multiomics analysis of cell physiological state after culture in a basket bioreactor. Sci Rep 2022; 12:20161. [PMID: 36424406 PMCID: PMC9686226 DOI: 10.1038/s41598-022-24687-4] [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: 09/13/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
Bioreactors are one of the most important, basic pieces of equipment in the biopharmaceutical industry. Understanding the effects of mechanical damage and other factors on the physiological state of cells during cell matrix culture is the basis for continuously achieving greater efficiency and higher product quality. In this study, Vero cells were used as a model and apoptosis, senescence, transcriptomics, proteomics, and metabolomics were carried out for analysis at the cellular and molecular levels. The results showed that compared with cells cultured in the simulated natural state, the cells cultured in the basket bioreactor displayed no obvious senescence. Additionally, the proportion of early apoptotic cells increased, but the proportions of damaged, late apoptotic and dead cells did not change significantly. The transcription levels of aminoacyl-tRNA synthetase and cyclin D1 and the expression levels of DNA replication licensing factor, methenyltetrahydrofolate cyclohydrolase, arachidonic acid and other metabolites of cells cultured in the basket bioreactor were significantly increased. These results suggest that DNA replication, protein translation and the metabolic activities in cells cultured in basket bioreactors are more active, which is more conducive to cell amplification and target product production. In this study, the growth and physiological state of cells in a basket bioreactor were characterized at the molecular level for the first time. Additionally, a tool to evaluate the physiological state of cells in a bioreactor was established, which can be used to guide the development and optimization of cell matrix culture conditions in industrial production and improve the production efficiency of the target products.
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Affiliation(s)
- Shouzhi Yu
- grid.419781.20000 0004 0388 5844Beijing Institute of Biological Products Company Limited, Beijing, China
| | - Miaomiao Guo
- grid.419781.20000 0004 0388 5844Beijing Institute of Biological Products Company Limited, Beijing, China
| | - Yadan Zhang
- grid.419781.20000 0004 0388 5844Beijing Institute of Biological Products Company Limited, Beijing, China
| | - Cunpei Bo
- grid.419781.20000 0004 0388 5844Beijing Institute of Biological Products Company Limited, Beijing, China
| | - Hongyang Liang
- grid.419781.20000 0004 0388 5844Beijing Institute of Biological Products Company Limited, Beijing, China
| | - Hui Wang
- grid.419781.20000 0004 0388 5844Beijing Institute of Biological Products Company Limited, Beijing, China
| | - Xiaoming Yang
- grid.419781.20000 0004 0388 5844Beijing Institute of Biological Products Company Limited, Beijing, China ,China National Biotec Group Company Limited, Beijing, China
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30
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Karagyaur M, Primak A, Efimenko A, Skryabina M, Tkachuk V. The Power of Gene Technologies: 1001 Ways to Create a Cell Model. Cells 2022; 11:cells11203235. [PMID: 36291103 PMCID: PMC9599997 DOI: 10.3390/cells11203235] [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: 09/05/2022] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 12/04/2022] Open
Abstract
Modern society faces many biomedical challenges that require urgent solutions. Two of the most important include the elucidation of mechanisms of socially significant diseases and the development of prospective drug treatments for these diseases. Experimental cell models are a convenient tool for addressing many of these problems. The power of cell models is further enhanced when combined with gene technologies, which allows the examination of even more subtle changes within the structure of the genome and permits testing of proteins in a native environment. The list and possibilities of these recently emerging technologies are truly colossal, which requires a rethink of a number of approaches for obtaining experimental cell models. In this review, we analyze the possibilities and limitations of promising gene technologies for obtaining cell models, and also give recommendations on the development and creation of relevant models. In our opinion, this review will be useful for novice cell biologists, as it provides some reference points in the rapidly growing universe of gene and cell technologies.
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Affiliation(s)
- Maxim Karagyaur
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
- Correspondence:
| | - Alexandra Primak
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Anastasia Efimenko
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Mariya Skryabina
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Vsevolod Tkachuk
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
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31
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Deng N, Minoche A, Harvey K, Li M, Winkler J, Goga A, Swarbrick A. Deep whole genome sequencing identifies recurrent genomic alterations in commonly used breast cancer cell lines and patient-derived xenograft models. Breast Cancer Res 2022; 24:63. [PMID: 36153537 PMCID: PMC9509640 DOI: 10.1186/s13058-022-01540-0] [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] [Received: 08/31/2021] [Accepted: 06/26/2022] [Indexed: 11/15/2022] Open
Abstract
Background Breast cancer cell lines (BCCLs) and patient-derived xenografts (PDXs) are the most frequently used models in breast cancer research. Despite their widespread usage, genome sequencing of these models is incomplete, with previous studies only focusing on targeted gene panels, whole exome or shallow whole genome sequencing. Deep whole genome sequencing is the most sensitive and accurate method to detect single nucleotide variants and indels, gene copy number and structural events such as gene fusions.
Results Here we describe deep whole genome sequencing (WGS) of commonly used BCCL and PDX models using the Illumina X10 platform with an average ~ 60 × coverage. We identify novel genomic alterations, including point mutations and genomic rearrangements at base-pair resolution, compared to previously available sequencing data. Through integrative analysis with publicly available functional screening data, we annotate new genomic features likely to be of biological significance. CSMD1, previously identified as a tumor suppressor gene in various cancer types, including head and neck, lung and breast cancers, has been identified with deletion in 50% of our PDX models, suggesting an important role in aggressive breast cancers. Conclusions Our WGS data provides a comprehensive genome sequencing resource of these models. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01540-0.
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Parisi A, Beltran CJ, Furutani KM. The Mayo Clinic Florida microdosimetric kinetic model of clonogenic survival: formalism and first benchmark against in vitro and in silico data. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac7375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/25/2022] [Indexed: 12/30/2022]
Abstract
Abstract
Objective. To develop a new model (Mayo Clinic Florida microdosimetric kinetic model, MCF MKM) capable of accurately describing the in vitro clonogenic survival at low and high linear energy transfer (LET) using single-event microdosimetric spectra in a single target. Methodology. The MCF MKM is based on the ‘post-processing average’ implementation of the non-Poisson microdosimetric kinetic model and includes a novel expression to compute the particle-specific quadratic-dependence of the cell survival with respect to dose (β of the linear-quadratic model). A new methodology to a priori calculate the mean radius of the MCF MKM subnuclear domains is also introduced. Lineal energy spectra were simulated with the Particle and Heavy Ion Transport code System (PHITS) for 1H, 4He, 12C, 20Ne, 40Ar, 56Fe, and 132Xe ions and used in combination with the MCF MKM to calculate the ion-specific LET-dependence of the relative biological effectiveness (RBE) for Chinese hamster lung fibroblasts (V79 cell line) and human salivary gland tumor cells (HSG cell line). The results were compared with in vitro data from the Particle Irradiation Data Ensemble (PIDE) and in silico results of different models. The possibility of performing experiment-specific predictions to explain the scatter in the in vitro RBE data was also investigated. Finally, a sensitivity analysis on the model parameters is also included. Main results. The RBE values predicted with the MCF MKM were found to be in good agreement with the in vitro data for all tested conditions. Though all MCF MKM model parameters were determined a priori, the accuracy of the MCF MKM was found to be comparable or superior to that of other models. The model parameters determined a priori were in good agreement with the ones obtained by fitting all available in vitro data. Significance. The MCF MKM will be considered for implementation in cancer radiotherapy treatment planning with accelerated ions.
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33
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Haber JE. A shattering experience. Mol Cell 2022; 82:2360-2362. [PMID: 35803217 DOI: 10.1016/j.molcel.2022.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Tang et al. (2022) report that the DNA breaks that provoke chromothripsis-the pulverization and dramatic assembly into a rearranged chromosome-are generated by the base excision repair APE1 endonuclease, triggered by removing deoxyinosines that are created in DNA::RNA hybrids.
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Affiliation(s)
- James E Haber
- Rosenstiel Center and Department of Biology, Brandeis University, Waltham, MA 02154, USA.
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34
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Dequeker BJH, Scherr MJ, Brandão HB, Gassler J, Powell S, Gaspar I, Flyamer IM, Lalic A, Tang W, Stocsits R, Davidson IF, Peters JM, Duderstadt KE, Mirny LA, Tachibana K. MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature 2022; 606:197-203. [PMID: 35585235 PMCID: PMC9159944 DOI: 10.1038/s41586-022-04730-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/06/2022] [Indexed: 12/23/2022]
Abstract
Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)1-3, which contribute to transcription, recombination and genomic stability4,5. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered6-12. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are 'active' barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.
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Affiliation(s)
- Bart J H Dequeker
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Hugo B Brandão
- Harvard Program in Biophysics, Harvard University, Cambridge, MA, USA
- Illumina Inc., San Diego, CA, USA
| | - Johanna Gassler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Sean Powell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Imre Gaspar
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, UK
| | - Aleksandar Lalic
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Roman Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany.
- Department of Physics, Technical University of Munich, Garching, Germany.
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany.
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35
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Bucher K, Rodriguez-Bocanegra E, Fischer MD. Benefits and Shortcomings of Laboratory Model Systems in the Development of Genetic Therapies. Klin Monbl Augenheilkd 2022; 239:263-269. [PMID: 35316853 DOI: 10.1055/a-1757-9879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Gene therapeutic approaches promise treatment or even a cure of diseases that were previously untreatable. Retinal gene therapies tested in clinical trials comprise a wide range of different strategies, including gene supplementation therapies, in vivo gene editing, modulation of splicing mechanisms, or the suppression of gene expression. To guarantee efficient transfer of genetic material into the respective target cells while avoiding major adverse effects, the development of genetic therapies requires appropriate in vitro model systems that allow tests of efficacy and safety of the gene therapeutic approach. In this review, we introduce various in vitro models of different levels of complexity used in the development of genetic therapies and discuss their respective benefits and shortcomings using the example of adeno-associated virus-based retinal gene therapy.
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Affiliation(s)
- Kirsten Bucher
- University Eye Hospital, University Hospital Tübingen Clinic of Ophthalmology, Tubingen, Germany.,Institute for Ophthalmic Research, University Hospital Tübingen Clinic of Ophthalmology, Tubingen, Germany
| | | | - M Dominik Fischer
- University Eye Hospital, University Hospital Tübingen Clinic of Ophthalmology, Tubingen, Germany.,Institute for Ophthalmic Research, University Hospital Tübingen Clinic of Ophthalmology, Tubingen, Germany.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom of Great Britain and Northern Ireland.,Department of Clinical Neurosciences, University of Oxford Nuffield Laboratory of Ophthalmology, Oxford, United Kingdom of Great Britain and Northern Ireland
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36
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Morozov V, Lagaye S, Morozov A. The TZM-bl Reporter Cell Line Expresses Kynureninase That Can Neutralize 2F5-like Antibodies in the HIV-1 Neutralization Assay. Int J Mol Sci 2022; 23:ijms23020641. [PMID: 35054825 PMCID: PMC8775840 DOI: 10.3390/ijms23020641] [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: 12/07/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Induction of broadly neutralizing antibodies targeting ectodomain of the transmembrane (TM) glycoprotein gp41 HIV-1 provides a basis for the development of a universal anti-viral vaccine. The HeLa cell-derived TZM-bl reporter cell line is widely used for the estimation of lentiviruses neutralization by immune sera. The cell line is highly permissive to infection by most strains of HIV, SIV, and SHIV. Here we demonstrated that TZM-bl cells express a 48 kDa non-glycosylated protein (p48) recognized by broadly neutralizing monoclonal antibody (mAb) 2F5 targeting the ELDKWA (aa 669–674) epitope of gp41TM of HIV-1. A significant amount of p48 was found in the cell supernatant. The protein was identified as human kynureninase (KYNU), which has the ELDKWA epitope. The protein is further called “p48 KYNU”. The HIV-1 neutralization by mAb 2F5 and 4E10 in the presence of p48KYNU was tested on Jurkat and TZM-bl cells. It was demonstrated that p48KYNU reduces neutralization by 2F5-like antibodies, but it has almost no effect on mAb 4E10. Therefore, p48KYNU can attenuate HIV-1 neutralization by 2F5-like antibodies and hence create false-negative results. Thus, previously tested immune sera that recognized the ELDKWA-epitope and demonstrated a “weak neutralization” of HIV-1 in TZM-bl assay should be reevaluated.
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Affiliation(s)
- Vladimir Morozov
- Institute of Human Virology, University of Maryland, Baltimore, MD 21201, USA
- Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
- Correspondence: (V.M.); (A.M.)
| | - Sylvie Lagaye
- Centre de Recherche Saint-Antoine (CRSA), INSERM—UMR-S 938/Sorbonne Université, CEDEX 12, 75571 Paris, France;
| | - Alexey Morozov
- Laboratory of Regulation of Intracellular Proteolysis, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence: (V.M.); (A.M.)
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Abstract
Many developments in biology and biotechnology have relied on the HeLa cell line, originally derived in 1951 from a Black cancer patient without her knowledge. This origin became generally known at the turn of the century, and the patient's descendants have sought and obtained some recognition and some control but little compensation. They have now retained two famous attorneys to sue a biotech firm for very extensive damages, with more legal action planned against other companies. This may have important repercussions for the biotech industry, and raises complex issues regarding ownership of biological material and compensation to patients from whom these materials have been obtained.
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Affiliation(s)
- Bertrand Jordan
- ADÉS (Anthropologie bioculturelle, droit, éthique et santé) UMR CNRS 7268, Aix Marseille université, Établissement français du sang. CoReBio PACA, case 901, Parc scientifique de Luminy, 13288 Marseille Cedex 09, France
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38
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Warburton A, Markowitz TE, Katz JP, Pipas JM, McBride AA. Recurrent integration of human papillomavirus genomes at transcriptional regulatory hubs. NPJ Genom Med 2021; 6:101. [PMID: 34848725 PMCID: PMC8632991 DOI: 10.1038/s41525-021-00264-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
Oncogenic human papillomavirus (HPV) genomes are often integrated into host chromosomes in HPV-associated cancers. HPV genomes are integrated either as a single copy or as tandem repeats of viral DNA interspersed with, or without, host DNA. Integration occurs frequently in common fragile sites susceptible to tandem repeat formation and the flanking or interspersed host DNA often contains transcriptional enhancer elements. When co-amplified with the viral genome, these enhancers can form super-enhancer-like elements that drive high viral oncogene expression. Here we compiled highly curated datasets of HPV integration sites in cervical (CESC) and head and neck squamous cell carcinoma (HNSCC) cancers, and assessed the number of breakpoints, viral transcriptional activity, and host genome copy number at each insertion site. Tumors frequently contained multiple distinct HPV integration sites but often only one “driver” site that expressed viral RNA. As common fragile sites and active enhancer elements are cell-type-specific, we mapped these regions in cervical cell lines using FANCD2 and Brd4/H3K27ac ChIP-seq, respectively. Large enhancer clusters, or super-enhancers, were also defined using the Brd4/H3K27ac ChIP-seq dataset. HPV integration breakpoints were enriched at both FANCD2-associated fragile sites and enhancer-rich regions, and frequently showed adjacent focal DNA amplification in CESC samples. We identified recurrent integration “hotspots” that were enriched for super-enhancers, some of which function as regulatory hubs for cell-identity genes. We propose that during persistent infection, extrachromosomal HPV minichromosomes associate with these transcriptional epicenters and accidental integration could promote viral oncogene expression and carcinogenesis.
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Affiliation(s)
- Alix Warburton
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, MSC3209, Bethesda, MD, 20892, USA
| | - Tovah E Markowitz
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua P Katz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison A McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, MSC3209, Bethesda, MD, 20892, USA.
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eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature 2021; 599:308-314. [PMID: 34671165 PMCID: PMC9295135 DOI: 10.1038/s41586-021-04009-w] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Extrachromosomal circular DNA elements (eccDNAs) have been described in the literature for several decades, and are known for their broad existence across different species1,2. However, their biogenesis and functions are largely unknown. By developing a new circular DNA enrichment method, here we purified and sequenced full-length eccDNAs with Nanopore sequencing. We found that eccDNAs map across the entire genome in a close to random manner, suggesting a biogenesis mechanism of random ligation of genomic DNA fragments. Consistent with this idea, we found that apoptosis inducers can increase eccDNA generation, which is dependent on apoptotic DNA fragmentation followed by ligation by DNA ligase 3. Importantly, we demonstrated that eccDNAs can function as potent innate immunostimulants in a manner that is independent of eccDNA sequence but dependent on eccDNA circularity and the cytosolic DNA sensor Sting. Collectively, our study not only revealed the origin, biogenesis and immunostimulant function of eccDNAs but also uncovered their sensing pathway and potential clinical implications in immune response.
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40
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Wnt-Signaling Regulated by Glucocorticoid-Induced miRNAs. Int J Mol Sci 2021; 22:ijms222111778. [PMID: 34769207 PMCID: PMC8584097 DOI: 10.3390/ijms222111778] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Glucocorticoids (GCs) are pleiotropic hormones which regulate innumerable physiological processes. Their comprehensive effects are due to the diversity of signaling mechanism networks. MiRNAs, small, non-coding RNAs contribute to the fine tuning of signaling pathways and reciprocal regulation between GCs and miRNAs has been suggested. Our aim was to investigate the expressional change and potential function of GC mediated miRNAs. The miRNA expression profile was measured in three models: human adrenocortical adenoma vs. normal tissue, steroid-producing H295R cells and in hormonally inactive HeLa cells before and after dexamethasone treatment. The gene expression profile in 82 control and 57 GC-affected samples was evaluated in GC producing and six different GC target tissue types. Tissue-specific target prediction (TSTP) was applied to identify the most relevant miRNA-mRNA interactions. Glucocorticoid treatment resulted in cell type-dependent miRNA expression changes. However, 19.5% of the influenced signaling pathways were common in all three experiments, of which the Wnt-signaling pathway seemed to be the most affected. Transcriptome data and TSTP showed similar results, as the Wnt pathway was significantly altered in both the GC-producing adrenal gland and all investigated GC target tissue types. In different cell types, different miRNAs led to the regulation of similar pathways. Wnt signaling may be one of the most important signaling pathways affected by hypercortisolism. It is, at least in part, regulated by miRNAs that mediate the glucocorticoid effect. Our findings on GC producing and GC target tissues suggest that the alteration of Wnt signaling (together with other pathways) may be responsible for the leading symptoms observed in Cushing's syndrome.
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Reduction in gene expression noise by targeted increase in accessibility at gene loci. Proc Natl Acad Sci U S A 2021; 118:2018640118. [PMID: 34625470 DOI: 10.1073/pnas.2018640118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 01/30/2023] Open
Abstract
Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by periods of quiescence. Here, we show that the intermittent access of the promoters to transcription factors through relatively impervious chromatin contributes to this "noisy" transcription. We tethered a nuclease-deficient Cas9 fused to a histone acetyl transferase at the promoters of two endogenous genes in HeLa cells. An assay for transposase-accessible chromatin using sequencing showed that the activity of the histone acetyl transferase altered the chromatin architecture locally without introducing global changes in the nucleus and rendered the targeted promoters constitutively accessible. We measured the gene expression variability from the gene loci by performing single-molecule fluorescence in situ hybridization against mature messenger RNAs (mRNAs) and by imaging nascent mRNA molecules present at active gene loci in single cells. Because of the increased accessibility of the promoter to transcription factors, the transcription from two genes became less noisy, even when the average levels of expression did not change. In addition to providing evidence for chromatin accessibility as a determinant of the noise in gene expression, our study offers a mechanism for controlling gene expression noise which is otherwise unavoidable.
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42
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St Germain C, Zhao H, Barlow JH. Transcription-Replication Collisions-A Series of Unfortunate Events. Biomolecules 2021; 11:1249. [PMID: 34439915 PMCID: PMC8391903 DOI: 10.3390/biom11081249] [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: 07/21/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Transcription-replication interactions occur when DNA replication encounters genomic regions undergoing transcription. Both replication and transcription are essential for life and use the same DNA template making conflicts unavoidable. R-loops, DNA supercoiling, DNA secondary structure, and chromatin-binding proteins are all potential obstacles for processive replication or transcription and pose an even more potent threat to genome integrity when these processes co-occur. It is critical to maintaining high fidelity and processivity of transcription and replication while navigating through a complex chromatin environment, highlighting the importance of defining cellular pathways regulating transcription-replication interaction formation, evasion, and resolution. Here we discuss how transcription influences replication fork stability, and the safeguards that have evolved to navigate transcription-replication interactions and maintain genome integrity in mammalian cells.
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Affiliation(s)
- Commodore St Germain
- School of Mathematics and Science, Solano Community College, 4000 Suisun Valley Road, Fairfield, CA 94534, USA
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
| | - Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
| | - Jacqueline H. Barlow
- Department of Microbiology and Molecular Genetics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA;
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43
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Hosseini S, Wetzel O, Kostka K, Heggen M, Loza K, Epple M. Pathways for Oral and Rectal Delivery of Gold Nanoparticles (1.7 nm) and Gold Nanoclusters into the Colon: Enteric-Coated Capsules and Suppositories. Molecules 2021; 26:5069. [PMID: 34443657 PMCID: PMC8401122 DOI: 10.3390/molecules26165069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 12/26/2022] Open
Abstract
Two ways to deliver ultrasmall gold nanoparticles and gold-bovine serum albumin (BSA) nanoclusters to the colon were developed. First, oral administration is possible by incorporation into gelatin capsules that were coated with an enteric polymer. These permit the transfer across the stomach whose acidic environment damages many drugs. The enteric coating dissolves due to the neutral pH of the colon and releases the capsule's cargo. Second, rectal administration is possible by incorporation into hard-fat suppositories that melt in the colon and then release the nanocarriers. The feasibility of the two concepts was demonstrated by in-vitro release studies and cell culture studies that showed the easy redispersibility after dissolution of the respective transport system. This clears a pathway for therapeutic applications of drug-loaded nanoparticles to address colon diseases, such as chronic inflammation and cancer.
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Affiliation(s)
- Shabnam Hosseini
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitaetsstr. 5-7, 45117 Essen, Germany; (S.H.); (O.W.); (K.K.); (K.L.)
| | - Oliver Wetzel
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitaetsstr. 5-7, 45117 Essen, Germany; (S.H.); (O.W.); (K.K.); (K.L.)
| | - Kathrin Kostka
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitaetsstr. 5-7, 45117 Essen, Germany; (S.H.); (O.W.); (K.K.); (K.L.)
| | - Marc Heggen
- Ernst Ruska Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
| | - Kateryna Loza
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitaetsstr. 5-7, 45117 Essen, Germany; (S.H.); (O.W.); (K.K.); (K.L.)
| | - Matthias Epple
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitaetsstr. 5-7, 45117 Essen, Germany; (S.H.); (O.W.); (K.K.); (K.L.)
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44
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Gunkel P, Iino H, Krull S, Cordes VC. ZC3HC1 Is a Novel Inherent Component of the Nuclear Basket, Resident in a State of Reciprocal Dependence with TPR. Cells 2021; 10:1937. [PMID: 34440706 PMCID: PMC8393659 DOI: 10.3390/cells10081937] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022] Open
Abstract
The nuclear basket (NB) scaffold, a fibrillar structure anchored to the nuclear pore complex (NPC), is regarded as constructed of polypeptides of the coiled-coil dominated protein TPR to which other proteins can bind without contributing to the NB's structural integrity. Here we report vertebrate protein ZC3HC1 as a novel inherent constituent of the NB, common at the nuclear envelopes (NE) of proliferating and non-dividing, terminally differentiated cells of different morphogenetic origin. Formerly described as a protein of other functions, we instead present the NB component ZC3HC1 as a protein required for enabling distinct amounts of TPR to occur NB-appended, with such ZC3HC1-dependency applying to about half the total amount of TPR at the NEs of different somatic cell types. Furthermore, pointing to an NB structure more complex than previously anticipated, we discuss how ZC3HC1 and the ZC3HC1-dependent TPR polypeptides could enlarge the NB's functional repertoire.
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Affiliation(s)
| | | | | | - Volker C. Cordes
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany; (P.G.); (H.I.); (S.K.)
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Abstract
The collection and use of human genetic data raise important ethical questions about how to balance individual autonomy and privacy with the potential for public good. The proliferation of local, national, and international efforts to collect genetic data and create linkages to support large-scale initiatives in precision medicine and the learning health system creates new demands for broad data sharing that involve managing competing interests and careful consideration of what constitutes appropriate ethical trade-offs. This review describes these emerging ethical issues with a focus on approaches to consent and issues related to justice in the shifting genomic research ecosystem.
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Affiliation(s)
- Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, NY 10032, USA;
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46
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Wey K, Schirrmann R, Diesing D, Lang S, Brandau S, Hansen S, Epple M. Coating of cochlear implant electrodes with bioactive DNA-loaded calcium phosphate nanoparticles for the local transfection of stimulatory proteins. Biomaterials 2021; 276:121009. [PMID: 34280824 DOI: 10.1016/j.biomaterials.2021.121009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/23/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022]
Abstract
Calcium phosphate nanoparticles were loaded with nucleic acids to enhance the on-growth of tissue to a cochlear implant electrode. The nanoparticle deposition on a metallic electrode surface is possible by electrophoretic deposition (EPD) or layer-by-layer deposition (LbL). Impedance spectroscopy showed that the coating layer did not interrupt the electrical conductance at physiological frequencies and beyond (1-40,000 Hz). The transfection was demonstrated with the model cell lines HeLa and 3T3 as well as with primary explanted spiral ganglion neurons (rat) with the model protein enhanced green fluorescent protein (EGFP). The expression of the functional protein brain-derived neurotrophic factor (BDNF) was also shown. Thus, a coating of inner-ear cochlear implant electrodes with nanoparticles that carry nucleic acids will enhance the ongrowth of spiral ganglion cell axons for an improved transmission of electrical pulses.
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Affiliation(s)
- Karolin Wey
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
| | - Ronja Schirrmann
- Department of Otorhinolaryngology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Detlef Diesing
- Physical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Stephan Lang
- Department of Otorhinolaryngology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sven Brandau
- Department of Otorhinolaryngology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Stefan Hansen
- Department of Otorhinolaryngology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Centre for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany.
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47
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Spiers H, Songhurst H, Nightingale L, de Folter J, Hutchings R, Peddie CJ, Weston A, Strange A, Hindmarsh S, Lintott C, Collinson LM, Jones ML. Deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations. Traffic 2021; 22:240-253. [PMID: 33914396 DOI: 10.1111/tra.12789] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 12/19/2022]
Abstract
Advancements in volume electron microscopy mean it is now possible to generate thousands of serial images at nanometre resolution overnight, yet the gold standard approach for data analysis remains manual segmentation by an expert microscopist, resulting in a critical research bottleneck. Although some machine learning approaches exist in this domain, we remain far from realizing the aspiration of a highly accurate, yet generic, automated analysis approach, with a major obstacle being lack of sufficient high-quality ground-truth data. To address this, we developed a novel citizen science project, Etch a Cell, to enable volunteers to manually segment the nuclear envelope (NE) of HeLa cells imaged with serial blockface scanning electron microscopy. We present our approach for aggregating multiple volunteer annotations to generate a high-quality consensus segmentation and demonstrate that data produced exclusively by volunteers can be used to train a highly accurate machine learning algorithm for automatic segmentation of the NE, which we share here, in addition to our archived benchmark data.
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Affiliation(s)
- Helen Spiers
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
- Department of Physics, University of Oxford, Oxford, UK
| | - Harry Songhurst
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
- Department of Computer Science, University of Manchester, Manchester, UK
| | - Luke Nightingale
- Scientific Computing Science Technology Platform, The Francis Crick Institute, London, UK
| | - Joost de Folter
- Scientific Computing Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Anne Weston
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Amy Strange
- Scientific Computing Science Technology Platform, The Francis Crick Institute, London, UK
| | - Steve Hindmarsh
- Scientific Computing Science Technology Platform, The Francis Crick Institute, London, UK
| | - Chris Lintott
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
- Department of Physics, University of Oxford, Oxford, UK
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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48
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Wurm MJ, Wurm FM. Naming CHO cells for bio-manufacturing: Genome plasticity and variant phenotypes of cell populations in bioreactors question the relevance of old names. Biotechnol J 2021; 16:e2100165. [PMID: 34050613 DOI: 10.1002/biot.202100165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 11/06/2022]
Abstract
Chinese Hamster Ovary [CHO] cells are the workhorse for production of modern biopharmaceuticals. They are however immortalized cells with a high propensity for genetic change. Judging from published culture records, CHO cell populations have undergone hundreds of population doublings since their origin in the late 1950s. Different cell populations were established and named from 1 to 3 decades after their generation, such as CHO-Pro-, CHO-K1, CHO-DG44, CHO-S, CHO-DUK, CHO-DXB-11 to indicate origin and certain phenotypic features. These names are commonly used in scientific publications still today. This article discusses the relevance of such names. We argue that they provide a false sense of identity. To substantiate this, we provide the long (and poorly recorded) history of CHO cells as well as their highly complex genetics. Finally, we suggest an alternative naming system for CHO cells which provides more relevant information. While the implementation of a new naming convention will require substantial discussions among members of the relevant community, it should improve interpretation and comparability between laboratories. This, in turn will help scientific communities and industrial users to attain and further the full potential of CHO cells.
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Affiliation(s)
- Maria J Wurm
- Life Science Faculty, Swiss Federal Institute of Technology Lausanne [EPFL], Lausanne, Switzerland
| | - Florian M Wurm
- Life Science Faculty, Swiss Federal Institute of Technology Lausanne [EPFL], Lausanne, Switzerland
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49
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McIntyre WD, Nemati R, Salehi M, Aldrich CC, FitzGibbon M, Deng L, Pazos MA, Rose RE, Toro B, Netzband RE, Pager CT, Robinson IP, Bialosuknia SM, Ciota AT, Fabris D. Agnostic Framework for the Classification/Identification of Organisms Based on RNA Post-Transcriptional Modifications. Anal Chem 2021; 93:7860-7869. [PMID: 34043326 PMCID: PMC8351319 DOI: 10.1021/acs.analchem.1c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We propose a novel approach for building a classification/identification framework based on the full complement of RNA post-transcriptional modifications (rPTMs) expressed by an organism at basal conditions. The approach relies on advanced mass spectrometry techniques to characterize the products of exonuclease digestion of total RNA extracts. Sample profiles comprising identities and relative abundances of all detected rPTM were used to train and test the capabilities of different machine learning (ML) algorithms. Each algorithm proved capable of identifying rigorous decision rules for differentiating closely related classes and correctly assigning unlabeled samples. The ML classifiers resolved different members of the Enterobacteriaceae family, alternative Escherichia coli serotypes, a series of Saccharomyces cerevisiae knockout mutants, and primary cells of the Homo sapiens central nervous system, which shared very similar genetic backgrounds. The excellent levels of accuracy and resolving power achieved by training on a limited number of classes were successfully replicated when the number of classes was significantly increased to escalate complexity. A dendrogram generated from ML-curated data exhibited a hierarchical organization that closely resembled those afforded by established taxonomic systems. Finer clustering patterns revealed the extensive effects induced by the deletion of a single pivotal gene. This information provided a putative roadmap for exploring the roles of rPTMs in their respective regulatory networks, which will be essential to decipher the epitranscriptomics code. The ubiquitous presence of RNA in virtually all living organisms promises to enable the broadest possible range of applications, with significant implications in the diagnosis of RNA-related diseases.
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Affiliation(s)
| | - Reza Nemati
- Dept. of Chemistry, University at Albany (SUNY), Albany, NY 12222, USA
| | - Mehraveh Salehi
- Dept. of Electrical Engineering, Yale University, New Haven, CT 06520, USA
| | - Colin C. Aldrich
- Dept. of Chemistry, University at Albany (SUNY), Albany, NY 12222, USA
| | - Molly FitzGibbon
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Limin Deng
- Dept. of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Manuel A. Pazos
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Rebecca E. Rose
- Dept. of Chemistry, University at Albany (SUNY), Albany, NY 12222, USA
| | - Botros Toro
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Rachel E. Netzband
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | - Cara T. Pager
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Ingrid P. Robinson
- Dept. of Biological Sciences, University at Albany, Albany, NY 12222, USA
| | | | | | - Daniele Fabris
- Dept. of Chemistry, University of Connecticut, Storrs, CT 06269, USA
- RNA Institute, University at Albany, Albany, NY 12222, USA
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50
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Extracts from Pulsatilla patens target cancer-related signaling pathways in HeLa cells. Sci Rep 2021; 11:10654. [PMID: 34017038 PMCID: PMC8138020 DOI: 10.1038/s41598-021-90136-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/30/2021] [Indexed: 01/19/2023] Open
Abstract
The purpose of this study was to determine if a methanolic extract of the Pulsatilla patens (L.) Mill. can inhibit the progression of cancer through the modulation of cancer-related metabolic signaling pathways. We analyzed a panel of 13 inducible luciferase reporter gene vectors which expression is driven by enhancer elements that bind to specific transcription factors for the evaluation of the activity of cancer signaling pathways. The root extract of P. patens exhibited strong inhibition of several signaling pathways in HeLa cells, a cervical cancer cell line, and was found to be the most potent in inhibiting the activation of Stat3, Smad, AP-1, NF-κB, MYC, Ets, Wnt and Hdghog, at a concentration of 40 µg/mL. The methanolic extracts of P. patens enhanced apoptotic death, deregulated cellular proliferation, differentiation, and progression towards the neoplastic phenotype by altering key signaling molecules required for cell cycle progression. This is the first study to report the influence of Pulsatilla species on cancer signaling pathways. Further, our detailed phytochemical analysis of the methanolic extracts of the P. patens allowed to deduce that compounds, which strongly suppressed the growth and proliferation of HeLa cancer cells were mainly triterpenoid saponins accompanied by phenolic acids.
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