1
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Haynes J, Palaniappan B, Crutchley JM, Sundaram U. Regulation of Enterocyte Brush Border Membrane Primary Na-Absorptive Transporters in Human Intestinal Organoid-Derived Monolayers. Cells 2024; 13:1623. [PMID: 39404387 PMCID: PMC11482628 DOI: 10.3390/cells13191623] [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: 08/26/2024] [Revised: 09/23/2024] [Accepted: 09/26/2024] [Indexed: 10/19/2024] Open
Abstract
In the small intestine, sodium (Na) absorption occurs primarily via two apical transporters, Na-hydrogen exchanger 3 (NHE3) and Na-glucose cotransporter 1 (SGLT1). The two primary Na-absorptive pathways were previously shown to compensatorily regulate each other in rabbit and rat intestinal epithelial cells. However, whether NHE3 and SGLT1 regulate one another in normal human enterocytes is unknown, mainly due to a lack of appropriate experimental models. To investigate this, we generated 2D enterocyte monolayers from human jejunal 3D organoids and used small interfering RNAs (siRNAs) to knock down NHE3 or SGLT1. Molecular and uptake studies were performed to determine the effects on NHE3 and SGLT1 expression and activity. Knockdown of NHE3 by siRNA in enterocyte monolayers was verified by qPCR and Western blot analysis and resulted in reduced NHE3 activity. However, in NHE3 siRNA-transfected cells, SGLT1 activity was significantly increased. siRNA knockdown of SGLT1 was confirmed by qPCR and Western blot analysis and resulted in reduced SGLT1 activity. However, in SGLT1 siRNA-transfected cells, NHE3 activity was significantly increased. These results demonstrate for the first time the functionality of siRNA in patient-derived organoid monolayers. Furthermore, they show that the two primary Na absorptive pathways in human enterocytes reciprocally regulate one another.
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Affiliation(s)
| | | | | | - Uma Sundaram
- Department of Clinical and Translational Sciences, Joan C. Edwards School of Medicine, Marshall University, 1600 Medical Center Drive, Huntington, WV 25701, USA
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2
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Avenel ICN, Ewald JD, Ariey-Bonnet J, Kristensen IH, Petterson SA, Thesbjerg MN, Burton M, Thomassen M, Wennerberg K, Michaelsen SR, Kristensen BW. GDNF/GFRA1 signaling contributes to chemo- and radioresistance in glioblastoma. Sci Rep 2024; 14:17639. [PMID: 39085346 PMCID: PMC11292001 DOI: 10.1038/s41598-024-68626-x] [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: 01/26/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults, characterized by an inherent aggressivity and resistance to treatment leading to poor prognoses. While some resistance mechanisms have been elucidated, a deeper understanding of these mechanisms is needed to increase therapeutic efficacy. In this study we first discovered glial-cell derived neurotrophic factor (GDNF) to be upregulated in patient-derived glioblastoma spheroid cultures after chemotherapeutic temozolomide treatment, through RNA-Seq experiments. Therefore, we investigated the role of the GDNF/GDNF receptor alpha 1 (GFRA1) signaling pathway as a resistance mechanism to chemotherapy with temozolomide and lomustine, as well as irradiation using patient-derived glioblastoma spheroid cultures. With qPCR experiments we showed a consistent upregulation of GDNF and its primary receptor GFRA1 following all three lines of treatment. Moreover, CRISPR/Cas9 knock-outs of GDNF in two patient-derived models sensitized these cells to chemotherapy treatment, but not radiotherapy. The increased sensitivity was completely reversed by the addition of exogeneous GDNF, confirming the key role of this factor in chemoresistance. Finally, a CRISPR KO of GFRA1 demonstrated a similar increased sensitivity to temozolomide and lomustine treatment, as well as radiotherapy. Together, our findings support the role of the GDNF/GFRA1 signaling pathway in glioblastoma chemo and radioresistance.
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Affiliation(s)
- Inès C N Avenel
- Department of Pathology, Bartholin Institute, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Jesper D Ewald
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Pathology Research Unit, Department of Clinical Research, University of Southern Denmark Odense, Odense, Denmark
| | - Jérémy Ariey-Bonnet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ida H Kristensen
- Department of Pathology, Bartholin Institute, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Stine A Petterson
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark Odense, Odense, Denmark
| | - Martin N Thesbjerg
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark Odense, Odense, Denmark
| | - Mark Burton
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark Odense, Odense, Denmark
| | - Mads Thomassen
- Clinical Genome Center, Department of Clinical Research, University of Southern Denmark Odense, Odense, Denmark
| | - Krister Wennerberg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Signe R Michaelsen
- Department of Pathology, Bartholin Institute, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bjarne W Kristensen
- Department of Pathology, Bartholin Institute, Rigshospitalet, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- DCCC Brain Tumor Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
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3
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Woo MS, Mayer C, Binkle-Ladisch L, Sonner JK, Rosenkranz SC, Shaposhnykov A, Rothammer N, Tsvilovskyy V, Lorenz SM, Raich L, Bal LC, Vieira V, Wagner I, Bauer S, Glatzel M, Conrad M, Merkler D, Freichel M, Friese MA. STING orchestrates the neuronal inflammatory stress response in multiple sclerosis. Cell 2024; 187:4043-4060.e30. [PMID: 38878778 DOI: 10.1016/j.cell.2024.05.031] [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: 01/16/2024] [Revised: 04/08/2024] [Accepted: 05/16/2024] [Indexed: 07/28/2024]
Abstract
Inflammation-induced neurodegeneration is a defining feature of multiple sclerosis (MS), yet the underlying mechanisms remain unclear. By dissecting the neuronal inflammatory stress response, we discovered that neurons in MS and its mouse model induce the stimulator of interferon genes (STING). However, activation of neuronal STING requires its detachment from the stromal interaction molecule 1 (STIM1), a process triggered by glutamate excitotoxicity. This detachment initiates non-canonical STING signaling, which leads to autophagic degradation of glutathione peroxidase 4 (GPX4), essential for neuronal redox homeostasis and thereby inducing ferroptosis. Both genetic and pharmacological interventions that target STING in neurons protect against inflammation-induced neurodegeneration. Our findings position STING as a central regulator of the detrimental neuronal inflammatory stress response, integrating inflammation with glutamate signaling to cause neuronal cell death, and present it as a tractable target for treating neurodegeneration in MS.
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Affiliation(s)
- Marcel S Woo
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christina Mayer
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lars Binkle-Ladisch
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jana K Sonner
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sina C Rosenkranz
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Artem Shaposhnykov
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Rothammer
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Volodymyr Tsvilovskyy
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Svenja M Lorenz
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lukas Raich
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas C Bal
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vanessa Vieira
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ingrid Wagner
- Department of Pathology and Immunology, Division of Clinical Pathology, Faculty of Medicine, University and University Hospital of Geneva, Geneva, Switzerland
| | - Simone Bauer
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Conrad
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany
| | - Doron Merkler
- Department of Pathology and Immunology, Division of Clinical Pathology, Faculty of Medicine, University and University Hospital of Geneva, Geneva, Switzerland
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Manuel A Friese
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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4
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Dupuy J, Fouché E, Noirot C, Martin P, Buisson C, Guéraud F, Pierre F, Héliès-Toussaint C. A dual model of normal vs isogenic Nrf2-depleted murine epithelial cells to explore oxidative stress involvement. Sci Rep 2024; 14:10905. [PMID: 38740939 DOI: 10.1038/s41598-024-60938-2] [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: 12/16/2022] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Cancer-derived cell lines are useful tools for studying cellular metabolism and xenobiotic toxicity, but they are not suitable for modeling the biological effects of food contaminants or natural biomolecules on healthy colonic epithelial cells in a normal genetic context. The toxicological properties of such compounds may rely on their oxidative properties. Therefore, it appears to be necessary to develop a dual-cell model in a normal genetic context that allows to define the importance of oxidative stress in the observed toxicity. Given that the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) is considered to be the master regulator of antioxidant defenses, our aim was to develop a cellular model comparing normal and Nrf2-depleted isogenic cells to qualify oxidative stress-related toxicity. We generated these cells by using the CRISPR/Cas9 technique. Whole-genome sequencing enabled us to confirm that our cell lines were free of cancer-related mutations. We used 4-hydroxy-2-nonenal (HNE), a lipid peroxidation product closely related to oxidative stress, as a model molecule. Here we report significant differences between the two cell lines in glutathione levels, gene regulation, and cell viability after HNE treatment. The results support the ability of our dual-cell model to study the role of oxidative stress in xenobiotic toxicity.
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Affiliation(s)
- Jacques Dupuy
- National Research Institute for Agriculture and Environment (INRAE), Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, BP93173, 31027, Toulouse Cedex 3, France
| | - Edwin Fouché
- National Research Institute for Agriculture and Environment (INRAE), Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, BP93173, 31027, Toulouse Cedex 3, France
| | - Céline Noirot
- National Research Institute for Agriculture and Environment (INRAE), Université Fédérale de Toulouse, INRAE, BioinfOmics, GenoToul Bioinformatics Facility, 31326, Castanet-Tolosan, France
| | - Pierre Martin
- National Research Institute for Agriculture and Environment (INRAE), Université Fédérale de Toulouse, INRAE, BioinfOmics, GenoToul Bioinformatics Facility, 31326, Castanet-Tolosan, France
| | - Charline Buisson
- National Research Institute for Agriculture and Environment (INRAE), Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, BP93173, 31027, Toulouse Cedex 3, France
| | - Françoise Guéraud
- National Research Institute for Agriculture and Environment (INRAE), Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, BP93173, 31027, Toulouse Cedex 3, France
| | - Fabrice Pierre
- National Research Institute for Agriculture and Environment (INRAE), Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, BP93173, 31027, Toulouse Cedex 3, France
| | - Cécile Héliès-Toussaint
- National Research Institute for Agriculture and Environment (INRAE), Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, BP93173, 31027, Toulouse Cedex 3, France.
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5
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Hub T, Cornean A, Round K, Fleming T, Freichel M, Medert R. Streamlined Generation of CRISPR/Cas9-Mediated Single-Cell Knockout Clones in Murine Cell Lines. ACS Pharmacol Transl Sci 2024; 7:1291-1301. [PMID: 38751646 PMCID: PMC11091971 DOI: 10.1021/acsptsci.3c00338] [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: 11/22/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024]
Abstract
Clonal cell lines harboring loss-of-function mutations in genes of interest are crucial for studying the cellular functions of the encoded proteins. Recent advances in genome engineering have converged on the CRISPR/Cas9 technology to quickly and reliably generate frameshift mutations in the target genes across various cell lines and species. Although high on-target cleavage efficiencies can be obtained reproducibly, screening and identifying clones with loss-of-function alleles remains a major bottleneck. Here, we describe a single sgRNA strategy to generate CRISPR/Cas9-mediated frameshift mutations in target genes of mammalian cell lines that can be easily and cost-effectively identified. Given the proliferation of workhorse cell lines such as N2a cells and the resulting clonal expansion of the cell type, our protocol can facilitate the isolation of knockout clonal cell lines and their genetic validation within a period of down to 6-8 weeks.
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Affiliation(s)
- Tobias Hub
- Institute
of Pharmacology, Heidelberg University, Heidelberg 69120, Germany
| | - Alex Cornean
- Institute
of Pharmacology, Heidelberg University, Heidelberg 69120, Germany
- Partner
Site Heidelberg/Mannheim, DZHK (German Centre
for Cardiovascular Research), Heidelberg, Germany
| | - Kellen Round
- Institute
of Pharmacology, Heidelberg University, Heidelberg 69120, Germany
| | - Thomas Fleming
- Department
of Internal Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg 69120, Germany
- German
Center for Diabetes Research (DZD), Neuherberg 85764, Germany
| | - Marc Freichel
- Institute
of Pharmacology, Heidelberg University, Heidelberg 69120, Germany
- Partner
Site Heidelberg/Mannheim, DZHK (German Centre
for Cardiovascular Research), Heidelberg, Germany
| | - Rebekka Medert
- Institute
of Pharmacology, Heidelberg University, Heidelberg 69120, Germany
- Partner
Site Heidelberg/Mannheim, DZHK (German Centre
for Cardiovascular Research), Heidelberg, Germany
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6
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Liu L, Manley JL. Non-canonical isoforms of the mRNA polyadenylation factor WDR33 regulate STING-mediated immune responses. Cell Rep 2024; 43:113886. [PMID: 38430516 PMCID: PMC11019558 DOI: 10.1016/j.celrep.2024.113886] [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: 06/05/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 03/04/2024] Open
Abstract
The human WDR33 gene encodes three major isoforms. The canonical isoform WDR33v1 (V1) is a well-characterized nuclear mRNA polyadenylation factor, while the other two, WDR33v2 (V2) and WDR33v3 (V3), have not been studied. Here, we report that V2 and V3 are generated by alternative polyadenylation, and neither protein contains all seven WD (tryptophan-aspartic acid) repeats that characterize V1. Surprisingly, V2 and V3 are not polyadenylation factors but localize to the endoplasmic reticulum and interact with stimulator of interferon genes (STING), the immune factor that induces the cellular response to cytosolic double-stranded DNA. V2 suppresses interferon-β induction by preventing STING disulfide oligomerization but promotes autophagy, likely by recruiting WIPI2 isoforms. V3, on the other hand, functions to increase STING protein levels. Our study has not only provided mechanistic insights into STING regulation but also revealed that protein isoforms can be functionally completely unrelated, indicating that alternative mRNA processing is a more powerful mechanism than previously appreciated.
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Affiliation(s)
- Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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7
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Hossain MJ, O’Connor TJ. An efficient and cost-effective method for disrupting genes in RAW264.7 macrophages using CRISPR-Cas9. PLoS One 2024; 19:e0299513. [PMID: 38483963 PMCID: PMC10939251 DOI: 10.1371/journal.pone.0299513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) are widely used for genome editing in cultured cell lines. However, the implementation of genome editing is still challenging due to the complex and often costly multi-step process associated with this technique. Moreover, the efficiency of genome editing varies across cell types, often limiting utility. Herein, we describe pCRISPR-EASY, a vector for simplified cloning of single guide RNAs (sgRNAs) and its simultaneous introduction with CRISPR-Cas9 into cultured cells using a non-viral delivery system. We outline a comprehensive, step-by-step protocol for genome editing in RAW264.7 macrophages, a mouse macrophage cell line widely used in biomedical research for which genome editing using CRISPR-Cas9 has been restricted to lentiviral or expensive commercial reagents. This provides an economical, highly efficient and reliable method for genome editing that can easily be adapted for use in other systems.
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Affiliation(s)
- Mohammad J. Hossain
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Tamara J. O’Connor
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
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8
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Choi N, Hwang J, Kim DY, Kim J, Song SY, Sung J. Involvement of DKK1 secreted from adipose-derived stem cells in alopecia areata. Cell Prolif 2024; 57:e13562. [PMID: 37991164 PMCID: PMC10905327 DOI: 10.1111/cpr.13562] [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: 07/04/2023] [Revised: 09/11/2023] [Accepted: 10/10/2023] [Indexed: 11/23/2023] Open
Abstract
Adipose-derived stem cells (ASCs) have shown efficacy in promoting hair growth, while DKK1 inhibits the WNT pathway, which is associated with hair loss. Our study focused on investigating the expression of DKK1 in alopecia areata (AA), a condition characterised by significant increases in the DKK1 levels in human and mouse ASCs. Treatment of interferon-γ increased the expression of DKK1 via STAT3 phosphorylation in ASCs. Treatment with recombinant DKK1 resulted in a decrease of cell growth in outer root sheath cells, whereas the use of a DKK1 neutralising antibody promoted hair growth. These results indicate that ASCs secrete DKK1, playing a crucial role in the progression and development of AA. Consequently, we generated DKK1 knockout (KO) ASCs using the Crispr/Cas9 system and evaluated their hair growth-promoting effects in an AA model. The DKK1 KO in ASCs led to enhanced cell motility and reduced cellular senescence by activating the WNT signalling pathway, while it reduced the expression of inflammatory cytokines by inactivating the NF-kB pathway. As expected, the intravenous injection of DKK1-KO-ASCs in AA mice, and the treatment with a conditioned medium derived from DKK1-KO-ASCs in hair organ culture proved to be more effective compared with the use of naïve ASCs and their conditioned medium. Overall, these findings suggest that DKK1 represents a novel therapeutic target for treating AA, and cell therapy using DKK1-KO-ASCs demonstrates greater efficiency.
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Affiliation(s)
| | | | - Doo Yeong Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical SciencesYonsei UniversityIncheonSouth Korea
| | - Jino Kim
- New Hair Plastic Surgery ClinicSeoulSouth Korea
| | - Seung Yong Song
- Institute for Human Tissue Restoration, Department of Plastic and Reconstructive SurgeryYonsei University College of MedicineSeoulSouth Korea
| | - Jong‐Hyuk Sung
- Epi Biotech Co., Ltd.IncheonSouth Korea
- College of Pharmacy, Yonsei Institute of Pharmaceutical SciencesYonsei UniversityIncheonSouth Korea
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9
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Wang M, Hong L, Cai L, Zhang Z, Jiang N, Chen Y, Ying Q, Kong L, Wei Z, Xu Y, Jin L. Novel LDLR variants affecting low density lipoprotein metabolism identified in familial hypercholesterolemia. Mol Biol Rep 2024; 51:153. [PMID: 38236436 DOI: 10.1007/s11033-023-09169-8] [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: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is an autosomal dominant disease of lipid metabolism mainly caused by mutations in the low-density lipoprotein receptor (LDLR) gene. Genetic detection of patients with FH help with precise diagnosis and treatment, thus reducing the risk of coronary heart disease (CHD) and other related diseases. The study aimed to identify the causative gene mutations in a Chinese FH family and reveal the pathogenicity and the mechanism of these mutations. METHODS AND RESULTS Whole exome sequencing was performed in a patient with severe lipid metabolism dysfunction seeking fertility guidance from a Chinese FH family. Two LDLR variants c.1875 C > G (p.N625K; novel variant) and c.1448G > A (p.W483*) were identified in the family. Wildtype and mutant LDLR constructs were established by the site-direct mutagenesis technique. Functional studies were carried out by cell transfection to evaluate the impact of detected variants on LDLR activity. The two variants were proven to affect LDL uptake and binding, resulting in cholesterol clearance reduction to different degrees. According to The American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines, the W483* variant was classified as "Pathogenic", while the N625K variant as "VUS". CONCLUSIONS Our results provide novel experimental evidence of functional alteration by LDLR variants identified in our study and expand the mutational spectrum of LDLR mutation induced FH.
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Affiliation(s)
- Miao Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ling Hong
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Luyi Cai
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ziyi Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ningdong Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yijing Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Qian Ying
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Lingpeng Kong
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Zhiyun Wei
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Yao Xu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Liping Jin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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10
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Doria-Borrell P, Moya-Navamuel M, Hemberger M, Pérez-García V. Generation of Knockout Mouse Trophoblast Stem Cells by CRISPR/Cas9. Methods Mol Biol 2024; 2781:81-91. [PMID: 38502445 DOI: 10.1007/978-1-0716-3746-3_8] [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] [Indexed: 03/21/2024]
Abstract
The placenta is the organ that dictates the reproductive outcome of mammalian pregnancy by supplying nutrients and oxygen to the developing fetus to sustain its normal growth. During early mammalian development, trophoblast cells are the earliest cell type to differentiate with multipotent capacity to generate the trophoblast components of the placenta. The isolation and use of mouse trophoblast stem cells (mTSCs) to model in vitro trophoblast differentiation, in combination with CRISPR/Cas9 genome editing technology, has provided tremendous insight into the molecular mechanisms governing early mouse placentation. By knocking out a specific gene of interest in mTSCs, researchers are shedding light onto the molecular pathways involved in normal placental development and pregnancy disorders associated with abnormal placentation. In this chapter, we provide a detailed protocol for the genetic modification of mTSCs by using CRISPR/Cas9 genome editing system.
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Affiliation(s)
- Paula Doria-Borrell
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, Valencia, Spain
| | - Maria Moya-Navamuel
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, Valencia, Spain
| | - Myriam Hemberger
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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11
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Gershoni A, Hassin O, Nataraj NB, Baruch S, Avioz‐Seligman A, Pirona AC, Fellus‐Alyagor L, Meir Salame T, Mukherjee S, Mallel G, Yarden Y, Aylon Y, Oren M. TAZ facilitates breast tumor growth by promoting an immune-suppressive tumor microenvironment. Mol Oncol 2023; 17:2675-2693. [PMID: 37716913 PMCID: PMC10701768 DOI: 10.1002/1878-0261.13525] [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: 08/26/2022] [Revised: 05/03/2023] [Accepted: 09/15/2023] [Indexed: 09/18/2023] Open
Abstract
The core Hippo pathway module consists of a tumour-suppressive kinase cascade that inhibits the transcriptional coactivators Yes-associated protein (YAP) and WW domain-containing transcription regulator protein 1 (WWTR1; also known as TAZ). When the Hippo pathway is downregulated, as often occurs in breast cancer, YAP/TAZ activity is induced. To elaborate the roles of TAZ in triple-negative breast cancer (TNBC), we depleted Taz in murine TNBC 4T1 cells, using either CRISPR/Cas9 or small hairpin RNA (shRNA). TAZ-depleted cells and their controls, harbouring wild-type levels of TAZ, were orthotopically injected into the mammary fat pads of syngeneic BALB/c female mice, and mice were monitored for tumour growth. TAZ depletion resulted in smaller tumours compared to the tumours generated by control cells, in line with the notion that TAZ functions as an oncogene in breast cancer. Tumours, as well as their corresponding in vitro cultured cells, were then subjected to gene expression profiling by RNA sequencing (RNA-seq). Interestingly, pathway analysis of the RNA-seq data indicated a TAZ-dependent enrichment of 'Inflammatory Response', a pathway correlated with TAZ expression levels also in human breast cancer tumours. Specifically, the RNA-seq analysis predicted a significant depletion of regulatory T cells (Tregs) in TAZ-deficient tumours, which was experimentally validated by the staining of tumour sections and by quantitative cytometry by time of flight (CyTOF). Strikingly, the differences in tumour size were completely abolished in immune-deficient mice, demonstrating that the immune-modulatory capacity of TAZ is critical for its oncogenic activity in this setting. Cytokine array analysis of conditioned medium from cultured cells revealed that TAZ increased the abundance of a small group of cytokines, including plasminogen activator inhibitor 1 (Serpin E1; also known as PAI-1), CCN family member 4 (CCN4; also known as WISP-1) and interleukin-23 (IL-23), suggesting a potential mechanistic explanation for its in vivo immunomodulatory effect. Together, our results imply that TAZ functions in a non-cell-autonomous manner to modify the tumour immune microenvironment and dampen the anti-tumour immune response, thereby facilitating tumour growth.
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Affiliation(s)
- Anat Gershoni
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Ori Hassin
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | | | - Sivan Baruch
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Adi Avioz‐Seligman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Anna Chiara Pirona
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Liat Fellus‐Alyagor
- Department of Veterinary ResourcesWeizmann Institute of ScienceRehovotIsrael
| | - Tomer Meir Salame
- Flow Cytometry Unit, Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | | | - Giuseppe Mallel
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Yosef Yarden
- Department of Immunology and Regenerative BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Yael Aylon
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Moshe Oren
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
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12
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Werner AN, Kumar AI, Charest PG. CRISPR-mediated reversion of oncogenic KRAS mutation results in increased proliferation and reveals independent roles of Ras and mTORC2 in the migration of A549 lung cancer cells. Mol Biol Cell 2023; 34:ar128. [PMID: 37729017 PMCID: PMC10848948 DOI: 10.1091/mbc.e23-05-0152] [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: 05/02/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
Although the RAS oncogene has been extensively studied, new aspects concerning its role and regulation in normal biology and cancer continue to be discovered. Recently, others and we have shown that the mechanistic Target of Rapamycin Complex 2 (mTORC2) is a Ras effector in Dictyostelium and mammalian cells. mTORC2 plays evolutionarily conserved roles in cell survival and migration and has been linked to tumorigenesis. Because RAS is often mutated in lung cancer, we investigated whether a Ras-mTORC2 pathway contributes to enhancing the migration of lung cancer cells expressing oncogenic Ras. We used A549 cells and CRISPR/Cas9 to revert the cells' KRAS G12S mutation to wild-type and establish A549 revertant (REV) cell lines, which we then used to evaluate the Ras-mediated regulation of mTORC2 and cell migration. Interestingly, our results suggest that K-Ras and mTORC2 promote A549 cell migration but as part of different pathways and independently of Ras's mutational status. Moreover, further characterization of the A549REV cells revealed that loss of mutant K-Ras expression for the wild-type protein leads to an increase in cell growth and proliferation, suggesting that the A549 cells have low KRAS-mutant dependency and that recovering expression of wild-type K-Ras protein increases these cells tumorigenic potential.
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Affiliation(s)
- Alyssa N. Werner
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Avani I. Kumar
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Pascale G. Charest
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- University of Arizona Cancer Center, Tucson, AZ 85721
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13
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Micalet A, Tappouni LJ, Peszko K, Karagianni D, Lam A, Counsell JR, Quezada SA, Moeendarbary E, Cheema U. Urokinase-type plasminogen activator (uPA) regulates invasion and matrix remodelling in colorectal cancer. Matrix Biol Plus 2023; 19-20:100137. [PMID: 38020586 PMCID: PMC10667746 DOI: 10.1016/j.mbplus.2023.100137] [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: 07/24/2023] [Revised: 11/02/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Background Cancer cells remodel their local physical environment through processes of matrix reorganisation, deposition, stiffening and degradation. Urokinase-type plasminogen activator (uPA), which is encoded by the PLAU gene, is an extracellular proteolytic enzyme known to be involved in cancer progression and tumour microenvironment (TME) remodelling. Perturbing uPA therefore has a strong potential as a mechano-based cancer therapy. This work is a bioengineering investigation to validate whether 1) uPA is involved in matrix degradation and 2) preventing matrix degradation by targeting uPA can reduce cancer cell invasion and metastasis. Methods To this aim, we used an engineered 3D in vitro model, termed the tumouroid, that appropriately mimics the tumour's native biophysical environment (3 kPa). A CRISPR-Cas9 mediated uPA knockout was performed to introduce a loss of function mutation in the gene coding sequence. Subsequently, to validate the translational potential of blocking uPA action, we tested a pharmacological inhibitor, UK-371,801. The changes in matrix stiffness were measured by atomic force microscopy (AFM). Invasion was quantified using images of the tumouroid, obtained after 21 days of culture. Results We showed that uPA is highly expressed in invasive breast and colorectal cancers, and these invasive cancer cells locally degrade their TME. PLAU (uPA) gene knock-out (KO) completely stopped matrix remodelling and significantly reduced cancer invasion. Many invasive cancer gene markers were also downregulated in the PLAU KO tumouroids. Pharmacological inhibition of uPA showed similarly promising results, where matrix degradation was reduced and so was the cancer invasion. Conclusion This work supports the role of uPA in matrix degradation. It demonstrates that the invasion of cancer cells was significantly reduced when enzymatic breakdown of the TME matrix was prevented. Collectively, this provides strong evidence of the effectiveness of targeting uPA as a mechano-based cancer therapy.
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Affiliation(s)
- Auxtine Micalet
- UCL Centre for 3D Models of Health and Disease, Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London W1W 7TS, United Kingdom
- Department of Mechanical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Luke J. Tappouni
- UCL Centre for Targeted Cancer Therapies, Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London W1W 7TS, United Kingdom
| | - Katarzyna Peszko
- UCL Centre for 3D Models of Health and Disease, Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London W1W 7TS, United Kingdom
| | - Despoina Karagianni
- Immune Regulation and Tumour Immunotherapy Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Ashley Lam
- UCL Centre for 3D Models of Health and Disease, Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London W1W 7TS, United Kingdom
| | - John R. Counsell
- UCL Centre for Targeted Cancer Therapies, Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London W1W 7TS, United Kingdom
| | - Sergio A. Quezada
- Immune Regulation and Tumour Immunotherapy Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Emad Moeendarbary
- Department of Mechanical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
- 199 Biotechnologies Ltd., Gloucester Road, London W2 6LD, United Kingdom
| | - Umber Cheema
- UCL Centre for 3D Models of Health and Disease, Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London W1W 7TS, United Kingdom
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14
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Patterson MT, Firulyova MM, Xu Y, Hillman H, Bishop C, Zhu A, Hickok GH, Schrank PR, Ronayne CE, Caillot Z, Fredrickson G, Kennedy AE, Acharya N, Neels JG, Chinetti G, Revelo X, Stromnes IM, Ivanov S, Bold TD, Zaitsev K, Williams JW. Trem2 promotes foamy macrophage lipid uptake and survival in atherosclerosis. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1015-1031. [PMID: 38646596 PMCID: PMC11031198 DOI: 10.1038/s44161-023-00354-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/22/2023] [Indexed: 04/23/2024]
Abstract
Atherosclerosis is driven by the expansion of cholesterol-loaded 'foamy' macrophages in the arterial intima. Factors regulating foamy macrophage differentiation and survival in plaque remain poorly understood. Here we show, using trajectory analysis of integrated single-cell RNA sequencing data and a genome-wide CRISPR screen, that triggering receptor expressed on myeloid cells 2 (Trem2) is associated with foamy macrophage specification. Loss of Trem2 led to a reduced ability of foamy macrophages to take up oxidized low-density lipoprotein (oxLDL). Myeloid-specific deletion of Trem2 showed an attenuation of plaque progression, even when targeted in established atherosclerotic lesions, and was independent of changes in circulating cytokines, monocyte recruitment or cholesterol levels. Mechanistically, we link Trem2-deficient macrophages with a failure to upregulate cholesterol efflux molecules, resulting in impaired proliferation and survival. Overall, we identify Trem2 as a regulator of foamy macrophage differentiation and atherosclerotic plaque growth and as a putative therapeutic target for atherosclerosis.
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Affiliation(s)
- Michael T. Patterson
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Maria M. Firulyova
- ITMO University, Saint Petersburg, Russia
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Yingzheng Xu
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Hannah Hillman
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Courtney Bishop
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Alisha Zhu
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Grant H. Hickok
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
| | - Patricia R. Schrank
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Christine E. Ronayne
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Medicine, University of Minnesota, Minneapolis, MN USA
| | | | - Gavin Fredrickson
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Ainsley E. Kennedy
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Nisha Acharya
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | | | | | - Xavier Revelo
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
| | - Ingunn M. Stromnes
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN USA
| | | | - Tyler D. Bold
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Medicine, University of Minnesota, Minneapolis, MN USA
| | | | - Jesse W. Williams
- Center for Immunology, University of Minnesota, Minneapolis, MN USA
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN USA
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15
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Bhattacharjee D, Bakar J, Chitnis SP, Sausville EL, Ashtekar KD, Mendelson BE, Long K, Smith JC, Heppner DE, Sheltzer JM. Inhibition of a lower potency target drives the anticancer activity of a clinical p38 inhibitor. Cell Chem Biol 2023; 30:1211-1222.e5. [PMID: 37827156 PMCID: PMC10715717 DOI: 10.1016/j.chembiol.2023.09.013] [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: 12/02/2022] [Revised: 06/27/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023]
Abstract
The small-molecule drug ralimetinib was developed as an inhibitor of the p38α mitogen-activated protein kinase, and it has advanced to phase 2 clinical trials in oncology. Here, we demonstrate that ralimetinib resembles EGFR-targeting drugs in pharmacogenomic profiling experiments and that ralimetinib inhibits EGFR kinase activity in vitro and in cellulo. While ralimetinib sensitivity is unaffected by deletion of the genes encoding p38α and p38β, its effects are blocked by expression of the EGFR-T790M gatekeeper mutation. Finally, we solved the cocrystal structure of ralimetinib bound to EGFR, providing further evidence that this drug functions as an ATP-competitive EGFR inhibitor. We conclude that, though ralimetinib is >30-fold less potent against EGFR compared to p38α, its ability to inhibit EGFR drives its primary anticancer effects. Our results call into question the value of p38α as an anticancer target, and we describe a multi-modal approach that can be used to uncover a drug's mechanism-of-action.
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Affiliation(s)
| | - Jaweria Bakar
- Yale University School of Medicine, New Haven, CT 06511, USA
| | - Surbhi P Chitnis
- Department of Chemistry, The University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | | | - Kumar Dilip Ashtekar
- Yale University School of Medicine, New Haven, CT 06511, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06511, USA; Yale Cancer Biology Institute, West Haven, CT 06516, USA
| | | | - Kaitlin Long
- Yale University School of Medicine, New Haven, CT 06511, USA
| | - Joan C Smith
- Yale University School of Medicine, New Haven, CT 06511, USA; Meliora Therapeutics, New Haven, CT 06511, USA
| | - David E Heppner
- Department of Chemistry, The University at Buffalo, State University of New York, Buffalo, NY 14260, USA; Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA.
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16
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Aboushousha R, van der Velden J, Hamilton N, Peng Z, MacPherson M, Erickson C, White S, Wouters EFM, Reynaert NL, Seward DJ, Li J, Janssen-Heininger YMW. Glutaredoxin attenuates glutathione levels via deglutathionylation of Otub1 and subsequent destabilization of system x C. SCIENCE ADVANCES 2023; 9:eadi5192. [PMID: 37703360 PMCID: PMC10499329 DOI: 10.1126/sciadv.adi5192] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023]
Abstract
Glutathione (GSH) is a critical component of the cellular redox system that combats oxidative stress. The glutamate-cystine antiporter, system xC-, is a key player in GSH synthesis that allows for the uptake of cystine, the rate-limiting building block of GSH. It is unclear whether GSH or GSH-dependent protein oxidation [protein S-glutathionylation (PSSG)] regulates the activity of system xC-. We demonstrate that an environment of enhanced PSSG promotes GSH increases via a system xC--dependent mechanism. Absence of the deglutathionylase, glutaredoxin (GLRX), augmented SLC7A11 protein and led to significant increases of GSH content. S-glutathionylation of C23 or C204 of the deubiquitinase OTUB1 promoted interaction with the E2-conjugating enzyme UBCH5A, leading to diminished ubiquitination and proteasomal degradation of SLC7A11 and augmentation of GSH, effects that were reversed by GLRX. These findings demonstrate an intricate link between GLRX and GSH via S-glutathionylation of OTUB1 and system xC- and illuminate a previously unknown feed-forward regulatory mechanism whereby enhanced GSH protein oxidation augments cellular GSH.
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Affiliation(s)
- Reem Aboushousha
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jos van der Velden
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Nicholas Hamilton
- Department of Chemistry, University of Vermont, Burlington, VT 05405, USA
| | - Zhihua Peng
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Maximilian MacPherson
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Cuixia Erickson
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Sheryl White
- Department of Neurological Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Emiel F. M. Wouters
- Department of Respiratory Medicine, NUTRIM School of nutrition and translational research in metabolism, Maastricht University Medical Center, Maastricht, Netherlands
- Ludwig Boltzmann Institute for Lung Research, Vienna, Austria
| | - Niki L. Reynaert
- Department of Respiratory Medicine, NUTRIM School of nutrition and translational research in metabolism, Maastricht University Medical Center, Maastricht, Netherlands
| | - David J. Seward
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jianing Li
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
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17
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Zheng G, Zhu Y, Xu L, Chen S, Zhang X, Li W, Chen W, Zhou Y, Gu W. LncRNA MACC1-AS1 associates with DDX5 to modulate MACC1 transcription in breast cancer cells. iScience 2023; 26:107642. [PMID: 37664587 PMCID: PMC10474461 DOI: 10.1016/j.isci.2023.107642] [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: 08/18/2022] [Revised: 03/31/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023] Open
Abstract
MACC1 is a master oncogene involved in multiple aspects of cancer metastasis in a broad variety of tumors. However, the molecular mechanism by which MACC1 transcription is regulated remains unclear. Here, we show that in breast cancer cells, lncRNA MACC1-AS1 serves as a cis-factor to up-regulate MACC1 transcription and this regulation increases the cell proliferation potential. Mechanistically, MACC1-AS1 forms a complex with DEAD-Box helicase 5 (DDX5) and simultaneously interacts with the distal region of the MACC1 promoter. The interaction allows its associated DDX5 to spatially contact the MACC1 core promoter and shift from MACC1-AS1 to the core promoter. Moreover, binding of DDX5 to the core promoter results in local recruitment of the transcription factor SP-1, thus enhancing MACC1 transcription. Our findings reveal a molecular mechanism by which MACC1-AS1 cis-regulates MACC1 transcription by interacting with the distal promoter region and delivering DDX5 to the core-promoter of the gene.
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Affiliation(s)
- Guiyu Zheng
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Yanmei Zhu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Liqun Xu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Shaoying Chen
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Xiaona Zhang
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Wei Li
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Weibin Chen
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Yanchun Zhou
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Wei Gu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
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18
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Jin S, Yong H, Liu Y, Bao W. CRISPR/Cas9-mediated high-mobility group A2 knockout inhibits cell proliferation and invasion in papillary thyroid carcinoma cells. Adv Med Sci 2023; 68:409-416. [PMID: 37837800 DOI: 10.1016/j.advms.2023.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/16/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023]
Abstract
PURPOSE Metastasis and recurrence are the prognostic risk factor in patients with thyroid carcinoma. High-mobility group A2 (HMGA2) protein plays a crucial role in papillary thyroid carcinoma (PTC) metastasis. The aim of this study was to investigate the mechanisms underlying the HMGA2 effect on PTC cell proliferation and invasion. MATERIALS AND METHODS We used the CRISPR/Cas9 system to perform knockout of the HMGA2 gene in the human PTC cell line TPC-1. The knockout monoclonal cells were screened and verified by PCR analysis and genomic sequencing. Cell proliferation was examined after the knockout of the HMGA2 gene using cell counting kit-8 (CCK-8) assays. Furthermore, cell migration and invasion after the knockout were examined by cell scratch tests. Additionally, the changes in cell cycle and apoptosis after the knockout were detected by flow cytometry. RESULTS The results of the PCR analysis and the genomic sequencing confirmed that the human PTC TPC-1 cell line with knockout of HMGA2 gene was successfully established. The knockout of the HMGA2 gene significantly reduced the cell proliferation, growth, and invasion. Meanwhile, the knockout of the HMGA2 gene delayed the conversion of the G2/M phase and promoted cell necrosis. CONCLUSION The CRISPR/Cas9-mediated HMGA2 knockout in the TPC-1 cell line inhibited cell proliferation and invasion, which might be due to the blockage of the cell cycle in the G2/M phase and the promotion of cell necrosis.
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Affiliation(s)
- Shan Jin
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China.
| | - Hong Yong
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yousheng Liu
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China
| | - Wuyuntu Bao
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Region, China
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19
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Recoules L, Tanguy Le Gac N, Moutahir F, Bystricky K, Lavigne AC. Recruitment of the Histone Variant MacroH2A1 to the Pericentric Region Occurs upon Chromatin Relaxation and Is Responsible for Major Satellite Transcriptional Regulation. Cells 2023; 12:2175. [PMID: 37681907 PMCID: PMC10486525 DOI: 10.3390/cells12172175] [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: 07/20/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
Heterochromatin formation plays a pivotal role in regulating chromatin organization and influences nuclear architecture and genome stability and expression. Amongst the locations where heterochromatin is found, the pericentric regions have the capability to attract the histone variant macroH2A1. However, the factors and mechanisms behind macroH2A1 incorporation into these regions have not been explored. In this study, we probe different conditions that lead to the recruitment of macroH2A1 to pericentromeric regions and elucidate its underlying functions. Through experiments conducted on murine fibroblastic cells, we determine that partial chromatin relaxation resulting from DNA damage, senescence, or histone hyper-acetylation is necessary for the recruitment of macroH2A1 to pericentric regions. Furthermore, macroH2A1 is required for upregulation of noncoding pericentric RNA expression but not for pericentric chromatin organization. Our findings shed light on the functional rather than structural significance of macroH2A1 incorporation into pericentric chromatin.
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Affiliation(s)
- Ludmila Recoules
- Centre de Biologie Intégrative (CBI), MCD, Université de Toulouse Paul Sabatier, UPS, Université de Toulouse, UT, CNRS, F-31062 Toulouse, France; (L.R.); (N.T.L.G.); (F.M.)
| | - Nicolas Tanguy Le Gac
- Centre de Biologie Intégrative (CBI), MCD, Université de Toulouse Paul Sabatier, UPS, Université de Toulouse, UT, CNRS, F-31062 Toulouse, France; (L.R.); (N.T.L.G.); (F.M.)
| | - Fatima Moutahir
- Centre de Biologie Intégrative (CBI), MCD, Université de Toulouse Paul Sabatier, UPS, Université de Toulouse, UT, CNRS, F-31062 Toulouse, France; (L.R.); (N.T.L.G.); (F.M.)
| | - Kerstin Bystricky
- Centre de Biologie Intégrative (CBI), MCD, Université de Toulouse Paul Sabatier, UPS, Université de Toulouse, UT, CNRS, F-31062 Toulouse, France; (L.R.); (N.T.L.G.); (F.M.)
- Institut Universitaire de France (IUF), F-75231 Paris, France
| | - Anne-Claire Lavigne
- Centre de Biologie Intégrative (CBI), MCD, Université de Toulouse Paul Sabatier, UPS, Université de Toulouse, UT, CNRS, F-31062 Toulouse, France; (L.R.); (N.T.L.G.); (F.M.)
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20
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Cuesta-Borràs E, Salvans C, Arqués O, Chicote I, Ramírez L, Cabellos L, Martínez-Quintanilla J, Mur-Espinosa A, García-Álvarez A, Hernando J, Tejedor JR, Mirallas O, Élez E, Fraga MF, Tabernero J, Nuciforo P, Capdevila J, Palmer HG, Puig I. DPPA3-HIF1α axis controls colorectal cancer chemoresistance by imposing a slow cell-cycle phenotype. Cell Rep 2023; 42:112927. [PMID: 37537841 DOI: 10.1016/j.celrep.2023.112927] [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: 12/29/2022] [Revised: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
Tumor relapse is linked to rapid chemoresistance and represents a bottleneck for cancer therapy success. Engagement of a reduced proliferation state is a non-mutational mechanism exploited by cancer cells to bypass therapy-induced cell death. Through combining functional pulse-chase experiments in engineered cells and transcriptomic analyses, we identify DPPA3 as a master regulator of slow-cycling and chemoresistant phenotype in colorectal cancer (CRC). We find a vicious DPPA3-HIF1α feedback loop that downregulates FOXM1 expression via DNA methylation, thereby delaying cell-cycle progression. Moreover, downregulation of HIF1α partially restores a chemosensitive proliferative phenotype in DPPA3-overexpressing cancer cells. In cohorts of CRC patient samples, DPPA3 overexpression acts as a predictive biomarker of chemotherapeutic resistance that subsequently requires reduction in its expression to allow metastatic outgrowth. Our work demonstrates that slow-cycling cancer cells exploit a DPPA3/HIF1α axis to support tumor persistence under therapeutic stress and provides insights on the molecular regulation of disease progression.
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Affiliation(s)
- Estefania Cuesta-Borràs
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Cándida Salvans
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Oriol Arqués
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Irene Chicote
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; CIBERONC, 08029 Madrid, Spain
| | - Lorena Ramírez
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Laia Cabellos
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | | | - Alex Mur-Espinosa
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Alejandro García-Álvarez
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Jorge Hernando
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Juan Ramón Tejedor
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), Health Research Institute of the Principality of Asturias (ISPA), Spanish Biomedical Research Network in Rare Diseases (CIBERER), Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33011 Oviedo, Asturias, Spain
| | - Oriol Mirallas
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Elena Élez
- CIBERONC, 08029 Madrid, Spain; Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), Health Research Institute of the Principality of Asturias (ISPA), Spanish Biomedical Research Network in Rare Diseases (CIBERER), Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33011 Oviedo, Asturias, Spain
| | - Josep Tabernero
- CIBERONC, 08029 Madrid, Spain; Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; UVic-UCC, IOB-Quiron, 08023 Barcelona, Spain
| | - Paolo Nuciforo
- CIBERONC, 08029 Madrid, Spain; Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Jaume Capdevila
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; IOB-Teknon, 08023 Barcelona, Spain
| | - Héctor G Palmer
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; CIBERONC, 08029 Madrid, Spain.
| | - Isabel Puig
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; CIBERONC, 08029 Madrid, Spain.
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21
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Girish V, Lakhani AA, Thompson SL, Scaduto CM, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Kandikuppa PK, Lukow DA, Yuan ML, Stevens EC, Lee SN, Schukken KM, Akalu SM, Vasudevan A, Zou C, Salovska B, Li W, Smith JC, Taylor AM, Martienssen RA, Liu Y, Sun R, Sheltzer JM. Oncogene-like addiction to aneuploidy in human cancers. Science 2023; 381:eadg4521. [PMID: 37410869 PMCID: PMC10753973 DOI: 10.1126/science.adg4521] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Most cancers exhibit aneuploidy, but its functional significance in tumor development is controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using CRISPR Targeting), a set of chromosome engineering tools that allow us to eliminate specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies, and we demonstrate that trisomy of chromosome 1q is required for malignant growth in cancers harboring this alteration. Mechanistically, gaining chromosome 1q increases the expression of MDM4 and suppresses p53 signaling, and we show that TP53 mutations are mutually exclusive with 1q aneuploidy in human cancers. Thus, tumor cells can be dependent on specific aneuploidies, raising the possibility that these "aneuploidy addictions" could be targeted as a therapeutic strategy.
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Affiliation(s)
- Vishruth Girish
- Yale University School of Medicine, New Haven, CT 06511
- Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | | | | | | | | | | | | | | | - Monet Lou Yuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | | | - Sophia N. Lee
- Yale University School of Medicine, New Haven, CT 06511
| | | | | | | | - Charles Zou
- Yale University School of Medicine, New Haven, CT 06511
| | | | - Wenxue Li
- Yale University School of Medicine, New Haven, CT 06511
| | - Joan C. Smith
- Yale University School of Medicine, New Haven, CT 06511
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Yansheng Liu
- Yale University School of Medicine, New Haven, CT 06511
| | - Ruping Sun
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
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22
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Ludwig MP, Galbraith MD, Eduthan NP, Hill AA, Clay MR, Tellez CM, Wilky BA, Elias A, Espinosa JM, Sullivan KD. Proteasome Inhibition Sensitizes Liposarcoma to MDM2 Inhibition with Nutlin-3 by Activating the ATF4/CHOP Stress Response Pathway. Cancer Res 2023; 83:2543-2556. [PMID: 37205634 PMCID: PMC10391328 DOI: 10.1158/0008-5472.can-22-3173] [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: 10/06/2022] [Revised: 03/14/2023] [Accepted: 05/17/2023] [Indexed: 05/21/2023]
Abstract
Liposarcoma is the most commonly occurring soft-tissue sarcoma and is frequently characterized by amplification of chromosome region 12q13-15 harboring the oncogenes MDM2 and CDK4. This unique genetic profile makes liposarcoma an attractive candidate for targeted therapeutics. While CDK4/6 inhibitors are currently employed for treatment of several cancers, MDM2 inhibitors have yet to attain clinical approval. Here, we report the molecular characterization of the response of liposarcoma to the MDM2 inhibitor nutlin-3. Treatment with nutlin-3 led to upregulation of two nodes of the proteostasis network: the ribosome and the proteasome. CRISPR/Cas9 was used to perform a genome-wide loss of function screen that identified PSMD9, which encodes a proteasome subunit, as a regulator of response to nutlin-3. Accordingly, pharmacologic studies with a panel of proteasome inhibitors revealed strong combinatorial induction of apoptosis with nutlin-3. Mechanistic studies identified activation of the ATF4/CHOP stress response axis as a potential node of interaction between nutlin-3 and the proteasome inhibitor carfilzomib. CRISPR/Cas9 gene editing experiments confirmed that ATF4, CHOP, and the BH3-only protein, NOXA, are all required for nutlin-3 and carfilzomib-induced apoptosis. Furthermore, activation of the unfolded protein response using tunicamycin and thapsigargin was sufficient to activate the ATF4/CHOP stress response axis and sensitize to nutlin-3. Finally, cell line and patient-derived xenograft models demonstrated combinatorial effects of treatment with idasanutlin and carfilzomib on liposarcoma growth in vivo. Together, these data indicate that targeting of the proteasome could improve the efficacy of MDM2 inhibitors in liposarcoma. SIGNIFICANCE Targeting the proteasome in combination with MDM2 inhibition activates the ATF4/CHOP stress response axis to induce apoptosis in liposarcoma, providing a potential therapeutic approach for the most common soft-tissue sarcoma.
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Affiliation(s)
- Michael P. Ludwig
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Matthew D. Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Neetha Paul Eduthan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Amanda A. Hill
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Michael R. Clay
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Cristiam Moreno Tellez
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Breelyn A. Wilky
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Anthony Elias
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Joaquin M. Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kelly D. Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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23
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Song Z, Zhang G, Huang S, Liu Y, Li G, Zhou X, Sun J, Gao P, Chen Y, Huang X, Liu J, Wang X. PE-STOP: A versatile tool for installing nonsense substitutions amenable for precise reversion. J Biol Chem 2023; 299:104942. [PMID: 37343700 PMCID: PMC10365944 DOI: 10.1016/j.jbc.2023.104942] [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: 04/03/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/23/2023] Open
Abstract
The rapid advances in genome editing technologies have revolutionized the study of gene functions in cell or animal models. The recent generation of double-stranded DNA cleavage-independent base editors has been suitably adapted for interrogation of protein-coding genes on the basis of introducing premature stop codons or disabling the start codons. However, such versions of stop/start codon-oriented genetic tools still present limitations on their versatility, base-level precision, and target specificity. Here, we exploit a newly developed prime editor (PE) that differs from base editors by its adoption of a reverse transcriptase activity, which enables incorporation of various types of precise edits templated by a specialized prime editing guide RNA. Based on such a versatile platform, we established a prime editing-empowered method (PE-STOP) for installation of nonsense substitutions, providing a complementary approach to the present gene-targeting tools. PE-STOP is bioinformatically predicted to feature substantially expanded coverage in the genome space. In practice, PE-STOP introduces stop codons with good efficiencies in human embryonic kidney 293T and N2a cells (with medians of 29% [ten sites] and 25% [four sites] editing efficiencies, respectively), while exhibiting minimal off-target effects and high on-target precision. Furthermore, given the fact that PE installs prime editing guide RNA-templated mutations, we introduce a unique strategy for precise genetic rescue of PE-STOP-dependent nonsense mutation via the same PE platform. Altogether, the present work demonstrates a versatile and specific tool for gene inactivation and for functional interrogation of nonsense mutations.
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Affiliation(s)
- Ziguo Song
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guiquan Zhang
- Zhejiang Lab, Hangzhou, Zhejiang, China; State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center at Medical School of Nanjing University, Nanjing, China
| | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Liu
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xianhui Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayuan Sun
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Gao
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingxu Huang
- Zhejiang Lab, Hangzhou, Zhejiang, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jianghuai Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center at Medical School of Nanjing University, Nanjing, China.
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China.
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24
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Kim C, Cnaani A, Kültz D. Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system. Sci Rep 2023; 13:12086. [PMID: 37495710 PMCID: PMC10371998 DOI: 10.1038/s41598-023-37928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
MYC transcription factors have critical roles in facilitating a variety of cellular functions that have been highly conserved among species during evolution. However, despite circumstantial evidence for an involvement of MYC in animal osmoregulation, mechanistic links between MYC function and osmoregulation are missing. Mozambique tilapia (Oreochromis mossambicus) represents an excellent model system to study these links because it is highly euryhaline and highly tolerant to osmotic (salinity) stress at both the whole organism and cellular levels of biological organization. Here, we utilize an O. mossambicus brain cell line and an optimized vector-based CRISPR/Cas9 system to functionally disrupt MYC in the tilapia genome and to establish causal links between MYC and cell functions, including cellular osmoregulation. A cell isolation and dilution strategy yielded polyclonal myca (a gene encoding MYC) knockout (ko) cell pools with low genetic variability and high gene editing efficiencies (as high as 98.2%). Subsequent isolation and dilution of cells from these pools produced a myca ko cell line harboring a 1-bp deletion that caused a frameshift mutation. This frameshift functionally inactivated the transcriptional regulatory and DNA-binding domains predicted by bioinformatics and structural analyses. Both the polyclonal and monoclonal myca ko cell lines were viable, propagated well in standard medium, and differed from wild-type cells in morphology. As such, they represent a new tool for causally linking myca to cellular osmoregulation and other cell functions.
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Affiliation(s)
- Chanhee Kim
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, 7528809, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA.
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25
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Xue W, Li T, Gu Y, Li S, Xia N. Molecular engineering tools for the development of vaccines against infectious diseases: current status and future directions. Expert Rev Vaccines 2023. [PMID: 37339445 DOI: 10.1080/14760584.2023.2227699] [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: 04/17/2023] [Accepted: 06/16/2023] [Indexed: 06/22/2023]
Abstract
INTRODUCTION The escalating global changes have fostered conditions for the expansion and transmission of diverse biological factors, leading to the rise of emerging and reemerging infectious diseases. Complex viral infections, such as COVID-19, influenza, HIV, and Ebola, continue to surface, necessitating the development of effective vaccine technologies. AREAS COVERED This review article highlights recent advancements in molecular biology, virology, and genomics that have propelled the design and development of innovative molecular tools. These tools have promoted new vaccine research platforms and directly improved vaccine efficacy. The review summarizes the cutting-edge molecular engineering tools used in creating novel vaccines and explores the rapidly expanding molecular tools landscape and potential directions for future vaccine development. EXPERT OPINION The strategic application of advanced molecular engineering tools can address conventional vaccine limitations, enhance the overall efficacy of vaccine products, promote diversification in vaccine platforms, and form the foundation for future vaccine development. Prioritizing safety considerations of these novel molecular tools during vaccine development is crucial.
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Affiliation(s)
- Wenhui Xue
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Tingting Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- Xiang an Biomedicine Laboratory, Xiamen, China
- The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen, China
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26
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Radoua A, Pernon B, Pernet N, Jean C, Elmallah M, Guerrache A, Constantinescu AA, Hadj Hamou S, Devy J, Micheau O. ptARgenOM-A Flexible Vector For CRISPR/CAS9 Nonviral Delivery. SMALL METHODS 2023:e2300069. [PMID: 37156748 DOI: 10.1002/smtd.202300069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/11/2023] [Indexed: 05/10/2023]
Abstract
Viral-mediated delivery of the CRISPR-Cas9 system is one the most commonly used techniques to modify the genome of a cell, with the aim of analyzing the function of the targeted gene product. While these approaches are rather straightforward for membrane-bound proteins, they can be laborious for intracellular proteins, given that selection of full knockout (KO) cells often requires the amplification of single-cell clones. Moreover, viral-mediated delivery systems, besides the Cas9 and gRNA, lead to the integration of unwanted genetic material, such as antibiotic resistance genes, introducing experimental biases. Here, an alternative non-viral delivery approach is presented for CRISPR/Cas9, allowing efficient and flexible selection of KO polyclonal cells. This all-in-one mammalian CRISPR-Cas9 expression vector, ptARgenOM, encodes the gRNA and the Cas9 linked to a ribosomal skipping peptide sequence followed by the enhanced green fluorescent protein and the puromycin N-acetyltransferase, allowing for transient, expression-dependent selection and enrichment of isogenic KO cells. After evaluation using more than 12 distinct targets in 6 cell lines, ptARgenOM is found to be efficient in producing KO cells, reducing the time required to obtain a polyclonal isogenic cell line by 4-6 folds. Altogether ptARgenOM provides a simple, fast, and cost-effective delivery tool for genome editing.
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Affiliation(s)
- Abdelmnim Radoua
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | - Baptiste Pernon
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
| | - Nicolas Pernet
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | - Chloé Jean
- UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne (URCA), Reims, Cedex, 51687, France
- Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, UMR 7369 CNRS, Reims, 51687, France
| | - Mohammed Elmallah
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- Chemistry Department, Faculty of Science, Helwan University, Ain Helwan, Cairo, 11795, Egypt
| | - Abderrahmane Guerrache
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
| | | | - Sofiane Hadj Hamou
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
| | - Jérôme Devy
- UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne (URCA), Reims, Cedex, 51687, France
- Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, UMR 7369 CNRS, Reims, 51687, France
| | - Olivier Micheau
- UFR des Sciences de Santé, Université de Bourgogne, Dijon, 21000, France
- INSERM, Université de Bourgogne Franche-Comté (UBFC), UMR1231, LNC, Dijon, 21000, France
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27
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Frank E, Cailleret M, Nelep C, Fragner P, Polentes J, Herardot E, El Kassar L, Giraud-Triboult K, Monville C, Ben M'Barek K. Semi-automated optimized method to isolate CRISPR/Cas9 edited human pluripotent stem cell clones. Stem Cell Res Ther 2023; 14:110. [PMID: 37106426 PMCID: PMC10142500 DOI: 10.1186/s13287-023-03327-2] [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: 12/14/2022] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND CRISPR/Cas9 editing systems are currently used to generate mutations in a particular gene to mimic a genetic disorder in vitro. Such "disease in a dish" models based on human pluripotent stem cells (hPSCs) offer the opportunity to have access to virtually all cell types of the human body. However, the generation of mutated hPSCs remains fastidious. Current CRISPR/Cas9 editing approaches lead to a mixed cell population containing simultaneously non-edited and a variety of edited cells. These edited hPSCs need therefore to be isolated through manual dilution cloning, which is time-consuming, labor intensive and tedious. METHODS Following CRISPR/Cas9 edition, we obtained a mixed cell population with various edited cells. We then used a semi-automated robotic platform to isolate single cell-derived clones. RESULTS We optimized CRISPR/Cas9 editing to knock out a representative gene and developed a semi-automated method for the clonal isolation of edited hPSCs. This method is faster and more reliable than current manual approaches. CONCLUSIONS This novel method of hPSC clonal isolation will greatly improve and upscale the generation of edited hPSCs required for downstream applications including disease modeling and drug screening.
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Affiliation(s)
- Elie Frank
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
| | - Michel Cailleret
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
| | | | - Pascal Fragner
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Jérome Polentes
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Elise Herardot
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
| | - Lina El Kassar
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Karine Giraud-Triboult
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Christelle Monville
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France.
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France.
| | - Karim Ben M'Barek
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France.
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France.
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France.
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28
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Simeoni F, Loukas I, Wilson TS, Scaffidi P. CRISPR-based large-scale modeling of loss-of-function mutations to investigate mechanisms of stress resistance in cancer. STAR Protoc 2023; 4:102097. [PMID: 36853711 PMCID: PMC9947008 DOI: 10.1016/j.xpro.2023.102097] [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: 11/23/2022] [Revised: 12/17/2022] [Accepted: 01/19/2023] [Indexed: 02/13/2023] Open
Abstract
Dissecting mechanisms driving subclone expansion in primary cancers has been challenging. Here, we present a protocol to systematically disrupt entire gene networks and assess the functional impact of this perturbation on cancer cell fitness. By combining arrayed CRISPR libraries and high-content microscopy, we describe steps to identify classes of genes whose inactivation promotes resistance to environmental challenges faced by cancer cells during tumor growth or upon therapy. A proof-of-principle interrogation of the epigenetic regulatory network is described. For complete details on the use and execution of this protocol, please refer to Loukas et al. (2022).1.
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Affiliation(s)
- Fabrizio Simeoni
- Cancer Epigenetics Laboratory, The Francis Crick Institute, NW1 1AT London, UK.
| | - Ioannis Loukas
- Cancer Epigenetics Laboratory, The Francis Crick Institute, NW1 1AT London, UK
| | | | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, NW1 1AT London, UK; Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy.
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29
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Jia Z, Yang M, Zhao Y, Li X, Yang C, Qiao L, Li H, Du J, Lin J, Guan L. CRISPR-Cas9-Mediated NPC1 Gene Deletion Enhances HEK 293 T Cell Adhesion by Regulating E-Cadherin. Mol Biotechnol 2023; 65:252-262. [PMID: 35587334 DOI: 10.1007/s12033-022-00503-2] [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] [Received: 03/01/2022] [Accepted: 04/25/2022] [Indexed: 01/18/2023]
Abstract
NPC1 gene encodes a transmembrane glycoprotein on the late endosome/lysosomal membrane. Its mutation leads to a rare and aggravated autosomal recessive neurovisceral condition, termed Niemann-Pick disease type C1 (NPC1), which is characterized by progressive neurodegeneration, visceral symptoms, and premature death. To investigate the influence of NPC1 gene deletion on cell morphology, adhesion, proliferation, and apoptosis, CRISPR-Cas9 technology was used to knockout the NPC1 gene in HEK 293 T cells. Sanger sequencing, western blotting, and immunofluorescence were used to confirm successful NPC1 ablation. Filipin staining results indicated that deletion of NPC1 gene led to accumulation of unesterified cholesterol in HEK 293 T cells. Phalloidin staining results revealed cell aggregation, synapse shortening, nuclear enlargement, and cytoskeleton filamentous actin thinning in HEK 293 T cells with NPC1 gene mutation. Furthermore, NPC1 gene mutated HEK 293 T cell showed enhanced cell adhesion, inhibited cell proliferation, and increased cell apoptosis. In addition, NPC1 gene mutations significantly increased the protein expression levels of E-cadherin and γ-catenin and significantly decreased the protein expression levels of Wnt 3a, c-Myc, and cyclin D1. These results suggest that NPC1 may regulate cell adhesion by affecting the cadherin-catenin complex through E-cadherin, and that the classical Wnt signaling pathway may be inhibited by restricting β-catenin from entering the nucleus to inhibit cell proliferation.
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Affiliation(s)
- Zisen Jia
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China
| | - Minlin Yang
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China
| | - Yanchun Zhao
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China
| | - Xiaoying Li
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China
| | - Ciqing Yang
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China
| | - Liang Qiao
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China
| | - Han Li
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China.,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China
| | - Jiang Du
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China.,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China.,School of Medical Engineering, Xinxiang Medical University, Xinxiang, China
| | - Juntang Lin
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China. .,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China. .,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China. .,School of Medical Engineering, Xinxiang Medical University, Xinxiang, China.
| | - Lihong Guan
- School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China. .,Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, China. .,Henan Joint International Research Laboratory of Stem Cell Medicine, Stem Cell and Biotherapy Engineering Research Center of Henan, Xinxiang, China.
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30
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Girish V, Lakhani AA, Scaduto CM, Thompson SL, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Lukow DA, Yuan ML, Kandikuppa PK, Stevens EC, Lee SN, Salovska B, Li W, Smith JC, Taylor AM, Martienssen RA, Liu Y, Sun R, Sheltzer JM. Oncogene-like addiction to aneuploidy in human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523344. [PMID: 36711674 PMCID: PMC9882055 DOI: 10.1101/2023.01.09.523344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Most cancers exhibit aneuploidy, but its functional significance in tumor development is controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using CRISPR Targeting), a set of chromosome engineering tools that allow us to eliminate specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies, and we demonstrate that trisomy of chromosome 1q is required for malignant growth in cancers harboring this alteration. Mechanistically, gaining chromosome 1q increases the expression of MDM4 and suppresses TP53 signaling, and we show that TP53 mutations are mutually-exclusive with 1q aneuploidy in human cancers. Thus, specific aneuploidies play essential roles in tumorigenesis, raising the possibility that targeting these "aneuploidy addictions" could represent a novel approach for cancer treatment.
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Affiliation(s)
- Vishruth Girish
- Yale University School of Medicine, New Haven, CT 06511
- Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | | | | | | | | | | | | | - Monet Lou Yuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | | | | | - Sophia N. Lee
- Yale University School of Medicine, New Haven, CT 06511
| | | | - Wenxue Li
- Yale University School of Medicine, New Haven, CT 06511
| | - Joan C. Smith
- Yale University School of Medicine, New Haven, CT 06511
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yansheng Liu
- Yale University School of Medicine, New Haven, CT 06511
| | - Ruping Sun
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
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31
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Maranda V, Zhang Y, Vizeacoumar FS, Freywald A, Vizeacoumar FJ. A CRISPR Platform for Targeted In Vivo Screens. Methods Mol Biol 2023; 2614:397-409. [PMID: 36587138 DOI: 10.1007/978-1-0716-2914-7_24] [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] [Indexed: 01/02/2023]
Abstract
Large-scale genetic screens are becoming increasingly used as powerful tools to query the genome to identify therapeutic targets in cancer. The advent of the CRISPR technology has revolutionized the effectiveness of these screens and has made it possible to carry out loss-of-function screens to identify cancer-specific genetic interactions. Such loss-of-function screens can be performed in silico, in vitro, and in vivo, depending on the scale of the screen, as well as research questions to be answered. Performing screens in vivo has its challenges but also advantages, providing opportunities to study the tumor microenvironment and cancer immunity. In this chapter, we present a procedural framework and associated notes for conducting in vivo CRISPR knockout screens in cancer models to study cancer biology, anti-tumor immune responses, tumor microenvironment, and predicting treatment responses.
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Affiliation(s)
- Vincent Maranda
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Yue Zhang
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | | | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
| | - Franco J Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
- Cancer Research Department, Saskatchewan Cancer Agency, Saskatoon, Canada.
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32
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Bahrami-Nejad Z, Zhang ZB, Tholen S, Sharma S, Rabiee A, Zhao ML, Kraemer FB, Teruel MN. Early enforcement of cell identity by a functional component of the terminally differentiated state. PLoS Biol 2022; 20:e3001900. [PMID: 36469503 PMCID: PMC9721491 DOI: 10.1371/journal.pbio.3001900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
How progenitor cells can attain a distinct differentiated cell identity is a challenging problem given the fluctuating signaling environment in which cells exist and that critical transcription factors are often not unique to a differentiation process. Here, we test the hypothesis that a unique differentiated cell identity can result from a core component of the differentiated state doubling up as a signaling protein that also drives differentiation. Using live single-cell imaging in the adipocyte differentiation system, we show that progenitor fat cells (preadipocytes) can only commit to terminally differentiate after up-regulating FABP4, a lipid buffer that is highly enriched in mature adipocytes. Upon induction of adipogenesis in mouse preadipocyte cells, we show that after a long delay, cells first abruptly start to engage a positive feedback between CEBPA and PPARG before then engaging, after a second delay, a positive feedback between FABP4 and PPARG. These sequential positive feedbacks both need to engage in order to drive PPARG levels past the threshold for irreversible differentiation. In the last step before commitment, PPARG transcriptionally increases FABP4 expression while fatty acid-loaded FABP4 increases PPARG activity. Together, our study suggests a control principle for robust cell identity whereby a core component of the differentiated state also promotes differentiation from its own progenitor state.
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Affiliation(s)
- Zahra Bahrami-Nejad
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Zhi-Bo Zhang
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
- Department of Biochemistry and the Drukier Institute for Children’s Health, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
| | - Stefan Tholen
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Sanjeev Sharma
- Department of Biochemistry and the Drukier Institute for Children’s Health, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
| | - Atefeh Rabiee
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, California, United States of America
| | - Michael L. Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Fredric B. Kraemer
- Department of Medicine/Division of Endocrinology, Stanford University, Stanford, California, United States of America
- VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Mary N. Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
- Department of Biochemistry and the Drukier Institute for Children’s Health, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, United States of America
- Weill Center for Metabolic Health, Division of Endocrinology, Diabetes & Metabolism, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
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33
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Holcomb EA, Pearson AN, Jungles KM, Tate A, James J, Jiang L, Huber AK, Green MD. High-content CRISPR screening in tumor immunology. Front Immunol 2022; 13:1041451. [PMID: 36479127 PMCID: PMC9721350 DOI: 10.3389/fimmu.2022.1041451] [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: 09/10/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
CRISPR screening is a powerful tool that links specific genetic alterations to corresponding phenotypes, thus allowing for high-throughput identification of novel gene functions. Pooled CRISPR screens have enabled discovery of innate and adaptive immune response regulators in the setting of viral infection and cancer. Emerging methods couple pooled CRISPR screens with parallel high-content readouts at the transcriptomic, epigenetic, proteomic, and optical levels. These approaches are illuminating cancer immune evasion mechanisms as well as nominating novel targets that augment T cell activation, increase T cell infiltration into tumors, and promote enhanced T cell cytotoxicity. This review details recent methodological advances in high-content CRISPR screens and highlights the impact this technology is having on tumor immunology.
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Affiliation(s)
- Erin A. Holcomb
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Ashley N. Pearson
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Kassidy M. Jungles
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Pharmacology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Akshay Tate
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jadyn James
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Long Jiang
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Amanda K. Huber
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Michael D. Green
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
- Department of Microbiology and Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
- Department of Radiation Oncology, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, United States
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34
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Wildtype heterogeneity contributes to clonal variability in genome edited cells. Sci Rep 2022; 12:18211. [PMID: 36307508 PMCID: PMC9616811 DOI: 10.1038/s41598-022-22885-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/20/2022] [Indexed: 12/31/2022] Open
Abstract
Genome editing tools such as CRISPR/Cas9 enable the rapid and precise manipulation of genomes. CRISPR-based genome editing has greatly simplified the study of gene function in cell lines, but its widespread use has also highlighted challenges of reproducibility. Phenotypic variability among different knockout clones of the same gene is a common problem confounding the establishment of robust genotype-phenotype correlations. Optimized genome editing protocols to enhance reproducibility include measures to reduce off-target effects. However, even if current state-of-the-art protocols are applied phenotypic variability is frequently observed. Here we identify heterogeneity of wild-type cells as an important and often neglected confounding factor in genome-editing experiments. We demonstrate that isolation of individual wild-type clones from an apparently homogenous stable cell line uncovers significant phenotypic differences between clones. Strikingly, we observe hundreds of differentially regulated transcripts (477 up- and 306 downregulated) when comparing two populations of wild-type cells. Furthermore, we show a variety of cellular and biochemical alterations in different wild-type clones in a range that is commonly interpreted as biologically relevant in genome-edited cells. Heterogeneity of wild-type cells thus contributes to variability in genome-edited cells when these are generated through isolation of clones. We show that the generation of monoclonal isogenic wild-type cells prior to genomic manipulation reduces phenotypic variability. We therefore propose to generate matched isogenic control cells prior to genome editing to increase reproducibility.
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35
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Hernandez D, Walsh S, Saavedra Sanchez L, Dickinson MS, Coers J. Interferon-Inducible E3 Ligase RNF213 Facilitates Host-Protective Linear and K63-Linked Ubiquitylation of Toxoplasma gondii Parasitophorous Vacuoles. mBio 2022; 13:e0188822. [PMID: 36154443 PMCID: PMC9601232 DOI: 10.1128/mbio.01888-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular protozoan pathogen Toxoplasma gondii infects a wide range of vertebrate hosts and frequently causes zoonotic infections in humans. Whereas infected immunocompetent individuals typically remain asymptomatic, toxoplasmosis in immunocompromised individuals can manifest as a severe, potentially lethal disease, and congenital Toxoplasma infections are associated with adverse pregnancy outcomes. The protective immune response of healthy individuals involves the production of lymphocyte-derived cytokines such as interferon gamma (IFN-γ), which elicits cell-autonomous immunity in host cells. IFN-γ-inducible antiparasitic defense programs comprise nutritional immunity, the production of noxious gases, and the ubiquitylation of the Toxoplasma-containing parasitophorous vacuole (PV). PV ubiquitylation prompts the recruitment of host defense proteins to the PV and the consequential execution of antimicrobial effector programs, which reduce parasitic burden. However, the ubiquitin E3 ligase orchestrating these events has remained unknown. Here, we demonstrate that the IFN-γ-inducible E3 ligase RNF213 translocates to Toxoplasma PVs and facilitates PV ubiquitylation in human cells. Toxoplasma PVs become decorated with linear and K63-linked ubiquitin and recruit ubiquitin adaptor proteins in a process that is RNF213 dependent but independent of the linear ubiquitin chain assembly complex (LUBAC). IFN-γ priming fails to restrict Toxoplasma growth in cells lacking RNF213 expression, thus identifying RNF213 as a potent executioner of ubiquitylation-driven antiparasitic host defense. IMPORTANCE Globally, approximately one out of three people become infected with the obligate intracellular parasite Toxoplasma. These infections are typically asymptomatic but can cause severe disease and mortality in immunocompromised individuals. Infections can also be passed on from mother to fetus during pregnancy, potentially causing miscarriage or stillbirth. Therefore, toxoplasmosis constitutes a substantial public health burden. A better understanding of mechanisms by which healthy individuals control Toxoplasma infections could provide roadmaps toward novel therapies for vulnerable groups. Our work reveals a fundamental mechanism controlling intracellular Toxoplasma infections. Cytokines produced during Toxoplasma infections instruct human cells to produce the enzyme RNF213. We find that RNF213 labels intracellular vacuoles containing Toxoplasma with the small protein ubiquitin, which functions as an "eat-me" signal, attracting antimicrobial defense programs to fight off infection. Our work therefore identified a novel antiparasitic protein orchestrating a central aspect of the human immune response to Toxoplasma.
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Affiliation(s)
- Dulcemaria Hernandez
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Stephen Walsh
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Luz Saavedra Sanchez
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Mary S. Dickinson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
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36
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Bernhard P, Feilen T, Rogg M, Fröhlich K, Cosenza-Contreras M, Hause F, Schell C, Schilling O. Proteome alterations during clonal isolation of established human pancreatic cancer cell lines. Cell Mol Life Sci 2022; 79:561. [PMID: 36271971 PMCID: PMC9587952 DOI: 10.1007/s00018-022-04584-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022]
Abstract
Clonal isolation is an integral step of numerous workflows in genome editing and cell engineering. It comprises the isolation of a single progenitor cell from a defined cell line population with subsequent expansion to obtain a monoclonal cell population. This process is associated with transient loss of cell–cell contacts and absence of a multicellular microenvironment. Previous studies have revealed transcriptomic changes upon clonal isolation with cell line specific extent. Since transcriptome alterations are only partially reflected on the proteome level, we sought to investigate the impact of clonal isolation on the cellular proteome to a depth of > 6000 proteins in three established pancreatic cancer cell lines. We show that clonal isolation does have an impact on the cellular proteome, however, with cell line specific extent, affecting different biological processes, and also depending on the isolation method. We demonstrate a different impact of clonal isolation on mesenchymal- and epithelial-derived cell lines mainly affecting cell proliferation, metabolism, cell adhesion and cellular stress. The results bear relevance to the field of genomic editing and cell engineering and highlight the need to consider the impact of clonal isolation when interpreting data stemming from experiments that include this step.
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Affiliation(s)
- P Bernhard
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - T Feilen
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - M Rogg
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany
| | - K Fröhlich
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - M Cosenza-Contreras
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - F Hause
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany
| | - C Schell
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - O Schilling
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Str. 115A, 79106, Freiburg, Germany. .,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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37
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Roy IM, Anu P, Zaunz S, Reddi S, Giri AM, Sankar RS, Schouteden S, Huelsken J, Verfaillie CM, Khurana S. Inhibition of SRC-mediated integrin signaling in bone marrow niche enhances hematopoietic stem cell function. iScience 2022; 25:105171. [PMID: 36204266 PMCID: PMC9530850 DOI: 10.1016/j.isci.2022.105171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 07/13/2022] [Accepted: 09/16/2022] [Indexed: 11/20/2022] Open
Abstract
Interaction with microenvironmental factors is crucial for the regulation of hematopoietic stem cell (HSC) function. Stroma derived factor (SDF)-1α supports HSCs in the quiescent state and is central to the homing of transplanted HSCs. Here, we show that integrin signaling regulates Sdf-1α expression transcriptionally. Systemic deletion of Periostin, an Integrin-αv ligand, showed increased expression of Sdf-1α in bone marrow (BM) niche. Pharmacological inhibition or CRISPR-Cas9-mediated deletion of SRC, resulted in a similar increase in the chemokine expression in vitro. Importantly, systemic SRC-inhibition led to increase in SDF-1α levels in BM plasma. This resulted in a robust increase (14.05 ± 1.22% to 29.11 ± 0.69%) in the homing efficiency of transplanted HSCs. In addition, we observed enhancement in the recovery of blood cell counts following radiation injury, indicating an enhanced hematopoietic function. These results establish a role of SRC-mediated integrin signaling in the transcriptional regulation of Sdf-1α. This mechanism could be harnessed further to improve the hematopoietic function.
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Affiliation(s)
- Irene Mariam Roy
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
| | - P.V. Anu
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
| | | | - Srinu Reddi
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
| | - Aravind M. Giri
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
| | - Rithika Saroj Sankar
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
| | | | - Joerg Huelsken
- École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | | | - Satish Khurana
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
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38
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Zhai LM, Zhao Y, Xiao RL, Zhang SQ, Tian BH, Li XX, Zhang R, Ma RS, Liang HX. Nuclear-targeted carbon quantum dot mediated CRISPR/Cas9 delivery for fluorescence visualization and efficient editing. NANOSCALE 2022; 14:14645-14660. [PMID: 36165075 DOI: 10.1039/d2nr04281a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nuclear targeted delivery has great potential in improving the efficiency of non-viral carrier mediated genome editing. However, direct and efficient delivery of CRISPR/Cas9 plasmid into the nucleus remains a challenge. In this study, a nuclear targeted gene delivery platform based on fluorescent carbon quantum dots (CQDs) was developed. Polyethylenimine (PEI) and polyethylene glycol (PEG) synergistically passivated the surface of CQDs, providing an excitation-independent green-emitting fluorescent CQDs-PEI-PEG conjugate (CQDs-PP) with an ultra-small size and positive surface charge. Here we show that CQDs-PP could bind CRISPR/Cas9 plasmid to form a nano-complex by electrostatic attraction, which can bypass lysosomes and enter the nucleus by passive diffusion, and thereby improve the transfection efficiency. Also, CQDs-PP could deliver CRISPR/Cas9 plasmid into HeLa cells, resulting in the insertion/deletion mutation of the target EFHD1 gene. More importantly, CQDs-PP exhibited a considerably higher gene editing efficiency as well as comparable or lower cytotoxicity relative to Lipo2000 and PEI-passivated CQDs-PEI (CQDs-P). Thus, the nuclear-targeted CQDs-PP is expected to constitute an efficient CRISPR/Cas9 delivery carrier in vitro with imaging-trackable ability.
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Affiliation(s)
- Li-Min Zhai
- College of Biomedical Engineering, Taiyuan University of Technology, Jinzhong, 030600, China.
- School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yan Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Rui-Lin Xiao
- School of Ecology, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Shi-Quan Zhang
- College of Biomedical Engineering, Taiyuan University of Technology, Jinzhong, 030600, China.
| | - Bao-Hua Tian
- School of Ecology, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Xin-Xin Li
- School of Ecology, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Rong Zhang
- Shanxi Eye Hospital Affiliated to Shanxi Medical University, Taiyuan, 030002, China
| | - Ri-Sheng Ma
- College of Biomedical Engineering, Taiyuan University of Technology, Jinzhong, 030600, China.
| | - Hai-Xia Liang
- College of Biomedical Engineering, Taiyuan University of Technology, Jinzhong, 030600, China.
- School of Ecology, Taiyuan University of Technology, Taiyuan, 030024, China
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Marker-free co-selection for successive rounds of prime editing in human cells. Nat Commun 2022; 13:5909. [PMID: 36207338 PMCID: PMC9546848 DOI: 10.1038/s41467-022-33669-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies. Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. Here the authors develop a co-selection strategy to facilitate prime editing in human cells and provide design principles to prevent the formation of undesired editing byproducts at the target site.
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40
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Banicka V, Martens MC, Panzer R, Schrama D, Emmert S, Boeckmann L, Thiem A. Homozygous CRISPR/Cas9 Knockout Generated a Novel Functionally Active Exon 1 Skipping XPA Variant in Melanoma Cells. Int J Mol Sci 2022; 23:ijms231911649. [PMID: 36232946 PMCID: PMC9569948 DOI: 10.3390/ijms231911649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022] Open
Abstract
Defects in DNA repair pathways have been associated with an improved response to immune checkpoint inhibition (ICI). In particular, patients with the nucleotide excision repair (NER) defect disease Xeroderma pigmentosum (XP) responded impressively well to ICI treatment. Recently, in melanoma patients, pretherapeutic XP gene expression was predictive for anti-programmed cell death-1 (PD-1) ICI response. The underlying mechanisms of this finding are still to be revealed. Therefore, we used CRISPR/Cas9 to disrupt XPA in A375 melanoma cells. The resulting subclonal cell lines were investigated by Sanger sequencing. Based on their genetic sequence, candidates from XPA exon 1 and 2 were selected and further analyzed by immunoblotting, immunofluorescence, HCR and MTT assays. In XPA exon 1, we established a homozygous (c.19delG; p.A7Lfs*8) and a compound heterozygous (c.19delG/c.19_20insG; p.A7Lfs*8/p.A7Gfs*55) cell line. In XPA exon 2, we generated a compound heterozygous mutated cell line (c.206_208delTTG/c.208_209delGA; p.I69_D70delinsN/p.D70Hfs*31). The better performance of the homozygous than the heterozygous mutated exon 1 cells in DNA damage repair (HCR) and post-UV-C cell survival (MTT), was associated with the expression of a novel XPA protein variant. The results of our study serve as the fundamental basis for the investigation of the immunological consequences of XPA disruption in melanoma.
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Affiliation(s)
- Veronika Banicka
- Clinic and Policlinic for Dermatology and Venereology, University Medical Center Rostock, 18057 Rostock, Germany
| | - Marie Christine Martens
- Clinic and Policlinic for Dermatology and Venereology, University Medical Center Rostock, 18057 Rostock, Germany
| | - Rüdiger Panzer
- Clinic and Policlinic for Dermatology and Venereology, University Medical Center Rostock, 18057 Rostock, Germany
| | - David Schrama
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Steffen Emmert
- Clinic and Policlinic for Dermatology and Venereology, University Medical Center Rostock, 18057 Rostock, Germany
| | - Lars Boeckmann
- Clinic and Policlinic for Dermatology and Venereology, University Medical Center Rostock, 18057 Rostock, Germany
| | - Alexander Thiem
- Clinic and Policlinic for Dermatology and Venereology, University Medical Center Rostock, 18057 Rostock, Germany
- Correspondence:
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41
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Ze Y, Wang R, Deng H, Zhou Z, Chen X, Huang L, Yao Y. Three-dimensional bioprinting: A cutting-edge tool for designing and fabricating engineered living materials. BIOMATERIALS ADVANCES 2022; 140:213053. [PMID: 35964390 DOI: 10.1016/j.bioadv.2022.213053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/12/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The design of engineered living materials (ELMs) is an emerging field developed from synthetic biology and materials science principles. ELMs are multi-scale bulk materials that combine the properties of self-healing and organism adaptability with the designed physicochemical or mechanical properties for functional applications in various fields, including therapy, electronics, and architecture. Among the many ELM design and manufacturing methods, three-dimensional (3D) bioprinting stands out for its precise control over the structure of the fabricated constructs and the spatial distribution of cells. In this review, we summarize the progress in the field, cell type and material selection, and the latest applications of 3D bioprinting to manufacture ELMs, as well as their advantages and limitations, hoping to deepen our understanding and provide new insights into ELM design. We believe that 3D bioprinting will become an important development direction and provide more contributions to this field.
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Affiliation(s)
- Yiting Ze
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ruixin Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Hanzhi Deng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zheqing Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoju Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Linyang Huang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yang Yao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
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42
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Anaganti N, Chattopadhyay A, Poirier JT, Hussain MM. Generation of hepatoma cell lines deficient in microsomal triglyceride transfer protein. J Lipid Res 2022; 63:100257. [PMID: 35931202 PMCID: PMC9405095 DOI: 10.1016/j.jlr.2022.100257] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 01/05/2023] Open
Abstract
The microsomal triglyceride transfer protein (MTP) is essential for the secretion of apolipoprotein B (apoB)48- and apoB100-containing lipoproteins in the intestine and liver, respectively. Loss of function mutations in MTP cause abetalipoproteinemia. Heterologous cells are used to evaluate the function of MTP in apoB secretion to avoid background MTP activity in liver and intestine-derived cells. However, these systems are not suitable to study the role of MTP in the secretion of apoB100-containing lipoproteins, as expression of a large apoB100 peptide using plasmids is difficult. Here, we report a new cell culture model amenable for studying the role of different MTP mutations on apoB100 secretion. The endogenous MTTP gene was ablated in human hepatoma Huh-7 cells using single guide RNA and RNA-guided clustered regularly interspaced short palindromic repeats-associated sequence 9 ribonucleoprotein complexes. We successfully established three different clones that did not express any detectable MTTP mRNA or MTP protein or activity. These cells were defective in secreting apoB-containing lipoproteins and accumulated lipids. Furthermore, we show that transfection of these cells with plasmids expressing human MTTP cDNA resulted in the expression of MTP protein, restoration of triglyceride transfer activity, and secretion of apoB100. Thus, these new cells can be valuable tools for studying structure-function of MTP, roles of different missense mutations in various lipid transfer activities of MTP, and their ability to support apoB100 secretion, compensatory changes associated with loss of MTP, and in the identification of novel proteins that may require MTP for their synthesis and secretion.
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Affiliation(s)
- Narasimha Anaganti
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, USA
| | - Atrayee Chattopadhyay
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, USA
| | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - M Mahmood Hussain
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, USA; VA New York Harbor Healthcare System, Brooklyn, NY, USA.
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43
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Arya SK, Goodman CL, Stanley D, Palli SR. A database of crop pest cell lines. In Vitro Cell Dev Biol Anim 2022; 58:719-757. [PMID: 35994130 DOI: 10.1007/s11626-022-00710-w] [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: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 11/27/2022]
Abstract
We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that were developed from agricultural pests. Cell line information has been primarily obtained from previous compilations of insect cell lines. We conducted in-depth Internet literature searches and drew on Internet sources such as the Cellosaurus database (https://web.expasy.org/cellosaurus/), and inventories from cell line depositories. Here, we report on a new database of insect cell lines, which covers 719 cell lines from 86 species. We have not included cell lines developed from Drosophila because they are already known from published databases, such as https://dgrc.bio.indiana.edu/cells/Catalog. We provide the designation, tissue and species of origin, cell line developer, unique characteristics, its use in various applications, publications, and patents, and, when known, insect virus susceptibility. This information has been assembled and organized into a searchable database available at the link https://entomology.ca.uky.edu/aginsectcellsdatabase which will be updated on an ongoing basis.
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Affiliation(s)
- Surjeet Kumar Arya
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Cynthia L Goodman
- Biological Control of Insects Research Laboratory, United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri, 65203, USA
| | - David Stanley
- Biological Control of Insects Research Laboratory, United States Department of Agriculture, Agricultural Research Service, Columbia, Missouri, 65203, USA
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA.
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44
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Han Z, Madhavan BK, Kaymak S, Nawroth P, Kumar V. A Fast and Reliable Method to Generate Pure, Single Cell-derived Clones of Mammalian Cells. Bio Protoc 2022; 12:e4490. [PMID: 36505273 PMCID: PMC9712125 DOI: 10.21769/bioprotoc.4490] [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: 04/19/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 12/29/2022] Open
Abstract
Stable cell cloning is an essential aspect of biological research. All advanced genome editing tools rely heavily on stable, pure, single cell-derived clones of genetically engineered cells. For years, researchers have depended on single-cell dilutions seeded in 96- or 192-well plates, followed by microscopic exclusion of the wells seeded with more than or without a cell. This method is not just laborious, time-consuming, and uneconomical but also liable to unintentional error in identifying the wells seeded with a single cell. All these disadvantages may increase the time needed to generate a stable clone. Here, we report an easy-to-follow and straightforward method to conveniently create pure, stable clones in less than half the time traditionally required. Our approach utilizes cloning cylinders with non-toxic tissue-tek gel, commonly used for immobilizing tissues for sectioning, followed by trypsinization and screening of the genome-edited clones. Our approach uses minimal cell handling steps, thus decreasing the time invested in generating the pure clones effortlessly and economically. Graphical abstract: A schematic comparison showing the traditional dilution cloning and the method described here. Here, a well-separated colony (in the green box) must be preferred over the colonies not well separated (in the red box).
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Affiliation(s)
- Zhe Han
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Bindhu K. Madhavan
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Serap Kaymak
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Peter Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
,
Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Varun Kumar
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
,
European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
,
Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
,
*For correspondence:
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45
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Wang Y, Huang C, Zhao W. Recent advances of the biological and biomedical applications of CRISPR/Cas systems. Mol Biol Rep 2022; 49:7087-7100. [PMID: 35705772 PMCID: PMC9199458 DOI: 10.1007/s11033-022-07519-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
Abstract
The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated endonuclease (Cas) system, referred to as CRISPR/Cas system, has attracted significant interest in scientific community due to its great potential in translating into versatile therapeutic tools in biomedical field. For instance, a myriad of studies has demonstrated that the CRISPR/Cas system is capable of detecting various types of viruses, killing antibiotic-resistant bacteria, treating inherited genetic diseases, and providing new strategies for cancer therapy. Furthermore, CRISPR/Cas systems are also exploited as research tools such as genome engineering tool that allows researchers to interrogate the biological roles of unexplored genes or uncover novel functions of known genes. Additionally, the CRISPR/Cas system has been employed to edit the genome of a wide range of eukaryotic, prokaryotic organisms and experimental models, including but not limited to mammalian cells, mice, zebrafish, plants, yeast, and Escherichia coli. The present review mainly focuses on summarizing recent discoveries regarding the type II CRISPR/Cas9 and type VI CRISPR/Cas13a systems to give researchers a glimpse of their potential applications in the biological and biomedical field.
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Affiliation(s)
- Yaya Wang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China.
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China.
| | - Chun Huang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China
| | - Weiqin Zhao
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China
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46
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George AJ, Dong B, Lail H, Gomez M, Hoffiz YC, Ware CB, Fang N, Murphy AZ, Hrabovszky E, Wanders D, Mabb AM. The E3 ubiquitin ligase RNF216/TRIAD3 is a key coordinator of the hypothalamic-pituitary-gonadal axis. iScience 2022; 25:104386. [PMID: 35620441 PMCID: PMC9126796 DOI: 10.1016/j.isci.2022.104386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 03/25/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022] Open
Abstract
Recessive mutations in RNF216/TRIAD3 cause Gordon Holmes syndrome (GHS), in which dysfunction of the hypothalamic-pituitary-gonadal (HPG) axis and neurodegeneration are thought to be core phenotypes. We knocked out Rnf216/Triad3 in a gonadotropin-releasing hormone (GnRH) hypothalamic cell line. Rnf216/Triad3 knockout (KO) cells had decreased steady-state GnRH and calcium transients. Rnf216/Triad3 KO adult mice had reductions in GnRH neuron soma size and GnRH production without changes in neuron densities. In addition, KO male mice had smaller testicular volumes that were accompanied by an abnormal release of inhibin B and follicle-stimulating hormone, whereas KO females exhibited irregular estrous cycling. KO males, but not females, had reactive microglia in the hypothalamus. Conditional deletion of Rnf216/Triad3 in neural stem cells caused abnormal microglia expression in males, but reproductive function remained unaffected. Our findings show that dysfunction of RNF216/TRIAD3 affects the HPG axis and microglia in a region- and sex-dependent manner, implicating sex-specific therapeutic interventions for GHS. Rnf216/Triad3 controls GnRH production and intrinsic hypothalamic cell activity Rnf216/Triad3 knockout male mice have greater reproductive impairments than females Rnf216/Triad3 controls the HPG axis differently in males and females Rnf216/Triad3 knockout male mice have reactive microglia in the hypothalamus
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47
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Lin SC, Haga K, Zeng XL, Estes MK. Generation of CRISPR-Cas9-mediated genetic knockout human intestinal tissue-derived enteroid lines by lentivirus transduction and single-cell cloning. Nat Protoc 2022; 17:1004-1027. [PMID: 35197604 PMCID: PMC9059808 DOI: 10.1038/s41596-021-00669-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022]
Abstract
Human intestinal tissue-derived enteroids (HIEs; also called organoids) are a powerful ex vivo model for gastrointestinal research. Genetic modification of these nontransformed cultures allows new insights into gene function and biological processes involved in intestinal diseases as well as gastrointestinal and donor segment-specific function. Here we provide a detailed technical pipeline and protocol for using the CRISPR-Cas9 genome editing system to knock out a gene of interest specifically in HIEs by lentiviral transduction and single-cell cloning. This protocol differs from a previously published alternative using electroporation of human colonoids to deliver piggyback transposons or CRISPR-Cas9 constructs, as this protocol uses a modified, fused LentiCRISPRv2-small-guiding RNA to express Cas9 and small-guiding RNA in a lentivirus. The protocol also includes the steps of gene delivery and subsequent single-cell cloning of the knockout cells as well as verification of clones and sequence identification of the mutation sites to establish knockout clones. An overview flowchart, step-by-step guidelines and troubleshooting suggestions are provided to aid the researcher in obtaining the genetic knockout HIE line within 2-3 months. In this protocol, we further describe how to use HIEs as an ex vivo model to assess host restriction factors for viral replication (using human norovirus replication as an example) by knocking out host attachment factors or innate immunity genes. Other applications are discussed to broaden the utility of this system, for example, to generate knockin or conditional knockout HIE lines to investigate the function of essential genes in many biological processes including other types of organoids.
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Affiliation(s)
- Shih-Ching Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kei Haga
- Department of Infection Control and Immunology, Kitasato University, Tokyo, Japan
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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48
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Heath NG, O’Geen H, Halmai NB, Corn JE, Segal DJ. Imaging Unique DNA Sequences in Individual Cells Using a CRISPR-Cas9-Based, Split Luciferase Biosensor. Front Genome Ed 2022; 4:867390. [PMID: 35403097 PMCID: PMC8990833 DOI: 10.3389/fgeed.2022.867390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
An extensive arsenal of biosensing tools has been developed based on the clustered regularly interspaced short palindromic repeat (CRISPR) platform, including those that detect specific DNA sequences both in vitro and in live cells. To date, DNA imaging approaches have traditionally used full fluorescent reporter-based fusion probes. Such “always-on” probes differentiate poorly between bound and unbound probe and are unable to sensitively detect unique copies of a target sequence in individual cells. Herein we describe a DNA biosensor that provides a sensitive readout for such low-copy DNA sequences through proximity-mediated reassembly of two independently optimized fragments of NanoLuc luciferase (NLuc), a small, bright luminescent reporter. Applying this “turn-on” probe in live cells, we demonstrate an application not easily achieved by fluorescent reporter-based probes, detection of individual endogenous genomic loci using standard epifluorescence microscopy. This approach could enable detection of gene edits during ex vivo editing procedures and should be a useful platform for many other live cell DNA biosensing applications.
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Affiliation(s)
- Nicholas G. Heath
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Nicole B. Halmai
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Biology, ETH, Zürich, Switzerland
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: David J. Segal,
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49
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Mamun MMA, Bukhari I. Fast-Track and Integration-Free Method of Genome Editing by CRISPR/Cas9 in Murine Pluripotent Stem Cells. Front Cell Dev Biol 2022; 10:819906. [PMID: 35372368 PMCID: PMC8972586 DOI: 10.3389/fcell.2022.819906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
The CRISPR/Cas9 system has unprecedentedly revolutionized genome-editing technology, which is being successfully applied virtually in all branches of biological sciences. Although much success has been attained in gene manipulation, still the majority of methods are laborious and non-integration-free, and require prolonged time for the expansion of mutant cell pools/clones, while fewer cells exhibit functional knockout efficiency. To overcome these obstacles, here, we describe an efficient, inexpensive, integration-free, and rapid one-step protocol for CRISPR/Cas9-assisted gene knockout in murine pluripotent stem cells (PSCs). Our protocol has streamlined both the liposome-based transfection system and screening strategy to work more efficiently with small numbers of PSCs (∼2.0 × 104 cells) and to minimize laborious steps of lentiviral packaging, transduction, and single-clone passaging. In our method, around 90% (CI = 95%, 79.5230%-100%) of PSC colonies harbored functional knockout in the context of protein expression. Therefore, the current protocol is technically feasible, time-saving, and highly efficient for genome editing in pluripotent stem cells.
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Affiliation(s)
- Md Mahfuz Al Mamun
- Translational Research Institute, Henan Provincial People’s Hospital, Henan Key Laboratory of Stem Cell Differentiation and Modification, School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Ihtisham Bukhari
- Translational Research Institute, Henan Provincial People’s Hospital, Henan Key Laboratory of Stem Cell Differentiation and Modification, School of Clinical Medicine, Henan University, Zhengzhou, China,Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Ihtisham Bukhari,
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50
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Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022; 19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
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Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Rebecca T Beuschel
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, MA, USA
| | | | - Julia Hatler
- Antibody Development Department, Bio-Techne, Minneapolis, MN, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA
| | - Josh Croteau
- Department of Applications Science, BioLegend, San Diego, CA, USA
| | | | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - R Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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