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Daley BR, Sealover NE, Sheffels E, Hughes JM, Gerlach D, Hofmann MH, Kostyrko K, Mair B, Linke A, Beckley Z, Frank A, Dalgard C, Kortum RL. SOS1 inhibition enhances the efficacy of and delays resistance to G12C inhibitors in lung adenocarcinoma. bioRxiv 2023:2023.12.07.570642. [PMID: 38106234 PMCID: PMC10723384 DOI: 10.1101/2023.12.07.570642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Clinical effectiveness of KRAS G12C inhibitors (G12Cis) is limited both by intrinsic and acquired resistance, necessitating the development of combination approaches. We found that targeting proximal receptor tyrosine kinase (RTK) signaling using the SOS1 inhibitor (SOS1i) BI-3406 both enhanced the potency of and delayed resistance to G12Ci treatment, but the extent of SOS1i effectiveness was modulated by both SOS2 expression and the specific mutational landscape. SOS1i enhanced the efficacy of G12Ci and limited rebound RTK/ERK signaling to overcome intrinsic/adaptive resistance, but this effect was modulated by SOS2 protein levels. Survival of drug-tolerant persister (DTP) cells within the heterogeneous tumor population and/or acquired mutations that reactivate RTK/RAS signaling can lead to outgrowth of tumor initiating cells (TICs) that drive therapeutic resistance. G12Ci drug tolerant persister cells showed a 2-3-fold enrichment of TICs, suggesting that these could be a sanctuary population of G12Ci resistant cells. SOS1i re-sensitized DTPs to G12Ci and inhibited G12C-induced TIC enrichment. Co-mutation of the tumor suppressor KEAP1 limits the clinical effectiveness of G12Cis, and KEAP1 and STK11 deletion increased TIC frequency and accelerated the development of acquired resistance to G12Ci in situ. SOS1i both delayed acquired G12Ci resistance and limited the total number of resistant colonies regardless of KEAP1 and STK11 mutational status. These data suggest that SOS1i could be an effective strategy to both enhance G12Ci efficacy and prevent G12Ci resistance regardless of co-mutations.
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Affiliation(s)
- Brianna R Daley
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Nancy E Sealover
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Erin Sheffels
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Jacob M. Hughes
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | | | | | - Kaja Kostyrko
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Amanda Linke
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Zaria Beckley
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Andrew Frank
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, MD, USA
- Student Bioinformatics Initiative, Center for Military Precision Health, Uniformed Services University of the Health Sciences; Bethesda, MD, USA
| | - Clifton Dalgard
- The American Genome Center, Department of Anatomy, Cell Biology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Robert L Kortum
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
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Kostyrko K, Román M, Lee AG, Simpson DR, Dinh PT, Leung SG, Marini KD, Kelly MR, Broyde J, Califano A, Jackson PK, Sweet-Cordero EA. UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma. Nat Commun 2023; 14:3966. [PMID: 37407562 PMCID: PMC10322837 DOI: 10.1038/s41467-023-39591-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
KRAS is a frequent driver in lung cancer. To identify KRAS-specific vulnerabilities in lung cancer, we performed RNAi screens in primary spheroids derived from a Kras mutant mouse lung cancer model and discovered an epigenetic regulator Ubiquitin-like containing PHD and RING finger domains 1 (UHRF1). In human lung cancer models UHRF1 knock-out selectively impaired growth and induced apoptosis only in KRAS mutant cells. Genome-wide methylation and gene expression analysis of UHRF1-depleted KRAS mutant cells revealed global DNA hypomethylation leading to upregulation of tumor suppressor genes (TSGs). A focused CRISPR/Cas9 screen validated several of these TSGs as mediators of UHRF1-driven tumorigenesis. In vivo, UHRF1 knock-out inhibited tumor growth of KRAS-driven mouse lung cancer models. Finally, in lung cancer patients high UHRF1 expression is anti-correlated with TSG expression and predicts worse outcomes for patients with KRAS mutant tumors. These results nominate UHRF1 as a KRAS-specific vulnerability and potential target for therapeutic intervention.
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Affiliation(s)
- Kaja Kostyrko
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
| | - Marta Román
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Alex G Lee
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - David R Simpson
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Phuong T Dinh
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Stanley G Leung
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Kieren D Marini
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Marcus R Kelly
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua Broyde
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - E Alejandro Sweet-Cordero
- Division of Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
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Moreno MR, Kostyrko K, Herrington K, Bassik M, Jackson P, Sweet-Cordero A. Abstract 3920: Functional analysis of the role of RAP1GDS1 and RhoA in KRAS-driven lung adenocarcinoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
While KRAS is among the most frequently mutated oncogenes, our understanding of the mechanisms of KRAS-driven oncogenesis remains limited. A significant remaining gap is a lack of understanding of tissue-specific effectors of Ras activation and the role of specific KRAS mutations in determining downstream vulnerabilities. Previously, we used a combination of proteomics and CRISPR/Cas9 screens in human lung adenocarcinoma (LUAD) cells to identify a KRAS-specific vulnerability induced by the combined loss of RHOA and the long isoform of RAP1GDS1, suggesting a potentially novel approach for targeting KRAS-driven cancer. Here we use biochemical, proteomic, and genetic approaches to dissect the isoform-specific roles of RAP1GDS1 to elucidate its synthetic lethal interaction with RHOA in KRAS-driven LUAD.
We performed AP/MS in KRAS-mutant A549 cells using both the long (RAP1GDS1-607) and the short (RAP1GDS1-558) isoforms of RAP1GDS1 as bait to identify overlapping and isoform-specific RAP1GDS1 interactors. We enriched this analysis with orthologous datasets from DepMap, published protein-protein interaction (PPI) data and RAP1GDS1-specific prenylome. This comprehensive analysis identified a cluster of RAB GTPases, proteins involved in vesicular transport and lysosomal function, as specific interactors of RAP1GDS1-607. We subsequently used the proximity ligation assay (PLA) to confirm the direct interaction between RAP1GDS1-607 and two of the strongest interactors - RAB7A and RAB22A – according to the PPI data. We also depleted either or both RAP1GDS1 isoforms in cells expressing GFP-tagged RAB7A, RAB22A or KRAS and used live cell imaging to determine how loss of RAP1GDS1 changes their subcellular localization. We found that depletion of both RAP1GDS1 isoforms and, to a lesser extent, single loss of RAP1GDS1-607, significantly decreased KRAS localization at the plasma membrane. We also used PLA to confirm that RAP1GDS1-607 has a stronger interaction with KRAS compared to the short isoform. Moreover, we demonstrated that loss of the long RAP1GDS1 isoform significantly decreased the membrane localization levels of GTP-bound KRAS, compared to the control or RAP1GDS1-558 knock-down. Finally, to identify the molecular mechanism of R1G1/RhoA synthetic lethality with KRAS, we performed a Genome Wide-CRISPR screen in R1G1-607 and RhoA knock-out cells. We identified the strongest hits and designed a focused CRISPR library of approximately 400 genes to screen a larger panel of KRAS-mutant LUAD cell lines (H23, A549 and H358). The aim is to identify other genes that are synthetic lethal in combination with RhoA or R1G1-607 loss and genes that could mediate the lethal effect of their combined loss.
In conclusion, these data demonstrate a specific role of the long RAP1GDS1 isoform in the membrane-localization and activation of KRAS, which supports its role as a potential therapeutic target for KRAS mutant tumors.
Citation Format: Marta Roman Moreno, Kaja Kostyrko, Kari Herrington, Michael Bassik, Peter Jackson, Alejandro Sweet-Cordero. Functional analysis of the role of RAP1GDS1 and RhoA in KRAS-driven lung adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3920.
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Affiliation(s)
| | - Kaja Kostyrko
- 1UCSF - University of California San Francisco, San Francisco, CA
| | - Kari Herrington
- 1UCSF - University of California San Francisco, San Francisco, CA
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Thatikonda V, Lu H, Jurado S, Kostyrko K, Bristow CA, Bosch K, Feng N, Gao S, Gerlach D, Gmachl M, Lieb S, Jeschko A, Machado AA, Marszalek ED, Mahendra M, Jaeger PA, Sorokin A, Strauss S, Trapani F, Kopetz S, Vellano CP, Petronczki M, Kraut N, Heffernan TP, Marszalek JR, Pearson M, Waizenegger I, Hofmann MH. Combined KRAS G12C and SOS1 inhibition enhances and extends the anti-tumor response in KRAS G12C-driven cancers by addressing intrinsic and acquired resistance. bioRxiv 2023:2023.01.23.525210. [PMID: 36747713 PMCID: PMC9900819 DOI: 10.1101/2023.01.23.525210] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Efforts to improve the anti-tumor response to KRASG12C targeted therapy have benefited from leveraging combination approaches. Here, we compare the anti-tumor response induced by the SOS1-KRAS interaction inhibitor, BI-3406, combined with a KRASG12C inhibitor (KRASG12Ci) to those induced by KRASG12Ci alone or combined with SHP2 or EGFR inhibitors. In lung cancer and colorectal cancer (CRC) models, BI-3406 plus KRASG12Ci induces an anti-tumor response stronger than that observed with KRASG12Ci alone and comparable to those by the other combinations. This enhanced anti-tumor response is associated with a stronger and extended suppression of RAS-MAPK signaling. Importantly, BI-3406 plus KRASG12Ci treatment delays the emergence of acquired adagrasib resistance in both CRC and lung cancer models and is associated with re-establishment of anti-proliferative activity in KRASG12Ci-resistant CRC models. Our findings position KRASG12C plus SOS1 inhibition therapy as a promising strategy for treating both KRASG12C-mutated tumors as well as for addressing acquired resistance to KRASG12Ci.
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Affiliation(s)
| | - Hengyu Lu
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sabine Jurado
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Kaja Kostyrko
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Christopher A. Bristow
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karin Bosch
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Ningping Feng
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sisi Gao
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Annette A. Machado
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ethan D. Marszalek
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mikhila Mahendra
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Alexey Sorokin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher P. Vellano
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Timothy P. Heffernan
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph R. Marszalek
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) Platform, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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Kostyrko K, Hinkel M, Traexler P, Arnold D, Melo-Zainzinger G, Gerlach D, Ruzicka R, Jacob R, Baum A, Lu H, Vellano C, Marszalek J, Heffernan T, Tontsch-Grunt U, Hofmann M. MEKi-based combination strategies for targeting KRAS-driven cancer. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00945-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Kostyrko K, Sweet-Cordero EA. An Expanded Tool Kit for Modeling the Oncogenic Functions of KRAS. Cancer Discov 2020; 10:1626-1628. [DOI: 10.1158/2159-8290.cd-20-1221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Summary:
Zafra and colleagues developed new mouse models to study the role of specific KRAS mutations in pancreatic, lung, and colon cancer pathogenesis. Their studies clearly describe the distinct ability of these mutations to drive pathogenesis in a tissue-specific fashion.
See related article by Zafra et al., p. 1654.
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Affiliation(s)
- Kaja Kostyrko
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
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7
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Kelly MR, Kostyrko K, Han K, Mooney NA, Jeng EE, Spees K, Dinh PT, Abbott KL, Gwinn DM, Sweet-Cordero EA, Bassik MC, Jackson PK. Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities. Cancer Discov 2020; 10:1950-1967. [PMID: 32727735 PMCID: PMC7710624 DOI: 10.1158/2159-8290.cd-19-1274] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/08/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022]
Abstract
Activating mutations in RAS GTPases drive many cancers, but limited understanding of less-studied RAS interactors, and of the specific roles of different RAS interactor paralogs, continues to limit target discovery. We developed a multistage discovery and screening process to systematically identify genes conferring RAS-related susceptibilities in lung adenocarcinoma. Using affinity purification mass spectrometry, we generated a protein-protein interaction map of RAS interactors and pathway components containing hundreds of interactions. From this network, we constructed a CRISPR dual knockout library targeting 119 RAS-related genes that we screened for KRAS-dependent genetic interactions (GI). This approach identified new RAS effectors, including the adhesion controller RADIL and the endocytosis regulator RIN1, and >250 synthetic lethal GIs, including a potent KRAS-dependent interaction between RAP1GDS1 and RHOA. Many GIs link specific paralogs within and between gene families. These findings illustrate the power of multiomic approaches to uncover synthetic lethal combinations specific for hitherto untreatable cancer genotypes. SIGNIFICANCE: We establish a deep network of protein-protein and genetic interactions in the RAS pathway. Many interactions validated here demonstrate important specificities and redundancies among paralogous RAS regulators and effectors. By comparing synthetic lethal interactions across KRAS-dependent and KRAS-independent cell lines, we identify several new combination therapy targets for RAS-driven cancers.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Marcus R Kelly
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California.,Program in Cancer Biology, Stanford University School of Medicine, Stanford, California
| | - Kaja Kostyrko
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Kyuho Han
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California
| | - Edwin E Jeng
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Kaitlyn Spees
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Phuong T Dinh
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Keene L Abbott
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California
| | - Dana M Gwinn
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California.
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, California. .,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California. .,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
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Kostyrko K, Kelly M, Han K, Jeng E, Morgens D, Bassik M, Jackson P, Sweet-Cordero A. Abstract PR07: Combinatorial knockout of Rap1GDS1 and RhoA leads to lethality in KRAS-driven non-small cell lung cancer. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-pr07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Synthetic lethal-based approaches to targeting KRAS driven cancers have recently been receiving increasing attention. However, as KRAS activates multiple effector pathways, targeting single genes may not be sufficient to fully inhibit KRAS-driven oncogenesis. In addition, genome-wide screens can be limited by high noise and low signal. Furthermore, it is increasingly clear that standard screens based on 2D proliferation can miss critical phenotypes relevant to cancer biology. Therefore, we developed a multistage screening strategy that includes a) identification of KRAS-proximal protein-protein interaction (PPI) networks, b) targeted CRISPR-based screening for pairs of genes that together are synthetic lethal with KRAS, and c) validation in a 3D sphere system using both human and mouse NSCLC cells. We used affinity purification/mass spectrometry (AP/MS) to construct a detailed map of protein-protein interactions centered on KRAS. Based on this network, we designed a CRISPR/Cas9 library targeting pairwise combinations of 119 KRAS-interacting genes. We screened two KRAS-driven non-small cell lung cancer (NSCLC) cell lines (A549 and H23). This screen yielded a large number of gene pairs that synergistically impaired cell growth. We selected the 20 most promising targets for further screening in a panel of 5 KRAS-mutant and 4 KRAS wild-type NSCLC cell lines. From these screens we identified a KRAS-specific synergistic interaction between two genes—Rap1GDS1 and RhoA. Validation in 3D cultures in a panel of cell lines showed that combinatorial Rap1GDS1 and RhoA knockout selectively impairs sphere growth of KRAS-mutant NSCLC cells but has minimal effects on KRAS wild-type NSCLC cell lines or nontransformed lung cells. We demonstrate that this effect is primarily due to the induction of apoptosis. Rap1GDS1 has previously been reported to encode two different isoforms with distinct cellular functions. We observe that only one of the isoforms is involved in the mediation of the KRAS-dependent lethal effect. Current efforts are directed at elucidating the mechanistic basis for the isoform-specific combinatorial lethality between Rap1GDS1 and RhoA. Furthermore, we are actively exploring how to exploit this knowledge to define potential novel therapies for KRAS-driven cancer. Overall, we demonstrate that an integrated strategy combining proteomics, paired CRISPR screens and innovative 3D validation systems can identify novel synthetic lethal combinations. This approach may help identify novel synthetic lethal drug combinations for KRAS and other to-date undruggable oncogenes.
This abstract is also being presented as Poster A40.
Citation Format: Kaja Kostyrko, Marcus Kelly, Kyuho Han, Edwin Jeng, David Morgens, Michael Bassik, Peter Jackson, Alejandro Sweet-Cordero. Combinatorial knockout of Rap1GDS1 and RhoA leads to lethality in KRAS-driven non-small cell lung cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr PR07.
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Affiliation(s)
- Kaja Kostyrko
- 1University of California San Francisco, San Francisco, CA,
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Kelly M, Han K, Kostyrko K, Mooney N, Jeng E, Demeter J, Sweet-Cordero A, Bassik M, Jackson PK. Abstract B25: Combined proteomic and genetic interaction mapping reveals new Ras pathway effectors and regulators. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-b25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite intensive study, no drugs in clinical use specifically target KRAS-mutant tumors. Uncharacterized feedback pathways and unmapped compensatory pathways, including compensation among paralogs, hinder our ability to target Ras effector pathways, requiring a better catalogue of pathways upstream and downstream of Ras. We used tandem affinity purification of Kras, Hras and Nras, their activated alleles and key proteins with known regulatory (GEFs, GAPs) or effectors (Raf, RalGDS1, RIN1/2) in both 293 cells and A549 NSCLC cells to generate a high-confidence protein-protein interaction (PPI) network of 220 proteins showing 1,400 physical interactions. The network was used to design an sgRNA library (10 sgRNAs/gene) and screen Cas9-expressing A549 cells for strong growth dependencies. These data were then used to select 120 genes and construct a 2-gene tandem sgRNA library of highest relevance to the Ras pathway (with 60 control sgRNAs). This 2-gene sgRNA library was tested in A549 and H23 NSCLC lines for quantitative single and two gene-dependent quantitative changes in growth, showing 100s of strong synthetic lethals among 14K pairwise tests. These genetic interactions in conjunction with PPIs and TCGA data identify extensive coupling between Raf/MEK/ERK kinases, Ral and Rap GTPases, the Rap1GDS1 small GTPase controller, and RADIL cell adhesion pathways. The screen identified new candidate effector pathways for cell adhesion, Rap GTPase regulation, and protein processing, including new understudied Kras direct effectors RADIL, RGL1/2/3, and RIN1/2. Additional 20 x 20 custom libraries were screened in a broader panel of Kras-mutant versus other NSCLC lines. These screens revealed systematic Kras-dependent synthetic lethality among components of the MAP kinase pathway (ERK1/ERK2, ERK1/RAF1, MEK1/MEK2 etc.) and other interactions between the MAPK pathway and components of the Ral and Rap GTPase, RADIL cell adhesion pathways and RIN1-dependent macropinocytosis pathways. Using the recent Kras G12C inhibitor in H23 cells, we have validated that sgRNA knockouts of these Kras effector affect these specific, new pathways: cell adhesion via RADIL, growth signaling via Rap1GDS1 and RhoA, and macropinocytosis via the Rab5 GEF RIN1. Application of the Kras inhibitor ARS-853 shows much-reduced effects on specific Kras effector pathways in cells deleted for these specific effectors, showing these effectors are highly coupled to Kras. Our systematic data reveal new genetic vulnerabilities and target candidates with potential for new therapeutics.
Citation Format: Marcus Kelly, Kyuho Han, Kaja Kostyrko, Nancie Mooney, Edwin Jeng, Janos Demeter, Alejandro Sweet-Cordero, Michael Bassik, Peter K. Jackson. Combined proteomic and genetic interaction mapping reveals new Ras pathway effectors and regulators [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B25.
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Affiliation(s)
| | | | - Kaja Kostyrko
- 2University of California San Francisco, San Francisco, CA
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10
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Valencia K, Erice O, Kostyrko K, Hausmann S, Guruceaga E, Tathireddy A, Flores NM, Sayles LC, Lee AG, Fragoso R, Sun TQ, Vallejo A, Roman M, Entrialgo-Cadierno R, Migueliz I, Razquin N, Fortes P, Lecanda F, Lu J, Ponz-Sarvise M, Chen CZ, Mazur PK, Sweet-Cordero EA, Vicent S. The Mir181ab1 cluster promotes KRAS-driven oncogenesis and progression in lung and pancreas. J Clin Invest 2020; 130:1879-1895. [PMID: 31874105 PMCID: PMC7108928 DOI: 10.1172/jci129012] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 12/19/2019] [Indexed: 02/03/2023] Open
Abstract
Few therapies are currently available for patients with KRAS-driven cancers, highlighting the need to identify new molecular targets that modulate central downstream effector pathways. Here we found that the microRNA (miRNA) cluster including miR181ab1 is a key modulator of KRAS-driven oncogenesis. Ablation of Mir181ab1 in genetically engineered mouse models of Kras-driven lung and pancreatic cancer was deleterious to tumor initiation and progression. Expression of both resident miRNAs in the Mir181ab1 cluster, miR181a1 and miR181b1, was necessary to rescue the Mir181ab1-loss phenotype, underscoring their nonredundant role. In human cancer cells, depletion of miR181ab1 impaired proliferation and 3D growth, whereas overexpression provided a proliferative advantage. Lastly, we unveiled miR181ab1-regulated genes responsible for this phenotype. These studies identified what we believe to be a previously unknown role for miR181ab1 as a potential therapeutic target in 2 highly aggressive and difficult to treat KRAS-mutated cancers.
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Affiliation(s)
- Karmele Valencia
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- University of Navarra, Department of Biochemistry and Genetics, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Oihane Erice
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
| | - Kaja Kostyrko
- Division of Hematology and Oncology, UCSF, San Francisco, California, USA
| | - Simone Hausmann
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Elizabeth Guruceaga
- Bioinformatics Platform, Center for Applied Medical Research, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | | | - Natasha M. Flores
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Leanne C. Sayles
- Division of Hematology and Oncology, UCSF, San Francisco, California, USA
| | - Alex G. Lee
- Division of Hematology and Oncology, UCSF, San Francisco, California, USA
| | - Rita Fragoso
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Adrian Vallejo
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain
| | - Marta Roman
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain
| | - Rodrigo Entrialgo-Cadierno
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- University of Navarra, Department of Biochemistry and Genetics, Pamplona, Spain
| | - Itziar Migueliz
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
| | - Nerea Razquin
- University of Navarra, Center for Applied Medical Research, Program in Gene Therapy and Regulation of Gene Expression, Pamplona, Spain
| | - Puri Fortes
- University of Navarra, Center for Applied Medical Research, Program in Gene Therapy and Regulation of Gene Expression, Pamplona, Spain
| | - Fernando Lecanda
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain
| | - Jun Lu
- Genetics Department, Yale University, New Haven, Connecticut, USA
| | - Mariano Ponz-Sarvise
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- Clínica Universidad de Navarra, Department of Medical Oncology, Pamplona, Spain
| | - Chang-Zheng Chen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Achelois Oncology, Redwood City, California, USA
| | - Pawel K. Mazur
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Silvestre Vicent
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
- University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain
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11
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Kim JW, Marquez CP, Kostyrko K, Koehne AL, Marini K, Simpson DR, Lee AG, Leung SG, Sayles LC, Shrager J, Ferrer I, Paz-Ares L, Gephart MH, Vicent S, Cochran JR, Sweet-Cordero EA. Antitumor activity of an engineered decoy receptor targeting CLCF1-CNTFR signaling in lung adenocarcinoma. Nat Med 2019; 25:1783-1795. [PMID: 31700175 DOI: 10.1038/s41591-019-0612-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/12/2019] [Indexed: 12/25/2022]
Abstract
Proinflammatory cytokines in the tumor microenvironment can promote tumor growth, yet their value as therapeutic targets remains underexploited. We validated the functional significance of the cardiotrophin-like cytokine factor 1 (CLCF1)-ciliary neurotrophic factor receptor (CNTFR) signaling axis in lung adenocarcinoma (LUAD) and generated a high-affinity soluble receptor (eCNTFR-Fc) that sequesters CLCF1, thereby inhibiting its oncogenic effects. eCNTFR-Fc inhibits tumor growth in multiple xenograft models and in an autochthonous, highly aggressive genetically engineered mouse model of LUAD, driven by activation of oncogenic Kras and loss of Trp53. Abrogation of CLCF1 through eCNTFR-Fc appears most effective in tumors driven by oncogenic KRAS. We observed a correlation between the effectiveness of eCNTFR-Fc and the presence of KRAS mutations that retain the intrinsic capacity to hydrolyze guanosine triphosphate, suggesting that the mechanism of action may be related to altered guanosine triphosphate loading. Overall, we nominate blockade of CLCF1-CNTFR signaling as a novel therapeutic opportunity for LUAD and potentially for other tumor types in which CLCF1 is present in the tumor microenvironment.
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Affiliation(s)
- Jun W Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Cesar P Marquez
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.,School of Medicine, Stanford University, Stanford, CA, USA
| | - Kaja Kostyrko
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda L Koehne
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.,School of Medicine, Stanford University, Stanford, CA, USA.,Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | - Kieren Marini
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - David R Simpson
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Alex G Lee
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Stanley G Leung
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Leanne C Sayles
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Shrager
- Division of Thoracic Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Irene Ferrer
- H120-CNIO Lung Cancer Clinical Research Unit, i+12 Research Institute, Spanish National Cancer Research Center and Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Luis Paz-Ares
- H120-CNIO Lung Cancer Clinical Research Unit, i+12 Research Institute, Spanish National Cancer Research Center and Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | | | - Silvestre Vicent
- Program in Solid Tumors and Biomarkers, Center for Applied Medical Research, Universidad de Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, University of Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | | | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
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12
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Marini KD, Croucher DR, McCloy RA, Vaghjiani V, Gonzalez-Rajal A, Hastings JF, Chin V, Szczepny A, Kostyrko K, Marquez C, Jayasekara WSN, Alamgeer M, Boolell V, Han JZR, Waugh T, Lee HC, Oakes SR, Kumar B, Harrison CA, Hedger MP, Lorensuhewa N, Kita B, Barrow R, Robinson BW, de Kretser DM, Wu J, Ganju V, Sweet-Cordero EA, Burgess A, Martelotto LG, Rossello FJ, Cain JE, Watkins DN. Inhibition of activin signaling in lung adenocarcinoma increases the therapeutic index of platinum chemotherapy. Sci Transl Med 2019; 10:10/451/eaat3504. [PMID: 30045976 DOI: 10.1126/scitranslmed.aat3504] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/30/2018] [Indexed: 12/14/2022]
Abstract
Resistance to platinum chemotherapy is a long-standing problem in the management of lung adenocarcinoma. Using a whole-genome synthetic lethal RNA interference screen, we identified activin signaling as a critical mediator of innate platinum resistance. The transforming growth factor-β (TGFβ) superfamily ligands activin A and growth differentiation factor 11 (GDF11) mediated resistance via their cognate receptors through TGFβ-activated kinase 1 (TAK1), rather than through the SMAD family of transcription factors. Inhibition of activin receptor signaling or blockade of activin A and GDF11 by the endogenous protein follistatin overcame this resistance. Consistent with the role of activin signaling in acute renal injury, both therapeutic interventions attenuated acute cisplatin-induced nephrotoxicity, its major dose-limiting side effect. This cancer-specific enhancement of platinum-induced cell death has the potential to dramatically improve the safety and efficacy of chemotherapy in lung cancer patients.
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Affiliation(s)
- Kieren D Marini
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia.,School of Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Rachael A McCloy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Vijesh Vaghjiani
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Alvaro Gonzalez-Rajal
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Jordan F Hastings
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Venessa Chin
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Department of Medical Oncology, St. Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
| | - Anette Szczepny
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Kaja Kostyrko
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Cesar Marquez
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA
| | | | - Muhammad Alamgeer
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia.,Department of Medical Oncology, Monash Medical Centre, East Bentleigh, Victoria 3165, Australia
| | - Vishal Boolell
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Medical Oncology, Monash Medical Centre, East Bentleigh, Victoria 3165, Australia
| | - Jeremy Z R Han
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Todd Waugh
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Hong Ching Lee
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Samantha R Oakes
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia
| | - Beena Kumar
- Department of Pathology, Monash Medical Centre, Clayton, Victoria 3168, Australia
| | - Craig A Harrison
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Mark P Hedger
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | | | - Badia Kita
- Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Ross Barrow
- Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Bruce W Robinson
- School of Medicine and Pharmacology, Queen Elizabeth II Medical Centre Unit, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - David M de Kretser
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia.,Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Jianmin Wu
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia.,Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing, China.,Center for Cancer Bioinformatics, Peking University Cancer Hospital and Institute, Hai-Dian District, Beijing 100142, China
| | - Vinod Ganju
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | | | - Andrew Burgess
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,ANZAC Research Institute, Concord, New South Wales 2139, Australia
| | - Luciano G Martelotto
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia.,Center for Cancer Research, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Fernando J Rossello
- Australian Regenerative Medicine Institute, Clayton, Victoria 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Jason E Cain
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.
| | - D Neil Watkins
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia. .,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia.,Department of Thoracic Medicine, St. Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
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13
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Kelly MR, Han K, Mooney N, Jeng E, Kostyrko K, Sweet-Cordero A, Bassik M, Jackson PK. Abstract PR12: A combined protein-protein interaction and genetic interaction map defines new and critical Kras effectors in non-small cell lung cancer. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-pr12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite intensive study, no drugs in clinical use specifically target KRAS-mutant tumors. Uncharacterized feedback mechanisms and parallel pathways have stymied the treatment of KRAS-mutant tumors with Raf and PI3K inhibitors, and the KRas protein itself does not easily accommodate binding of small-molecule inhibitors. These challenges demand more systematic and quantitative characterization of the physical and genetic relationships between Ras regulators and effectors.
To that end, we used tandem affinity purification of Kras, Hras and Nras, their activated alleles and key proteins with known regulatory (GEFs, GAPs) or effector (Raf, RalGDS, RIN1/2) roles in both 293 cells and A549 NSCLC cells to generate a high-confidence protein-protein interaction (PPI) network. This map of 220 proteins and 1,400 physical interactions was used to design an sgRNA library with 10 guides/gene. This library was screened in Cas9-expressing A549 cells and grown for 14 days before analysis for dropout or enhanced representation of sgRNAs. Approximately 120 genes showed positive or negative growth effects. PPIs and genetic interactions (GIs) were cross-referenced with public PPI data and TCGA patient data to assemble a combined physical PPI and genetic map informed by cancer mutations. This map suggests many hypotheses for PPIs critical for growth control. This set was used to construct a sgRNA library covering 120 genes of probable relevance to the Ras pathway with ~60 “safe harbor” control sgRNAs. This library was screened in a two-cassette sgRNA system testing 14K pairwise genetic effects to identify quantitative changes in growth in A549 and H23 NSCLC lines. This screen showed >100 genetic interactions, which in conjunction with PPIs, identify coupling between the Raf/MEK/ERK kinase, Ral and Rap GTPase, RNA processing, and cell adhesion pathways. The screen identified new candidate effector pathways for cell adhesion, RNA processing, Rap GTPase regulation, and protein processing, including the RADIL, RGL, and RIN Kras effectors. Validation focused using the synthetic lethal interactions observed in the sgRNA screen to predict drug combinations showing drug synergy in A549 and H23 cells. Using 11-point dose titrations and isobologram analysis of drug combinations, we see strong synergy among PI3 kinase, Raf, and Erk inhibitors in these cells. Using the recently described Kras G12C inhibitor, expressed in H23 cells, we have validated that sgRNA deletion of the the key Kras effector for specific pathways including cell adhesion (RADIL), growth signaling (RAF), and endocytosis/ macropinocytosis (RIN) are affected and that use of the Kras inhibitor ARS-853 shows much reduced effects on specific Kras effector pathways in cells deleted for these effectors. These systematic data underscore the limitations of our current understanding of Kras-driven cancers, revealing new genetic vulnerabilities and target candidates.
This abstract is also being presented as Poster A28.
Citation Format: Marcus R. Kelly, Kyuho Han, Nancie Mooney, Edwin Jeng, Kaja Kostyrko, Alejandro Sweet-Cordero, Michael Bassik, Peter K. Jackson. A combined protein-protein interaction and genetic interaction map defines new and critical Kras effectors in non-small cell lung cancer [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr PR12.
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Affiliation(s)
| | - Kyuho Han
- 1Stanford University School of Medicine, Stanford, CA,
| | - Nancie Mooney
- 1Stanford University School of Medicine, Stanford, CA,
| | - Edwin Jeng
- 1Stanford University School of Medicine, Stanford, CA,
| | - Kaja Kostyrko
- 2University of California San Francisco, San Francisco, CA
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14
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Kostyrko K, Kelly MR, Han K, Jeng EE, Morgens DW, Bassik MC, Jackson PK, Sweet-Cordero A. Abstract 4362: Identification of novel combinatorial synthetic lethal vulnerabilities in KRAS-driven lung cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung cancer is the number one cause of cancer-related deaths worldwide. The most prevalent type of lung cancer is Non-Small Cell Lung Cancer (NSCLC). A significant number of patients with NSCLC carry oncogenic KRAS mutations. However, the efforts to target KRAS directly have thus far proven unsuccessful and tumors harboring mutations in this gene remain the most difficult to treat, highlighting the need for alternative approaches. One promising strategy is to target KRAS-dependent cancers through synthetic lethality. However, KRAS activates multiple effector pathways, suggesting that targeting one gene may not be sufficient to fully inhibit KRAS oncogenesis. Therefore, we propose that targeting combinations of genes that together are synthetic lethal with KRAS may constitute a better therapeutic strategy. Furthermore, we hypothesize that a targeted approach focused on the protein-protein interaction network proximal to KRAS may be more effective than the current emphasis on genome-wide screens. To discover novel, combinatorial KRAS synthetic lethal genes, we used affinity purification/mass spectrometry (AP/MS), to systematically identify KRAS interacting proteins and construct a detailed map of protein-protein interactions centered on KRAS. Based on this network we designed a CRISPR/Cas9 library targeting pairwise combinations of KRAS-interacting genes. Using this library we simultaneously knocked-out pairs of 119 genes in two KRAS-driven non-small cell lung cancer (NSCLC) cell lines (A549 and H23). Knock-out of many gene pairs synergistically impaired growth of these cells, while the knock-out of each of the genes alone had no or little effect. We chose 20 most promising targets for further screening in vitro and in vivo in a panel of 9 KRAS-mutant and KRAS wild type Cas9-expressing NSCLC cell lines. We also selected six gene pairs that had the most synergistic effect on growth in A549 and H23 cells for individual validation in Cas9-expressing NSCLC cell lines and normal human bronchial epithelial cells (HBECs). We found that the simultaneous knock-out of one pair of genes, Rap1GDS1 and RhoA, significantly decreased growth of KRAS-dependent NSCLC cells, while having a limited effect on KRAS-independent cells or HBECs. Moreover the knock-out of either of these genes alone had no effect on growth in any of the cell lines, suggesting that only the combination of these two genes is synthetically lethal with KRAS. We are currently performing further validation in organoid cultures and in vivo. Additional validation and human relevance will be determined using patient-derived xenografts (PDX).
Citation Format: Kaja Kostyrko, Marcus R. Kelly, Kyuho Han, Edwin E. Jeng, David W. Morgens, Michael C. Bassik, Peter K. Jackson, Alejandro Sweet-Cordero. Identification of novel combinatorial synthetic lethal vulnerabilities in KRAS-driven lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4362.
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15
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Kostyrko K, Han K, Kelly M, Jeng E, Morgens D, Bassik M, Jackson P, Sweet-Cordero A. SPOT-007 Identifying novel combinatorial synthetic lethal vulnerabilities in KRAS-driven lung cancer. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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16
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Kelly MR, Kyuho H, Jeng EE, Morgans D, Kostyrko K, Simpson D, Gwinn D, Sweet-Cordero A, Bassik MC, Jackson PK. Abstract PR03: Linking AP/MS-driven protein-protein interaction networks and combination CRISPR/sgRNA screens defines new Kras effectors and target candidates for non-small cell lung cancer. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-pr03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Kras pathway is a central driver in prevalent and deadly cancers including pancreas, colon and lung. Despite decades of work studying the Raf and PI3 kinase pathways downstream of Kras, therapies targeted to these pathways have shown varied responses in tumors
To better understand whether important Kras dependences have been overlooked, we used tandem affinity purification of Kras, Hras, and Nras interactors and a set of baits representing ~50 interacting pathway regulators, and have compared these interactions in Kras transformed A549 NSCLC lines versus an isogenic shRNA Kras knockdown line, to identify key protein-protein interactions (PPIs) linked to Kras effector activity. These interactions were curated and compared to public PPI, genetic susceptibility, and other multiomics data to assemble a physical PPI map annotated with important functional determinants. This functional map was used to construct a library of 114 selected sgRNAs (10 guides per gene) and screened in a 1140 x 1140 dual sgRNA vector system to look for quantitative changes in single and dual genetic dependencies in A549 cell growth. We discovered a considerable number of new KRAS GTP-specific effectors important in NSCLC cancer, many with strong mutations patterns supported by TCGA data and validated by in vitro biochemical assay. We will present these data and additional validation studies on two pathways including the Radil-Rap1-Kif14 pathway for cell migration and an extensive interaction of the Kras pathway with Ral and Rap GTPase family guanine nucleotide exchange factors. These new effectors underscore limitations in our functional understanding of transformation in Kras-driven tumors and suggest specific new targets for these critical tumors.
Citation Format: Marcus R. Kelly, Han Kyuho, Edwin E. Jeng, David Morgans, Kaja Kostyrko, David Simpson, Dana Gwinn, Alejandro Sweet-Cordero, Michael C. Bassik, Peter K. Jackson. Linking AP/MS-driven protein-protein interaction networks and combination CRISPR/sgRNA screens defines new Kras effectors and target candidates for non-small cell lung cancer [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR03.
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Affiliation(s)
| | - Han Kyuho
- Stanford University School of Medicine, Stanford, CA
| | - Edwin E. Jeng
- Stanford University School of Medicine, Stanford, CA
| | - David Morgans
- Stanford University School of Medicine, Stanford, CA
| | - Kaja Kostyrko
- Stanford University School of Medicine, Stanford, CA
| | - David Simpson
- Stanford University School of Medicine, Stanford, CA
| | - Dana Gwinn
- Stanford University School of Medicine, Stanford, CA
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17
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Kostyrko K, Neuenschwander S, Junier T, Regamey A, Iseli C, Schmid-Siegert E, Bosshard S, Majocchi S, Le Fourn V, Girod PA, Xenarios I, Mermod N. MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering. Biotechnol Bioeng 2016; 114:384-396. [PMID: 27575535 PMCID: PMC5215416 DOI: 10.1002/bit.26086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/03/2016] [Accepted: 08/25/2016] [Indexed: 12/27/2022]
Abstract
Untargeted plasmid integration into mammalian cell genomes remains a poorly understood and inefficient process. The formation of plasmid concatemers and their genomic integration has been ascribed either to non-homologous end-joining (NHEJ) or homologous recombination (HR) DNA repair pathways. However, a direct involvement of these pathways has remained unclear. Here, we show that the silencing of many HR factors enhanced plasmid concatemer formation and stable expression of the gene of interest in Chinese hamster ovary (CHO) cells, while the inhibition of NHEJ had no effect. However, genomic integration was decreased by the silencing of specific HR components, such as Rad51, and DNA synthesis-dependent microhomology-mediated end-joining (SD-MMEJ) activities. Genome-wide analysis of the integration loci and junction sequences validated the prevalent use of the SD-MMEJ pathway for transgene integration close to cellular genes, an effect shared with matrix attachment region (MAR) DNA elements that stimulate plasmid integration and expression. Overall, we conclude that SD-MMEJ is the main mechanism driving the illegitimate genomic integration of foreign DNA in CHO cells, and we provide a recombination engineering approach that increases transgene integration and recombinant protein expression in these cells. Biotechnol. Bioeng. 2017;114: 384-396. © 2016 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals, Inc.
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Affiliation(s)
- Kaja Kostyrko
- Department of Fundamental Microbiology, Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | | | - Thomas Junier
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | | | - Sandra Bosshard
- Department of Fundamental Microbiology, Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | - Stefano Majocchi
- Department of Fundamental Microbiology, Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | | | | | | | - Nicolas Mermod
- Department of Fundamental Microbiology, Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
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Kostyrko K, Mermod N. Assays for DNA double-strand break repair by microhomology-based end-joining repair mechanisms. Nucleic Acids Res 2016; 44:e56. [PMID: 26657630 PMCID: PMC4824085 DOI: 10.1093/nar/gkv1349] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/17/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022] Open
Abstract
DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collectively termed microhomology-mediated end-joining (MMEJ), relies on short homologies for the end-joining process. Here, we constructed GFP reporter assays to characterize and distinguish MMEJ variant pathways, namely the simple MMEJ and the DNA synthesis-dependent (SD)-MMEJ mechanisms. Transfection of these assay vectors in Chinese hamster ovary (CHO) cells and characterization of the repaired DNA sequences indicated that while simple MMEJ is able to mediate relatively efficient DSB repair if longer microhomologies are present, the majority of DSBs were repaired using the highly error-prone SD-MMEJ pathway. To validate the involvement of DNA synthesis in the repair process, siRNA knock-down of different genes proposed to play a role in MMEJ were performed, revealing that the knock-down of DNA polymerase θ inhibited DNA end resection and repair through simple MMEJ, thus favoring the other repair pathway. Overall, we conclude that this approach provides a convenient assay to study MMEJ-related DNA repair pathways.
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Affiliation(s)
- Kaja Kostyrko
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
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Abstract
Eukaryotic cells respond to DNA breaks, especially double-stranded breaks (DSBs), by activating the DNA damage response (DDR), which encompasses DNA repair and cell cycle checkpoint signaling. The DNA damage signal is transmitted to the checkpoint machinery by a network of specialized DNA damage-recognizing and signal-transducing molecules. However, recent evidence suggests that DNA repair proteins themselves may also directly contribute to the checkpoint control. Here, we investigated the role of homologous recombination (HR) proteins in normal cell cycle regulation in the absence of exogenous DNA damage. For this purpose, we used Chinese Hamster Ovary (CHO) cells expressing the Fluorescent ubiquitination-based cell cycle indicators (Fucci). Systematic siRNA-mediated knockdown of HR genes in these cells demonstrated that the lack of several of these factors alters cell cycle distribution, albeit differentially. The knock-down of MDC1, Rad51 and Brca1 caused the cells to arrest in the G2 phase, suggesting that they may be required for the G2/M transition. In contrast, inhibition of the other HR factors, including several Rad51 paralogs and Rad50, led to the arrest in the G1/G0 phase. Moreover, reduced expression of Rad51B, Rad51C, CtIP and Rad50 induced entry into a quiescent G0-like phase. In conclusion, the lack of many HR factors may lead to cell cycle checkpoint activation, even in the absence of exogenous DNA damage, indicating that these proteins may play an essential role both in DNA repair and checkpoint signaling.
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Affiliation(s)
- Kaja Kostyrko
- a Institute of Biotechnology ; University of Lausanne ; and Center for Biotechnology UNIL-EPFL ; Lausanne , Switzerland
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Kostyrko K, Mermod N. siRNA-mediated engineering of DNA recombination for improved transgene integration and expression. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Grandjean M, Girod PA, Calabrese D, Kostyrko K, Wicht M, Yerly F, Mazza C, Beckmann JS, Martinet D, Mermod N. High-level transgene expression by homologous recombination-mediated gene transfer. Nucleic Acids Res 2011; 39:e104. [PMID: 21652640 PMCID: PMC3159483 DOI: 10.1093/nar/gkr436] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Gene transfer and expression in eukaryotes is often limited by a number of stably maintained gene copies and by epigenetic silencing effects. Silencing may be limited by the use of epigenetic regulatory sequences such as matrix attachment regions (MAR). Here, we show that successive transfections of MAR-containing vectors allow a synergistic increase of transgene expression. This finding is partly explained by an increased entry into the cell nuclei and genomic integration of the DNA, an effect that requires both the MAR element and iterative transfections. Fluorescence in situ hybridization analysis often showed single integration events, indicating that DNAs introduced in successive transfections could recombine. High expression was also linked to the cell division cycle, so that nuclear transport of the DNA occurs when homologous recombination is most active. Use of cells deficient in either non-homologous end-joining or homologous recombination suggested that efficient integration and expression may require homologous recombination-based genomic integration of MAR-containing plasmids and the lack of epigenetic silencing events associated with tandem gene copies. We conclude that MAR elements may promote homologous recombination, and that cells and vectors can be engineered to take advantage of this property to mediate highly efficient gene transfer and expression.
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Affiliation(s)
- Mélanie Grandjean
- Laboratory of Molecular Biotechnology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland
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