CRISPR/Cas9 and targeted cancer therapy
Liu, Bin
DOI:
10.33612/diss.99103461
IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below.
Document Version
Publisher's PDF, also known as Version of record
Publication date: 2019
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Liu, B. (2019). CRISPR/Cas9 and targeted cancer therapy. University of Groningen. https://doi.org/10.33612/diss.99103461
Copyright
Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).
Take-down policy
If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.
Conventional cancer therapies, including resection surgery, chemotherapy, radiotherapy and their combinations have been the primary therapeutic options for cancers for decades1. However, the improved survival of patients with advanced cancer, such as lung carcinoma and renal cell carcinoma, is usually months instead of years. Side effects of these conventional therapies significantly affect the living quality2.
Targeted therapy by small molecular compounds or antibodies seems better at least to reduce side effects. Targeted therapy is mainly based on the knowledge of tumor biology, such as targeting some essential proteins in oncogenic molecular pathways, for instance, EGFR-Tyrosine kinase inhibitors (TKIs) for lung cancer and EGFR-antibodies for colorectal cancer. Although small molecular inhibitors and antibodies have achieved some successes in cancer treatment, drug resistance inevitably occurs after a short term treatment, which limits the efficacy of targeted drugs3,4. Therefore, finding more novel targets, new combination therapeutic options and alternative therapies are urgently required.
CRISPR/Cas-based technologies are revolutionizing every field of research in life sciences and medicine, cancer treatment research is certainly not an exception5. The applications of CRISPR/Cas9 in cancer research and therapy are mainly focused on two aspects. One is screening and identifying therapeutic targets6, which may include a deeper understanding of old targets and finding novel targets using “CRISPR Way”. The other is directly using CRISPR/Cas9 as a therapy for cancer. Although a few clinical trials using CRISPR against cancer have been ongoing7, these clinical trials can only be regarded as first proof-of-concept studies due to many unknowns.
Therefore, the aim for this thesis is exploring the potential of CRISPR/Cas9 in discovering therapeutic targets and in cancer therapy. Herein, three parts are presented in this thesis. Chapters 2, 3, 4, 5, and 6 present the applications of CRISPR/Cas9 in cancer target identification and treatment. Chapter 7 presents a strategy for improving CRISPR/Cas9 targeting efficiency for cancer treatment by HDAC inhibition. Finally a summary of the studies is presented in this thesis and future perspectives are drawn.
CHAPTER 1
Scope and Outline of This Thesis
Conventional cancer therapies, including resection surgery, chemotherapy, radiotherapy and their combinations have been the primary therapeutic options for cancers for decades1. However, the improved survival of patients with advanced cancer, such as lung carcinoma and renal cell carcinoma, is usually months instead of years. Side effects of these conventional therapies significantly affect the living quality2.
Targeted therapy by small molecular compounds or antibodies seems better at least to reduce side effects. Targeted therapy is mainly based on the knowledge of tumor biology, such as targeting some essential proteins in oncogenic molecular pathways, for instance, EGFR-Tyrosine kinase inhibitors (TKIs) for lung cancer and EGFR-antibodies for colorectal cancer. Although small molecular inhibitors and antibodies have achieved some successes in cancer treatment, drug resistance inevitably occurs after a short term treatment, which limits the efficacy of targeted drugs3,4. Therefore, finding more novel targets, new combination therapeutic options and alternative therapies are urgently required.
CRISPR/Cas-based technologies are revolutionizing every field of research in life sciences and medicine, cancer treatment research is certainly not an exception5. The applications of CRISPR/Cas9 in cancer research and therapy are mainly focused on two aspects. One is screening and identifying therapeutic targets6, which may include a deeper understanding of old targets and finding novel targets using “CRISPR Way”. The other is directly using CRISPR/Cas9 as a therapy for cancer. Although a few clinical trials using CRISPR against cancer have been ongoing7, these clinical trials can only be regarded as first proof-of-concept studies due to many unknowns.
Therefore, the aim for this thesis is exploring the potential of CRISPR/Cas9 in discovering therapeutic targets and in cancer therapy. Herein, three parts are presented in this thesis. Chapters 2, 3, 4, 5, and 6 present the applications of CRISPR/Cas9 in cancer target identification and treatment. Chapter 7 presents a strategy for improving CRISPR/Cas9 targeting efficiency for cancer treatment by HDAC inhibition. Finally a summary of the studies is presented in this thesis and future perspectives are drawn.
Selection of the right target is crucial for developing an effective treatment strategy for cancer8. A candidate protein or molecule cannot be considered as an appropriate target only based on its expression level or mutation status. Recently, application of CRISPR/Cas9 have enabled greatly successful validation of potential therapeutic targets for cancer therapy7. Thus, in
Chapter 2, we provide a comprehensive overview of using CRISPR/Cas9 for identification of new
targets for cancer treatment. Furthermore, we summarized the delivery of CRISPR/Cas9 and provided an approach for specifically disrupting cancer driver mutations9–11. In the end, we discussed the challenges and the opportunities of CRISPR/Cas9 for cancer therapy.
However, resistance inevitably occurs in almost all cancer patients with drug treatment. The resistant mechanisms are complicated. CRISPR/Cas9 has been successfully used in elucidating some drug resistant mechanisms for cancer treatment. Understanding resistant mechanisms could provide useful guidance for personalized medicine in cancer12. Therefore, in chapter 3, we focus specifically on the use of CRISPR/Cas9 for understanding drug resistance mechanisms and identification of resistance-related genes in solid tumors.
Lung cancer is the leading cause of cancer mortality worldwide13. Mechanisms of EGFR-TKI resistance in NSCLC are complicated14. In Chapter 4, we aimed to characterize cellular and molecular changes of HER family receptors upon EGFR ablation by CRISPR/Cas9 or acquisition of TKI resistance. We have characterized EGFR ablation by CRISPR/Cas9 and TKI resistance in lung cancer cell lines with different genotypes. We further reveal that HER2 and HER3 nuclear translocation mediated-cyclin D1 overexpression contributes to cell proliferation, survival and resistance in lung cancer cells upon EGFR targeting.
KRAS-driven non-small cell lung cancer patients have no effective targeted treatment15,16. EGFR targeted therapy shows little or no efficacy in non-small-cell lung carcinoma (NSCLC) patients with KRAS mutation. We aimed to find a new therapeutic option for the treatment of NSCLC patients with KRAS mutation. To this end, in Chapter 5, we report that CXCR7 overexpression is a novel compensation and survival mechanism in EGFR targeted therapy (CRISPR/Cas9 and TKIs) in in KRAS-driven lung cancer cells. We show that EGFR and CXCR7 have a crucial interaction in
NSCLC. Dual EGFR and CXCR7 inhibition led to substantial reduction of MAPK (pERK) and synergistic inhibition of cell growth. Therefore, a combination therapy by dual inhibition EGFR and CXCR7 may be a potential therapeutic option for a subtype of patients with NSCLC. In addition, we observed that EGF-induced phosphorylation of Akt may be independent of EGFR, which to our knowledge has not been reported previously. One hypothesis is that EGF stimulates pAkt via CXCR7, because previous studies have shown that CXCR7 associated pathways can induce Akt phosphorylation.
Recently, CXCR7 has been classified as a novel receptor for human macrophage migration inhibitory factor (MIF)17–19. However, D-dopachrome tautomerase(D-DT), also called MIF2, is a newly described cytokine, which is an analogue of MIF20. I hypothesized that D-DT may be a ligand of CXCR7. The new mechanism of DDT/CXCR7 signaling may deepen our understanding of some diseases development, such as COPD and cancer.
We concentrate on EGFR targeting and expand our study from lung cancer to renal cancer. RCC (Renal cell carcinoma) is one of the most aggressive malignant tumors. The 5-year survival rate of metastatic RCC is less than 10%. In Chapter 6, we show that ablation of EGFR by CRISPR/Cas9 significantly restrained tumor cell growth and activated the MAPK (pERK1/2) pathway. The VEGFR and PDGFR inhibitor, sunitinib, attenuated the expression of MAPK (pERK1/2) and pAKT induced by EGFR loss and further inhibited EGFR-/- cell proliferation.
Despite the rapid development of CRISPR/Cas9-mediated gene editing technology, the gene editing potential of CRISPR/Cas9 is hampered by low efficiency21,22, especially for cancer gene therapy. Therefore, in Chapter 7, we provide a practical and clinically applicable approach for precise control of CRISPR/Cas9 mediated gene editing by modulation of HDAC and HAT activity in host cells. In this study, we hypothesized that regulation of chromatin compaction by inhibiting HAT and/or HDAC activity can modulate CRISPR-Cas9 based gene editing. We comprehensively investigated the impact of HDACs and HATs on CRISPR/Cas9 mediated gene editing. Our findings demonstrate that attenuation of HDAC1 and HDAC2 activity, but not other HDACs, leads to an open chromatin state, facilitates Cas9 access and binding to the targeted
CHAPTER 1
Selection of the right target is crucial for developing an effective treatment strategy for cancer8. A candidate protein or molecule cannot be considered as an appropriate target only based on its expression level or mutation status. Recently, application of CRISPR/Cas9 have enabled greatly successful validation of potential therapeutic targets for cancer therapy7. Thus, in
Chapter 2, we provide a comprehensive overview of using CRISPR/Cas9 for identification of new
targets for cancer treatment. Furthermore, we summarized the delivery of CRISPR/Cas9 and provided an approach for specifically disrupting cancer driver mutations9–11. In the end, we discussed the challenges and the opportunities of CRISPR/Cas9 for cancer therapy.
However, resistance inevitably occurs in almost all cancer patients with drug treatment. The resistant mechanisms are complicated. CRISPR/Cas9 has been successfully used in elucidating some drug resistant mechanisms for cancer treatment. Understanding resistant mechanisms could provide useful guidance for personalized medicine in cancer12. Therefore, in chapter 3, we focus specifically on the use of CRISPR/Cas9 for understanding drug resistance mechanisms and identification of resistance-related genes in solid tumors.
Lung cancer is the leading cause of cancer mortality worldwide13. Mechanisms of EGFR-TKI resistance in NSCLC are complicated14. In Chapter 4, we aimed to characterize cellular and molecular changes of HER family receptors upon EGFR ablation by CRISPR/Cas9 or acquisition of TKI resistance. We have characterized EGFR ablation by CRISPR/Cas9 and TKI resistance in lung cancer cell lines with different genotypes. We further reveal that HER2 and HER3 nuclear translocation mediated-cyclin D1 overexpression contributes to cell proliferation, survival and resistance in lung cancer cells upon EGFR targeting.
KRAS-driven non-small cell lung cancer patients have no effective targeted treatment15,16. EGFR targeted therapy shows little or no efficacy in non-small-cell lung carcinoma (NSCLC) patients with KRAS mutation. We aimed to find a new therapeutic option for the treatment of NSCLC patients with KRAS mutation. To this end, in Chapter 5, we report that CXCR7 overexpression is a novel compensation and survival mechanism in EGFR targeted therapy (CRISPR/Cas9 and TKIs) in in KRAS-driven lung cancer cells. We show that EGFR and CXCR7 have a crucial interaction in
Scope and Outline of This Thesis
NSCLC. Dual EGFR and CXCR7 inhibition led to substantial reduction of MAPK (pERK) and synergistic inhibition of cell growth. Therefore, a combination therapy by dual inhibition EGFR and CXCR7 may be a potential therapeutic option for a subtype of patients with NSCLC. In addition, we observed that EGF-induced phosphorylation of Akt may be independent of EGFR, which to our knowledge has not been reported previously. One hypothesis is that EGF stimulates pAkt via CXCR7, because previous studies have shown that CXCR7 associated pathways can induce Akt phosphorylation.
Recently, CXCR7 has been classified as a novel receptor for human macrophage migration inhibitory factor (MIF)17–19. However, D-dopachrome tautomerase(D-DT), also called MIF2, is a newly described cytokine, which is an analogue of MIF20. I hypothesized that D-DT may be a ligand of CXCR7. The new mechanism of DDT/CXCR7 signaling may deepen our understanding of some diseases development, such as COPD and cancer.
We concentrate on EGFR targeting and expand our study from lung cancer to renal cancer. RCC (Renal cell carcinoma) is one of the most aggressive malignant tumors. The 5-year survival rate of metastatic RCC is less than 10%. In Chapter 6, we show that ablation of EGFR by CRISPR/Cas9 significantly restrained tumor cell growth and activated the MAPK (pERK1/2) pathway. The VEGFR and PDGFR inhibitor, sunitinib, attenuated the expression of MAPK (pERK1/2) and pAKT induced by EGFR loss and further inhibited EGFR-/- cell proliferation.
Despite the rapid development of CRISPR/Cas9-mediated gene editing technology, the gene editing potential of CRISPR/Cas9 is hampered by low efficiency21,22, especially for cancer gene therapy. Therefore, in Chapter 7, we provide a practical and clinically applicable approach for precise control of CRISPR/Cas9 mediated gene editing by modulation of HDAC and HAT activity in host cells. In this study, we hypothesized that regulation of chromatin compaction by inhibiting HAT and/or HDAC activity can modulate CRISPR-Cas9 based gene editing. We comprehensively investigated the impact of HDACs and HATs on CRISPR/Cas9 mediated gene editing. Our findings demonstrate that attenuation of HDAC1 and HDAC2 activity, but not other HDACs, leads to an open chromatin state, facilitates Cas9 access and binding to the targeted
DNA, and consequently enhances CRISPR/Cas9-mediated gene knockout frequencies by NHEJ as well as gene knock-in by HDR. Conversely, inhibition of HDAC3 attenuates the ability of CRISPR/Cas9 mediated gene editing.
The studies presented in this thesis are summarized and discussed in Chapter 8 along with future perspectives.
1. Tannock, I. F. Conventional cancer therapy: promise broken or promise delayed? Lancet 351, SII9–SII16 (1998).
2. Baudino, T. A. Targeted Cancer Therapy: The Next Generation of Cancer Treatment. Curr. Drug Discov. Technol. 12, 3–20 (2015).
3. Holohan, C., Van Schaeybroeck, S., Longley, D. B. & Johnston, P. G. Cancer drug resistance: an evolving paradigm. Nat. Rev. Cancer 13, 714 (2013).
4. Saber, A., Liu, B., Ebrahimi, P. & Haisma, H. J. CRISPR/Cas9 for overcoming drug resistance in solid tumors. DARU J. Pharm. Sci. (2019). doi:10.1007/s40199-019-00240-z
5. Zhan, T., Rindtorff, N., Betge, J., Ebert, M. P. & Boutros, M. CRISPR/Cas9 for cancer research and therapy. Semin. Cancer Biol. (2018). doi:10.1016/J.SEMCANCER.2018.04.001 6. Wang, T., Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells using
the CRISPR-Cas9 system. Science 343, 80–84 (2014).
7. Liu, B., Saber, A. & Haisma, H. J. CRISPR/Cas9: a powerful tool for identification of new targets for cancer treatment. Drug Discov. Today (2019).
doi:10.1016/j.drudis.2019.02.011
8. Ahmad, G. & Amiji, M. Use of CRISPR/Cas9 gene-editing tools for developing models in drug discovery. Drug Discov. Today 23, 519–533 (2018).
9. Guernet, A. et al. CRISPR-Barcoding for Intratumor Genetic Heterogeneity Modeling and Functional Analysis of Oncogenic Driver Mutations. Mol. Cell 63, 526–538 (2016).
10. Kiessling, M. K. et al. Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics 17, 723 (2016).
11. Gebler, C. et al. Inactivation of Cancer Mutations Utilizing CRISPR/Cas9. J. Natl. Cancer Inst. 109, (2017).
12. Fellmann, C., Gowen, B. G., Lin, P., Doudna, J. A. & Corn, J. E. Cornerstones of CRISPR–Cas in drug discovery and therapy. Nat. Publ. Gr. 4–7 (2016). doi:10.1038/nrd.2016.238 13. Park, K. et al. Afatinib versus gefitinib as first-line treatment of patients with EGFR
mutation-positive non-small-cell lung cancer (LUX-Lung 7): a phase 2B, open-label, randomised controlled trial. Lancet Oncol. 17, 577–589 (2016).
14. Soria, J.-C. et al. Gefitinib plus chemotherapy versus placebo plus chemotherapy in EGFR-mutation-positive non-small-cell lung cancer after progression on first-line gefitinib (IMPRESS): a phase 3 randomised trial. Lancet Oncol. 16, 990–998 (2015).
15. Mao, C. et al. KRAS mutations and resistance to EGFR-TKIs treatment in patients with non-small cell lung cancer: A meta-analysis of 22 studies. Lung Cancer 69, 272–278 (2010). 16. Riely, G. J., Marks, J. & Pao, W. KRAS mutations in non-small cell lung cancer. Proc. Am.
Thorac. Soc. 6, 201–205 (2009).
17. Chatterjee, M. et al. Macrophage migration inhibitory factor limits activation-induced apoptosis of platelets via CXCR7-dependent Akt signaling. Circ. Res. 115, 939–949 (2014). 18. Alampour-Rajabi, S. et al. MIF interacts with CXCR7 to promote receptor internalization,
ERK1/2 and ZAP-70 signaling, and lymphocyte chemotaxis. FASEB J. 29, 4497–511 (2015). 19. Alampour-Rajabi, S. et al. MIF interacts with CXCR7 to promote receptor internalization,
ERK1/2 and ZAP-70 signaling, and lymphocyte chemotaxis. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 29, 4497–4511 (2015).
CHAPTER 1
DNA, and consequently enhances CRISPR/Cas9-mediated gene knockout frequencies by NHEJ as well as gene knock-in by HDR. Conversely, inhibition of HDAC3 attenuates the ability of CRISPR/Cas9 mediated gene editing.
The studies presented in this thesis are summarized and discussed in Chapter 8 along with future perspectives.
1. Tannock, I. F. Conventional cancer therapy: promise broken or promise delayed? Lancet 351, SII9–SII16 (1998).
2. Baudino, T. A. Targeted Cancer Therapy: The Next Generation of Cancer Treatment. Curr. Drug Discov. Technol. 12, 3–20 (2015).
3. Holohan, C., Van Schaeybroeck, S., Longley, D. B. & Johnston, P. G. Cancer drug resistance: an evolving paradigm. Nat. Rev. Cancer 13, 714 (2013).
4. Saber, A., Liu, B., Ebrahimi, P. & Haisma, H. J. CRISPR/Cas9 for overcoming drug resistance in solid tumors. DARU J. Pharm. Sci. (2019). doi:10.1007/s40199-019-00240-z
5. Zhan, T., Rindtorff, N., Betge, J., Ebert, M. P. & Boutros, M. CRISPR/Cas9 for cancer research and therapy. Semin. Cancer Biol. (2018). doi:10.1016/J.SEMCANCER.2018.04.001 6. Wang, T., Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells using
the CRISPR-Cas9 system. Science 343, 80–84 (2014).
7. Liu, B., Saber, A. & Haisma, H. J. CRISPR/Cas9: a powerful tool for identification of new targets for cancer treatment. Drug Discov. Today (2019).
doi:10.1016/j.drudis.2019.02.011
8. Ahmad, G. & Amiji, M. Use of CRISPR/Cas9 gene-editing tools for developing models in drug discovery. Drug Discov. Today 23, 519–533 (2018).
9. Guernet, A. et al. CRISPR-Barcoding for Intratumor Genetic Heterogeneity Modeling and Functional Analysis of Oncogenic Driver Mutations. Mol. Cell 63, 526–538 (2016).
Scope and Outline of This Thesis
10. Kiessling, M. K. et al. Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics 17, 723 (2016).
11. Gebler, C. et al. Inactivation of Cancer Mutations Utilizing CRISPR/Cas9. J. Natl. Cancer Inst. 109, (2017).
12. Fellmann, C., Gowen, B. G., Lin, P., Doudna, J. A. & Corn, J. E. Cornerstones of CRISPR–Cas in drug discovery and therapy. Nat. Publ. Gr. 4–7 (2016). doi:10.1038/nrd.2016.238 13. Park, K. et al. Afatinib versus gefitinib as first-line treatment of patients with EGFR
mutation-positive non-small-cell lung cancer (LUX-Lung 7): a phase 2B, open-label, randomised controlled trial. Lancet Oncol. 17, 577–589 (2016).
14. Soria, J.-C. et al. Gefitinib plus chemotherapy versus placebo plus chemotherapy in EGFR-mutation-positive non-small-cell lung cancer after progression on first-line gefitinib (IMPRESS): a phase 3 randomised trial. Lancet Oncol. 16, 990–998 (2015).
15. Mao, C. et al. KRAS mutations and resistance to EGFR-TKIs treatment in patients with non-small cell lung cancer: A meta-analysis of 22 studies. Lung Cancer 69, 272–278 (2010). 16. Riely, G. J., Marks, J. & Pao, W. KRAS mutations in non-small cell lung cancer. Proc. Am.
Thorac. Soc. 6, 201–205 (2009).
17. Chatterjee, M. et al. Macrophage migration inhibitory factor limits activation-induced apoptosis of platelets via CXCR7-dependent Akt signaling. Circ. Res. 115, 939–949 (2014). 18. Alampour-Rajabi, S. et al. MIF interacts with CXCR7 to promote receptor internalization,
ERK1/2 and ZAP-70 signaling, and lymphocyte chemotaxis. FASEB J. 29, 4497–511 (2015). 19. Alampour-Rajabi, S. et al. MIF interacts with CXCR7 to promote receptor internalization,
ERK1/2 and ZAP-70 signaling, and lymphocyte chemotaxis. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 29, 4497–4511 (2015).
functional homolog of macrophage migration inhibitory factor (MIF). Proc. Natl. Acad. Sci. 108, E577–E585 (2011).
21. Chu, V. T. et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 33, 543–548 (2015). 22. Paix, A., Folkmann, A., Rasoloson, D. & Seydoux, G. High Efficiency, Homology-Directed
Genome Editing in Caenorhabditis elegans Using CRISPR-Cas9 Ribonucleoprotein Complexes. Genetics 201, 47–54 (2015).
CHAPTER 1
functional homolog of macrophage migration inhibitory factor (MIF). Proc. Natl. Acad. Sci. 108, E577–E585 (2011).
21. Chu, V. T. et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 33, 543–548 (2015). 22. Paix, A., Folkmann, A., Rasoloson, D. & Seydoux, G. High Efficiency, Homology-Directed
Genome Editing in Caenorhabditis elegans Using CRISPR-Cas9 Ribonucleoprotein Complexes. Genetics 201, 47–54 (2015).
Chapter 2 CRISPR/Cas9: A powerful tool for
identification of new targets for cancer treatment
Bin Liu, Ali Saber, Hidde J. Haisma
