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Dziubańska-Kusibab PJ, Nevedomskaya E, Haendler B. Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review. Int J Mol Sci 2024; 25:705. [PMID: 38255778 PMCID: PMC10815614 DOI: 10.3390/ijms25020705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.
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Affiliation(s)
| | | | - Bernard Haendler
- Research and Early Development Oncology, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (P.J.D.-K.); (E.N.)
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2
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Mali SB, Dahivelkar S. Cancer management in terms of precision oncology. Oral Oncol 2024; 148:106658. [PMID: 38056061 DOI: 10.1016/j.oraloncology.2023.106658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/08/2023]
Abstract
Cancer processes have been studied for over a century, but clinical care still relies on morphological and histological approaches. Modern diagnostic and therapy options include molecular characterisation of abnormal genes, cell surface indicators, hormonal/endocrine mediators, and signaling pathways. Targeted medicines, synthetic lethal targeting, and immune checkpoint inhibitors have spurred hope for molecular targets in cancer management. Precision medicine programs aim to transform population-based research into biomarker-driven clinical trials, but disparities in access to genetic profiling and inexpensive precision oncology drugs must be addressed to ensure cost-effective therapies are available to all patients.
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Affiliation(s)
- Shrikant B Mali
- Mahatma Gandhi Vidya Mandir's Dental College and Hospital Nashik, India.
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3
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Pogacar Z, Johnson JL, Krenning L, De Conti G, Jochems F, Lieftink C, Velds A, Wardak L, Groot K, Schepers A, Wang L, Song JY, van de Ven M, van Tellingen O, Medema RH, Beijersbergen RL, Bernards R, Leite de Oliveira R. Indisulam synergizes with palbociclib to induce senescence through inhibition of CDK2 kinase activity. PLoS One 2022; 17:e0273182. [PMID: 36067171 PMCID: PMC9447877 DOI: 10.1371/journal.pone.0273182] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 08/03/2022] [Indexed: 11/19/2022] Open
Abstract
Inducing senescence in cancer cells is emerging as a new therapeutic strategy. In order to find ways to enhance senescence induction by palbociclib, a CDK4/6 inhibitor approved for treatment of metastatic breast cancer, we performed functional genetic screens in palbociclib-resistant cells. Using this approach, we found that loss of CDK2 results in strong senescence induction in palbociclib-treated cells. Treatment with the CDK2 inhibitor indisulam, which phenocopies genetic CDK2 inactivation, led to sustained senescence induction when combined with palbociclib in various cell lines and lung cancer xenografts. Treating cells with indisulam led to downregulation of cyclin H, which prevented CDK2 activation. Combined treatment with palbociclib and indisulam induced a senescence program and sensitized cells to senolytic therapy. Our data indicate that inhibition of CDK2 through indisulam treatment can enhance senescence induction by CDK4/6 inhibition.
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Affiliation(s)
- Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jackie L. Johnson
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lenno Krenning
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leyma Wardak
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Division of Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rene H. Medema
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- The NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rene Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail: (RB); (RLO)
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail: (RB); (RLO)
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4
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Pogacar Z, Groot K, Jochems F, Dos Santos Dias M, Mulero-Sánchez A, Morris B, Roosen M, Wardak L, De Conti G, Velds A, Lieftink C, Thijssen B, Beijersbergen RL, Bernards R, Leite de Oliveira R. Genetic and compound screens uncover factors modulating cancer cell response to indisulam. Life Sci Alliance 2022; 5:5/9/e202101348. [PMID: 35534224 PMCID: PMC9095732 DOI: 10.26508/lsa.202101348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/28/2022] Open
Abstract
The authors identify that loss of SRPK1 sensitises cancer cells to indisulam treatment and loss of CAND1 confers resistance. Resistance is mediated through RBM39. Furthermore, pharmacological Bcl-xL inhibition prevents acquired resistance to indisulam. Discovering biomarkers of drug response and finding powerful drug combinations can support the reuse of previously abandoned cancer drugs in the clinic. Indisulam is an abandoned drug that acts as a molecular glue, inducing degradation of splicing factor RBM39 through interaction with CRL4DCAF15. Here, we performed genetic and compound screens to uncover factors mediating indisulam sensitivity and resistance. First, a dropout CRISPR screen identified SRPK1 loss as a synthetic lethal interaction with indisulam that can be exploited therapeutically by the SRPK1 inhibitor SPHINX31. Moreover, a CRISPR resistance screen identified components of the degradation complex that mediate resistance to indisulam: DCAF15, DDA1, and CAND1. Last, we show that cancer cells readily acquire spontaneous resistance to indisulam. Upon acquiring indisulam resistance, pancreatic cancer (Panc10.05) cells still degrade RBM39 and are vulnerable to BCL-xL inhibition. The better understanding of the factors that influence the response to indisulam can assist rational reuse of this drug in the clinic.
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Affiliation(s)
- Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Matheus Dos Santos Dias
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antonio Mulero-Sánchez
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ben Morris
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mieke Roosen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leyma Wardak
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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5
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Manjón AG, Linder S, Teunissen H, Friskes A, Zwart W, de Wit E, Medema RH. Unexpected gene activation following CRISPR-Cas9-mediated genome editing. EMBO Rep 2021; 23:e53902. [PMID: 34927791 PMCID: PMC8811649 DOI: 10.15252/embr.202153902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
The discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its development as a genome editing tool has revolutionized the field of molecular biology. In the DNA damage field, CRISPR has brought an alternative to induce endogenous double-strand breaks (DSBs) at desired genomic locations and study the DNA damage response and its consequences. Many systems for sgRNA delivery have been reported in order to efficiently generate this DSB, including lentiviral vectors. However, some of the consequences of these systems are not yet well understood. Here, we report that lentiviral-based sgRNA vectors can integrate into the endogenous genomic target location, leading to undesired activation of the target gene. By generating a DSB in the regulatory region of the ABCB1 gene using a lentiviral sgRNA vector, we can induce the formation of Taxol-resistant colonies. We show that these colonies upregulate ABCB1 via integration of the EEF1A1 and the U6 promoters from the sgRNA vector. We believe that this is an unreported CRISPR/Cas9 on-target effect that researchers need to be aware of when using lentiviral vectors for genome editing.
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Affiliation(s)
- Anna G Manjón
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simon Linder
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hans Teunissen
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anoek Friskes
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elzo de Wit
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René H Medema
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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6
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Genomic profiling in oncology clinical practice. Clin Transl Oncol 2020; 22:1430-1439. [PMID: 31981077 DOI: 10.1007/s12094-020-02296-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/08/2020] [Indexed: 02/04/2023]
Abstract
The development of high-throughput technologies such as next-generation sequencing for DNA sequencing together with the decrease in their cost has led to the progressive introduction of genomic profiling in our daily practice in oncology. Nowadays, genomic profiling is part of genetic counseling, cancer diagnosis, molecular characterization, and as a biomarker of prognosis and response to treatment. Furthermore, germline or somatic genomic characterization of the tumor may provide new treatment opportunities for patients with cancer. In this review, we will summarize the clinical applications and limitations of genomic profiling in oncology clinical practice, focusing on next-generation sequencing.
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7
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Cefalì M, Efstathopoulou A, De Dosso S, Saletti P. Lymphocyte count and lymphocyte-to-white blood cells ratio as indicators of survival in specific cancer subtypes. Int Immunopharmacol 2019; 77:105982. [PMID: 31677993 DOI: 10.1016/j.intimp.2019.105982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/07/2019] [Accepted: 10/13/2019] [Indexed: 10/25/2022]
Affiliation(s)
- M Cefalì
- Medical Oncology Clinic, Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland.
| | - A Efstathopoulou
- Medical Oncology Clinic, Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - S De Dosso
- Medical Oncology Clinic, Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
| | - P Saletti
- Medical Oncology Clinic, Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
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