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Previtali V, Bagnolini G, Ciamarone A, Ferrandi G, Rinaldi F, Myers SH, Roberti M, Cavalli A. New Horizons of Synthetic Lethality in Cancer: Current Development and Future Perspectives. J Med Chem 2024; 67:11488-11521. [PMID: 38955347 DOI: 10.1021/acs.jmedchem.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
In recent years, synthetic lethality has been recognized as a solid paradigm for anticancer therapies. The discovery of a growing number of synthetic lethal targets has led to a significant expansion in the use of synthetic lethality, far beyond poly(ADP-ribose) polymerase inhibitors used to treat BRCA1/2-defective tumors. In particular, molecular targets within DNA damage response have provided a source of inhibitors that have rapidly reached clinical trials. This Perspective focuses on the most recent progress in synthetic lethal targets and their inhibitors, within and beyond the DNA damage response, describing their design and associated therapeutic strategies. We will conclude by discussing the current challenges and new opportunities for this promising field of research, to stimulate discussion in the medicinal chemistry community, allowing the investigation of synthetic lethality to reach its full potential.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Ciamarone
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giovanni Ferrandi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesco Rinaldi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel Harry Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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2
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Liu M, Zhao Z, Wang C, Sang S, Cui Y, Lv C, Yang X, Zhang N, Xiong K, Chen B, Dong Q, Liu K, Gu Y. Harnessing genetic interactions for prediction of immune checkpoint inhibitors response signature in cancer cells. Cancer Lett 2024; 594:216991. [PMID: 38797232 DOI: 10.1016/j.canlet.2024.216991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Genetic interactions (GIs) refer to two altered genes having a combined effect that is not seen individually. They play a crucial role in influencing drug efficacy. We utilized CGIdb 2.0 (http://www.medsysbio.org/CGIdb2/), an updated database of comprehensively published GIs information, encompassing synthetic lethality (SL), synthetic viability (SV), and chemical-genetic interactions. CGIdb 2.0 elucidates GIs relationships between or within protein complex models by integrating protein-protein physical interactions. Additionally, we introduced GENIUS (GENetic Interactions mediated drUg Signature) to leverage GIs for identifying the response signature of immune checkpoint inhibitors (ICIs). GENIUS identified high MAP4K4 expression as a resistant signature and high HERC4 expression as a sensitive signature for ICIs treatment. Melanoma patients with high expression of MAP4K4 were associated with decreased efficacy and poorer survival following ICIs treatment. Conversely, overexpression of HERC4 in melanoma patients correlated with a positive response to ICIs. Notably, HERC4 enhances sensitivity to immunotherapy by facilitating antigen presentation. Analyses of immune cell infiltration and single-cell data revealed that B cells expressing MAP4K4 may contribute to resistance to ICIs in melanoma. Overall, CGIdb 2.0, provides integrated GIs data, thus serving as a crucial tool for exploring drug effects.
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Affiliation(s)
- Mingyue Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhangxiang Zhao
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC), Chongqing University Three Gorges Hospital, Chongqing University, Wanzhou, Chongqing, China
| | - Chengyu Wang
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shaocong Sang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanrui Cui
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chen Lv
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiuqi Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Nan Zhang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Xiong
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Bo Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qi Dong
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Kaidong Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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Krieg S, Rohde T, Rausch T, Butthof L, Wendler-Link L, Eckert C, Breuhahn K, Galy B, Korbel J, Billmann M, Breinig M, Tschaharganeh DF. Mitoferrin2 is a synthetic lethal target for chromosome 8p deleted cancers. Genome Med 2024; 16:83. [PMID: 38886830 PMCID: PMC11181659 DOI: 10.1186/s13073-024-01357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Somatic copy number alterations are a hallmark of cancer that offer unique opportunities for therapeutic exploitation. Here, we focused on the identification of specific vulnerabilities for tumors harboring chromosome 8p deletions. METHODS We developed and applied an integrative analysis of The Cancer Genome Atlas (TCGA), the Cancer Dependency Map (DepMap), and the Cancer Cell Line Encyclopedia to identify chromosome 8p-specific vulnerabilities. We employ orthogonal gene targeting strategies, both in vitro and in vivo, including short hairpin RNA-mediated gene knockdown and CRISPR/Cas9-mediated gene knockout to validate vulnerabilities. RESULTS We identified SLC25A28 (also known as MFRN2), as a specific vulnerability for tumors harboring chromosome 8p deletions. We demonstrate that vulnerability towards MFRN2 loss is dictated by the expression of its paralog, SLC25A37 (also known as MFRN1), which resides on chromosome 8p. In line with their function as mitochondrial iron transporters, MFRN1/2 paralog protein deficiency profoundly impaired mitochondrial respiration, induced global depletion of iron-sulfur cluster proteins, and resulted in DNA-damage and cell death. MFRN2 depletion in MFRN1-deficient tumors led to impaired growth and even tumor eradication in preclinical mouse xenograft experiments, highlighting its therapeutic potential. CONCLUSIONS Our data reveal MFRN2 as a therapeutic target of chromosome 8p deleted cancers and nominate MFNR1 as the complimentary biomarker for MFRN2-directed therapies.
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Affiliation(s)
- Stephan Krieg
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Rohde
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Luise Butthof
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lena Wendler-Link
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Eckert
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kai Breuhahn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bruno Galy
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Maximilian Billmann
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany.
| | - Marco Breinig
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
| | - Darjus F Tschaharganeh
- Helmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ), Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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4
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Ye BJ, Li DF, Li XY, Hao JL, Liu DJ, Yu H, Zhang CD. Methylation synthetic lethality: Exploiting selective drug targets for cancer therapy. Cancer Lett 2024; 597:217010. [PMID: 38849016 DOI: 10.1016/j.canlet.2024.217010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024]
Abstract
In cancer, synthetic lethality refers to the drug-induced inactivation of one gene and the inhibition of another in cancer cells by a drug, resulting in the death of only cancer cells; however, this effect is not present in normal cells, leading to targeted killing of cancer cells. Recent intensive epigenetic research has revealed that aberrant epigenetic changes are more frequently observed than gene mutations in certain cancers. Recently, numerous studies have reported various methylation synthetic lethal combinations involving DNA damage repair genes, metabolic pathway genes, and paralogs with significant results in cellular models, some of which have already entered clinical trials with promising results. This review systematically introduces the advantages of methylation synthetic lethality and describes the lethal mechanisms of methylation synthetic lethal combinations that have recently demonstrated success in cellular models. Furthermore, we discuss the future opportunities and challenges of methylation synthetic lethality in targeted anticancer therapies.
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Affiliation(s)
- Bing-Jie Ye
- Clinical Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Di-Fei Li
- Clinical Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Xin-Yun Li
- Clinical Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Jia-Lin Hao
- Central Laboratory, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Di-Jie Liu
- Central Laboratory, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Hang Yu
- Department of Surgical Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
| | - Chun-Dong Zhang
- Central Laboratory, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; Department of Surgical Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
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5
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Li S, Han T. Frequent loss of FAM126A expression in colorectal cancer results in selective FAM126B dependency. iScience 2024; 27:109646. [PMID: 38638566 PMCID: PMC11025007 DOI: 10.1016/j.isci.2024.109646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/01/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Most advanced colorectal cancer (CRC) patients cannot benefit from targeted therapy due to lack of actionable targets. By mining data from the DepMap, we identified FAM126B as a specific vulnerability in CRC cell lines exhibiting low FAM126A expression. Employing a combination of genetic perturbation and inducible protein degradation techniques, we demonstrate that FAM126A and FAM126B function in a redundant manner to facilitate the recruitment of PI4KIIIα to the plasma membrane for PI4P synthesis. Examination of data from TCGA and GTEx revealed that over 7% of CRC tumor samples exhibited loss of FAM126A expression, contrasting with uniform FAM126A expression in normal tissues. In both CRC cell lines and tumor samples, promoter hypermethylation correlated with the loss of FAM126A expression, which could be reversed by DNA methylation inhibitors. In conclusion, our study reveals that loss of FAM126A expression results in FAM126B dependency, thus proposing FAM126B as a therapeutic target for CRC treatment.
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Affiliation(s)
- Shuang Li
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ting Han
- PTN Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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Navarro-Carrasco E, Monte-Serrano E, Campos-Díaz A, Rolfs F, de Goeij-de Haas R, Pham TV, Piersma SR, González-Alonso P, Jiménez CR, Lazo PA. VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells. Int J Mol Sci 2024; 25:4874. [PMID: 38732093 PMCID: PMC11084957 DOI: 10.3390/ijms25094874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
The chromatin organization and its dynamic remodeling determine its accessibility and sensitivity to DNA damage oxidative stress, the main source of endogenous DNA damage. We studied the role of the VRK1 chromatin kinase in the response to oxidative stress. which alters the nuclear pattern of histone epigenetic modifications and phosphoproteome pathways. The early effect of oxidative stress on chromatin was studied by determining the levels of 8-oxoG lesions and the alteration of the epigenetic modification of histones. Oxidative stress caused an accumulation of 8-oxoG DNA lesions that were increased by VRK1 depletion, causing a significant accumulation of DNA strand breaks detected by labeling free 3'-DNA ends. In addition, oxidative stress altered the pattern of chromatin epigenetic marks and the nuclear phosphoproteome pathways that were impaired by VRK1 depletion. Oxidative stress induced the acetylation of H4K16ac and H3K9 and the loss of H3K4me3. The depletion of VRK1 altered all these modifications induced by oxidative stress and resulted in losses of H4K16ac and H3K9ac and increases in the H3K9me3 and H3K4me3 levels. All these changes were induced by the oxidative stress in the epigenetic pattern of histones and impaired by VRK1 depletion, indicating that VRK1 plays a major role in the functional reorganization of chromatin in the response to oxidative stress. The analysis of the nuclear phosphoproteome in response to oxidative stress detected an enrichment of the phosphorylated proteins associated with the chromosome organization and chromatin remodeling pathways, which were significantly decreased by VRK1 depletion. VRK1 depletion alters the histone epigenetic pattern and nuclear phosphoproteome pathways in response to oxidative stress. The enzymes performing post-translational epigenetic modifications are potential targets in synthetic lethality strategies for cancer therapies.
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Affiliation(s)
- Elena Navarro-Carrasco
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Eva Monte-Serrano
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Aurora Campos-Díaz
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Frank Rolfs
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Richard de Goeij-de Haas
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Thang V. Pham
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Sander R. Piersma
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Paula González-Alonso
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Pedro A. Lazo
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
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Cai C, Tu J, Najarro J, Zhang R, Fan H, Zhang FQ, Li J, Xie Z, Su R, Dong L, Arellano N, Ciboddo M, Elf SE, Gao X, Chen J, Wu R. NRAS Mutant Dictates AHCYL1-Governed ER Calcium Homeostasis for Melanoma Tumor Growth. Mol Cancer Res 2024; 22:386-401. [PMID: 38294692 PMCID: PMC10987265 DOI: 10.1158/1541-7786.mcr-23-0445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/27/2023] [Accepted: 01/29/2024] [Indexed: 02/01/2024]
Abstract
Calcium homeostasis is critical for cell proliferation, and emerging evidence shows that cancer cells exhibit altered calcium signals to fulfill their need for proliferation. However, it remains unclear whether there are oncogene-specific calcium homeostasis regulations that can expose novel therapeutic targets. Here, from RNAi screen, we report that adenosylhomocysteinase like protein 1 (AHCYL1), a suppressor of the endoplasmic reticulum (ER) calcium channel protein inositol trisphosphate receptor (IP3R), is selectively upregulated and critical for cell proliferation and tumor growth potential of human NRAS-mutated melanoma, but not for melanoma expressing BRAF V600E. Mechanistically, AHCYL1 deficiency results in decreased ER calcium levels, activates the unfolded protein response (UPR), and triggers downstream apoptosis. In addition, we show that AHCYL1 transcription is regulated by activating transcription factor 2 (ATF2) in NRAS-mutated melanoma. Our work provides evidence for oncogene-specific calcium regulations and suggests AHCYL1 as a novel therapeutic target for RAS mutant-expressing human cancers, including melanoma. IMPLICATIONS Our findings suggest that targeting the AHCYL1-IP3R axis presents a novel therapeutic approach for NRAS-mutated melanomas, with potential applicability to all cancers harboring RAS mutations, such as KRAS-mutated human colorectal cancers.
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Affiliation(s)
- Chufan Cai
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jiayi Tu
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jeronimo Najarro
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Rukang Zhang
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Hao Fan
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Freya Q. Zhang
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Jiacheng Li
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Zhicheng Xie
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Nicole Arellano
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Michele Ciboddo
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Shannon E. Elf
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Xue Gao
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Current address: Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jing Chen
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Rong Wu
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
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8
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Liu F, Xin M, Feng H, Zhang W, Liao Z, Sheng T, Wen P, Wu Q, Liang T, Shi J, Zhou R, He K, Gu Z, Li H. Cryo-shocked tumor cells deliver CRISPR-Cas9 for lung cancer regression by synthetic lethality. SCIENCE ADVANCES 2024; 10:eadk8264. [PMID: 38552011 PMCID: PMC10980270 DOI: 10.1126/sciadv.adk8264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/23/2024] [Indexed: 04/01/2024]
Abstract
Although CRISPR-mediated genome editing holds promise for cancer therapy, inadequate tumor targeting and potential off-target side effects hamper its outcomes. In this study, we present a strategy using cryo-shocked lung tumor cells as a CRISPR-Cas9 delivery system for cyclin-dependent kinase 4 (CDK4) gene editing, which initiates synthetic lethal in KRAS-mutant non-small cell lung cancer (NSCLC). By rapidly liquid nitrogen shocking, we effectively eliminate the pathogenicity of tumor cells while preserving their structure and surface receptor activity. This delivery system enables the loaded CRISPR-Cas9 to efficiently target to lung through the capture in pulmonary capillaries and interactions with endothelial cells. In a NSCLC-bearing mouse model, the drug accumulation is increased nearly fourfold in lung, and intratumoral CDK4 expression is substantially down-regulated compared to CRISPR-Cas9 lipofectamine nanoparticles administration. Furthermore, CRISPR-Cas9 editing-mediated CDK4 ablation triggers synthetic lethal in KRAS-mutant NSCLC and prolongs the survival of mice.
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Affiliation(s)
- Feng Liu
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Minhang Xin
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huiheng Feng
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Wentao Zhang
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziyan Liao
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Tao Sheng
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ping Wen
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Qing Wu
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Tingxizi Liang
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Jiaqi Shi
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Ruyi Zhou
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kaixin He
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
| | - Zhen Gu
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongjun Li
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
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9
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Lajmi N, Alves-Vasconcelos S, Tsiachristas A, Haworth A, Woods K, Crichton C, Noble T, Salih H, Várnai KA, Branford-White H, Orrell L, Osman A, Bradley KM, Bonney L, McGowan DR, Davies J, Prime MS, Hassan AB. Challenges and solutions to system-wide use of precision oncology as the standard of care paradigm. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e4. [PMID: 38699518 PMCID: PMC11062796 DOI: 10.1017/pcm.2024.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/02/2024] [Accepted: 03/12/2024] [Indexed: 05/05/2024]
Abstract
The personalised oncology paradigm remains challenging to deliver despite technological advances in genomics-based identification of actionable variants combined with the increasing focus of drug development on these specific targets. To ensure we continue to build concerted momentum to improve outcomes across all cancer types, financial, technological and operational barriers need to be addressed. For example, complete integration and certification of the 'molecular tumour board' into 'standard of care' ensures a unified clinical decision pathway that both counteracts fragmentation and is the cornerstone of evidence-based delivery inside and outside of a research setting. Generally, integrated delivery has been restricted to specific (common) cancer types either within major cancer centres or small regional networks. Here, we focus on solutions in real-world integration of genomics, pathology, surgery, oncological treatments, data from clinical source systems and analysis of whole-body imaging as digital data that can facilitate cost-effectiveness analysis, clinical trial recruitment, and outcome assessment. This urgent imperative for cancer also extends across the early diagnosis and adjuvant treatment interventions, individualised cancer vaccines, immune cell therapies, personalised synthetic lethal therapeutics and cancer screening and prevention. Oncology care systems worldwide require proactive step-changes in solutions that include inter-operative digital working that can solve patient centred challenges to ensure inclusive, quality, sustainable, fair and cost-effective adoption and efficient delivery. Here we highlight workforce, technical, clinical, regulatory and economic challenges that prevent the implementation of precision oncology at scale, and offer a systematic roadmap of integrated solutions for standard of care based on minimal essential digital tools. These include unified decision support tools, quality control, data flows within an ethical and legal data framework, training and certification, monitoring and feedback. Bridging the technical, operational, regulatory and economic gaps demands the joint actions from public and industry stakeholders across national and global boundaries.
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Affiliation(s)
- Nesrine Lajmi
- Diagnostics Division, Roche Information Solutions, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Sofia Alves-Vasconcelos
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Apostolos Tsiachristas
- Nuffield Department of Primary Care Health Sciences, Radcliffe Observatory Quarter, Oxford, UK
| | - Andrew Haworth
- Diagnostics Division, Roche Information Solutions, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Kerrie Woods
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Theresa Noble
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Hizni Salih
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kinga A. Várnai
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Liam Orrell
- Diagnostics Division, Roche Information Solutions, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Andrew Osman
- Roche Healthcare Consulting, Roche Diagnostics Limited, West Sussex, UK
| | - Kevin M. Bradley
- Wales Research and Diagnostic PET Imaging Centre, University Hospital of Wales, Cardiff, UK
| | - Lara Bonney
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Jim Davies
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
| | - Matthew S. Prime
- Diagnostics Division, Roche Information Solutions, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Andrew Bassim Hassan
- Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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10
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Tien JCY, Chang Y, Zhang Y, Chou J, Cheng Y, Wang X, Yang J, Mannan R, Shah P, Wang XM, Todd AJ, Eyunni S, Cheng C, Rebernick RJ, Xiao L, Bao Y, Neiswender J, Brough R, Pettitt SJ, Cao X, Miner SJ, Zhou L, Wu YM, Labanca E, Wang Y, Parolia A, Cieslik M, Robinson DR, Wang Z, Feng FY, Lord CJ, Ding K, Chinnaiyan AM. CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585990. [PMID: 38562774 PMCID: PMC10983964 DOI: 10.1101/2024.03.20.585990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration-resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development-either alone, or in the context of other genetic alterations-and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions and robust T cell infiltration in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with Trp53 inactivation but negatively associated with Pten inactivation-akin to what is observed in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent Trp53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12 knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic Cdk12 and Trp53 loss allografts represent a new syngeneic model for the study of androgen receptor (AR)-positive, luminal prostate cancer. Notably, Cdk12/Trp53 loss prostate tumors are sensitive to immune checkpoint blockade. Cdk12-null organoids (either with or without Trp53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fide tumor suppressor gene with impact on tumor progression and lends support to paralog-based synthetic lethality as a promising strategy for treating CDK12-mutant mCRPC.
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Affiliation(s)
- Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- These authors contributed equally to this work
| | - Yunhui Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally to this work
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jianzhang Yang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Palak Shah
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiao-Ming Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Abigail J. Todd
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ryan J. Rebernick
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Bao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - James Neiswender
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Licheng Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Estefania Labanca
- Department of Genitourinary Medical Oncology and David H. Koch Center for Applied Research of Genitourinary Cancer, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Vancouver General Hospital and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, V6H 3Z6, Canada
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Dan R. Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Zhen Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, College of Pharmacy, Jinan University, Guangzhou 511400, People’s Republic of China
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People’s Republic of China
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Lead contact
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11
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Liu X, Hu J, Zheng J. SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality. Bioinformatics 2024; 40:btae016. [PMID: 38244572 PMCID: PMC10868331 DOI: 10.1093/bioinformatics/btae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
SUMMARY Synthetic lethality (SL) refers to a type of genetic interaction in which the simultaneous inactivation of two genes leads to cell death, while the inactivation of a single gene does not affect cell viability. It significantly expands the range of potential therapeutic targets for anti-cancer treatments. SL interactions are primarily identified through experimental screening and computational prediction. Although various computational methods have been proposed, they tend to ignore providing evidence to support their predictions of SL. Besides, they are rarely user-friendly for biologists who likely have limited programming skills. Moreover, the genetic context specificity of SL interactions is often not taken into consideration. Here, we introduce a web server called SL-Miner, which is designed to mine the evidence of SL relationships between a primary gene and a few candidate SL partner genes in a specific type of cancer, and to prioritize these candidate genes by integrating various types of evidence. For intuitive data visualization, SL-Miner provides a range of charts (e.g. volcano plot and box plot) to help users get insights from the data. AVAILABILITY AND IMPLEMENTATION SL-Miner is available at https://slminer.sist.shanghaitech.edu.cn.
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Affiliation(s)
- Xin Liu
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jieni Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jie Zheng
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Engineering Research Center of Intelligent Vision and Imaging, Shanghai 201210, China
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12
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Zhang Y, Liu Z, Hirschi M, Brodsky O, Johnson E, Won SJ, Nagata A, Petroski MD, Majmudar JD, Niessen S, VanArsdale T, Gilbert AM, Hayward MM, Stewart AE, Nager AR, Melillo B, Cravatt B. Expanding the ligandable proteome by paralog hopping with covalent probes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576274. [PMID: 38293178 PMCID: PMC10827202 DOI: 10.1101/2024.01.18.576274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.
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Affiliation(s)
- Yuanjin Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Zhonglin Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Marsha Hirschi
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Oleg Brodsky
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Eric Johnson
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Sang Joon Won
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Asako Nagata
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | | | - Jaimeen D Majmudar
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Cambridge, MA 02139, USA
| | - Sherry Niessen
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
- Current address: Belharra Therapeutics, 3985 Sorrento Valley Blvd suite c, San Diego, CA 92121
| | - Todd VanArsdale
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Adam M Gilbert
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - Matthew M Hayward
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
- Current address: Magnet Biomedicine, 321 Harrison Ave., Suite 600, Boston, MA 02118, USA
| | - Al E Stewart
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Andrew R Nager
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Benjamin Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
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13
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De Kegel B, Ryan CJ. Paralog dispensability shapes homozygous deletion patterns in tumor genomes. Mol Syst Biol 2023; 19:e11987. [PMID: 37963083 DOI: 10.15252/msb.202311987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023] Open
Abstract
Genomic instability is a hallmark of cancer, resulting in tumor genomes having large numbers of genetic aberrations, including homozygous deletions of protein coding genes. That tumor cells remain viable in the presence of such gene loss suggests high robustness to genetic perturbation. In model organisms and cancer cell lines, paralogs have been shown to contribute substantially to genetic robustness-they are generally more dispensable for growth than singletons. Here, by analyzing copy number profiles of > 10,000 tumors, we test the hypothesis that the increased dispensability of paralogs shapes tumor genome evolution. We find that genes with paralogs are more likely to be homozygously deleted and that this cannot be explained by other factors known to influence copy number variation. Furthermore, features that influence paralog dispensability in cancer cell lines correlate with paralog deletion frequency in tumors. Finally, paralogs that are broadly essential in cancer cell lines are less frequently deleted in tumors than non-essential paralogs. Overall, our results suggest that homozygous deletions of paralogs are more frequently observed in tumor genomes because paralogs are more dispensable.
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Affiliation(s)
- Barbara De Kegel
- School of Computer Science and Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Colm J Ryan
- School of Computer Science and Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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14
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Ryan CJ, Devakumar LPS, Pettitt SJ, Lord CJ. Complex synthetic lethality in cancer. Nat Genet 2023; 55:2039-2048. [PMID: 38036785 DOI: 10.1038/s41588-023-01557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/04/2023] [Indexed: 12/02/2023]
Abstract
The concept of synthetic lethality has been widely applied to identify therapeutic targets in cancer, with varying degrees of success. The standard approach normally involves identifying genetic interactions between two genes, a driver and a target. In reality, however, most cancer synthetic lethal effects are likely complex and also polygenic, being influenced by the environment in addition to involving contributions from multiple genes. By acknowledging and delineating this complexity, we describe in this article how the success rate in cancer drug discovery and development could be improved.
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Affiliation(s)
- Colm J Ryan
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland.
| | - Lovely Paul Solomon Devakumar
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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15
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Liu F, Liao Z, Zhang Z. MYC in liver cancer: mechanisms and targeted therapy opportunities. Oncogene 2023; 42:3303-3318. [PMID: 37833558 DOI: 10.1038/s41388-023-02861-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
MYC, a major oncogenic transcription factor, regulates target genes involved in various pathways such as cell proliferation, metabolism and immune evasion, playing a critical role in the tumor initiation and development in multiple types of cancer. In liver cancer, MYC and its signaling pathways undergo significant changes, exerting a profound impact on liver cancer progression, including tumor proliferation, metastasis, dedifferentiation, metabolism, immune microenvironment, and resistance to comprehensive therapies. This makes MYC an appealing target, despite it being previously considered an undruggable protein. In this review, we discuss the role and mechanisms of MYC in liver physiology, chronic liver diseases, hepatocarcinogenesis, and liver cancer progression, providing a theoretical basis for targeting MYC as an ideal therapeutic target for liver cancer. We also summarize and prospect the strategies for targeting MYC, including direct and indirect approaches to abolish the oncogenic function of MYC in liver cancer.
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Affiliation(s)
- Furong Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhanguo Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China.
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
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16
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Pu M, Cheng K, Li X, Xin Y, Wei L, Jin S, Zheng W, Peng G, Tang Q, Zhou J, Zhang Y. Using graph-based model to identify cell specific synthetic lethal effects. Comput Struct Biotechnol J 2023; 21:5099-5110. [PMID: 37920819 PMCID: PMC10618116 DOI: 10.1016/j.csbj.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023] Open
Abstract
Synthetic lethal (SL) pairs are pairs of genes whose simultaneous loss-of-function results in cell death, while a damaging mutation of either gene alone does not affect the cell's survival. This makes SL pairs attractive targets for precision cancer therapies, as targeting the unimpaired gene of the SL pair can selectively kill cancer cells that already harbor the impaired gene. Limited by the difficulty of finding true SL pairs, especially on specific cell types, current computational approaches provide only limited insights because of overlooking the crucial aspects of cellular context dependency and mechanistic understanding of SL pairs. As a result, the identification of SL targets still relies on expensive, time-consuming experimental approaches. In this work, we applied cell-line specific multi-omics data to a specially designed deep learning model to predict cell-line specific SL pairs. Through incorporating multiple types of cell-specific omics data with a self-attention module, we represent gene relationships as graphs. Our approach achieves the prediction of SL pairs in a cell-specific manner and demonstrates the potential to facilitate the discovery of cell-specific SL targets for cancer therapeutics, providing a tool to unearth mechanisms underlying the origin of SL in cancer biology. The code and data of our approach can be found at https://github.com/promethiume/SLwise.
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Affiliation(s)
| | - Kaiyang Cheng
- StoneWise, AI, Ltd., Beijing, China
- Nanjing University of Chinese Medicine, Shanghai, China
| | - Xiaorong Li
- StoneWise, AI, Ltd., Beijing, China
- Minzu University of China, Beijing, China
| | | | | | - Sutong Jin
- StoneWise, AI, Ltd., Beijing, China
- Harbin Institute of Technology, Weihai, China
| | | | | | - Qihong Tang
- StoneWise, AI, Ltd., Beijing, China
- Guilin University of Electronic Science and Technology, Guangxi, China
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17
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Mirzayans R, Murray D. Intratumor Heterogeneity and Treatment Resistance of Solid Tumors with a Focus on Polyploid/Senescent Giant Cancer Cells (PGCCs). Int J Mol Sci 2023; 24:11534. [PMID: 37511291 PMCID: PMC10380821 DOI: 10.3390/ijms241411534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Single cell biology has revealed that solid tumors and tumor-derived cell lines typically contain subpopulations of cancer cells that are readily distinguishable from the bulk of cancer cells by virtue of their enormous size. Such cells with a highly enlarged nucleus, multiple nuclei, and/or multiple micronuclei are often referred to as polyploid giant cancer cells (PGCCs), and may exhibit features of senescence. PGCCs may enter a dormant phase (active sleep) after they are formed, but a subset remain viable, secrete growth promoting factors, and can give rise to therapy resistant and tumor repopulating progeny. Here we will briefly discuss the prevalence and prognostic value of PGCCs across different cancer types, the current understanding of the mechanisms of their formation and fate, and possible reasons why these tumor repopulating "monsters" continue to be ignored in most cancer therapy-related preclinical studies. In addition to PGCCs, other subpopulations of cancer cells within a solid tumor (such as oncogenic caspase 3-activated cancer cells and drug-tolerant persister cancer cells) can also contribute to therapy resistance and pose major challenges to the delivery of cancer therapy.
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Affiliation(s)
- Razmik Mirzayans
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - David Murray
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
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