1
|
Jyakhwo S, Serov N, Dmitrenko A, Vinogradov VV. Machine Learning Reinforced Genetic Algorithm for Massive Targeted Discovery of Selectively Cytotoxic Inorganic Nanoparticles. Small 2024; 20:e2305375. [PMID: 37771186 DOI: 10.1002/smll.202305375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/11/2023] [Indexed: 09/30/2023]
Abstract
Nanoparticles (NPs) have been employed as drug delivery systems (DDSs) for several decades, primarily as passive carriers, with limited selectivity. However, recent publications have shed light on the emerging phenomenon of NPs exhibiting selective cytotoxicity against cancer cell lines, attributable to distinct metabolic disparities between healthy and pathological cells. This study revisits the concept of NPs selective cytotoxicity, and for the first time proposes a high-throughput in silico screening approach to massive targeted discovery of selectively cytotoxic inorganic NPs. In the first step, this work trains a gradient boosting regression model to predict viability of NP-treated cell lines. The model achieves mean cross-validation (CV) Q2 = 0.80 and root mean square error (RMSE) of 13.6. In the second step, this work develops a machine learning (ML) reinforced genetic algorithm (GA), capable of screening >14 900 candidates/min, to identify the best-performing selectively cytotoxic NPs. As proof-of-concept, DDS candidates for the treatment of liver cancer are screened on HepG2 and hepatocytes cell lines resulting in Ag NPs with selective toxicity score of 42%. This approach opens the door for clinical translation of NPs, expanding their therapeutic application to a wider range of chemical space of NPs and living organisms such as bacteria and fungi.
Collapse
Affiliation(s)
- Susan Jyakhwo
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
| | - Nikita Serov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
| | - Andrei Dmitrenko
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
| | - Vladimir V Vinogradov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
| |
Collapse
|
2
|
Ben Toumia I, Bachetti T, Chekir-Ghedira L, Profumo A, Ponassi M, Di Domizio A, Izzotti A, Sciacca S, Puglisi C, Forte S, Giuffrida R, Colarossi C, Milardi D, Grasso G, Lanza V, Fiordoro S, Drago G, Tkachenko K, Cardinali B, Romano P, Iervasi E, Vargas GC, Barboro P, Kohnke FH, Rosano C. Fraisinib: a calixpyrrole derivative reducing A549 cell-derived NSCLC tumor in vivo acts as a ligand of the glycine-tRNA synthase, a new molecular target in oncology. Front Pharmacol 2024; 14:1258108. [PMID: 38235113 PMCID: PMC10791888 DOI: 10.3389/fphar.2023.1258108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024] Open
Abstract
Background and purpose: Lung cancer is the leading cause of death in both men and women, constituting a major public health problem worldwide. Non-small-cell lung cancer accounts for 85%-90% of all lung cancers. We propose a compound that successfully fights tumor growth in vivo by targeting the enzyme GARS1. Experimental approach: We present an in-depth investigation of the mechanism through which Fraisinib [meso-(p-acetamidophenyl)-calix(4)pyrrole] affects the human lung adenocarcinoma A549 cell line. In a xenografted model of non-small-cell lung cancer, Fraisinib was found to reduce tumor mass volume without affecting the vital parameters or body weight of mice. Through a computational approach, we uncovered that glycyl-tRNA synthetase is its molecular target. Differential proteomics analysis further confirmed that pathways regulated by Fraisinib are consistent with glycyl-tRNA synthetase inhibition. Key results: Fraisinib displays a strong anti-tumoral potential coupled with limited toxicity in mice. Glycyl-tRNA synthetase has been identified and validated as a protein target of this compound. By inhibiting GARS1, Fraisinib modulates different key biological processes involved in tumoral growth, aggressiveness, and invasiveness. Conclusion and implications: The overall results indicate that Fraisinib is a powerful inhibitor of non-small-cell lung cancer growth by exerting its action on the enzyme GARS1 while displaying marginal toxicity in animal models. Together with the proven ability of this compound to cross the blood-brain barrier, we can assess that Fraisinib can kill two birds with one stone: targeting the primary tumor and its metastases "in one shot." Taken together, we suggest that inhibiting GARS1 expression and/or GARS1 enzymatic activity may be innovative molecular targets for cancer treatment.
Collapse
Affiliation(s)
| | | | - Leila Chekir-Ghedira
- Unit of Bioactive Natural Substances and Biotechnology, Faculty of Dental Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Aldo Profumo
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Marco Ponassi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Alberto Izzotti
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Stefano Forte
- Istituto Oncologico del Mediterraneo, Viagrande, Italy
| | | | | | - Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Valeria Lanza
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Stefano Fiordoro
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Giacomo Drago
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Paolo Romano
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Erika Iervasi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Paola Barboro
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Franz Heinrich Kohnke
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), University of Messina, Messina, Italy
| | | |
Collapse
|
3
|
Pun FW, Leung GHD, Leung HW, Rice J, Schmauck-Medina T, Lautrup S, Long X, Liu BHM, Wong CW, Ozerov IV, Aliper A, Ren F, Rosenberg AJ, Agrawal N, Izumchenko E, Fang EF, Zhavoronkov A. A comprehensive AI-driven analysis of large-scale omic datasets reveals novel dual-purpose targets for the treatment of cancer and aging. Aging Cell 2023; 22:e14017. [PMID: 37888486 PMCID: PMC10726874 DOI: 10.1111/acel.14017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
As aging and tumorigenesis are tightly interconnected biological processes, targeting their common underlying driving pathways may induce dual-purpose anti-aging and anti-cancer effects. Our transcriptomic analyses of 16,740 healthy samples demonstrated tissue-specific age-associated gene expression, with most tumor suppressor genes downregulated during aging. Furthermore, a large-scale pan-cancer analysis of 11 solid tumor types (11,303 cases and 4431 control samples) revealed that many cellular processes, such as protein localization, DNA replication, DNA repair, cell cycle, and RNA metabolism, were upregulated in cancer but downregulated in healthy aging tissues, whereas pathways regulating cellular senescence were upregulated in both aging and cancer. Common cancer targets were identified by the AI-driven target discovery platform-PandaOmics. Age-associated cancer targets were selected and further classified into four groups based on their reported roles in lifespan. Among the 51 identified age-associated cancer targets with anti-aging experimental evidence, 22 were proposed as dual-purpose targets for anti-aging and anti-cancer treatment with the same therapeutic direction. Among age-associated cancer targets without known lifespan-regulating activity, 23 genes were selected based on predicted dual-purpose properties. Knockdown of histone demethylase KDM1A, one of these unexplored candidates, significantly extended lifespan in Caenorhabditis elegans. Given KDM1A's anti-cancer activities reported in both preclinical and clinical studies, our findings propose KDM1A as a promising dual-purpose target. This is the first study utilizing an innovative AI-driven approach to identify dual-purpose target candidates for anti-aging and anti-cancer treatment, supporting the value of AI-assisted target identification for drug discovery.
Collapse
Affiliation(s)
- Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong, China
| | | | | | - Jared Rice
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Tomas Schmauck-Medina
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Xi Long
- Insilico Medicine Hong Kong Ltd., Hong Kong, China
| | | | | | | | - Alex Aliper
- Insilico Medicine AI Ltd., Masdar City, United Arab Emirates
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Ari J Rosenberg
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, Illinois, USA
| | - Nishant Agrawal
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, Illinois, USA
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
- The Norwegian Centre On Healthy Ageing (NO-Age), Oslo, Norway
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong, China
- Insilico Medicine AI Ltd., Masdar City, United Arab Emirates
- Buck Institute for Research on Aging, Novato, California, USA
| |
Collapse
|
4
|
Nakken S, Gundersen S, Bernal FLM, Polychronopoulos D, Hovig E, Wesche J. Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR. Int J Cancer 2023; 153:1819-1828. [PMID: 37551617 DOI: 10.1002/ijc.34666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 08/09/2023]
Abstract
Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based service hosted by the Galaxy platform (https://oncotools.elixir.no), and can also be accessed as a stand-alone R package (https://github.com/sigven/oncoEnrichR).
Collapse
Affiliation(s)
- Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Sveinung Gundersen
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Fabian L M Bernal
- University Center for Information Technology, University of Oslo, Oslo, Norway
| | | | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Jørgen Wesche
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
5
|
Peng R, Deng M. Mapping the protein-protein interactome in the tumor immune microenvironment. Antib Ther 2023; 6:311-321. [PMID: 38098892 PMCID: PMC10720949 DOI: 10.1093/abt/tbad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/01/2023] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
The cell-to-cell communication primarily occurs through cell-surface and secreted proteins, which form a sophisticated network that coordinates systemic immune function. Uncovering these protein-protein interactions (PPIs) is indispensable for understanding the molecular mechanism and elucidating immune system aberrances under diseases. Traditional biological studies typically focus on a limited number of PPI pairs due to the relative low throughput of commonly used techniques. Encouragingly, classical methods have advanced, and many new systems tailored for large-scale protein-protein screening have been developed and successfully utilized. These high-throughput PPI investigation techniques have already made considerable achievements in mapping the immune cell interactome, enriching PPI databases and analysis tools, and discovering therapeutic targets for cancer and other diseases, which will definitely bring unprecedented insight into this field.
Collapse
Affiliation(s)
- Rui Peng
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, PR China
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, PR China
| | - Mi Deng
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, PR China
- School of Basic Medical Sciences, Health Science Center, Peking University, Beijing 100191, PR China
- Peking University Cancer Hospital and Institute, Peking University, Beijing 100142, PR China
| |
Collapse
|
6
|
Brown AC, Cohen CJ, Mielczarek O, Migliorini G, Costantino F, Allcock A, Davidson C, Elliott KS, Fang H, Lledó Lara A, Martin AC, Osgood JA, Sanniti A, Scozzafava G, Vecellio M, Zhang P, Black MH, Li S, Truong D, Molineros J, Howe T, Wordsworth BP, Bowness P, Knight JC. Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis. Cell Genom 2023; 3:100306. [PMID: 37388915 PMCID: PMC10300554 DOI: 10.1016/j.xgen.2023.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/30/2023] [Accepted: 03/27/2023] [Indexed: 07/01/2023]
Abstract
Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis characterized by enthesitis of the spine and sacroiliac joints. Genome-wide association studies (GWASs) have revealed more than 100 genetic associations whose functional effects remain largely unresolved. Here, we present a comprehensive transcriptomic and epigenomic map of disease-relevant blood immune cell subsets from AS patients and healthy controls. We find that, while CD14+ monocytes and CD4+ and CD8+ T cells show disease-specific differences at the RNA level, epigenomic differences are only apparent upon multi-omics integration. The latter reveals enrichment at disease-associated loci in monocytes. We link putative functional SNPs to genes using high-resolution Capture-C at 10 loci, including PTGER4 and ETS1, and show how disease-specific functional genomic data can be integrated with GWASs to enhance therapeutic target discovery. This study combines epigenetic and transcriptional analysis with GWASs to identify disease-relevant cell types and gene regulation of likely pathogenic relevance and prioritize drug targets.
Collapse
Affiliation(s)
- Andrew C. Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Carla J. Cohen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Olga Mielczarek
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Horizon Discovery (PerkinElmer) Cambridge Research Park, 8100 Beach Dr., Waterbeach, Cambridge CB25 9TL, UK
| | - Gabriele Migliorini
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Félicie Costantino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- UVSQ, INSERM UMR1173, Infection et Inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Paris, France
- Rheumatology Department, AP-HP, Ambroise Paré Hospital, Paris, France
| | - Alice Allcock
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Connor Davidson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | | | - Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Alicia Lledó Lara
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alice C. Martin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Julie A. Osgood
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Anna Sanniti
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Giuseppe Scozzafava
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- Centro Ricerche Fondazione Italiana Ricerca sull’Artrite (FIRA), Fondazione Pisana per la Scienza ONLUS, Via Ferruccio Giovannini 13, 56017 San Giuliano Terme (Pisa), Italy
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mary Helen Black
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Shuwei Li
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Dongnhu Truong
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Julio Molineros
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Trevor Howe
- Data Science, External Innovation, Janssen R&D, London W1G 0BG, UK
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| |
Collapse
|
7
|
Olsen A, Harpaz Z, Ren C, Shneyderman A, Veviorskiy A, Dralkina M, Konnov S, Shcheglova O, Pun FW, Leung GHD, Leung HW, Ozerov IV, Aliper A, Korzinkin M, Zhavoronkov A. Identification of dual-purpose therapeutic targets implicated in aging and glioblastoma multiforme using PandaOmics - an AI-enabled biological target discovery platform. Aging (Albany NY) 2023; 15:2863-2876. [PMID: 37100462 DOI: 10.18632/aging.204678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023]
Abstract
Glioblastoma Multiforme (GBM) is the most aggressive and most common primary malignant brain tumor. The age of GBM patients is considered as one of the disease's negative prognostic factors and the mean age of diagnosis is 62 years. A promising approach to preventing both GBM and aging is to identify new potential therapeutic targets that are associated with both conditions as concurrent drivers. In this work, we present a multi-angled approach of identifying targets, which takes into account not only the disease-related genes but also the ones important in aging. For this purpose, we developed three strategies of target identification using the results of correlation analysis augmented with survival data, differences in expression levels and previously published information of aging-related genes. Several studies have recently validated the robustness and applicability of AI-driven computational methods for target identification in both cancer and aging-related diseases. Therefore, we leveraged the AI predictive power of the PandaOmics TargetID engine in order to rank the resulting target hypotheses and prioritize the most promising therapeutic gene targets. We propose cyclic nucleotide gated channel subunit alpha 3 (CNGA3), glutamate dehydrogenase 1 (GLUD1) and sirtuin 1 (SIRT1) as potential novel dual-purpose therapeutic targets to treat aging and GBM.
Collapse
Affiliation(s)
- Andrea Olsen
- The Youth Longevity Association, Sevenoaks, NA, United Kingdom
| | - Zachary Harpaz
- The Youth Longevity Association, Sevenoaks, NA, United Kingdom
- Pine Crest School Science Research Department, Fort Lauderdale, Florida 33334, USA
| | - Christopher Ren
- Shanghai High School International Division, Shanghai 200231, China
| | - Anastasia Shneyderman
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alexander Veviorskiy
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Maria Dralkina
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Simon Konnov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Olga Shcheglova
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Geoffrey Ho Duen Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Hoi Wing Leung
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alex Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Mikhail Korzinkin
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, New Territories, Hong Kong, China
| |
Collapse
|
8
|
Górnicki T, Lambrinow J, Mrozowska M, Romanowicz H, Smolarz B, Piotrowska A, Gomułkiewicz A, Podhorska-Okołów M, Dzięgiel P, Grzegrzółka J. Expression of RBMS3 in Breast Cancer Progression. Int J Mol Sci 2023; 24. [PMID: 36769184 DOI: 10.3390/ijms24032866] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The aim of the study was to evaluate the localization and intensity of RNA-binding motif single-stranded-interacting protein 3 (RBMS3) expression in clinical material using immunohistochemical (IHC) reactions in cases of ductal breast cancer (in vivo), and to determine the level of RBMS3 expression at both the protein and mRNA levels in breast cancer cell lines (in vitro). Moreover, the data obtained in the in vivo and in vitro studies were correlated with the clinicopathological profiles of the patients. Material for the IHC studies comprised 490 invasive ductal carcinoma (IDC) cases and 26 mastopathy tissues. Western blot and RT-qPCR were performed on four breast cancer cell lines (MCF-7, BT-474, SK-BR-3 and MDA-MB-231) and the HME1-hTERT (Me16C) normal immortalized breast epithelial cell line (control). The Kaplan-Meier plotter tool was employed to analyze the predictive value of overall survival of RBMS3 expression at the mRNA level. Cytoplasmatic RBMS3 IHC expression was observed in breast cancer cells and stromal cells. The statistical analysis revealed a significantly decreased RBMS3 expression in the cancer specimens when compared with the mastopathy tissues (p < 0.001). An increased expression of RBMS3 was corelated with HER2(+) cancer specimens (p < 0.05) and ER(-) cancer specimens (p < 0.05). In addition, a statistically significant higher expression of RBMS3 was observed in cancer stromal cells in comparison to the control and cancer cells (p < 0.0001). The statistical analysis demonstrated a significantly higher expression of RBMS3 mRNA in the SK-BR-3 cell line compared with all other cell lines (p < 0.05). A positive correlation was revealed between the expression of RBMS3, at both the mRNA and protein levels, and longer overall survival. The differences in the expression of RBMS3 in cancer cells (both in vivo and in vitro) and the stroma of breast cancer with regard to the molecular status of the tumor may indicate that RBMS3 could be a potential novel target for the development of personalized methods of treatment. RBMS3 can be an indicator of longer overall survival for potential use in breast cancer diagnostic process.
Collapse
|
9
|
Feng Z, Shen Z, Li H, Li S. e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature. Brief Bioinform 2022; 23:6809962. [PMID: 36347537 PMCID: PMC9677481 DOI: 10.1093/bib/bbac465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
Target discovery and identification processes are driven by the increasing amount of biomedical data. The vast numbers of unstructured texts of biomedical publications provide a rich source of knowledge for drug target discovery research and demand the development of specific algorithms or tools to facilitate finding disease genes and proteins. Text mining is a method that can automatically mine helpful information related to drug target discovery from massive biomedical literature. However, there is a substantial lag between biomedical publications and the subsequent abstraction of information extracted by text mining to databases. The knowledge graph is introduced to integrate heterogeneous biomedical data. Here, we describe e-TSN (Target significance and novelty explorer, http://www.lilab-ecust.cn/etsn/), a knowledge visualization web server integrating the largest database of associations between targets and diseases from the full scientific literature by constructing significance and novelty scoring methods based on bibliometric statistics. The platform aims to visualize target-disease knowledge graphs to assist in prioritizing candidate disease-related proteins. Approved drugs and associated bioactivities for each interested target are also provided to facilitate the visualization of drug-target relationships. In summary, e-TSN is a fast and customizable visualization resource for investigating and analyzing the intricate target-disease networks, which could help researchers understand the mechanisms underlying complex disease phenotypes and improve the drug discovery and development efficiency, especially for the unexpected outbreak of infectious disease pandemics like COVID-19.
Collapse
Affiliation(s)
- Ziyan Feng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zihao Shen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China,Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China,Lingang Laboratory, Shanghai 200031, China
| | - Shiliang Li
- Corresponding author: Shiliang Li, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China. E-mail:
| |
Collapse
|
10
|
Freed DM, Sommer J, Punturi N. Emerging target discovery and drug repurposing opportunities in chordoma. Front Oncol 2022; 12:1009193. [PMID: 36387127 PMCID: PMC9647139 DOI: 10.3389/fonc.2022.1009193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/11/2022] [Indexed: 09/01/2023] Open
Abstract
The development of effective and personalized treatment options for patients with rare cancers like chordoma is hampered by numerous challenges. Biomarker-guided repurposing of therapies approved in other indications remains the fastest path to redefining the treatment paradigm, but chordoma's low mutation burden limits the impact of genomics in target discovery and precision oncology efforts. As our knowledge of oncogenic mechanisms across various malignancies has matured, it's become increasingly clear that numerous properties of tumors transcend their genomes - leading to new and uncharted frontiers of therapeutic opportunity. In this review, we discuss how the implementation of cutting-edge tools and approaches is opening new windows into chordoma's vulnerabilities. We also note how a convergence of emerging observations in chordoma and other cancers is leading to the identification and evaluation of new therapeutic hypotheses for this rare cancer.
Collapse
|
11
|
Gómez-Castañeda E, Hopcroft LEM, Rogers S, Munje C, Bittencourt-Silvestre J, Copland M, Vetrie D, Holyoake T, Jørgensen HG. Tyrosine Kinase Inhibitor Independent Gene Expression Signature in CML Offers New Targets for LSPC Eradication Therapy. Cancers (Basel) 2022; 14:5253. [PMID: 36358672 PMCID: PMC9655972 DOI: 10.3390/cancers14215253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
Tyrosine kinase inhibitors (TKI) have revolutionised the treatment of CML. However, TKI do not eliminate the leukaemia stem cells (LSC), which can re-initiate the disease. Thus, finding new therapeutic targets in CML LSC is key to finding a curative treatment. Using microarray datasets, we defined a list of 227 genes that were differentially expressed in CML LSC compared to the healthy controls but were not affected by TKI in vitro. Two of them, CD33 and PPIF, are targeted by gemtuzumab-ozogamicin and cyclosporin A, respectively. We treated CML and the control CD34+ cells with either drug with or without imatinib to investigate the therapeutic potential of the TKI-independent gene expression programme. Cyclosporine A, in combination with imatinib, reduced the number of CML CFC compared with non-CML controls, but only at supra-therapeutic concentrations. Gemtuzumab-ozogamicin showed an EC50 of 146 ng/mL, below the plasma peak concentration of 630 ng/mL observed in the AML patients and below the EC50 of 3247 ng/mL observed in the non-CML cells. Interestingly, gemtuzumab-ozogamicin seems to promote cell cycle progression in CML CD34+ cells and demonstrated activation of the RUNX1 pathway in an RNAseq experiment. This suggests that targeting the TKI-independent genes in CML LSC could be exploited for the development of new therapies in CML.
Collapse
Affiliation(s)
- Eduardo Gómez-Castañeda
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK
| | - Lisa E. M. Hopcroft
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK
| | - Simon Rogers
- School of Computing Science, College of Science and Engineering, University of Glasgow, 18 Lilybank Gardens, Glasgow G12 8RZ, UK
| | - Chinmay Munje
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK
| | - Joana Bittencourt-Silvestre
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK
| | - Mhairi Copland
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK
| | - David Vetrie
- Wolfson Wohl Translational Cancer Research Centre, Institute of Cancer Science, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Tessa Holyoake
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK
| | - Heather G. Jørgensen
- Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK
| |
Collapse
|
12
|
Górnicki T, Lambrinow J, Mrozowska M, Podhorska-Okołów M, Dzięgiel P, Grzegrzółka J. Role of RBMS3 Novel Potential Regulator of the EMT Phenomenon in Physiological and Pathological Processes. Int J Mol Sci 2022; 23:ijms231810875. [PMID: 36142783 PMCID: PMC9503485 DOI: 10.3390/ijms231810875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
RNA-binding protein 3 (RBMS3) plays a significant role in embryonic development and the pathogenesis of many diseases, especially cancer initiation and progression. The multiple roles of RBMS3 are conditioned by its numerous alternative expression products. It has been proven that the main form of RBMS3 influences the regulation of microRNA expression or stabilization. The absence of RBMS3 activates the Wnt/β-catenin pathway. The expression of c-Myc, another target of the Wnt/β-catenin pathway, is correlated with the RBMS3 expression. Numerous studies have focused solely on the interaction of RBMS3 with the epithelial-mesenchymal transition (EMT) protein machinery. EMT plays a vital role in cancer progression, in which RBMS3 is a new potential regulator. It is also significant that RBMS3 may act as a prognostic factor of overall survival (OS) in different types of cancer. This review presents the current state of knowledge about the role of RBMS3 in physiological and pathological processes, with particular emphasis on carcinogenesis. The molecular mechanisms underlying the role of RBMS3 are not fully understood; hence, a broader explanation and understanding is still needed.
Collapse
Affiliation(s)
- Tomasz Górnicki
- Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Jakub Lambrinow
- Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Monika Mrozowska
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | | | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Jędrzej Grzegrzółka
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland
| |
Collapse
|
13
|
Amen AM, Loughran RM, Huang CH, Lew RJ, Ravi A, Guan Y, Schatoff EM, Dow LE, Emerling BM, Fellmann C. Endogenous spacing enables co-processing of microRNAs and efficient combinatorial RNAi. Cell Rep Methods 2022; 2:100239. [PMID: 35880017 PMCID: PMC9308131 DOI: 10.1016/j.crmeth.2022.100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/21/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
We present Multi-miR, a microRNA-embedded shRNA system modeled after endogenous microRNA clusters that enables simultaneous expression of up to three or four short hairpin RNAs (shRNAs) from a single promoter without loss of activity, enabling robust combinatorial RNA interference (RNAi). We further developed complementary all-in-one vectors that are over one log-scale more sensitive to doxycycline-mediated activation in vitro than previous methods and resistant to shRNA inactivation in vivo. We demonstrate the utility of this system for intracranial expression of shRNAs in a glioblastoma model. Additionally, we leverage this platform to target the redundant RAF signaling node in a mouse model of KRAS-mutant cancer and show that robust combinatorial synthetic lethality efficiently abolishes tumor growth.
Collapse
Affiliation(s)
- Alexandra M. Amen
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ryan M. Loughran
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Chun-Hao Huang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Rachel J. Lew
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Archna Ravi
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | | | - Emma M. Schatoff
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Lukas E. Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Brooke M. Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Christof Fellmann
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- Mirimus Inc., Brooklyn, NY, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
14
|
Yim S, Hwang W, Han N, Lee D. Computational Discovery of Cancer Immunotherapy Targets by Intercellular CRISPR Screens. Front Immunol 2022; 13:884561. [PMID: 35651625 PMCID: PMC9149307 DOI: 10.3389/fimmu.2022.884561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer immunotherapy targets the interplay between immune and cancer cells. In particular, interactions between cytotoxic T lymphocytes (CTLs) and cancer cells, such as PD-1 (PDCD1) binding PD-L1 (CD274), are crucial for cancer cell clearance. However, immune checkpoint inhibitors targeting these interactions are effective only in a subset of patients, requiring the identification of novel immunotherapy targets. Genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screening in either cancer or immune cells has been employed to discover regulators of immune cell function. However, CRISPR screens in a single cell type complicate the identification of essential intercellular interactions. Further, pooled screening is associated with high noise levels. Herein, we propose intercellular CRISPR screens, a computational approach for the analysis of genome-wide CRISPR screens in every interacting cell type for the discovery of intercellular interactions as immunotherapeutic targets. We used two publicly available genome-wide CRISPR screening datasets obtained while triple-negative breast cancer (TNBC) cells and CTLs were interacting. We analyzed 4825 interactions between 1391 ligands and receptors on TNBC cells and CTLs to evaluate their effects on CTL function. Intercellular CRISPR screens discovered targets of approved drugs, a few of which were not identifiable in single datasets. To evaluate the method's performance, we used data for cytokines and costimulatory molecules as they constitute the majority of immunotherapeutic targets. Combining both CRISPR datasets improved the recall of discovering these genes relative to using single CRISPR datasets over two-fold. Our results indicate that intercellular CRISPR screens can suggest novel immunotherapy targets that are not obtained through individual CRISPR screens. The pipeline can be extended to other cancer and immune cell types to discover important intercellular interactions as potential immunotherapeutic targets.
Collapse
Affiliation(s)
- Soorin Yim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,Bio-Synergy Research Center, Daejeon, South Korea
| | - Woochang Hwang
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom.,Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Doheon Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,Bio-Synergy Research Center, Daejeon, South Korea
| |
Collapse
|
15
|
Lu C, Glisovic-Aplenc T, Bernt KM, Nestler K, Cesare J, Cao L, Lee H, Fazelinia H, Chinwalla A, Xu Y, Shestova O, Xing Y, Gill S, Li M, Garcia B, Aplenc R. Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms. J Proteome Res 2021; 20:5203-5211. [PMID: 34669412 DOI: 10.1021/acs.jproteome.1c00624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative proteomics has become an increasingly popular tool for profiling global protein abundances in an unbiased manner. However, the reproducibility of these data across time and LC-MS platforms is not well characterized. Here, we evaluate the performance of three LC-MS platforms (Orbitrap Elite, Q Exactive HF, and Orbitrap Fusion) in label-free semiquantitative analysis of cell surface proteins over a six-year period. Sucrose gradient ultracentrifugation was used for surfaceome enrichment, following gel separation for in-depth protein identification. With our established workflow, we consistently detected and reproducibly quantified >2300 putative cell surface proteins in a human acute myeloid leukemia (AML) cell line on all three platforms. To our knowledge this is the first study reporting highly reproducible semiquantitative proteomic data collection of biological replicates across multiple years and LC-MS platforms. These data provide experimental justification for semiquantitative proteomic study designs that are executed over multiyear time intervals and on different platforms. Multiyear and multiplatform experimental designs will likely enable larger scale proteomic studies and facilitate longitudinal proteomic studies by investigators lacking access to high throughput MS facilities. Data are available via ProteomeXchange with identifier PXD022721.
Collapse
Affiliation(s)
- Congcong Lu
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Tina Glisovic-Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Kathrin M Bernt
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Kevin Nestler
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Joseph Cesare
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Lusha Cao
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Hyoungjoo Lee
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Hossein Fazelinia
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Asif Chinwalla
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Yang Xu
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Olga Shestova
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Yi Xing
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Saar Gill
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin Garcia
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Richard Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
16
|
Osgood C, Ahmed Z, Di Pietro V. Co-Expression Network Analysis of MicroRNAs and Proteins in Severe Traumatic Brain Injury: A Systematic Review. Cells 2021; 10:cells10092425. [PMID: 34572074 PMCID: PMC8465595 DOI: 10.3390/cells10092425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023] Open
Abstract
Traumatic brain injury (TBI) represents one of the leading causes of mortality and morbidity worldwide, placing an enormous socioeconomic burden on healthcare services and communities around the world. Survivors of TBI can experience complications ranging from temporary neurological and psychosocial problems to long-term, severe disability and neurodegenerative disease. The current lack of therapeutic agents able to mitigate the effects of secondary brain injury highlights the urgent need for novel target discovery. This study comprises two independent systematic reviews, investigating both microRNA (miRNA) and proteomic expression in rat models of severe TBI (sTBI). The results were combined to perform integrated miRNA-protein co-expression analyses with the aim of uncovering the potential roles of miRNAs in sTBI and to ultimately identify new targets for therapy. Thirty-four studies were included in total. Bioinformatic analysis was performed to identify any miRNA–protein associations. Endocytosis and TNF signalling pathways were highlighted as common pathways involving both miRNAs and proteins found to be differentially expressed in rat brain tissue following sTBI, suggesting efforts to find novel therapeutic targets that should be focused here. Further high-quality investigations are required to ascertain the involvement of these pathways and their miRNAs in the pathogenesis of TBI and other CNS diseases and to therefore uncover those targets with the greatest therapeutic potential.
Collapse
Affiliation(s)
- Claire Osgood
- Neuroscience and Ophthalmology Group, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Zubair Ahmed
- Neuroscience and Ophthalmology Group, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
- Centre for Trauma Sciences Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham B15 2TH, UK
- Correspondence: (Z.A.); (V.D.P.)
| | - Valentina Di Pietro
- Neuroscience and Ophthalmology Group, Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
- Centre for Trauma Sciences Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham B15 2TH, UK
- Correspondence: (Z.A.); (V.D.P.)
| |
Collapse
|
17
|
Mohanty V, Wang F, Mills GB, Chen K. Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers. Cell Rep Med 2021; 2:100349. [PMID: 34337565 PMCID: PMC8324495 DOI: 10.1016/j.xcrm.2021.100349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/11/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022]
Abstract
Uncoupling of mRNA expression from copy number (UECN) might be a strategy for cancer cells to a tolerate high degree of aneuploidy. To test the extent and role of UECN across cancers, we perform integrative multiomic analysis of The Cancer Genome Atlas (TCGA) dataset, encompassing ∼5,000 individual tumors. We find UECN is common in cancers and is associated with increased oncogenic signaling, proliferation, and immune suppression. UECN appears to be orchestrated by complex regulatory changes, with transcription factors (TFs) playing a prominent role. To further dissect the regulatory mechanisms, we develop a systems-biology approach to identify candidate TFs, which could serve as targets to disrupt UECN and reduce tumor fitness. Applying our approach to TCGA data, we identify 21 putative targets, 42.8% of which are validated by independent sources. Together, our study indicates that UECN is likely an important mechanism in development of aneuploid tumors and might be therapeutically targetable.
Collapse
Affiliation(s)
- Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B. Mills
- Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health University, Portland, OR 97201, USA
| | - CTD2 Research Network
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health University, Portland, OR 97201, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
18
|
He C, Han S, Chang Y, Wu M, Zhao Y, Chen C, Chu X. CRISPR screen in cancer: status quo and future perspectives. Am J Cancer Res 2021; 11:1031-1050. [PMID: 33948344 PMCID: PMC8085856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) system offers a powerful platform for genome manipulation, including protein-coding genes, noncoding RNAs and regulatory elements. The development of CRISPR screen enables high-throughput interrogation of gene functions in diverse tumor biologies, such as tumor growth, metastasis, synthetic lethal interactions, therapeutic resistance and immunotherapy response, which are mostly performed in vitro or in transplant models. Recently, direct in vivo CRISPR screens have been developed to identify drivers of tumorigenesis in native microenvironment. Key parameters of CRISPR screen are constantly being optimized to achieve higher targeting efficiency and lower off-target effect. Here, we review the recent advances of CRISPR screen in cancer studies both in vitro and in vivo, with a particular focus on identifying cancer immunotherapy targets, and propose optimizing strategies and future perspectives for CRISPR screen.
Collapse
Affiliation(s)
- Chenglong He
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
| | - Siqi Han
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
| | - Yue Chang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
| | - Meijuan Wu
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
| | - Yulu Zhao
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical UniversityNanjing 210002, China
| | - Cheng Chen
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical UniversityNanjing 210002, China
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing UniversityNanjing 210002, China
- Department of Medical Oncology, Jinling Hospital, Nanjing Medical UniversityNanjing 210002, China
| |
Collapse
|
19
|
Dubrot J, Lane-Reticker SK, Kessler EA, Ayer A, Mishra G, Wolfe CH, Zimmer MD, Du PP, Mahapatra A, Ockerman KM, Davis TGR, Kohnle IC, Pope HW, Allen PM, Olander KE, Iracheta-Vellve A, Doench JG, Haining WN, Yates KB, Manguso RT. In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma. Immunity 2021; 54:571-585.e6. [PMID: 33497609 DOI: 10.1016/j.immuni.2021.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/20/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas9 genome engineering has increased the pace of discovery for immunology and cancer biology, revealing potential therapeutic targets and providing insight into mechanisms underlying resistance to immunotherapy. However, endogenous immune recognition of Cas9 has limited the applicability of CRISPR technologies in vivo. Here, we characterized immune responses against Cas9 and other expressed CRISPR vector components that cause antigen-specific tumor rejection in several mouse cancer models. To avoid unwanted immune recognition, we designed a lentiviral vector system that allowed selective CRISPR antigen removal (SCAR) from tumor cells. The SCAR system reversed immune-mediated rejection of CRISPR-modified tumor cells in vivo and enabled high-throughput genetic screens in previously intractable models. A pooled in vivo screen using SCAR in a CRISPR-antigen-sensitive renal cell carcinoma revealed resistance pathways associated with autophagy and major histocompatibility complex class I (MHC class I) expression. Thus, SCAR presents a resource that enables CRISPR-based studies of tumor-immune interactions and prevents unwanted immune recognition of genetically engineered cells, with implications for clinical applications.
Collapse
Affiliation(s)
- Juan Dubrot
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Emily A Kessler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Austin Ayer
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gargi Mishra
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Clara H Wolfe
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret D Zimmer
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter P Du
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Animesh Mahapatra
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle M Ockerman
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas G R Davis
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian C Kohnle
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hans W Pope
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter M Allen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kira E Olander
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arvin Iracheta-Vellve
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - W Nicholas Haining
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Pediatric Hematology and Oncology, Children's Hospital, Boston, MA, USA; Merck Research Laboratories, Boston, MA, USA
| | - Kathleen B Yates
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Robert T Manguso
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| |
Collapse
|
20
|
Grand Moursel L, Visser M, Servant G, Durmus S, Zuurmond AM. CRISPRing future medicines. Expert Opin Drug Discov 2021; 16:463-473. [PMID: 33322954 DOI: 10.1080/17460441.2021.1850687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: The ability to engineer mammalian genomes in a quick and cost-effective way has led to rapid adaptation of CRISPR technology in biomedical research. CRISPR-based engineering has the potential to accelerate drug discovery, to support the reduction of high attrition rate in drug development and to enhance development of cell and gene-based therapies.Areas covered: How CRISPR technology is transforming drug discovery is discussed in this review. From target identification to target validation in both in vitro and in vivo models, CRISPR technology is positively impacting the early stages of drug development by providing a straightforward way to genome engineering. This property also attracted attention for CRISPR application in the cell and gene therapy area.Expert opinion: CRISPR technology is rapidly becoming the preferred tool for genome engineering and nowadays it is hard to imagine the drug discovery pipeline without this technology. With the years to come, CRISPR technology will undoubtedly be further refined and will flourish into a mature technology that will play a key role in supporting genome engineering requirements in the drug discovery pipeline as well as in cell and gene therapy development.
Collapse
Affiliation(s)
| | - Mijke Visser
- Charles River Laboratories, Leiden, The Netherlands
| | | | - Selvi Durmus
- Charles River Laboratories, Leiden, The Netherlands
| | | |
Collapse
|
21
|
Ding M, Tegel H, Sivertsson Å, Hober S, Snijder A, Ormö M, Strömstedt PE, Davies R, Holmberg Schiavone L. Secretome-Based Screening in Target Discovery. SLAS Discov 2020; 25:535-551. [PMID: 32425085 PMCID: PMC7309359 DOI: 10.1177/2472555220917113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.
Collapse
Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Mats Ormö
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rick Davies
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | |
Collapse
|
22
|
Jelcic M, Wang K, Hui KL, Cai XC, Enyedi B, Luo M, Niethammer P. A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. Cell Chem Biol 2020; 27:1073-1083.e12. [PMID: 32521230 DOI: 10.1016/j.chembiol.2020.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/13/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
Abstract
ATP is an important energy metabolite and allosteric signal in health and disease. ATP-interacting proteins, such as P2 receptors, control inflammation, cell death, migration, and wound healing. However, identification of allosteric ATP sites remains challenging, and our current inventory of ATP-controlled pathways is likely incomplete. Here, we develop and verify mipATP as a minimally invasive photoaffinity probe for ATP-interacting proteins. Its N6 functionalization allows target enrichment by UV crosslinking and conjugation to reporter tags by "click" chemistry. The additions are compact, allowing mipATP to completely retain the calcium signaling responses of native ATP in vitro and in vivo. mipATP specifically enriched for known nucleotide binders in A549 cell lysates and membrane fractions. In addition, it retrieved unannotated ATP interactors, such as the FAS receptor, CD44, and various SLC transporters. Thus, mipATP is a promising tool to identify allosteric ATP sites in the proteome.
Collapse
Affiliation(s)
- Mark Jelcic
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ke Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - King Lam Hui
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiao-Chuan Cai
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Balázs Enyedi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Lendület Tissue Damage Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary; HCEMM-SE Inflammatory Signaling Research Group, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
23
|
Ross-Thriepland D, Bornot A, Butler L, Desai A, Jaiswal H, Peel S, Hunter MR, Odunze U, Isherwood B, Gianni D. Arrayed CRISPR Screening Identifies Novel Targets That Enhance the Productive Delivery of mRNA by MC3-Based Lipid Nanoparticles. SLAS Discov 2020; 25:605-617. [PMID: 32441189 PMCID: PMC7309353 DOI: 10.1177/2472555220925770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Modified messenger RNAs (mRNAs) hold great potential as therapeutics by using the body’s own processes for protein production. However, a key challenge is efficient delivery of therapeutic mRNA to the cell cytosol and productive protein translation. Lipid nanoparticles (LNPs) are the most clinically advanced system for nucleic acid delivery; however, a relatively narrow therapeutic index makes them unsuitable for many therapeutic applications. A key obstacle to the development of more potent LNPs is a limited mechanistic understanding of the interaction of LNPs with cells. To address this gap, we performed an arrayed CRISPR screen to identify novel pathways important for the functional delivery of MC3 lipid-based LNP encapsulated mRNA (LNP-mRNA). Here, we have developed and validated a robust, high-throughput screening–friendly phenotypic assay to identify novel targets that modulate productive LNP-mRNA delivery. We screened the druggable genome (7795 genes) and validated 44 genes that either increased (37 genes) or inhibited (14 genes) the productive delivery of LNP-mRNA. Many of these genes clustered into families involved with host cell transcription, protein ubiquitination, and intracellular trafficking. We show that both UDP-glucose ceramide glucosyltransferase and V-type proton ATPase can significantly modulate the productive delivery of LNP-mRNA, increasing and decreasing, respectively, with both genetic perturbation and by small-molecule inhibition. Taken together, these findings shed new light into the molecular machinery regulating the delivery of LNPs into cells and improve our mechanistic understanding of the cellular processes modulating the interaction of LNPs with cells.
Collapse
Affiliation(s)
| | - Aurelie Bornot
- Quantitative Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Larissa Butler
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Arpan Desai
- Advanced Drug Delivery, Pharmaceutical Science, R&D, AstraZeneca, Cambridge, UK
| | - Himjyot Jaiswal
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Molndal, Sweden
| | - Samantha Peel
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Morag Rose Hunter
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Uchechukwu Odunze
- Advanced Drug Delivery, Pharmaceutical Science, R&D, AstraZeneca, Cambridge, UK
| | | | - Davide Gianni
- Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| |
Collapse
|
24
|
Chen B, Long QS, Meng J, Zhou X, Wu ZB, Tuo XX, Ding Y, Zhang L, Wang PY, Li Z, Yang S. Target Discovery in Ralstonia solanacearum through an Activity-Based Protein Profiling Technique Based on Bioactive Oxadiazole Sulfones. J Agric Food Chem 2020; 68:2340-2346. [PMID: 32017553 DOI: 10.1021/acs.jafc.9b07192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ralstonia solanacearum is an extremely destructive and rebellious phytopathogen that can cause bacterial wilt diseases in more than 200 plant species. To explore and discover the potential targets in R. solanacearum for the purpose of developing new agrochemicals targeting this infection, here, we exploited a typical activity-based protein profiling technique for target discovery in R. solanacearum based on an activity-based probe 1 derived from bioactive oxadiazole sulfones. A total of 65 specific targets were identified with high confidence through a quantitative chemical proteomic approach. Three representative proteins (glycine cleavage system H protein, thiol peroxidase, and dihydrolipoamide S-succinyltransferase) were validated as the targets by using the immunoblotting analysis with their respective antibodies. Additionally, the in vitro interaction between the recombinant thiol peroxidase and probe 1 further confirmed that this protein was a target of oxadiazole sulfones. We anticipated that these discovered protein targets in R. solanacearum can stimulate the discovery and development of novel agrochemicals targeting bacterial infections caused by R. solanacearum.
Collapse
Affiliation(s)
- Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Qing-Su Long
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Jiao Meng
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Xiang Zhou
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Zhi-Bing Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Xin-Xin Tuo
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Yue Ding
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Ling Zhang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Pei-Yi Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
| | - Zhong Li
- College of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Center for R&D of Fine Chemicals of Guizhou University , Guiyang 550025 , China
- College of Pharmacy , East China University of Science & Technology , Shanghai 200237 , China
| |
Collapse
|
25
|
Morretta E, Tosco A, Festa C, Mozzicafreddo M, Monti MC, Casapullo A. Crellastatin A, a PARP-1 Inhibitor Discovered by Complementary Proteomic Approaches. ChemMedChem 2020; 15:317-323. [PMID: 31829516 DOI: 10.1002/cmdc.201900634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Indexed: 12/13/2022]
Abstract
Crellastatin A, a cytotoxic sulfated bis-steroid isolated from the Vanuatu Island marine sponge Crella sp., was selected as an interesting probe for a comprehensive proteomic analysis directed at the characterization of its protein interactors. Given its peculiar structural features, A was submitted to a mass spectrometry-based drug affinity responsive target stability (DARTS) assay combined with (targeted-limited proteolysis-multiple reaction monitoring (t-LiP MRM), rather than a classical affinity purification strategy. Poly-ADP-ribose-polymerase-1 (PARP-1) emerged as the main crellastatin A cellular partner. This result was confirmed by both biochemical and in silico analyses. Further in vitro biological assays highlighted an interesting crellastatin A inhibitory activity on PARP-1.
Collapse
Affiliation(s)
- Elva Morretta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano Salerno, Italy.,Department of Pharmacy PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano Salerno, Italy
| | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano Salerno, Italy
| | - Carmen Festa
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano 49, 80131, Napoli, Italy
| | - Matteo Mozzicafreddo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Maria C Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano Salerno, Italy
| | - Agostino Casapullo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano Salerno, Italy
| |
Collapse
|
26
|
Abstract
Activity-based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high-throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity-based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.
Collapse
Affiliation(s)
- Jiaqian Xu
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR, 999077, China
| | - Xiaoqian Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| |
Collapse
|
27
|
Monkman JH, Thompson EW, Nagaraj SH. Targeting Epithelial Mesenchymal Plasticity in Pancreatic Cancer: A Compendium of Preclinical Discovery in a Heterogeneous Disease. Cancers (Basel) 2019; 11:cancers11111745. [PMID: 31703358 PMCID: PMC6896204 DOI: 10.3390/cancers11111745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is a particularly insidious and aggressive disease that causes significant mortality worldwide. The direct correlation between PDAC incidence, disease progression, and mortality highlights the critical need to understand the mechanisms by which PDAC cells rapidly progress to drive metastatic disease in order to identify actionable vulnerabilities. One such proposed vulnerability is epithelial mesenchymal plasticity (EMP), a process whereby neoplastic epithelial cells delaminate from their neighbours, either collectively or individually, allowing for their subsequent invasion into host tissue. This disruption of tissue homeostasis, particularly in PDAC, further promotes cellular transformation by inducing inflammatory interactions with the stromal compartment, which in turn contributes to intratumoural heterogeneity. This review describes the role of EMP in PDAC, and the preclinical target discovery that has been conducted to identify the molecular regulators and effectors of this EMP program. While inhibition of individual targets may provide therapeutic insights, a single ‘master-key’ remains elusive, making their collective interactions of greater importance in controlling the behaviours’ of heterogeneous tumour cell populations. Much work has been undertaken to understand key transcriptional programs that drive EMP in certain contexts, however, a collaborative appreciation for the subtle, context-dependent programs governing EMP regulation is needed in order to design therapeutic strategies to curb PDAC mortality.
Collapse
Affiliation(s)
- James H. Monkman
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia;
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia
- Translational Research Institute, Brisbane, QLD 4102, Australia
- Correspondence: (J.H.M.); (S.H.N.)
| | - Erik W. Thompson
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia;
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia
- Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Shivashankar H. Nagaraj
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia;
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4059, Australia
- Translational Research Institute, Brisbane, QLD 4102, Australia
- Correspondence: (J.H.M.); (S.H.N.)
| |
Collapse
|
28
|
Dong MB, Wang G, Chow RD, Ye L, Zhu L, Dai X, Park JJ, Kim HR, Errami Y, Guzman CD, Zhou X, Chen KY, Renauer PA, Du Y, Shen J, Lam SZ, Zhou JJ, Lannin DR, Herbst RS, Chen S. Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells. Cell 2019; 178:1189-1204.e23. [PMID: 31442407 PMCID: PMC6719679 DOI: 10.1016/j.cell.2019.07.044] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/17/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
CD8 T cells play essential roles in anti-tumor immune responses. Here, we performed genome-scale CRISPR screens in CD8 T cells directly under cancer immunotherapy settings and identified regulators of tumor infiltration and degranulation. The in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. The infiltration and degranulation screens converged on an RNA helicase Dhx37. Dhx37 knockout enhanced the efficacy of antigen-specific CD8 T cells against triple-negative breast cancer in vivo. Immunological characterization in mouse and human CD8 T cells revealed that DHX37 suppresses effector functions, cytokine production, and T cell activation. Transcriptomic profiling and biochemical interrogation revealed a role for DHX37 in modulating NF-κB. These data demonstrate high-throughput in vivo genetic screens for immunotherapy target discovery and establishes DHX37 as a functional regulator of CD8 T cells.
Collapse
Affiliation(s)
- Matthew B Dong
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Guangchuan Wang
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Ryan D Chow
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Lupeng Ye
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Lvyun Zhu
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Hyunu R Kim
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Youssef Errami
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Christopher D Guzman
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Krista Y Chen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Paul A Renauer
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yaying Du
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA
| | - Johanna Shen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Stanley Z Lam
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Jingjia J Zhou
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; The College, Yale University, New Haven, CT 06520, USA
| | - Donald R Lannin
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06510, USA; Breast Cancer Program, Yale University School of Medicine, New Haven, CT06510, USA; Smilow Cancer Hospital, 35 Park Street, New Haven, CT 06510; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Roy S Herbst
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA; Smilow Cancer Hospital, 35 Park Street, New Haven, CT 06510; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; System Biology Institute, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Center for Cancer Systems Biology, Integrated Science & Technology Center, Yale University, 850 W Campus Drive, West Haven, CT 06516, USA; Yale MD-PhD Program, Yale University School of Medicine, New Haven, CT 06510, USA; Immunobiology Program, Yale University School of Medicine, New Haven, CT 06510, USA; Combined Program in the Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Liver Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
29
|
O’Donnell P, Rosen L, Alexander R, Murthy V, Davies CH, Ratti E. Strategies to Address Challenges in Neuroscience Drug Discovery and Development. Int J Neuropsychopharmacol 2019; 22:445-448. [PMID: 31139821 PMCID: PMC6600465 DOI: 10.1093/ijnp/pyz027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/06/2019] [Accepted: 05/27/2019] [Indexed: 01/17/2023] Open
Abstract
The paucity of novel drugs for neuropsychiatric indications contrasts with the remarkable recent advances in neuroscience research. We have identified 5 challenges the field needs to address and recommend potential solutions. First, we need to drive discovery efforts based on human data. Second, we need to think more carefully about animal models, embracing them as tools to test pathophysiological alterations. Third, we need to develop strategies to select more homogenous groups of patients in our clinical trials. Fourth, we need to develop and validate translational biomarkers, which can be used for pharmacodynamic assessments as well as for patient selection. Fifth, we need to adopt more reliable and objective measures to capture clinical efficacy. The tools that will allow these solutions to be implemented may already be in place but not routinely adopted or are still being developed. Overall, a change in mindset to adopt science- and data-driven paths is needed.
Collapse
Affiliation(s)
- Patricio O’Donnell
- Takeda Pharmaceuticals, Cambridge, Massachusetts,Correspondence: Patricio O’Donnell, MD, PhD, Takeda Pharmaceuticals, 350 Massachusetts Ave., Cambridge, MA 02139 ()
| | - Laura Rosen
- Takeda Pharmaceuticals, Cambridge, Massachusetts
| | | | | | - Ceri H Davies
- Takeda Pharmaceuticals Company Limited, Fujisawa, Kanagawa, Japan
| | | |
Collapse
|
30
|
Duarte Y, Márquez-Miranda V, Miossec MJ, González-Nilo F. Integration of target discovery, drug discovery and drug delivery: A review on computational strategies. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2019; 11:e1554. [PMID: 30932351 DOI: 10.1002/wnan.1554] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/14/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
Most of the computational tools involved in drug discovery developed during the 1980s were largely based on computational chemistry, quantitative structure-activity relationship (QSAR) and cheminformatics. Subsequently, the advent of genomics in the 2000s gave rise to a huge number of databases and computational tools developed to analyze large quantities of data, through bioinformatics, to obtain valuable information about the genomic regulation of different organisms. Target identification and validation is a long process during which evidence for and against a target is accumulated in the pursuit of developing new drugs. Finally, the drug delivery system appears as a novel approach to improve drug targeting and releasing into the cells, leading to new opportunities to improve drug efficiency and avoid potential secondary effects. In each area: target discovery, drug discovery and drug delivery, different computational strategies are being developed to accelerate the process of selection and discovery of new tools to be applied to different scientific fields. Research on these three topics is growing rapidly, but still requires a global view of this landscape to detect the most challenging bottleneck and how computational tools could be integrated in each topic. This review describes the current state of the art in computational strategies for target discovery, drug discovery and drug delivery and how these fields could be integrated. Finally, we will discuss about the current needs in these fields and how the continuous development of databases and computational tools will impact on the improvement of those areas. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
Collapse
Affiliation(s)
- Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| |
Collapse
|
31
|
Abstract
With the rise in novel infectious agents and disease pandemics, a new era of vaccine discovery is necessary. To address this, the new field of immunomics is described, which is synergistically powered by integrating bioinformatics methodologies with technological advances in biology and high-throughput instrumentation. By incorporating biological data from immunology and molecular biology with current genomics and proteomics, immunomics is geared to deliver an insight into immune function, optimal stimulation of immune responses and precise mapping and rational selection of immune targets that cover antigenic diversity. These efforts are expected to contribute towards the development of new generation of vaccines, tailored to both the genetic make-up of the human population and of the pathogen. Vaccine technologies are also being explored for prevention or control of non-communicable diseases.
Collapse
|
32
|
Leung KK, Nguyen A, Shi T, Tang L, Ni X, Escoubet L, MacBeth KJ, DiMartino J, Wells JA. Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome. Proc Natl Acad Sci U S A 2019; 116:695-700. [PMID: 30584089 DOI: 10.1073/pnas.1813666116] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor widely used to treat MDS and AML, yet the impact of AZA on the cell-surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome, the transcriptome, and the cell-surface proteome. Untreated AML cell lines showed substantial overlap at all three omics levels; however, while AZA treatment globally reduced DNA methylation in all cell lines, changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteome analysis found no commonly regulated proteins. Gene set enrichment analysis of differentially regulated RNA and surface proteins showed a decrease in metabolic pathways and an increase in immune defense response pathways. As such, AZA treatment led to diverse effects at the individual gene and protein levels but converged to common responses at the pathway level. Given the heterogeneous responses in the four cell lines, we discuss potential therapeutic strategies for AML in combination with AZA.
Collapse
|
33
|
Kinchen J, Chen HH, Parikh K, Antanaviciute A, Jagielowicz M, Fawkner-Corbett D, Ashley N, Cubitt L, Mellado-Gomez E, Attar M, Sharma E, Wills Q, Bowden R, Richter FC, Ahern D, Puri KD, Henault J, Gervais F, Koohy H, Simmons A. Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease. Cell 2018; 175:372-386.e17. [PMID: 30270042 PMCID: PMC6176871 DOI: 10.1016/j.cell.2018.08.067] [Citation(s) in RCA: 379] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 06/08/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022]
Abstract
Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD. Single-cell census of the colonic mesenchyme reveals unexpected heterogeneity Identification of the colonic crypt niche mesenchymal cell expressing SOX6 and Wnts Definition of fundamental aspects of mesenchymal remodeling in colitis Analysis of colitis-associated mesenchymal cells reveals pathogenicity drivers
Collapse
Affiliation(s)
- James Kinchen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Hannah H Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Kaushal Parikh
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Agne Antanaviciute
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK; MRC WIMM Centre For Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Marta Jagielowicz
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - David Fawkner-Corbett
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Neil Ashley
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Laura Cubitt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Esther Mellado-Gomez
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Eshita Sharma
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Quin Wills
- Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Felix C Richter
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - David Ahern
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | | | - Jill Henault
- Translational Development, Celgene Corporation, Cambridge, MA, USA
| | - Francois Gervais
- Translational Development, Celgene Corporation, Cambridge, MA, USA
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; MRC WIMM Centre For Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK.
| |
Collapse
|
34
|
Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y. Aberration hubs in protein interaction networks highlight actionable targets in cancer. Oncotarget 2018; 9:25166-25180. [PMID: 29861861 PMCID: PMC5982744 DOI: 10.18632/oncotarget.25382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/24/2018] [Indexed: 01/08/2023] Open
Abstract
Despite efforts for extensive molecular characterization of cancer patients, such as the international cancer genome consortium (ICGC) and the cancer genome atlas (TCGA), the heterogeneous nature of cancer and our limited knowledge of the contextual function of proteins have complicated the identification of targetable genes. Here, we present Aberration Hub Analysis for Cancer (AbHAC) as a novel integrative approach to pinpoint aberration hubs, i.e. individual proteins that interact extensively with genes that show aberrant mutation or expression. Our analysis of the breast cancer data of the TCGA and the renal cancer data from the ICGC shows that aberration hubs are involved in relevant cancer pathways, including factors promoting cell cycle and DNA replication in basal-like breast tumors, and Src kinase and VEGF signaling in renal carcinoma. Moreover, our analysis uncovers novel functionally relevant and actionable targets, among which we have experimentally validated abnormal splicing of spleen tyrosine kinase as a key factor for cell proliferation in renal cancer. Thus, AbHAC provides an effective strategy to uncover novel disease factors that are only identifiable by examining mutational and expression data in the context of biological networks.
Collapse
Affiliation(s)
- Mehran Karimzadeh
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Pouria Jandaghi
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Andreas I. Papadakis
- Department of Biochemistry, The Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sebastian Trainor
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, LS9 7TF, UK
| | - Johan Rung
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Mar Gonzàlez-Porta
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, 69008, France
| | - Naveen S. Vasudev
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, LS9 7TF, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Sidong Huang
- Department of Biochemistry, The Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Rosamonde E. Banks
- Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James's University Hospital, Leeds, LS9 7TF, UK
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Hamed S. Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada
| |
Collapse
|
35
|
Baptista R, Bhowmick S, Nash RJ, Baillie L, Mur LA. Target discovery focused approaches to overcome bottlenecks in the exploitation of antimycobacterial natural products. Future Med Chem 2018; 10:811-22. [PMID: 29569936 DOI: 10.4155/fmc-2017-0273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis is a major global health hazard. The search for new antimycobacterials has focused on such as screening combinational chemistry libraries or designing chemicals to target predefined pockets of essential bacterial proteins. The relative ineffectiveness of these has led to a reappraisal of natural products for new antimycobacterial drug leads. However, progress has been limited, we suggest through a failure in many cases to define the drug target and optimize the hits using this information. We highlight methods of target discovery needed to develop a drug into a candidate for clinical trials. We incorporate these into suggested analysis pipelines which could inform the research strategies to accelerate the development of new drug leads from natural products.
Collapse
|
36
|
Frédérick R, Pochet L, De Tullio P, Dufrasne F. 31ièmes Journées Franco-Belges de Pharmacochimie: Meeting Report. Pharmaceuticals (Basel) 2017; 10:ph10040094. [PMID: 29207523 PMCID: PMC5748649 DOI: 10.3390/ph10040094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 11/27/2017] [Indexed: 11/16/2022] Open
Abstract
The "Journées Franco-Belges de Pharmacochimie" is a recognized two-day annual meeting on Medicinal Chemistry that is renowned for the advanced science presented, conviviality, and outstanding opportunities for senior and young scientists to exchange knowledge. Abstracts of plenary lectures, oral communications, and posters presented during the meeting are collected in this report.
Collapse
Affiliation(s)
- Raphaël Frédérick
- Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain, Woluwé-Saint-Lambert 1200, Belgium.
| | - Lionel Pochet
- Department of Pharmacy, Namur Medicine & Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, 61, Rue de Bruxelles, Namur B-5000, Belgium.
| | - Pascal De Tullio
- Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Liège 4000, Belgium.
| | - François Dufrasne
- Laboratoire de Chimie Pharmaceutique Organique, Faculté de Pharmacie, Université Libre de Bruxelles Campus Plaine CP 205/5, Brussels 1050, Belgium.
| |
Collapse
|
37
|
Perna F, Berman SH, Soni RK, Mansilla-Soto J, Eyquem J, Hamieh M, Hendrickson RC, Brennan CW, Sadelain M. Integrating Proteomics and Transcriptomics for Systematic Combinatorial Chimeric Antigen Receptor Therapy of AML. Cancer Cell 2017; 32:506-519.e5. [PMID: 29017060 PMCID: PMC7025434 DOI: 10.1016/j.ccell.2017.09.004] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/02/2017] [Accepted: 09/07/2017] [Indexed: 02/07/2023]
Abstract
Chimeric antigen receptor (CAR) therapy targeting CD19 has yielded remarkable outcomes in patients with acute lymphoblastic leukemia. To identify potential CAR targets in acute myeloid leukemia (AML), we probed the AML surfaceome for overexpressed molecules with tolerable systemic expression. We integrated large transcriptomics and proteomics datasets from malignant and normal tissues, and developed an algorithm to identify potential targets expressed in leukemia stem cells, but not in normal CD34+CD38- hematopoietic cells, T cells, or vital tissues. As these investigations did not uncover candidate targets with a profile as favorable as CD19, we developed a generalizable combinatorial targeting strategy fulfilling stringent efficacy and safety criteria. Our findings indicate that several target pairings hold great promise for CAR therapy of AML.
Collapse
Affiliation(s)
- Fabiana Perna
- Center for Cell Engineering and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Samuel H Berman
- Center for Cell Engineering and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rajesh K Soni
- Microchemistry and Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jorge Mansilla-Soto
- Center for Cell Engineering and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Justin Eyquem
- Center for Cell Engineering and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mohamad Hamieh
- Center for Cell Engineering and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronald C Hendrickson
- Microchemistry and Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cameron W Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michel Sadelain
- Center for Cell Engineering and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
38
|
Sharifnia T, Hong AL, Painter CA, Boehm JS. Emerging Opportunities for Target Discovery in Rare Cancers. Cell Chem Biol 2017; 24:1075-1091. [PMID: 28938087 PMCID: PMC5857178 DOI: 10.1016/j.chembiol.2017.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/26/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022]
Abstract
Rare cancers pose unique challenges to research due to their low incidence. Barriers include a scarcity of tissue and experimental models to enable basic research and insufficient patient accrual for clinical studies. Consequently, an understanding of the genetic and cellular features of many rare cancer types and their associated vulnerabilities has been lacking. However, new opportunities are emerging to facilitate discovery of therapeutic targets in rare cancers. Online platforms are allowing patients with rare cancers to organize on an unprecedented scale, tumor genome sequencing is now routinely performed in research and clinical settings, and the efficiency of patient-derived model generation has improved. New CRISPR/Cas9 and small-molecule libraries permit cancer dependency discovery in a rapid and systematic fashion. In parallel, large-scale studies of common cancers now provide reference datasets to help interpret rare cancer profiling data. Together, these advances motivate consideration of new research frameworks to accelerate rare cancer target discovery.
Collapse
Affiliation(s)
- Tanaz Sharifnia
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew L Hong
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Jesse S Boehm
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| |
Collapse
|
39
|
Beninger P, Connelly J, Natarajan C. Data Sharing in the Pharmaceutical Enterprise: The Genie's Out of the Bottle. Clin Ther 2017; 39:1890-1894. [PMID: 28823517 DOI: 10.1016/j.clinthera.2017.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 07/30/2017] [Accepted: 08/01/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This Commentary shows that the present emphasis on the sharing of data from clinical trials can be extended to the entire pharmaceutical enterprise. METHODS The authors constructed a Data Sharing Dashboard that shows the relationship between all of the life-cycle domains of the pharmaceutical enterprise from discovery to obsolescence and the domain-bridging disciplines, such as target credentialing, structure-activity relationships, and exposure-effect relationships. FINDINGS The published literature encompassing the pharmaceutical enterprise is expansive, covering the major domains of discovery, translation, clinical development, and post-marketing outcomes research, all of which have even larger, though generally inaccessible, troves of legacy data bases. Notable exceptions include the fields of genomics and bioinformatics. IMPLICATIONS We have the opportunity to broaden the present momentum of interest in data sharing to the entire pharmaceutical enterprise, beginning with discovery and extending into health technology assessment and post-patent expiry generic use with the plan of integrating new levels and disciplines of knowledge and with the ultimate goal of improving the care of our patients.
Collapse
Affiliation(s)
- Paul Beninger
- Public Health & Community Medicine, Tufts University School of Medicine, Boston, Massachusetts.
| | | | | |
Collapse
|
40
|
Aci-Sèche S, Buron F, Plé K, Robin L, Suzenet F, Routier S. 30ièmes Journées Franco-Belges de Pharmacochimie. Pharmaceuticals (Basel) 2016; 9:ph9040073. [PMID: 27869720 PMCID: PMC5198048 DOI: 10.3390/ph9040073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/10/2016] [Indexed: 11/16/2022] Open
Abstract
The "Journées Franco-Belges de Pharmacochimie" is a recognized annual meeting in organic and medicinal chemistry known for the quality of scientific exchange and conviviality. Young researchers were encouraged to present their work and share ideas with senior scientists. Abstracts of plenary lectures, oral communications, and posters presented during the meeting are collected in this report.
Collapse
Affiliation(s)
- Samia Aci-Sèche
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, Université d'Orléans, F-45067 Orléans, France.
| | - Frédéric Buron
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, Université d'Orléans, F-45067 Orléans, France.
| | - Karen Plé
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, Université d'Orléans, F-45067 Orléans, France.
| | - Laurent Robin
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, Université d'Orléans, F-45067 Orléans, France.
| | - Franck Suzenet
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, Université d'Orléans, F-45067 Orléans, France.
| | - Sylvain Routier
- Institut de Chimie Organique et Analytique, CNRS UMR 7311, Université d'Orléans, F-45067 Orléans, France.
| |
Collapse
|
41
|
Committee TM. 29ièmes Journées Franco-Belges de Pharmacochimie: Meeting Report. Pharmaceuticals (Basel) 2015; 8:758-77. [PMID: 26593925 DOI: 10.3390/ph8040758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 11/17/2022] Open
Abstract
The "Journées Franco-Belges de Pharmacochimie" is a recognized two-day annual meeting on Medicinal Chemistry that is renowned for the advanced science presented, conviviality, and outstanding opportunities for senior and young scientists to exchange knowledge. Abstracts of plenary lectures, oral communications, and posters presented during the meeting are collected in this report.
Collapse
|
42
|
Czopka T. Insights into mechanisms of central nervous system myelination using zebrafish. Glia 2015; 64:333-49. [PMID: 26250418 DOI: 10.1002/glia.22897] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 12/12/2022]
Abstract
Myelin is the multi-layered membrane that surrounds most axons and is produced by oligodendrocytes in the central nervous system (CNS). In addition to its important role in enabling rapid nerve conduction, it has become clear in recent years that myelin plays additional vital roles in CNS function. Myelinating oligodendrocytes provide metabolic support to axons and active myelination is even involved in regulating forms of learning and memory formation. However, there are still large gaps in our understanding of how myelination by oligodendrocytes is regulated. The small tropical zebrafish has become an increasingly popular model organism to investigate many aspects of nervous system formation, function, and regeneration. This is mainly due to two approaches for which the zebrafish is an ideally suited vertebrate model--(1) in vivo live cell imaging using vital dyes and genetically encoded reporters, and (2) gene and target discovery using unbiased screens. This review summarizes how the use of zebrafish has helped understand mechanisms of oligodendrocyte behavior and myelination in vivo and discusses the potential use of zebrafish to shed light on important future questions relating to myelination in the context of CNS development, function and repair.
Collapse
Affiliation(s)
- Tim Czopka
- Institute of Neuronal Cell Biology, Technische Universität München, Munich, Germany
| |
Collapse
|
43
|
Augustyn A, Borromeo M, Wang T, Fujimoto J, Shao C, Dospoy PD, Lee V, Tan C, Sullivan JP, Larsen JE, Girard L, Behrens C, Wistuba II, Xie Y, Cobb MH, Gazdar AF, Johnson JE, Minna JD. ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers. Proc Natl Acad Sci U S A 2014; 111:14788-93. [PMID: 25267614 DOI: 10.1073/pnas.1410419111] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aggressive neuroendocrine lung cancers, including small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), represent an understudied tumor subset that accounts for approximately 40,000 new lung cancer cases per year in the United States. No targeted therapy exists for these tumors. We determined that achaete-scute homolog 1 (ASCL1), a transcription factor required for proper development of pulmonary neuroendocrine cells, is essential for the survival of a majority of lung cancers (both SCLC and NSCLC) with neuroendocrine features. By combining whole-genome microarray expression analysis performed on lung cancer cell lines with ChIP-Seq data designed to identify conserved transcriptional targets of ASCL1, we discovered an ASCL1 target 72-gene expression signature that (i) identifies neuroendocrine differentiation in NSCLC cell lines, (ii) is predictive of poor prognosis in resected NSCLC specimens from three datasets, and (iii) represents novel "druggable" targets. Among these druggable targets is B-cell CLL/lymphoma 2, which when pharmacologically inhibited stops ASCL1-dependent tumor growth in vitro and in vivo and represents a proof-of-principle ASCL1 downstream target gene. Analysis of downstream targets of ASCL1 represents an important advance in the development of targeted therapy for the neuroendocrine class of lung cancers, providing a significant step forward in the understanding and therapeutic targeting of the molecular vulnerabilities of neuroendocrine lung cancer.
Collapse
|
44
|
Abstract
Therapeutic antibodies may mediate antineoplastic effects by altering the biological functions of their target, by directly stimulating the demise of cancer cells or by activating antibody-dependent immune effector mechanisms. We have recently provided in vivo proof-of-concept for a "function-first" target and drug discovery platform in which antibodies against a multitude of tumor-associated antigens are screened for biological effects in a target-unbiased manner.
Collapse
|