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Sobczyk MK, Zheng J, Davey Smith G, Gaunt TR. Systematic comparison of Mendelian randomisation studies and randomised controlled trials using electronic databases. BMJ Open 2023; 13:e072087. [PMID: 37751957 PMCID: PMC10533809 DOI: 10.1136/bmjopen-2023-072087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
OBJECTIVE To scope the potential for (semi)-automated triangulation of Mendelian randomisation (MR) and randomised controlled trials (RCTs) evidence since the two methods have distinct assumptions that make comparisons between their results invaluable. METHODS We mined ClinicalTrials.Gov, PubMed and EpigraphDB databases and carried out a series of 26 manual literature comparisons among 54 MR and 77 RCT publications. RESULTS We found that only 13% of completed RCTs identified in ClinicalTrials.Gov submitted their results to the database. Similarly low coverage was revealed for Semantic Medline (SemMedDB) semantic triples derived from MR and RCT publications -36% and 12%, respectively. Among intervention types that can be mimicked by MR, only trials of pharmaceutical interventions could be automatically matched to MR results due to insufficient annotation with Medical Subject Headings ontology. A manual survey of the literature highlighted the potential for triangulation across a number of exposure/outcome pairs if these challenges can be addressed. CONCLUSIONS We conclude that careful triangulation of MR with RCT evidence should involve consideration of similarity of phenotypes across study designs, intervention intensity and duration, study population demography and health status, comparator group, intervention goal and quality of evidence.
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Affiliation(s)
- Maria K Sobczyk
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
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Mitchell DC, Kuljanin M, Li J, Van Vranken JG, Bulloch N, Schweppe DK, Huttlin EL, Gygi SP. A proteome-wide atlas of drug mechanism of action. Nat Biotechnol 2023; 41:845-857. [PMID: 36593396 PMCID: PMC11069389 DOI: 10.1038/s41587-022-01539-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/30/2022] [Indexed: 01/03/2023]
Abstract
Defining the cellular response to pharmacological agents is critical for understanding the mechanism of action of small molecule perturbagens. Here, we developed a 96-well-plate-based high-throughput screening infrastructure for quantitative proteomics and profiled 875 compounds in a human cancer cell line with near-comprehensive proteome coverage. Examining the 24-h proteome changes revealed ligand-induced changes in protein expression and uncovered rules by which compounds regulate their protein targets while identifying putative dihydrofolate reductase and tankyrase inhibitors. We used protein-protein and compound-compound correlation networks to uncover mechanisms of action for several compounds, including the adrenergic receptor antagonist JP1302, which we show disrupts the FACT complex and degrades histone H1. By profiling many compounds with overlapping targets covering a broad chemical space, we linked compound structure to mechanisms of action and highlighted off-target polypharmacology for molecules within the library.
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Affiliation(s)
- Dylan C Mitchell
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Miljan Kuljanin
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Nathan Bulloch
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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Levy S, Arthur JD, Banks M, Kok NFM, Fenwick SW, Diaz-Nieto R, van Leerdam ME, Cuthbertson DJ, Valk GD, Kuhlmann KFD, Tesselaar MET. Primary Tumor Resection is Associated with Improved Disease-Specific Mortality in Patients with Stage IV Small Intestinal Neuroendocrine Tumors (NETs): A Comparison of Upfront Surgical Resection Versus a Watch and Wait Strategy in Two Specialist NET Centers. Ann Surg Oncol 2022; 29:7822-7832. [PMID: 35842528 DOI: 10.1245/s10434-022-12030-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Small intestinal neuroendocrine tumors (SI-NETs) often present with metastatic disease. An ongoing debate exists on whether to perform primary tumor resection (PTR) in patients with stage IV SI-NETs, without symptoms of the primary tumor and inoperable metastatic disease. OBJECTIVE The aim of this study was to compare a treatment strategy of upfront surgical resection versus a surveillance strategy of watch and wait. METHODS This was a retrospective cohort study of patients with stage IV SI-NETs at diagnosis, between 2000 and 2018, from two tertiary referral centers (Netherlands Cancer Institute [NKI] and Aintree University Hospital [AUH]) who had adopted contrasting treatment approaches: upfront surgical resection and watch and wait, respectively. Patients without symptoms related to the primary tumor were included. Multivariable intention-to-treat (ITT), per-protocol (PP), and instrumental variable (IV) analyses using 'institute' as an IV were performed to assess the influence of PTR on disease-specific mortality (DSM). RESULTS A total of 557 patients were identified, with 145 patients remaining after exclusion of stage I-III disease or symptoms of the primary tumor (93 from the NKI and 52 from AUH). The cohorts differed in performance status (PS; p = 0.006) and tumor grade (p < 0.001). PTR was independently associated with reduced DSM irrespective of statistical methods employed: ITT hazard ratio [HR] 0.60, p = 0.005; PP HR 0.58, p < 0.001; and IV HR 0.07, p = 0.019. Other factors associated with DSM were age, PS, high chromogranin A, and somatostatin analog treatment. CONCLUSION Taking advantage of contrasting institutional treatment strategies, this study identified PTR as an independent predictor of DSM. Future prospective studies should aim to validate these results.
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Affiliation(s)
- Sonja Levy
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - James D Arthur
- Department of Surgery, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Melissa Banks
- Department of Surgery, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Niels F M Kok
- Department of Surgical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Stephen W Fenwick
- Department of Surgery, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Rafael Diaz-Nieto
- Department of Surgery, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Monique E van Leerdam
- Department of Gastroenterologic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel J Cuthbertson
- Institute of Cardiovascular and Metabolic Medicine, University of Liverpool, Liverpool, UK.,Department of Endocrinology, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Gerlof D Valk
- Department of Endocrine Oncology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Koert F D Kuhlmann
- Department of Surgical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Margot E T Tesselaar
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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Pathak K, Pathak MP, Saikia R, Gogoi U, Sahariah JJ, Zothantluanga JH, Samanta A, Das A. Cancer Chemotherapy via Natural Bioactive Compounds. Curr Drug Discov Technol 2022; 19:e310322202888. [PMID: 35362385 DOI: 10.2174/1570163819666220331095744] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/29/2021] [Accepted: 12/17/2021] [Indexed: 12/09/2022]
Abstract
BACKGROUND Cancer-induced mortality is increasingly prevalent globally which skyrocketed the necessity to discover new/novel safe and effective anticancer drugs. Cancer is characterized by the continuous multiplication of cells in the human which is unable to control. Scientific research is drawing its attention towards naturally-derived bioactive compounds as they have fewer side effects compared to the current synthetic drugs used for chemotherapy. OBJECTIVE Drugs isolated from natural sources and their role in the manipulation of epigenetic markers in cancer are discussed briefly in this review article. METHODS With advancing medicinal plant biotechnology and microbiology in the past century, several anticancer phytomedicines were developed. Modern pharmacopeia contains at least 25% herbal-based remedy including clinically used anticancer drugs. These drugs mainly include the podophyllotoxin derivatives vinca alkaloids, curcumin, mistletoe plant extracts, taxanes, camptothecin, combretastatin, and others including colchicine, artesunate, homoharringtonine, ellipticine, roscovitine, maytanasin, tapsigargin,andbruceantin. RESULTS Compounds (psammaplin, didemnin, dolastin, ecteinascidin,and halichondrin) isolated from marine sources and animals such as microalgae, cyanobacteria, heterotrophic bacteria, invertebrates. They have been evaluated for their anticancer activity on cells and experimental animal models and used chemotherapy.Drug induced manipulation of epigenetic markers plays an important role in the treatment of cancer. CONCLUSION The development of a new drug from isolated bioactive compounds of plant sources has been a feasible way to lower the toxicity and increase their effectiveness against cancer. Potential anticancer therapeutic leads obtained from various ethnomedicinal plants, foods, marine, and microorganisms are showing effective yet realistically safe pharmacological activity. This review will highlight important plant-based bioactive compounds like curcumin, stilbenes, terpenes, other polyphenolic phyto-compounds, and structurally related families that are used to prevent/ ameliorate cancer. However, a contribution from all possible fields of science is still a prerequisite for discovering safe and effective anticancer drugs.
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Affiliation(s)
- Kalyani Pathak
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786004, Assam, India
| | - Manash Pratim Pathak
- Faculty of Pharmaceutical Sciences, Assam down town University, Panikhaiti, Guwahati-781026, Assam, India
| | - Riya Saikia
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786004, Assam, India
| | - Urvashee Gogoi
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786004, Assam, India
| | - Jon Jyoti Sahariah
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786004, Assam, India
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786004, Assam, India
| | - Abhishek Samanta
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786004, Assam, India
| | - Aparoop Das
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh - 786004, Assam, India
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Cho-Clark MJ, Sukumar G, Vidal NM, Raiciulescu S, Oyola MG, Olsen C, Mariño-Ramírez L, Dalgard CL, Wu TJ. Comparative transcriptome analysis between patient and endometrial cancer cell lines to determine common signaling pathways and markers linked to cancer progression. Oncotarget 2021; 12:2500-2513. [PMID: 34966482 PMCID: PMC8711572 DOI: 10.18632/oncotarget.28161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/10/2021] [Indexed: 01/08/2023] Open
Abstract
The rising incidence and mortality of endometrial cancer (EC) in the United States calls for an improved understanding of the disease's progression. Current methodologies for diagnosis and treatment rely on the use of cell lines as models for tumor biology. However, due to inherent heterogeneity and differential growing environments between cell lines and tumors, these comparative studies have found little parallels in molecular signatures. As a consequence, the development and discovery of preclinical models and reliable drug targets are delayed. In this study, we established transcriptome parallels between cell lines and tumors from The Cancer Genome Atlas (TCGA) with the use of optimized normalization methods. We identified genes and signaling pathways associated with regulating the transformation and progression of EC. Specifically, the LXR/RXR activation, neuroprotective role for THOP1 in Alzheimer's disease, and glutamate receptor signaling pathways were observed to be mostly downregulated in advanced cancer stage. While some of these highlighted markers and signaling pathways are commonly found in the central nervous system (CNS), our results suggest a novel function of these genes in the periphery. Finally, our study underscores the value of implementing appropriate normalization methods in comparative studies to improve the identification of accurate and reliable markers.
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Affiliation(s)
- Madelaine J. Cho-Clark
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gauthaman Sukumar
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sorana Raiciulescu
- Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Mario G. Oyola
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Cara Olsen
- Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Leonardo Mariño-Ramírez
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20814, USA
| | - Clifton L. Dalgard
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - T. John Wu
- Department of Gynecologic Surgery & Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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Tumor-Associated Macrophages Induce Endocrine Therapy Resistance in ER+ Breast Cancer Cells. Cancers (Basel) 2019; 11:cancers11020189. [PMID: 30736340 PMCID: PMC6406935 DOI: 10.3390/cancers11020189] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/09/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Antiestrogenic adjuvant treatments are first-line therapies in patients with breast cancer positive for estrogen receptor (ER+). Improvement of their treatment strategies is needed because most patients eventually acquire endocrine resistance and many others are initially refractory to anti-estrogen treatments. The tumor microenvironment plays essential roles in cancer development and progress; however, the molecular mechanisms underlying such effects remain poorly understood. Breast cancer cell lines co-cultured with TNF-α-conditioned macrophages were used as pro-inflammatory tumor microenvironment models. Proliferation, migration, and colony formation assays were performed to evaluate tamoxifen and ICI 182,780 resistance and confirmed in a mouse-xenograft model. Molecular mechanisms were investigated using cytokine antibody arrays, WB, ELISA, ChIP, siRNA, and qPCR-assays. In our simulated pro-inflammatory tumor microenvironment, tumor-associated macrophages promoted proliferation, migration, invasiveness, and breast tumor growth of ER+ cells, rendering these estrogen-dependent breast cancer cells resistant to estrogen withdrawal and tamoxifen or ICI 182,780 treatment. Crosstalk between breast cancer cells and conditioned macrophages induced sustained release of pro-inflammatory cytokines from both cell types, activation of NF-κB/STAT3/ERK in the cancer cells and hyperphosphorylation of ERα, which resulted constitutively active. Our simulated tumor microenvironment strongly altered endocrine and inflammatory signaling pathways in breast cancer cells, leading to endocrine resistance in these cells.
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