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Goetz A, Shanahan F, Brooks L, Lin E, Mroue R, Cruz DD, Hunsaker T, Czech B, Dixit P, Segal U, Martin S, Foster SA, Gerosa L. Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606432. [PMID: 39149377 PMCID: PMC11326189 DOI: 10.1101/2024.08.02.606432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Purpose This study explores the potential of preclinical in vitro cell line response data and computational modeling in identifying optimal dosage requirements of pan-RAF (Belvarafenib) and MEK (Cobimetinib) inhibitors in melanoma treatment. Our research is motivated by the critical role of drug combinations in enhancing anti-cancer responses and the need to close the knowledge gap around selecting effective dosing strategies to maximize their potential. Results In a drug combination screen of 43 melanoma cell lines, we identified unique dosage landscapes of panRAF and MEK inhibitors for NRAS vs BRAF mutant melanomas. Both experienced benefits, but with a notably more synergistic and narrow dosage range for NRAS mutant melanoma. Computational modeling and molecular experiments attributed the difference to a mechanism of adaptive resistance by negative feedback. We validated in vivo translatability of in vitro dose-response maps by accurately predicting tumor growth in xenografts. Then, we analyzed pharmacokinetic and tumor growth data from Phase 1 clinical trials of Belvarafenib with Cobimetinib to show that the synergy requirement imposes stricter precision dose constraints in NRAS mutant melanoma patients. Conclusion Leveraging pre-clinical data and computational modeling, our approach proposes dosage strategies that can optimize synergy in drug combinations, while also bringing forth the real-world challenges of staying within a precise dose range.
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Affiliation(s)
- Andrew Goetz
- gRED Computational Sciences, Genentech, South San Francisco, CA, US
- Department of Biomedical Engineering, Yale University, New Haven, CT, US
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
| | - Logan Brooks
- Department of Modeling and Simulation Clinical Pharmacology, Genentech, South San Francisco, CA, US
| | - Eva Lin
- Department of Functional Genomics, Genentech, South San Francisco, CA, US
| | - Rana Mroue
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
| | - Darlene Dela Cruz
- Department of Translational Oncology, Genentech, South San Francisco, CA, US
| | - Thomas Hunsaker
- Department of Translational Oncology, Genentech, South San Francisco, CA, US
| | | | - Purushottam Dixit
- Department of Biomedical Engineering, Yale University, New Haven, CT, US
| | - Udi Segal
- Department of Translational Oncology, Genentech, South San Francisco, CA, US
| | - Scott Martin
- Department of Functional Genomics, Genentech, South San Francisco, CA, US
| | - Scott A. Foster
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
| | - Luca Gerosa
- gRED Computational Sciences, Genentech, South San Francisco, CA, US
- Department of Discovery Oncology, Genentech, South San Francisco, CA, US
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Wen S, Lin X, Luo W, Pan Y, Liao F, Wang Z, Zhan B, Feng J, Huang H. Metabolic difference between patient-derived xenograft model of pancreatic ductal adenocarcinoma and corresponding primary tumor. BMC Cancer 2024; 24:485. [PMID: 38632504 PMCID: PMC11022326 DOI: 10.1186/s12885-024-12193-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Patients-derived xenograft (PDX) model have been widely used for tumor biological and pathological studies. However, the metabolic similarity of PDX tumor to the primary cancer (PC) is still unknown. METHODS In present study, we established PDX model by engrafting primary tumor of pancreatic ductal adenocarcinoma (PDAC), and then compared the tumor metabolomics of PC, the first generation of PDX tumor (PDXG1), and the third generation of PDX tumor (PDXG3) by using 1H NMR spectroscopy. Then, we assessed the differences in response to chemotherapy between PDXG1 and PDXG3 and corresponding metabolomic differences in drug-resistant tumor tissues. To evaluate the metabolomic similarity of PDX to PC, we also compared the metabolomic difference of cell-derived xenograft (CDX) vs. PC and PDX vs. PC. RESULTS After engraftment, PDXG1 tumor had a low level of lactate, pyruvate, citrate and multiple amino acids (AAs) compared with PC. Metabolite sets enrichment and metabolic pathway analyses implied that glycolysis metabolisms were suppressed in PDXG1 tumor, and tricarboxylic acid cycle (TCA)-associated anaplerosis pathways, such as amino acids metabolisms, were enhanced. Then, after multiple passages of PDX, the altered glycolysis and TCA-associated anaplerosis pathways were partially recovered. Although no significant difference was observed in the response of PDXG1 and PDXG3 to chemotherapy, the difference in glycolysis and amino acids metabolism between PDXG1 and PDXG3 could still be maintained. In addition, the metabolomic difference between PC and CDX models were much larger than that of PDX model and PC, indicating that PDX model still retain more metabolic characteristics of primary tumor which is more suitable for tumor-associated metabolism research. CONCLUSIONS Compared with primary tumor, PDX models have obvious difference in metabolomic level. These findings can help us design in vivo tumor metabolomics research legitimately and analyze the underlying mechanism of tumor metabolic biology thoughtfully.
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Affiliation(s)
- Shi Wen
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Xianchao Lin
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Wei Luo
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Yu Pan
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Fei Liao
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China
| | - Zhenzhao Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China
| | - Bohan Zhan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, No. 422, Siming South Road, Siming District, 361005, Xiamen, China.
| | - Heguang Huang
- Department of General Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, 351001, Fuzhou, China.
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Reyes-Aldasoro CC. Modelling the Tumour Microenvironment, but What Exactly Do We Mean by "Model"? Cancers (Basel) 2023; 15:3796. [PMID: 37568612 PMCID: PMC10416922 DOI: 10.3390/cancers15153796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The Oxford English Dictionary includes 17 definitions for the word "model" as a noun and another 11 as a verb. Therefore, context is necessary to understand the meaning of the word model. For instance, "model railways" refer to replicas of railways and trains at a smaller scale and a "model student" refers to an exemplary individual. In some cases, a specific context, like cancer research, may not be sufficient to provide one specific meaning for model. Even if the context is narrowed, specifically, to research related to the tumour microenvironment, "model" can be understood in a wide variety of ways, from an animal model to a mathematical expression. This paper presents a review of different "models" of the tumour microenvironment, as grouped by different definitions of the word into four categories: model organisms, in vitro models, mathematical models and computational models. Then, the frequencies of different meanings of the word "model" related to the tumour microenvironment are measured from numbers of entries in the MEDLINE database of the United States National Library of Medicine at the National Institutes of Health. The frequencies of the main components of the microenvironment and the organ-related cancers modelled are also assessed quantitatively with specific keywords. Whilst animal models, particularly xenografts and mouse models, are the most commonly used "models", the number of these entries has been slowly decreasing. Mathematical models, as well as prognostic and risk models, follow in frequency, and these have been growing in use.
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Stella GM, Lettieri S, Piloni D, Ferrarotti I, Perrotta F, Corsico AG, Bortolotto C. Smart Sensors and Microtechnologies in the Precision Medicine Approach against Lung Cancer. Pharmaceuticals (Basel) 2023; 16:1042. [PMID: 37513953 PMCID: PMC10385174 DOI: 10.3390/ph16071042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND AND RATIONALE The therapeutic interventions against lung cancer are currently based on a fully personalized approach to the disease with considerable improvement of patients' outcome. Alongside continuous scientific progresses and research investments, massive technologic efforts, innovative challenges, and consolidated achievements together with research investments are at the bases of the engineering and manufacturing revolution that allows a significant gain in clinical setting. AIM AND METHODS The scope of this review is thus to focus, rather than on the biologic traits, on the analysis of the precision sensors and novel generation materials, as semiconductors, which are below the clinical development of personalized diagnosis and treatment. In this perspective, a careful revision and analysis of the state of the art of the literature and experimental knowledge is presented. RESULTS Novel materials are being used in the development of personalized diagnosis and treatment for lung cancer. Among them, semiconductors are used to analyze volatile cancer compounds and allow early disease diagnosis. Moreover, they can be used to generate MEMS which have found an application in advanced imaging techniques as well as in drug delivery devices. CONCLUSIONS Overall, these issues represent critical issues only partially known and generally underestimated by the clinical community. These novel micro-technology-based biosensing devices, based on the use of molecules at atomic concentrations, are crucial for clinical innovation since they have allowed the recent significant advances in cancer biology deciphering as well as in disease detection and therapy. There is an urgent need to create a stronger dialogue between technologists, basic researchers, and clinicians to address all scientific and manufacturing efforts towards a real improvement in patients' outcome. Here, great attention is focused on their application against lung cancer, from their exploitations in translational research to their application in diagnosis and treatment development, to ensure early diagnosis and better clinical outcomes.
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Affiliation(s)
- Giulia Maria Stella
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Sara Lettieri
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Davide Piloni
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Ilaria Ferrarotti
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Fabio Perrotta
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", 80131 Napoli, Italy
- U.O.C. Clinica Pneumologica "L. Vanvitelli", A.O. dei Colli, Ospedale Monaldi, 80131 Napoli, Italy
| | - Angelo Guido Corsico
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Chandra Bortolotto
- Department of Clinical-Surgical, Diagnostic and Paediatric Sciences, University of Pavia Medical School, 27100 Pavia, Italy
- Department of Diagnostic Services and Imaging, Unit of Radiology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Howell R, Davies J, Clarke MA, Appios A, Mesquita I, Jayal Y, Ringham-Terry B, Boned Del Rio I, Fisher J, Bennett CL. Localized immune surveillance of primary melanoma in the skin deciphered through executable modeling. SCIENCE ADVANCES 2023; 9:eadd1992. [PMID: 37043573 PMCID: PMC10096595 DOI: 10.1126/sciadv.add1992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
While skin is a site of active immune surveillance, primary melanomas often escape detection. Here, we have developed an in silico model to determine the local cross-talk between melanomas and Langerhans cells (LCs), the primary antigen-presenting cells at the site of melanoma development. The model predicts that melanomas fail to activate LC migration to lymph nodes until tumors reach a critical size, which is determined by a positive TNF-α feedback loop within melanomas, in line with our observations of murine tumors. In silico drug screening, supported by subsequent experimental testing, shows that treatment of primary tumors with MAPK pathway inhibitors may further prevent LC migration. In addition, our in silico model predicts treatment combinations that bypass LC dysfunction. In conclusion, our combined approach of in silico and in vivo studies suggests a molecular mechanism that explains how early melanomas develop under the radar of immune surveillance by LC.
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Affiliation(s)
| | | | - Matthew A. Clarke
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Anna Appios
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Inês Mesquita
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Yashoda Jayal
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Ben Ringham-Terry
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Isabel Boned Del Rio
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
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Padmanabhan R, Kheraldine H, Gupta I, Meskin N, Hamad A, Vranic S, Al Moustafa AE. Quantification of the growth suppression of HER2+ breast cancer colonies under the effect of trastuzumab and PD-1/PD-L1 inhibitor. Front Oncol 2022; 12:977664. [PMID: 36568154 PMCID: PMC9769711 DOI: 10.3389/fonc.2022.977664] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Immune checkpoint blockade (ICB)-based therapy is revolutionizing cancer treatment by fostering successful immune surveillance and effector cell responses against various types of cancers. However, patients with HER2+ cancers are yet to benefit from this therapeutic strategy. Precisely, several questions regarding the right combination of drugs, drug modality, and effective dose recommendations pertaining to the use of ICB-based therapy for HER2+ patients remain unanswered. Methods In this study, we use a mathematical modeling-based approach to quantify the growth inhibition of HER2+ breast cancer (BC) cell colonies (ZR75) when treated with anti-HER2; trastuzumab (TZ) and anti-PD-1/PD-L1 (BMS-202) agents. Results and discussion Our data show that a combination therapy of TZ and BMS-202 can significantly reduce the viability of ZR75 cells and trigger several morphological changes. The combination decreased the cell's invasiveness along with altering several key pathways, such as Akt/mTor and ErbB2 compared to monotherapy. In addition, BMS-202 causes dose-dependent growth inhibition of HER2+ BC cell colonies alone, while this effect is significantly improved when used in combination with TZ. Based on the in-vitro monoculture experiments conducted, we argue that BMS-202 can cause tumor growth suppression not only by mediating immune response but also by interfering with the growth signaling pathways of HER2+BC. Nevertheless, further studies are imperative to substantiate this argument and to uncover the potential crosstalk between PD-1/PD-L1 inhibitors and HER2 growth signaling pathways in breast cancer.
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Affiliation(s)
| | - Hadeel Kheraldine
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar,Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Ishita Gupta
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar,Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Nader Meskin
- Department of Electrical Engineering, Qatar University, Doha, Qatar,*Correspondence: Nader Meskin, ; Ala-Eddin Al Moustafa,
| | - Anas Hamad
- Pharmaceutical Department at Hamad Medical Corporation, Hamad Medical Corporation, Doha, Qatar
| | - Semir Vranic
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar
| | - Ala-Eddin Al Moustafa
- College of Medicine, Qatar University (QU) Health, Qatar University, Doha, Qatar,Biomedical Research Centre, Qatar University, Doha, Qatar,*Correspondence: Nader Meskin, ; Ala-Eddin Al Moustafa,
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7
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Cesaro G, Milia M, Baruzzo G, Finco G, Morandini F, Lazzarini A, Alotto P, da Cunha Carvalho de Miranda NF, Trajanoski Z, Finotello F, Di Camillo B. MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach. BIOINFORMATICS ADVANCES 2022; 2:vbac092. [PMID: 36699399 PMCID: PMC9744439 DOI: 10.1093/bioadv/vbac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/03/2022] [Indexed: 12/10/2022]
Abstract
Motivation Recently, several computational modeling approaches, such as agent-based models, have been applied to study the interaction dynamics between immune and tumor cells in human cancer. However, each tumor is characterized by a specific and unique tumor microenvironment, emphasizing the need for specialized and personalized studies of each cancer scenario. Results We present MAST, a hybrid Multi-Agent Spatio-Temporal model which can be informed using a data-driven approach to simulate unique tumor subtypes and tumor-immune dynamics starting from high-throughput sequencing data. It captures essential components of the tumor microenvironment by coupling a discrete agent-based model with a continuous partial differential equations-based model.The application to real data of human colorectal cancer tissue investigating the spatio-temporal evolution and emergent properties of four simulated human colorectal cancer subtypes, along with their agreement with current biological knowledge of tumors and clinical outcome endpoints in a patient cohort, endorse the validity of our approach. Availability and implementation MAST, implemented in Python language, is freely available with an open-source license through GitLab (https://gitlab.com/sysbiobig/mast), and a Docker image is provided to ease its deployment. The submitted software version and test data are available in Zenodo at https://dx.doi.org/10.5281/zenodo.7267745. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Giovanni Finco
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Francesco Morandini
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Alessio Lazzarini
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Piergiorgio Alotto
- Department of Industrial Engineering, University of Padova, 35131 Padova, Italy
| | | | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria,Institute of Molecular Biology, University Innsbruck, 6020 Innsbruck, Austria,Digital Science Center (DiSC), University Innsbruck, 6020 Innsbruck, Austria
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8
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Butner JD, Dogra P, Chung C, Pasqualini R, Arap W, Lowengrub J, Cristini V, Wang Z. Mathematical modeling of cancer immunotherapy for personalized clinical translation. NATURE COMPUTATIONAL SCIENCE 2022; 2:785-796. [PMID: 38126024 PMCID: PMC10732566 DOI: 10.1038/s43588-022-00377-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2023]
Abstract
Encouraging advances are being made in cancer immunotherapy modeling, especially in the key areas of developing personalized treatment strategies based on individual patient parameters, predicting treatment outcomes and optimizing immunotherapy synergy when used in combination with other treatment approaches. Here we present a focused review of the most recent mathematical modeling work on cancer immunotherapy with a focus on clinical translatability. It can be seen that this field is transitioning from pure basic science to applications that can make impactful differences in patients' lives. We discuss how researchers are integrating experimental and clinical data to fully inform models so that they can be applied for clinical predictions, and present the challenges that remain to be overcome if widespread clinical adaptation is to be realized. Lastly, we discuss the most promising future applications and areas that are expected to be the focus of extensive upcoming modeling studies.
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Affiliation(s)
- Joseph D. Butner
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Prashant Dogra
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Department of Radiation Oncology, Division of Cancer Biology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ, USA
- Department of Medicine, Division of Hematology/Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - John Lowengrub
- Department of Mathematics, University of California at Irvine, Irvine, CA, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
- Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
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Abramson A, Chan CT, Khan Y, Mermin-Bunnell A, Matsuhisa N, Fong R, Shad R, Hiesinger W, Mallick P, Gambhir SS, Bao Z. A flexible electronic strain sensor for the real-time monitoring of tumor regression. SCIENCE ADVANCES 2022; 8:eabn6550. [PMID: 36112679 PMCID: PMC9481124 DOI: 10.1126/sciadv.abn6550] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 07/12/2022] [Indexed: 05/02/2023]
Abstract
Assessing the efficacy of cancer therapeutics in mouse models is a critical step in treatment development. However, low-resolution measurement tools and small sample sizes make determining drug efficacy in vivo a difficult and time-intensive task. Here, we present a commercially scalable wearable electronic strain sensor that automates the in vivo testing of cancer therapeutics by continuously monitoring the micrometer-scale progression or regression of subcutaneously implanted tumors at the minute time scale. In two in vivo cancer mouse models, our sensor discerned differences in tumor volume dynamics between drug- and vehicle-treated tumors within 5 hours following therapy initiation. These short-term regression measurements were validated through histology, and caliper and bioluminescence measurements taken over weeklong treatment periods demonstrated the correlation with longer-term treatment response. We anticipate that real-time tumor regression datasets could help expedite and automate the process of screening cancer therapies in vivo.
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Affiliation(s)
- Alex Abramson
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Carmel T. Chan
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford (MIPS) and Bio-X Program, Stanford University, Stanford CA, 94305, USA
| | - Yasser Khan
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alana Mermin-Bunnell
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Naoji Matsuhisa
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Robyn Fong
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rohan Shad
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William Hiesinger
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Parag Mallick
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA 94305, USA
| | - Sanjiv Sam Gambhir
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford (MIPS) and Bio-X Program, Stanford University, Stanford CA, 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zhenan Bao
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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Salman G, Pehlivanoglu S, Aydin Acar C, Yesilot S. Anticancer Effects of Vitis vinifera L. Mediated Biosynthesized Silver Nanoparticles and Cotreatment with 5 Fluorouracil on HT-29 Cell Line. Biol Trace Elem Res 2022; 200:3159-3170. [PMID: 34546492 DOI: 10.1007/s12011-021-02923-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022]
Abstract
The aim of this study was to evaluate the anticancer effects of biosynthesized silver nanoparticles (Vv-AgNPs) from grape (Vitis vinifera L.) seed aqueous extract, alone or in combination with 5-Fluorouracil (5-FU) on HT-29 cell line. Vv-AgNPs were characterized by techniques such as UV-vis spectrophotometer (surface plasmon peak 454 nm), scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDX). HT-29 cells were treated with different concentrations (0-80 μg/mL for MTT) and (0-20 μg/mL for BrdU) of Vv-AgNPs alone and combined with (200 μg/mL) 5-FU for 72 h. The cytotoxic effects were analyzed by [3-(4,5-dimethylthiazol-2- yl)-2,5-diphenyl tetrazolium bromide] (MTT) assay (IC50 values 13.74 and 5.35 μg/mL, respectively). Antiproliferative effects were examined 5-bromo-2'-deoxyuridine (BrdU) assay (IC50 values 9.65 and 5.00 μg/mL, respectively). Activation of caspase-3 and protein expression levels of p53 were determined by Western blotting analysis. It was observed that Vv-AgNPs significantly increased the cleavage of the proapoptotic proteins caspase 3 and obviously enhanced the expression of p53 in a dose-dependent manner. The increased amount of total oxidant status (TOS) in the 10 μg/mL Vv-AgNPs + 5-FU treatment group, despite the increasing amount of total antioxidant status (TAS), caused an increase in Oxidative Stress Index (OSI) compared to the control. In this study, it has been shown in vitro that the use of successfully biosynthesized Vv-AgNPs in combination with 5-FU exhibits synergistic cytotoxic, antiproliferative, apoptotic, and oxidative effects against HT-29 cell line.
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Affiliation(s)
- Giray Salman
- Department of Health and Biomedical Sciences, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
| | - Suray Pehlivanoglu
- Department of Molecular Biology and Genetics, Necmettin Erbakan University, Konya, Turkey
| | - Cigdem Aydin Acar
- Department of Health and Biomedical Sciences, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
- Department of Nursing, Bucak School of Health, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
| | - Sukriye Yesilot
- Department of Health and Biomedical Sciences, Burdur Mehmet Akif Ersoy University, Burdur, Turkey.
- Department of Nursing, Bucak School of Health, Burdur Mehmet Akif Ersoy University, Burdur, Turkey.
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11
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Nilsson A, Peters JM, Meimetis N, Bryson B, Lauffenburger DA. Artificial neural networks enable genome-scale simulations of intracellular signaling. Nat Commun 2022; 13:3069. [PMID: 35654811 PMCID: PMC9163072 DOI: 10.1038/s41467-022-30684-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Mammalian cells adapt their functional state in response to external signals in form of ligands that bind receptors on the cell-surface. Mechanistically, this involves signal-processing through a complex network of molecular interactions that govern transcription factor activity patterns. Computer simulations of the information flow through this network could help predict cellular responses in health and disease. Here we develop a recurrent neural network framework constrained by prior knowledge of the signaling network with ligand-concentrations as input and transcription factor-activity as output. Applied to synthetic data, it predicts unseen test-data (Pearson correlation r = 0.98) and the effects of gene knockouts (r = 0.8). We stimulate macrophages with 59 different ligands, with and without the addition of lipopolysaccharide, and collect transcriptomics data. The framework predicts this data under cross-validation (r = 0.8) and knockout simulations suggest a role for RIPK1 in modulating the lipopolysaccharide response. This work demonstrates the feasibility of genome-scale simulations of intracellular signaling.
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Affiliation(s)
- Avlant Nilsson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE 41296, Sweden
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Joshua M Peters
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Nikolaos Meimetis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan Bryson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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12
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Computational drug repurposing in the age of COVID-19: mixing antiviral cocktails in silico. NPJ Digit Med 2022; 5:52. [PMID: 35459899 PMCID: PMC9033809 DOI: 10.1038/s41746-022-00599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/29/2022] [Indexed: 11/20/2022] Open
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13
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Imoto H, Yamashiro S, Okada M. A text-based computational framework for patient -specific modeling for classification of cancers. iScience 2022; 25:103944. [PMID: 35535207 PMCID: PMC9076893 DOI: 10.1016/j.isci.2022.103944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/03/2022] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
Abstract
Patient heterogeneity precludes cancer treatment and drug development; hence, development of methods for finding prognostic markers for individual treatment is urgently required. Here, we present Pasmopy (Patient-Specific Modeling in Python), a computational framework for stratification of patients using in silico signaling dynamics. Pasmopy converts texts and sentences on biochemical systems into an executable mathematical model. Using this framework, we built a model of the ErbB receptor signaling network, trained in cultured cell lines, and performed in silico simulation of 377 patients with breast cancer using The Cancer Genome Atlas (TCGA) transcriptome datasets. The temporal dynamics of Akt, extracellular signal-regulated kinase (ERK), and c-Myc in each patient were able to accurately predict the difference in prognosis and sensitivity to kinase inhibitors in triple-negative breast cancer (TNBC). Our model applies to any type of signaling network and facilitates the network-based use of prognostic markers and prediction of drug response. A text file describing biochemical systems is converted into an executable model Patient-specific models incorporate individual gene expression profiles In silico signaling dynamics can be utilized as prognostic biomarkers Personalized kinetic models are capable of predicting potential drug targets
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14
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Hassan G, Zahra MH, Seno A, Seno M. The significance of ErbB2/3 in the conversion of induced pluripotent stem cells into cancer stem cells. Sci Rep 2022; 12:2711. [PMID: 35177646 PMCID: PMC8854581 DOI: 10.1038/s41598-022-04980-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/15/2021] [Indexed: 11/27/2022] Open
Abstract
Cancer stem cells (CSCs) are suggested to be responsible for drug resistance and aggressive phenotypes of tumors. Mechanisms of CSC induction are still under investigation. Our lab has established a novel method to generate CSCs from iPSCs under a cancerous microenvironment mimicked by the conditioned medium (CM) of cancer-derived cells. Here, we analyzed the transcriptome of CSCs, which were converted from iPSCs with CM from pancreatic ductal adenocarcinoma cells. The differentially expressed genes were identified and used to explore pathway enrichment. From the comparison of the CSCs with iPSCs, genes with elevated expression were related to the ErbB2/3 signaling pathway. Inhibition of either ErbB2 with lapatinib as a tyrosine kinase inhibitor or ErbB3 with TX1-85-1 or siRNAs arrested cell proliferation, inhibited the in vitro tumorigenicity, and lead to loss of stemness in the converting cells. The self-renewal and tube formation abilities of cells were also abolished while CD24 and Oct3/4 levels were reduced, and the MAPK pathway was overactivated. This study shows a potential involvement of the ErbB2/ErbB3 pathway in CSC generation and could lead to new insight into the mechanism of tumorigenesis and the way of cancer prevention.
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Affiliation(s)
- Ghmkin Hassan
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3.1.1 Tsushima-Naka, Kita, Okayama, 700-8530, Japan
- Department of Genomic Oncology and Oral Medicine, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Maram H Zahra
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3.1.1 Tsushima-Naka, Kita, Okayama, 700-8530, Japan
| | - Akimasa Seno
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3.1.1 Tsushima-Naka, Kita, Okayama, 700-8530, Japan
- The Laboratory of Natural Food and Medicine, Co., Ltd., Okayama, 700-8530, Japan
| | - Masaharu Seno
- Department of Biotechnology and Drug Discovery, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3.1.1 Tsushima-Naka, Kita, Okayama, 700-8530, Japan.
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15
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Haga M, Okada M. Systems approaches to investigate the role of NF-κB signaling in aging. Biochem J 2022; 479:161-183. [PMID: 35098992 PMCID: PMC8883486 DOI: 10.1042/bcj20210547] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 12/14/2022]
Abstract
The nuclear factor-κB (NF-κB) signaling pathway is one of the most well-studied pathways related to inflammation, and its involvement in aging has attracted considerable attention. As aging is a complex phenomenon and is the result of a multi-step process, the involvement of the NF-κB pathway in aging remains unclear. To elucidate the role of NF-κB in the regulation of aging, different systems biology approaches have been employed. A multi-omics data-driven approach can be used to interpret and clarify unknown mechanisms but cannot generate mechanistic regulatory structures alone. In contrast, combining this approach with a mathematical modeling approach can identify the mechanistics of the phenomena of interest. The development of single-cell technologies has also helped clarify the heterogeneity of the NF-κB response and underlying mechanisms. Here, we review advances in the understanding of the regulation of aging by NF-κB by focusing on omics approaches, single-cell analysis, and mathematical modeling of the NF-κB network.
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Affiliation(s)
- Masatoshi Haga
- Laboratory for Cell Systems, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Basic Research Development Division, ROHTO Pharmaceutical Co., Ltd., Ikuno-ku, Osaka 544-8666, Japan
| | - Mariko Okada
- Laboratory for Cell Systems, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Center for Drug Design and Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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16
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Rocca A, Kholodenko BN. Can Systems Biology Advance Clinical Precision Oncology? Cancers (Basel) 2021; 13:6312. [PMID: 34944932 PMCID: PMC8699328 DOI: 10.3390/cancers13246312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Precision oncology is perceived as a way forward to treat individual cancer patients. However, knowing particular cancer mutations is not enough for optimal therapeutic treatment, because cancer genotype-phenotype relationships are nonlinear and dynamic. Systems biology studies the biological processes at the systems' level, using an array of techniques, ranging from statistical methods to network reconstruction and analysis, to mathematical modeling. Its goal is to reconstruct the complex and often counterintuitive dynamic behavior of biological systems and quantitatively predict their responses to environmental perturbations. In this paper, we review the impact of systems biology on precision oncology. We show examples of how the analysis of signal transduction networks allows to dissect resistance to targeted therapies and inform the choice of combinations of targeted drugs based on tumor molecular alterations. Patient-specific biomarkers based on dynamical models of signaling networks can have a greater prognostic value than conventional biomarkers. These examples support systems biology models as valuable tools to advance clinical and translational oncological research.
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Affiliation(s)
- Andrea Rocca
- Hygiene and Public Health, Local Health Unit of Romagna, 47121 Forlì, Italy
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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17
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Pedersen RK, Andersen M, Knudsen TA, Skov V, Kjær L, Hasselbalch HC, Ottesen JT. Dose‐dependent mathematical modeling of interferon‐α‐treatment for personalized treatment of myeloproliferative neoplasms. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021. [DOI: 10.1002/cso2.1030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Rasmus K. Pedersen
- Centre for Mathematical Modeling ‐ Human Health and Disease (COMMAND) IMFUFA Department of Science and Environment Roskilde University Roskilde Denmark
| | - Morten Andersen
- Centre for Mathematical Modeling ‐ Human Health and Disease (COMMAND) IMFUFA Department of Science and Environment Roskilde University Roskilde Denmark
| | - Trine A. Knudsen
- Department of Hematology Zealand University Hospital Roskilde Denmark
| | - Vibe Skov
- Department of Hematology Zealand University Hospital Roskilde Denmark
| | - Lasse Kjær
- Department of Hematology Zealand University Hospital Roskilde Denmark
| | | | - Johnny T. Ottesen
- Centre for Mathematical Modeling ‐ Human Health and Disease (COMMAND) IMFUFA Department of Science and Environment Roskilde University Roskilde Denmark
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18
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Ganini C, Amelio I, Bertolo R, Bove P, Buonomo OC, Candi E, Cipriani C, Di Daniele N, Juhl H, Mauriello A, Marani C, Marshall J, Melino S, Marchetti P, Montanaro M, Natale ME, Novelli F, Palmieri G, Piacentini M, Rendina EA, Roselli M, Sica G, Tesauro M, Rovella V, Tisone G, Shi Y, Wang Y, Melino G. Global mapping of cancers: The Cancer Genome Atlas and beyond. Mol Oncol 2021; 15:2823-2840. [PMID: 34245122 PMCID: PMC8564642 DOI: 10.1002/1878-0261.13056] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/04/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Cancer genomes have been explored from the early 2000s through massive exome sequencing efforts, leading to the publication of The Cancer Genome Atlas in 2013. Sequencing techniques have been developed alongside this project and have allowed scientists to bypass the limitation of costs for whole-genome sequencing (WGS) of single specimens by developing more accurate and extensive cancer sequencing projects, such as deep sequencing of whole genomes and transcriptomic analysis. The Pan-Cancer Analysis of Whole Genomes recently published WGS data from more than 2600 human cancers together with almost 1200 related transcriptomes. The application of WGS on a large database allowed, for the first time in history, a global analysis of features such as molecular signatures, large structural variations and noncoding regions of the genome, as well as the evaluation of RNA alterations in the absence of underlying DNA mutations. The vast amount of data generated still needs to be thoroughly deciphered, and the advent of machine-learning approaches will be the next step towards the generation of personalized approaches for cancer medicine. The present manuscript wants to give a broad perspective on some of the biological evidence derived from the largest sequencing attempts on human cancers so far, discussing advantages and limitations of this approach and its power in the era of machine learning.
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Affiliation(s)
- Carlo Ganini
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- IDI‐IRCCSRomeItaly
| | - Ivano Amelio
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Riccardo Bertolo
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Pierluigi Bove
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Oreste Claudio Buonomo
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Eleonora Candi
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- IDI‐IRCCSRomeItaly
| | - Chiara Cipriani
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Nicola Di Daniele
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Alessandro Mauriello
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Carla Marani
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - John Marshall
- Medstar Georgetown University HospitalGeorgetown UniversityWashingtonDCUSA
| | - Sonia Melino
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Manuela Montanaro
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Maria Emanuela Natale
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Flavia Novelli
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giampiero Palmieri
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Mauro Piacentini
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Mario Roselli
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giuseppe Sica
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Manfredi Tesauro
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Valentina Rovella
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giuseppe Tisone
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Yufang Shi
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- CAS Key Laboratory of Tissue Microenvironment and TumorShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina
- The First Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and ProtectionInstitutes for Translational MedicineSoochow UniversityChina
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and TumorShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina
| | - Gerry Melino
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
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19
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Srinivasan A, Bain M, Baskar A. Learning explanations for biological feedback with delays using an event calculus. Mach Learn 2021. [DOI: 10.1007/s10994-021-06038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Semenova N, Tuchin VV. 3D models of the dynamics of cancer cells under external pressure. CHAOS (WOODBURY, N.Y.) 2021; 31:083122. [PMID: 34470224 DOI: 10.1063/5.0056764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Skin cancer is one of the most frequent cancers worldwide. Recently, it has been shown that the tumor proliferation rate in skin and its dynamics can be changed by an osmotic pressure. However, these findings are rather unstructured. A weak pressure can slow down the tumor growth, while a very high pressure can, on the contrary, lead to accelerated growth and metastases. The magnitude and spatial distribution of osmotic pressures in tumors at present cannot be measured experimentally. Therefore, it is of particular interest to find appropriate models that would simulate the effects of additional osmotic pressures in skin and assess the features of its implementation. In this paper, we suggest an improved model based on the principles of the conventional hydrodynamic model for macrophase separations, which allows one to include not only the properties of healthy and cancer cells but also the microenvironment. We study and analyze the proliferation of cancer cells in 3D models of the epidermal layer of skin under an osmotic pressure. There are two suggested 3D models that are based on the same principles: (1) cellular cubic lattice and (2) cell spheroid. This allows expanding the application of the model depending on a given task. Here, we are focused on the study of melanoma at an early stage when there are not many cancer cells. Additional compressive and expansive pressures are added to the central part of the system. Both systems demonstrate similar results in slowing down the rate of tumor growth with a small pressure.
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Affiliation(s)
- Nadezhda Semenova
- Department of Fundamental Medicine and Medical Technology, Institute of Physics, Saratov State University, 83 Astrakhanskaya str., Saratov 410012, Russia
| | - Valery V Tuchin
- Laboratory of Biomedical Photoacoustics, Science Medical Center, Saratov State University, 112A Bolshaya Kazachya, Saratov 410012, Russia
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21
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Gómez Tejeda Zañudo J, Mao P, Alcon C, Kowalski K, Johnson GN, Xu G, Baselga J, Scaltriti M, Letai A, Montero J, Albert R, Wagle N. Cell Line-Specific Network Models of ER + Breast Cancer Identify Potential PI3Kα Inhibitor Resistance Mechanisms and Drug Combinations. Cancer Res 2021; 81:4603-4617. [PMID: 34257082 PMCID: PMC8744502 DOI: 10.1158/0008-5472.can-21-1208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/18/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022]
Abstract
Durable control of invasive solid tumors necessitates identifying therapeutic resistance mechanisms and effective drug combinations. In this work, we used a network-based mathematical model to identify sensitivity regulators and drug combinations for the PI3Kα inhibitor alpelisib in estrogen receptor positive (ER+) PIK3CA-mutant breast cancer. The model-predicted efficacious combination of alpelisib and BH3 mimetics, for example, MCL1 inhibitors, was experimentally validated in ER+ breast cancer cell lines. Consistent with the model, FOXO3 downregulation reduced sensitivity to alpelisib, revealing a novel potential resistance mechanism. Cell line-specific sensitivity to combinations of alpelisib and BH3 mimetics depended on which BCL2 family members were highly expressed. On the basis of these results, newly developed cell line-specific network models were able to recapitulate the observed differential response to alpelisib and BH3 mimetics. This approach illustrates how network-based mathematical models can contribute to overcoming the challenge of cancer drug resistance. SIGNIFICANCE: Network-based mathematical models of oncogenic signaling and experimental validation of its predictions can identify resistance mechanisms for targeted therapies, as this study demonstrates for PI3Kα-specific inhibitors in breast cancer.
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Affiliation(s)
- Jorge Gómez Tejeda Zañudo
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Pingping Mao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Clara Alcon
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Kailey Kowalski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Gabriela N Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Guotai Xu
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jose Baselga
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maurizio Scaltriti
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Joan Montero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. .,Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Réka Albert
- Department of Physics, The Pennsylvania State University, Pennsylvania. .,Department of Biology, The Pennsylvania State University, Pennsylvania
| | - Nikhil Wagle
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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22
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Prugger M, Einkemmer L, Beik SP, Wasdin PT, Harris LA, Lopez CF. Unsupervised logic-based mechanism inference for network-driven biological processes. PLoS Comput Biol 2021; 17:e1009035. [PMID: 34077417 PMCID: PMC8202945 DOI: 10.1371/journal.pcbi.1009035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/14/2021] [Accepted: 05/03/2021] [Indexed: 01/21/2023] Open
Abstract
Modern analytical techniques enable researchers to collect data about cellular states, before and after perturbations. These states can be characterized using analytical techniques, but the inference of regulatory interactions that explain and predict changes in these states remains a challenge. Here we present a generalizable, unsupervised approach to generate parameter-free, logic-based models of cellular processes, described by multiple discrete states. Our algorithm employs a Hamming-distance based approach to formulate, test, and identify optimized logic rules that link two states. Our approach comprises two steps. First, a model with no prior knowledge except for the mapping between initial and attractor states is built. We then employ biological constraints to improve model fidelity. Our algorithm automatically recovers the relevant dynamics for the explored models and recapitulates key aspects of the biochemical species concentration dynamics in the original model. We present the advantages and limitations of our work and discuss how our approach could be used to infer logic-based mechanisms of signaling, gene-regulatory, or other input-output processes describable by the Boolean formalism.
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Affiliation(s)
- Martina Prugger
- Department of Biochemistry, University of Innsbruck, Innsbruck, Austria
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Lukas Einkemmer
- Department of Mathematics, University of Innsbruck, Innsbruck, Austria
| | - Samantha P. Beik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Perry T. Wasdin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Leonard A. Harris
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, United States of America
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Carlos F. Lopez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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23
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Cirillo D, Núñez‐Carpintero I, Valencia A. Artificial intelligence in cancer research: learning at different levels of data granularity. Mol Oncol 2021; 15:817-829. [PMID: 33533192 PMCID: PMC8024732 DOI: 10.1002/1878-0261.12920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/20/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
From genome-scale experimental studies to imaging data, behavioral footprints, and longitudinal healthcare records, the convergence of big data in cancer research and the advances in Artificial Intelligence (AI) is paving the way to develop a systems view of cancer. Nevertheless, this biomedical area is largely characterized by the co-existence of big data and small data resources, highlighting the need for a deeper investigation about the crosstalk between different levels of data granularity, including varied sample sizes, labels, data types, and other data descriptors. This review introduces the current challenges, limitations, and solutions of AI in the heterogeneous landscape of data granularity in cancer research. Such a variety of cancer molecular and clinical data calls for advancing the interoperability among AI approaches, with particular emphasis on the synergy between discriminative and generative models that we discuss in this work with several examples of techniques and applications.
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Affiliation(s)
| | | | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
- ICREABarcelonaSpain
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24
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Ebata K, Yamashiro S, Iida K, Okada M. Building patient-specific models for receptor tyrosine kinase signaling networks. FEBS J 2021; 289:90-101. [PMID: 33755310 DOI: 10.1111/febs.15831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022]
Abstract
Cancer progresses due to changes in the dynamic interactions of multidimensional factors associated with gene mutations. Cancer research has actively adopted computational methods, including data-driven and mathematical model-driven approaches, to identify causative factors and regulatory rules that can explain the complexity and diversity of cancers. A data-driven, statistics-based approach revealed correlations between gene alterations and clinical outcomes in many types of cancers. A model-driven mathematical approach has elucidated the dynamic features of cancer networks and identified the mechanisms of drug efficacy and resistance. More recently, machine learning methods have emerged that can be used for mining omics data and classifying patient. However, as the strengths and weaknesses of each method becoming apparent, new analytical tools are emerging to combine and improve the methodologies and maximize their predictive power for classifying cancer subtypes and prognosis. Here, we introduce recent advances in cancer systems biology aimed at personalized medicine, with focus on the receptor tyrosine kinase signaling network.
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Affiliation(s)
- Kyoichi Ebata
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Sawa Yamashiro
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Keita Iida
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Mariko Okada
- Institute for Protein Research, Osaka University, Suita, Japan.,Center for Drug Design and Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan.,Institute for Chemical Research, Kyoto University, Japan
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25
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Li ZZ, Liu PF, An TT, Yang HC, Zhang W, Wang JX. Construction of a prognostic immune signature for lower grade glioma that can be recognized by MRI radiomics features to predict survival in LGG patients. Transl Oncol 2021; 14:101065. [PMID: 33761371 PMCID: PMC8020484 DOI: 10.1016/j.tranon.2021.101065] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study aimed to identify a series of prognostically relevant immune features by immunophenoscore. Immune features were explored using MRI radiomics features to prediction the overall survival (OS) of lower-grade glioma (LGG) patients and their response to immune checkpoints. METHOD LGG data were retrieved from TCGA and categorized into training and internal validation datasets. Patients attending the First Affiliated Hospital of Harbin Medical University were included in an external validation cohort. An immunophenoscore-based signature was built to predict malignant potential and response to immune checkpoint inhibitors in LGG patients. In addition, a deep learning neural network prediction model was built for validation of the immunophenoscore-based signature. RESULTS Immunophenotype-associated mRNA signatures (IMriskScore) for outcome prediction and ICB therapeutic effects in LGG patients were constructed. Deep learning of neural networks based on radiomics showed that MRI radiomic features determined IMriskScore. Enrichment analysis and ssGSEA correlation analysis were performed. Mutations in CIC significantly improved the prognosis of patients in the high IMriskScore group. Therefore, CIC is a potential therapeutic target for patients in the high IMriskScore group. Moreover, IMriskScore is an independent risk factor that can be used clinically to predict LGG patient outcomes. CONCLUSIONS The IMriskScore model consisting of a sets of biomarkers, can independently predict the prognosis of LGG patients and provides a basis for the development of personalized immunotherapy strategies. In addition, IMriskScore features were predicted by MRI radiomics using a deep learning approach using neural networks. Therefore, they can be used for the prognosis of LGG patients.
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Affiliation(s)
- Zi-Zhuo Li
- Department of Abdominal Ultrasound, The First Affiliated Hospital of Harbin Medical University China
| | - Peng-Fei Liu
- Department of Magnetic Resonance, The First Affiliated Hospital of Harbin Medical University China.
| | - Ting-Ting An
- Department of Abdominal Ultrasound, The First Affiliated Hospital of Harbin Medical University China
| | - Hai-Chao Yang
- Department of Abdominal Ultrasound, The First Affiliated Hospital of Harbin Medical University China
| | - Wei Zhang
- Department of Abdominal Ultrasound, The First Affiliated Hospital of Harbin Medical University China
| | - Jia-Xu Wang
- Department of Abdominal Ultrasound, The First Affiliated Hospital of Harbin Medical University China
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26
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Abdul Pari AA, Singhal M, Augustin HG. Emerging paradigms in metastasis research. J Exp Med 2021; 218:e20190218. [PMID: 33601416 PMCID: PMC7754674 DOI: 10.1084/jem.20190218] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/17/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022] Open
Abstract
Historically, therapy of metastatic disease has essentially been limited to using strategies that were identified and established to shrink primary tumors. The limited efficacy of such treatments on overall patient survival stems from diverging intrinsic and extrinsic characteristics of a primary tumor and metastases originating therefrom. To develop better therapeutic strategies to treat metastatic disease, there is an urgent need to shift the paradigm in preclinical metastasis research by conceptualizing metastatic dissemination, colonization, and growth as spatiotemporally dynamic processes and identifying rate-limiting vulnerabilities of the metastatic cascade. Clinically, while metastatic colonization remains the most attractive therapeutic avenue, comprehensive understanding of earlier steps may unravel novel metastasis-restricting therapies for presurgical neoadjuvant application. Moving beyond a primary tumor-centric view, this review adopts a holistic approach to understanding the spatial and temporal progression of metastasis. After reviewing recent developments in metastasis research, we highlight some of the grand challenges and propose a framework to expedite mechanism-based discovery research feeding the translational pipeline.
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Affiliation(s)
- Ashik Ahmed Abdul Pari
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Mahak Singhal
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hellmut G. Augustin
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Kuijjer ML. Predicting Cancer Evolution Using Cell State Dynamics. Cancer Res 2020; 80:3072-3073. [PMID: 32753487 DOI: 10.1158/0008-5472.can-20-1878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 11/16/2022]
Abstract
One of the biggest challenges in cancer is predicting its initiation and course of progression. In this issue of Cancer Research, Rockne and colleagues use state transition theory to predict how peripheral mononuclear blood cells in mice transition from a healthy state to acute myeloid leukemia. They found that critical transcriptomic perturbations could predict initiation and progression of the disease. This is an important step toward accurately predicting cancer evolution, which may eventually facilitate early diagnosis of cancer and disease recurrence, and which could potentially inform on timing of therapeutic interventions.See related article by Rockne et al., 3157.
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Affiliation(s)
- Marieke L Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.
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A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data-Application to the ErbB Receptor Signaling Pathway. Cancers (Basel) 2020; 12:cancers12102878. [PMID: 33036375 PMCID: PMC7650612 DOI: 10.3390/cancers12102878] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Temporal signaling dynamics are important for controlling the fate decisions of mammalian cells. In this study, we developed BioMASS, a computational platform for prediction and analysis of signaling dynamics using RNA-sequencing gene expression data. We first constructed a detailed mechanistic model of early transcriptional regulation mediated by ErbB receptor signaling pathway. After training the model parameters against phosphoprotein time-course datasets obtained from breast cancer cell lines, the model successfully predicted signaling activities of another untrained cell line. The result indicates that the parameters of molecular interactions in these different cell types are not particularly unique to the cell type, and the expression levels of the components of the signaling network are sufficient to explain the complex dynamics of the networks. Our method can be further expanded to predict signaling activity from clinical gene expression data for in silico drug screening for personalized medicine. Abstract A current challenge in systems biology is to predict dynamic properties of cell behaviors from public information such as gene expression data. The temporal dynamics of signaling molecules is critical for mammalian cell commitment. We hypothesized that gene expression levels are tightly linked with and quantitatively control the dynamics of signaling networks regardless of the cell type. Based on this idea, we developed a computational method to predict the signaling dynamics from RNA sequencing (RNA-seq) gene expression data. We first constructed an ordinary differential equation model of ErbB receptor → c-Fos induction using a newly developed modeling platform BioMASS. The model was trained with kinetic parameters against multiple breast cancer cell lines using autologous RNA-seq data obtained from the Cancer Cell Line Encyclopedia (CCLE) as the initial values of the model components. After parameter optimization, the model proceeded to prediction in another untrained breast cancer cell line. As a result, the model learned the parameters from other cells and was able to accurately predict the dynamics of the untrained cells using only the gene expression data. Our study suggests that gene expression levels of components within the ErbB network, rather than rate constants, can explain the cell-specific signaling dynamics, therefore playing an important role in regulating cell fate.
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Bates M, Boland A, McDermott N, Marignol L. YB-1: The key to personalised prostate cancer management? Cancer Lett 2020; 490:66-75. [PMID: 32681926 DOI: 10.1016/j.canlet.2020.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Y-box-binding protein 1 (YB-1) is a DNA/RNA binding protein increasingly implicated in the regulation of cancer cell biology. Normally located in the cytoplasm, nuclear localisation in prostate cancer is associated with more aggressive, potentially treatment-resistant disease. This is attributed to the ability of YB-1 to act as a transcription factor for various target genes associated with androgen receptor signalling, survival, DNA repair, proliferation, invasion, differentiation, angiogenesis and hypoxia. This review aims to examine the clinical potential of YB-1 in the detection and therapeutic management of prostate cancer.
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Affiliation(s)
- Mark Bates
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland
| | - Anna Boland
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland
| | - Niamh McDermott
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland
| | - Laure Marignol
- Translational Radiobiology and Molecular Oncology Group, Applied Radiation Therapy Trinity, Discipline of Radiation Therapy, Trinity College Dublin, Dublin 2, Ireland.
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