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Kim Y, Han Y, Hopper C, Lee J, Joo JI, Gong JR, Lee CK, Jang SH, Kang J, Kim T, Cho KH. A gray box framework that optimizes a white box logical model using a black box optimizer for simulating cellular responses to perturbations. CELL REPORTS METHODS 2024; 4:100773. [PMID: 38744288 PMCID: PMC11133856 DOI: 10.1016/j.crmeth.2024.100773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Predicting cellular responses to perturbations requires interpretable insights into molecular regulatory dynamics to perform reliable cell fate control, despite the confounding non-linearity of the underlying interactions. There is a growing interest in developing machine learning-based perturbation response prediction models to handle the non-linearity of perturbation data, but their interpretation in terms of molecular regulatory dynamics remains a challenge. Alternatively, for meaningful biological interpretation, logical network models such as Boolean networks are widely used in systems biology to represent intracellular molecular regulation. However, determining the appropriate regulatory logic of large-scale networks remains an obstacle due to the high-dimensional and discontinuous search space. To tackle these challenges, we present a scalable derivative-free optimizer trained by meta-reinforcement learning for Boolean network models. The logical network model optimized by the trained optimizer successfully predicts anti-cancer drug responses of cancer cell lines, while simultaneously providing insight into their underlying molecular regulatory mechanisms.
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Affiliation(s)
- Yunseong Kim
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Younghyun Han
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Corbin Hopper
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jonghoon Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jae Il Joo
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jeong-Ryeol Gong
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Chun-Kyung Lee
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Seong-Hoon Jang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Junsoo Kang
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Taeyoung Kim
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Kwang-Hyun Cho
- Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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Chen L, Zhang D, Chen Y, Zhu H, Liu Z, Yu Z, Xie J. ORC6 acts as an effective prognostic predictor for non‑small cell lung cancer and is closely associated with tumor progression. Oncol Lett 2024; 27:96. [PMID: 38288041 PMCID: PMC10823314 DOI: 10.3892/ol.2024.14229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
Origin recognition complexes (ORCs) are vital in the control of DNA replication and the progression of the cell cycle, however the precise function and mechanism of ORC6 in non-small cell lung cancer (NSCLC) is still not well understood. The present study used bioinformatics methods to assess the predictive significance of ORC6 expression in NSCLC. Moreover, the expression of ORC6 was further evaluated using reverse transcription-quantitative PCR and western blotting, and its functional significance in lung cancer was assessed via knockdown experiments using small interfering RNA. A significant association was demonstrated between the expression of ORC6 and the clinical features of NSCLC. In particular, elevated levels of ORC6 were significantly strongly correlated with an unfavorable prognosis. Multivariate analysis demonstrated that increased ORC6 expression independently contributed to the risk of overall survival (HR 1.304; P=0.015) in individuals diagnosed with NSCLC. Analysis of Kaplan-Meier plots demonstrated that ORC6 expression served as a valuable indicator for diagnosing and predicting the prognosis of NSCLC. Moreover, in vitro studies demonstrated that modified ORC6 expression had a significant impact on the proliferation, migration and metastasis of NSCLC cells. NSCLC cell lines (H1299 and mH1650) exhibited markedly higher ORC6 expression than normal lung cell lines. The results of the present study indicated a strong association between the expression of ORC6 and the clinicopathological characteristics of NSCLC, which suggested its potential as a reliable biomarker for predicting NSCLC. Furthermore, ORC6 may have important therapeutic implications in the management of NSCLC.
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Affiliation(s)
- Letian Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Dongdong Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Yujuan Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Huilan Zhu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Zhipeng Liu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Zhiping Yu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Junping Xie
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
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Leggett SE, Brennan MC, Martinez S, Tien J, Nelson CM. Relatively Rare Populations of Invasive Cells Drive Progression of Heterogeneous Tumors. Cell Mol Bioeng 2024; 17:7-24. [PMID: 38435793 PMCID: PMC10902221 DOI: 10.1007/s12195-023-00792-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/19/2023] [Indexed: 03/05/2024] Open
Abstract
Introduction Breast tumors often display an astonishing degree of spatial and temporal heterogeneity, which are associated with cancer progression, drug resistance, and relapse. Triple-negative breast cancer (TNBC) is a particularly aggressive and heterogeneous subtype for which targeted therapies are scarce. Consequently, patients with TNBC have a poorer overall prognosis compared to other breast cancer patients. Within heterogeneous tumors, individual clonal subpopulations may exhibit differences in their rates of growth and degrees of invasiveness. We hypothesized that such phenotypic heterogeneity at the single-cell level may accelerate tumor progression by enhancing the overall growth and invasion of the entire tumor. Methods To test this hypothesis, we isolated and characterized clonal subpopulations with distinct morphologies and biomarker expression from the inherently heterogeneous 4T1 mouse mammary carcinoma cell line. We then leveraged a 3D microfluidic tumor model to reverse-engineer intratumoral heterogeneity and thus investigate how interactions between phenotypically distinct subpopulations affect tumor growth and invasion. Results We found that the growth and invasion of multiclonal tumors were largely dictated by the presence of cells with epithelial and mesenchymal traits, respectively. The latter accelerated overall tumor invasion, even when these cells comprised less than 1% of the initial population. Consistently, tumor progression was delayed by selectively targeting the mesenchymal subpopulation. Discussion This work reveals that highly invasive cells can dominate tumor phenotype and that specifically targeting these cells can slow the progression of heterogeneous tumors, which may help inform therapeutic approaches. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-023-00792-w.
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Affiliation(s)
- Susan E. Leggett
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Molly C. Brennan
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
| | - Sophia Martinez
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
| | - Joe Tien
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
| | - Celeste M. Nelson
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
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4
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Domingo E, Martínez-González B, García-Crespo C, Somovilla P, de Ávila AI, Soria ME, Durán-Pastor A, Perales C. Puzzles, challenges, and information reservoir of SARS-CoV-2 quasispecies. J Virol 2023; 97:e0151123. [PMID: 38092661 PMCID: PMC10734546 DOI: 10.1128/jvi.01511-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
Upon the emergence of SARS-CoV-2 in the human population, it was conjectured that for this coronavirus the dynamic intra-host heterogeneity typical of RNA viruses would be toned down. Nothing of this sort is observed. Here we review the main observations on the complexity and diverse composition of SARS-CoV-2 mutant spectra sampled from infected patients, within the framework of quasispecies dynamics. The analyses suggest that the information provided by myriads of genomic sequences within infected individuals may have a predictive value of the genomic sequences that acquire epidemiological relevance. Possibilities to reconcile the presence of broad mutant spectra in the large RNA coronavirus genome with its encoding a 3' to 5' exonuclease proofreading-repair activity are considered. Indeterminations in the behavior of individual viral genomes provide a benefit for the survival of the ensemble. We propose that this concept falls in the domain of "stochastic thinking," a notion that applies also to cellular processes, as a means for biological systems to face unexpected needs.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Brenda Martínez-González
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - María Eugenia Soria
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Antoni Durán-Pastor
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
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5
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Dinić J, Podolski-Renić A, Dragoj M, Jovanović Stojanov S, Stepanović A, Lupšić E, Pajović M, Jovanović M, Petrović Rodić D, Marić D, Ercegovac M, Pešić M. Immunofluorescence-Based Assay for High-Throughput Analysis of Multidrug Resistance Markers in Non-Small Cell Lung Carcinoma Patient-Derived Cells. Diagnostics (Basel) 2023; 13:3617. [PMID: 38132201 PMCID: PMC10743086 DOI: 10.3390/diagnostics13243617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Lung cancer remains the leading cause of cancer death globally, with non-small cell lung cancer (NSCLC) accounting for the majority of cases. Multidrug resistance (MDR), often caused by ATP-binding cassette (ABC) transporters, represents a significant obstacle in the treatment of NSCLC. While genetic profiling has an important role in personalized therapy, functional assays that measure cellular responses to drugs are gaining in importance. We developed an automated microplate-based immunofluorescence assay for the evaluation of MDR markers ABCB1, ABCC1, and ABCG2 in cells obtained from NSCLC patients through high-content imaging and image analysis, as part of a functional diagnostic approach. This assay effectively discriminated cancer from non-cancer cells within mixed cultures, which is vital for accurate assessment of changes in MDR marker expression in different cell populations in response to anticancer drugs. Validation was performed using established drug-sensitive (NCI-H460) and drug-resistant (NCI-H460/R) NSCLC cell lines, demonstrating the assay's capacity to distinguish and evaluate different MDR profiles. The obtained results revealed wide-ranging effects of various chemotherapeutic agents on MDR marker expression in different patient-derived NSCLC cultures, emphasizing the need for MDR diagnostics in NSCLC. In addition to being a valuable tool for assessing drug effects on MDR markers in different cell populations, the assay can complement genetic profiling to optimize treatment. Further assay adaptations may extend its application to other cancer types, improving treatment efficacy while minimizing the development of resistance.
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Affiliation(s)
- Jelena Dinić
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Ana Podolski-Renić
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Miodrag Dragoj
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Sofija Jovanović Stojanov
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Ana Stepanović
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Ema Lupšić
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Milica Pajović
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Mirna Jovanović
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
| | - Dušica Petrović Rodić
- Department of Thoracic Pathology, Clinical Center of Serbia, Service of Pathohistology, University of Belgrade, Pasterova 2, 11000 Belgrade, Serbia;
| | - Dragana Marić
- Clinic for Pulmonology, Faculty of Medicine, University of Belgrade, Dr Koste Todorovića 26, 11000 Belgrade, Serbia;
| | - Maja Ercegovac
- Clinic for Thoracic Surgery, Faculty of Medicine, University of Belgrade, Pasterova 2, 11000 Belgrade, Serbia;
| | - Milica Pešić
- Department of Neurobiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11108 Belgrade, Serbia; (A.P.-R.); (M.D.); (S.J.S.); (A.S.); (E.L.); (M.P.); (M.J.)
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6
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Beumers L, Vlachavas EI, Borgoni S, Schwarzmüller L, Penso-Dolfin L, Michels BE, Sofyali E, Burmester S, Heiss D, Wilhelm H, Yarden Y, Helm D, Will R, Goncalves A, Wiemann S. Clonal heterogeneity in ER+ breast cancer reveals the proteasome and PKC as potential therapeutic targets. NPJ Breast Cancer 2023; 9:97. [PMID: 38042915 PMCID: PMC10693625 DOI: 10.1038/s41523-023-00604-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Intratumoral heterogeneity impacts the success or failure of anti-cancer therapies. Here, we investigated the evolution and mechanistic heterogeneity in clonal populations of cell models for estrogen receptor positive breast cancer. To this end, we established barcoded models of luminal breast cancer and rendered them resistant to commonly applied first line endocrine therapies. By isolating single clones from the resistant cell pools and characterizing replicates of individual clones we observed inter- (between cell lines) and intra-tumor (between different clones from the same cell line) heterogeneity. Molecular characterization at RNA and phospho-proteomic levels revealed private clonal activation of the unfolded protein response and respective sensitivity to inhibition of the proteasome, and potentially shared sensitivities for repression of protein kinase C. Our in vitro findings are consistent with tumor-heterogeneity that is observed in breast cancer patients thus highlighting the need to uncover heterogeneity at an individual patient level and to adjust therapies accordingly.
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Affiliation(s)
- Lukas Beumers
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.
| | - Efstathios-Iason Vlachavas
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Luisa Schwarzmüller
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Luca Penso-Dolfin
- Division of Somatic Evolution and Early Detection, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Birgitta E Michels
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Emre Sofyali
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Sara Burmester
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Daniela Heiss
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Heike Wilhelm
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Rainer Will
- Cellular Tools Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Angela Goncalves
- Division of Somatic Evolution and Early Detection, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany.
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7
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Jain P, Pillai M, Duddu AS, Somarelli JA, Goyal Y, Jolly MK. Dynamical hallmarks of cancer: Phenotypic switching in melanoma and epithelial-mesenchymal plasticity. Semin Cancer Biol 2023; 96:48-63. [PMID: 37788736 DOI: 10.1016/j.semcancer.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
Phenotypic plasticity was recently incorporated as a hallmark of cancer. This plasticity can manifest along many interconnected axes, such as stemness and differentiation, drug-sensitive and drug-resistant states, and between epithelial and mesenchymal cell-states. Despite growing acceptance for phenotypic plasticity as a hallmark of cancer, the dynamics of this process remains poorly understood. In particular, the knowledge necessary for a predictive understanding of how individual cancer cells and populations of cells dynamically switch their phenotypes in response to the intensity and/or duration of their current and past environmental stimuli remains far from complete. Here, we present recent investigations of phenotypic plasticity from a systems-level perspective using two exemplars: epithelial-mesenchymal plasticity in carcinomas and phenotypic switching in melanoma. We highlight how an integrated computational-experimental approach has helped unravel insights into specific dynamical hallmarks of phenotypic plasticity in different cancers to address the following questions: a) how many distinct cell-states or phenotypes exist?; b) how reversible are transitions among these cell-states, and what factors control the extent of reversibility?; and c) how might cell-cell communication be able to alter rates of cell-state switching and enable diverse patterns of phenotypic heterogeneity? Understanding these dynamic features of phenotypic plasticity may be a key component in shifting the paradigm of cancer treatment from reactionary to a more predictive, proactive approach.
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Affiliation(s)
- Paras Jain
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA
| | | | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India.
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8
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Groves SM, Quaranta V. Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics. FRONTIERS IN NETWORK PHYSIOLOGY 2023; 3:1225736. [PMID: 37731743 PMCID: PMC10507267 DOI: 10.3389/fnetp.2023.1225736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
Phenotypic plasticity of cancer cells can lead to complex cell state dynamics during tumor progression and acquired resistance. Highly plastic stem-like states may be inherently drug-resistant. Moreover, cell state dynamics in response to therapy allow a tumor to evade treatment. In both scenarios, quantifying plasticity is essential for identifying high-plasticity states or elucidating transition paths between states. Currently, methods to quantify plasticity tend to focus on 1) quantification of quasi-potential based on the underlying gene regulatory network dynamics of the system; or 2) inference of cell potency based on trajectory inference or lineage tracing in single-cell dynamics. Here, we explore both of these approaches and associated computational tools. We then discuss implications of each approach to plasticity metrics, and relevance to cancer treatment strategies.
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Affiliation(s)
- Sarah M. Groves
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Vito Quaranta
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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9
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Beik SP, Harris LA, Kochen MA, Sage J, Quaranta V, Lopez CF. Unified tumor growth mechanisms from multimodel inference and dataset integration. PLoS Comput Biol 2023; 19:e1011215. [PMID: 37406008 DOI: 10.1371/journal.pcbi.1011215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/25/2023] [Indexed: 07/07/2023] Open
Abstract
Mechanistic models of biological processes can explain observed phenomena and predict responses to a perturbation. A mathematical model is typically constructed using expert knowledge and informal reasoning to generate a mechanistic explanation for a given observation. Although this approach works well for simple systems with abundant data and well-established principles, quantitative biology is often faced with a dearth of both data and knowledge about a process, thus making it challenging to identify and validate all possible mechanistic hypothesis underlying a system behavior. To overcome these limitations, we introduce a Bayesian multimodel inference (Bayes-MMI) methodology, which quantifies how mechanistic hypotheses can explain a given experimental datasets, and concurrently, how each dataset informs a given model hypothesis, thus enabling hypothesis space exploration in the context of available data. We demonstrate this approach to probe standing questions about heterogeneity, lineage plasticity, and cell-cell interactions in tumor growth mechanisms of small cell lung cancer (SCLC). We integrate three datasets that each formulated different explanations for tumor growth mechanisms in SCLC, apply Bayes-MMI and find that the data supports model predictions for tumor evolution promoted by high lineage plasticity, rather than through expanding rare stem-like populations. In addition, the models predict that in the presence of cells associated with the SCLC-N or SCLC-A2 subtypes, the transition from the SCLC-A subtype to the SCLC-Y subtype through an intermediate is decelerated. Together, these predictions provide a testable hypothesis for observed juxtaposed results in SCLC growth and a mechanistic interpretation for tumor treatment resistance.
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Affiliation(s)
- Samantha P Beik
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Leonard A Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, United States of America
- Interdisciplinary Graduate Program in Cell & 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
| | - Michael A Kochen
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Julien Sage
- Departments of Pediatrics, Stanford University, Stanford, California, United States of America
- Departments of Genetics, Stanford University, Stanford, California, United States of America
| | - Vito Quaranta
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Carlos F Lopez
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Altos Laboratories, Redwood City, California, United States of America
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10
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Pillai M, Hojel E, Jolly MK, Goyal Y. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools. NATURE COMPUTATIONAL SCIENCE 2023; 3:301-313. [PMID: 38177938 DOI: 10.1038/s43588-023-00427-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/03/2023] [Indexed: 01/06/2024]
Abstract
Individual cells within an otherwise genetically homogenous population constantly undergo fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity is being increasingly implicated in cancer therapy resistance and metastasis. Identifying the origins of non-genetic heterogeneity is therefore crucial for making clinical breakthroughs. We discuss with examples how dynamical models and computational tools have provided critical multiscale insights into the nature and consequences of non-genetic heterogeneity in cancer. We demonstrate how mechanistic modeling has been pivotal in establishing key concepts underlying non-genetic diversity at various biological scales, from population dynamics to gene regulatory networks. We discuss advances in single-cell longitudinal profiling techniques to reveal patterns of non-genetic heterogeneity, highlighting the ongoing efforts and challenges in statistical frameworks to robustly interpret such multimodal datasets. Moving forward, we stress the need for data-driven statistical and mechanistically motivated dynamical frameworks to come together to develop predictive cancer models and inform therapeutic strategies.
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Affiliation(s)
- Maalavika Pillai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Emilia Hojel
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA.
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11
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Groves SM, Ildefonso GV, McAtee CO, Ozawa PMM, Ireland AS, Stauffer PE, Wasdin PT, Huang X, Qiao Y, Lim JS, Bader J, Liu Q, Simmons AJ, Lau KS, Iams WT, Hardin DP, Saff EB, Holmes WR, Tyson DR, Lovly CM, Rathmell JC, Marth G, Sage J, Oliver TG, Weaver AM, Quaranta V. Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer. Cell Syst 2022; 13:690-710.e17. [PMID: 35981544 PMCID: PMC9615940 DOI: 10.1016/j.cels.2022.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/10/2022] [Accepted: 07/25/2022] [Indexed: 01/26/2023]
Abstract
Small cell lung cancer (SCLC) tumors comprise heterogeneous mixtures of cell states, categorized into neuroendocrine (NE) and non-neuroendocrine (non-NE) transcriptional subtypes. NE to non-NE state transitions, fueled by plasticity, likely underlie adaptability to treatment and dismal survival rates. Here, we apply an archetypal analysis to model plasticity by recasting SCLC phenotypic heterogeneity through multi-task evolutionary theory. Cell line and tumor transcriptomics data fit well in a five-dimensional convex polytope whose vertices optimize tasks reminiscent of pulmonary NE cells, the SCLC normal counterparts. These tasks, supported by knowledge and experimental data, include proliferation, slithering, metabolism, secretion, and injury repair, reflecting cancer hallmarks. SCLC subtypes, either at the population or single-cell level, can be positioned in archetypal space by bulk or single-cell transcriptomics, respectively, and characterized as task specialists or multi-task generalists by the distance from archetype vertex signatures. In the archetype space, modeling single-cell plasticity as a Markovian process along an underlying state manifold indicates that task trade-offs, in response to microenvironmental perturbations or treatment, may drive cell plasticity. Stifling phenotypic transitions and plasticity may provide new targets for much-needed translational advances in SCLC. A record of this paper's Transparent Peer Review process is included in the supplemental information.
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Affiliation(s)
- Sarah M Groves
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Geena V Ildefonso
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Caitlin O McAtee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Patricia M M Ozawa
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Abbie S Ireland
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Philip E Stauffer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Perry T Wasdin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Xiaomeng Huang
- Utah Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Yi Qiao
- Utah Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Jing Shan Lim
- Department of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jackie Bader
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Alan J Simmons
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Wade T Iams
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Doug P Hardin
- Department of Mathematics and Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA
| | - Edward B Saff
- Department of Mathematics, Vanderbilt University, Nashville, TN 37235, USA
| | - William R Holmes
- Department of Mathematics, Vanderbilt University, Nashville, TN 37235, USA; Department of Physics, Vanderbilt University, Nashville, TN 37235, USA
| | - Darren R Tyson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Christine M Lovly
- Department of Mathematics and Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gabor Marth
- Utah Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Julien Sage
- Department of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Trudy G Oliver
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37235, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA.
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12
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Stochastic population dynamics of cancer stemness and adaptive response to therapies. Essays Biochem 2022; 66:387-398. [PMID: 36073715 DOI: 10.1042/ebc20220038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 02/07/2023]
Abstract
Intratumoral heterogeneity can exist along multiple axes: Cancer stem cells (CSCs)/non-CSCs, drug-sensitive/drug-tolerant states, and a spectrum of epithelial-hybrid-mesenchymal phenotypes. Further, these diverse cell-states can switch reversibly among one another, thereby posing a major challenge to therapeutic efficacy. Therefore, understanding the origins of phenotypic plasticity and heterogeneity remains an active area of investigation. While genomic components (mutations, chromosomal instability) driving heterogeneity have been well-studied, recent reports highlight the role of non-genetic mechanisms in enabling both phenotypic plasticity and heterogeneity. Here, we discuss various processes underlying phenotypic plasticity such as stochastic gene expression, chromatin reprogramming, asymmetric cell division and the presence of multiple stable gene expression patterns ('attractors'). These processes can facilitate a dynamically evolving cell population such that a subpopulation of (drug-tolerant) cells can survive lethal drug exposure and recapitulate population heterogeneity on drug withdrawal, leading to relapse. These drug-tolerant cells can be both pre-existing and also induced by the drug itself through cell-state reprogramming. The dynamics of cell-state transitions both in absence and presence of the drug can be quantified through mathematical models. Such a dynamical systems approach to elucidating patterns of intratumoral heterogeneity by integrating longitudinal experimental data with mathematical models can help design effective combinatorial and/or sequential therapies for better clinical outcomes.
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13
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Mahfoudhi E, Ricordel C, Lecuyer G, Mouric C, Lena H, Pedeux R. Preclinical Models for Acquired Resistance to Third-Generation EGFR Inhibitors in NSCLC: Functional Studies and Drug Combinations Used to Overcome Resistance. Front Oncol 2022; 12:853501. [PMID: 35463360 PMCID: PMC9023070 DOI: 10.3389/fonc.2022.853501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022] Open
Abstract
Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) are currently recommended as first-line treatment for advanced non-small-cell lung cancer (NSCLC) with EGFR-activating mutations. Third-generation (3rd G) EGFR-TKIs, including osimertinib, offer an effective treatment option for patients with NSCLC resistant 1st and 2nd EGFR-TKIs. However, the efficacy of 3rd G EGFR-TKIs is limited by acquired resistance that has become a growing clinical challenge. Several clinical and preclinical studies are being carried out to better understand the mechanisms of resistance to 3rd G EGFR-TKIs and have revealed various genetic aberrations associated with molecular heterogeneity of cancer cells. Studies focusing on epigenetic events are limited despite several indications of their involvement in the development of resistance. Preclinical models, established in most cases in a similar manner, have shown different prevalence of resistance mechanisms from clinical samples. Clinically identified mechanisms include EGFR mutations that were not identified in preclinical models. Thus, NRAS genetic alterations were not observed in patients but have been described in cell lines resistant to 3rd G EGFR-TKI. Mainly, resistance to 3rd G EGFR-TKI in preclinical models is related to the activation of alternative signaling pathways through tyrosine kinase receptor (TKR) activation or to histological and phenotypic transformations. Yet, preclinical models have provided some insight into the complex network between dominant drivers and associated events that lead to the emergence of resistance and consequently have identified new therapeutic targets. This review provides an overview of preclinical studies developed to investigate the mechanisms of acquired resistance to 3rd G EGFR-TKIs, including osimertinib and rociletinib, across all lines of therapy. In fact, some of the models described were first generated to be resistant to first- and second-generation EGFR-TKIs and often carried the T790M mutation, while others had never been exposed to TKIs. The review further describes the therapeutic opportunities to overcome resistance, based on preclinical studies.
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Affiliation(s)
- Emna Mahfoudhi
- Univ Rennes, Institut Nationale de la Santé et de la Recherche Médicale (INSERM), COSS (Chemistry Oncogenesis Stress Signaling), UMR_S 1242, Centre de Lutte Contre le Cancer (CLOC) Eugène Marquis, Rennes, France
| | - Charles Ricordel
- Univ Rennes, Institut Nationale de la Santé et de la Recherche Médicale (INSERM), COSS (Chemistry Oncogenesis Stress Signaling), UMR_S 1242, Centre de Lutte Contre le Cancer (CLOC) Eugène Marquis, Rennes, France.,Centre Hospitalier Universitaire de Rennes, Service de Pneumologie, Université de Rennes 1, Rennes, France
| | - Gwendoline Lecuyer
- Univ Rennes, Institut Nationale de la Santé et de la Recherche Médicale (INSERM), COSS (Chemistry Oncogenesis Stress Signaling), UMR_S 1242, Centre de Lutte Contre le Cancer (CLOC) Eugène Marquis, Rennes, France
| | - Cécile Mouric
- Univ Rennes, Institut Nationale de la Santé et de la Recherche Médicale (INSERM), COSS (Chemistry Oncogenesis Stress Signaling), UMR_S 1242, Centre de Lutte Contre le Cancer (CLOC) Eugène Marquis, Rennes, France
| | - Hervé Lena
- Univ Rennes, Institut Nationale de la Santé et de la Recherche Médicale (INSERM), COSS (Chemistry Oncogenesis Stress Signaling), UMR_S 1242, Centre de Lutte Contre le Cancer (CLOC) Eugène Marquis, Rennes, France.,Centre Hospitalier Universitaire de Rennes, Service de Pneumologie, Université de Rennes 1, Rennes, France
| | - Rémy Pedeux
- Univ Rennes, Institut Nationale de la Santé et de la Recherche Médicale (INSERM), COSS (Chemistry Oncogenesis Stress Signaling), UMR_S 1242, Centre de Lutte Contre le Cancer (CLOC) Eugène Marquis, Rennes, France
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14
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Cancer: More than a geneticist’s Pandora’s box. J Biosci 2022. [DOI: 10.1007/s12038-022-00254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Rosati D, Giordano A. Single-cell RNA sequencing and bioinformatics as tools to decipher cancer heterogenicity and mechanisms of drug resistance. Biochem Pharmacol 2021; 195:114811. [PMID: 34673017 DOI: 10.1016/j.bcp.2021.114811] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022]
Abstract
It is well known that cancer is an aggressive disease, often associated with relapse, in many cases due to drug resistance. Cancer stem cell and clonal evolution are frequently causes of innate or acquired drug resistance. Current RNA sequencing technologies do not distinguish gene expression of different cell lineages because they are based on bulk cell studies. Single-cell RNA sequencing technologies and related bioinformatics clustering and differential expression analysis represent a turning point in cancer research. They are emerging as essential tools for dissecting tumors at single-cell resolution and represent novel tools to understand carcinogenesis and drug response. In this review, we will outline the role of these new technologies in addressing cancer heterogeneity and cell lineage-dependent drug resistance.
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Affiliation(s)
- Diletta Rosati
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Antonio Giordano
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA.
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16
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Cai Y, Chen T, Liu J, Peng S, Liu H, Lv M, Ding Z, Zhou Z, Li L, Zeng S, Xiao E. Orthotopic Versus Allotopic Implantation: Comparison of Radiological and Pathological Characteristics. J Magn Reson Imaging 2021; 55:1133-1140. [PMID: 34611963 PMCID: PMC9291575 DOI: 10.1002/jmri.27940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/11/2022] Open
Abstract
Background In experimental animal models, implantation location might influence the heterogeneity and overall development of the tumor, leading to an interpretation bias. Purpose To investigate the effects of implantation location in experimental tumor model using magnetic resonance imaging (MRI) and pathological findings. Study Type Prospective. Subjects Forty‐five breast cancer‐bearing mice underwent orthotopic (N = 15) and heterotopic (intrahepatic [N = 15] and subcutaneous [N = 15]) implantation. Field Strength/Sequence Sequences including: T1‐weighted turbo spin echo sequence, T2‐weighted blade sequence, diffusion‐weighted imaging, pre‐ and post‐contrast T1 mapping, multi‐echo T2 mapping at 3.0 T. Assessment MRI was performed at 7, 14, and 21 days after implantation. Native T1, post‐contrast T1, T2, and apparent diffusion coefficient (ADC) of tumors, the tumor volume and necrosis volume within tumor were obtained. Lymphocyte cells from H&E staining, Ki67‐positive, and CD31‐positive cells from immunohistochemistry were determined. Statistical Tests One‐way analysis of variance and Spearman's rank correlation were performed. P value <0.05 was considered statistically significant. Results The tumor volume (intrahepatic vs. orthotopic vs. subcutaneous: 587.50 ± 77.62 mm3 vs. 814.00 ± 43.85 mm3 vs. 956.13 ± 119.22 mm3), necrosis volume within tumor (89.10 ± 26.60 mm3 vs. 292.41 ± 57.92 mm3 vs. 179.91 ± 31.73 mm3, respectively), ADC at day 21 (543.41 ± 42.28 vs. 542.92 ± 99.67 vs. 369.83 ± 42.90, respectively), and post‐contrast T1 at all timepoints (day 7: 442.00 ± 11.52 vs. 435.00 ± 22.90 vs. 394.33 ± 29.95; day 14: 459.00 ± 26.11 vs. 436.83 ± 26.01 vs. 377.00 ± 27.83; day 21: 463.50 ± 23.49 vs. 458.00 ± 34.28 vs. 375.00 ± 30.55) were significantly different between three groups. Necrosis volumes of subcutaneous and intrahepatic tumors were significantly lower than those of orthotopic tumors. The CD31‐positive rate in the intrahepatic implantation was significantly higher than in orthotopic and subcutaneous groups. Necrosis volume (r = −0.71), ADC (r = −0.85), and post‐contrast T1 (r = −0.75) were strongly correlated with vascular invasion index. Data Conclusion Orthotopic and heterotopic tumors have their unique growth kinetics, necrosis volume, and vascular invasion. Non‐invasive MR quantitative parameters, including ADC and post‐contrast T1, may reflect vascular invasion in mice. Level of Evidence 1 Technical Efficacy Stage 3
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Affiliation(s)
- YeYu Cai
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - TaiLi Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - JiaYi Liu
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - ShuHui Peng
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Huan Liu
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Min Lv
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - ZhuYuan Ding
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - ZiYi Zhou
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lan Li
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - EnHua Xiao
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, China.,Molecular Imaging Research Center, Central South University, Changsha, China.,Clinical Research Center for Medical Imaging in Hunan Province, Changsha, China
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17
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Alarcón T, Sardanyés J, Guillamon A, Menendez JA. Bivalent chromatin as a therapeutic target in cancer: An in silico predictive approach for combining epigenetic drugs. PLoS Comput Biol 2021; 17:e1008408. [PMID: 34153035 PMCID: PMC8248646 DOI: 10.1371/journal.pcbi.1008408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 07/01/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022] Open
Abstract
Tumour cell heterogeneity is a major barrier for efficient design of targeted anti-cancer therapies. A diverse distribution of phenotypically distinct tumour-cell subpopulations prior to drug treatment predisposes to non-uniform responses, leading to the elimination of sensitive cancer cells whilst leaving resistant subpopulations unharmed. Few strategies have been proposed for quantifying the variability associated to individual cancer-cell heterogeneity and minimizing its undesirable impact on clinical outcomes. Here, we report a computational approach that allows the rational design of combinatorial therapies involving epigenetic drugs against chromatin modifiers. We have formulated a stochastic model of a bivalent transcription factor that allows us to characterise three different qualitative behaviours, namely: bistable, high- and low-gene expression. Comparison between analytical results and experimental data determined that the so-called bistable and high-gene expression behaviours can be identified with undifferentiated and differentiated cell types, respectively. Since undifferentiated cells with an aberrant self-renewing potential might exhibit a cancer/metastasis-initiating phenotype, we analysed the efficiency of combining epigenetic drugs against the background of heterogeneity within the bistable sub-ensemble. Whereas single-targeted approaches mostly failed to circumvent the therapeutic problems represented by tumour heterogeneity, combinatorial strategies fared much better. Specifically, the more successful combinations were predicted to involve modulators of the histone H3K4 and H3K27 demethylases KDM5 and KDM6A/UTX. Those strategies involving the H3K4 and H3K27 methyltransferases MLL2 and EZH2, however, were predicted to be less effective. Our theoretical framework provides a coherent basis for the development of an in silico platform capable of identifying the epigenetic drugs combinations best-suited to therapeutically manage non-uniform responses of heterogenous cancer cell populations.
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Affiliation(s)
- Tomás Alarcón
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre de Recerca Matemàtica, Cerdanyola del Vallès, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Antoni Guillamon
- Centre de Recerca Matemàtica, Cerdanyola del Vallès, Spain
- Departament de Matemàtiques, EPSEB, Universitat Politècnica de Catalunya, Barcelona, Spain
- Institut de Matemàtiques de la UPC-BarcelonaTech (IMTech), Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Javier A. Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain
- Girona Biomedical Research Institute, Salt, Girona, Spain
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