1
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Blanchard CE, Gomeiz AT, Avery K, Gazzah EE, Alsubaie AM, Sikaroodi M, Chiari Y, Ward C, Sanchez J, Espina V, Petricoin E, Baldelli E, Pierobon M. Signaling dynamics in coexisting monoclonal cell subpopulations unveil mechanisms of resistance to anti-cancer compounds. Cell Commun Signal 2024; 22:377. [PMID: 39061010 PMCID: PMC11282632 DOI: 10.1186/s12964-024-01742-3] [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: 03/29/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Tumor heterogeneity is a main contributor of resistance to anti-cancer targeted agents though it has proven difficult to study. Unfortunately, model systems to functionally characterize and mechanistically study dynamic responses to treatment across coexisting subpopulations of cancer cells remain a missing need in oncology. METHODS Using single cell cloning and expansion techniques, we established monoclonal cell subpopulations (MCPs) from a commercially available epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer cell line. We then used this model sensitivity to the EGFR inhibitor osimertinib across coexisting cell populations within the same tumor. Pathway-centered signaling dynamics associated with response to treatment and morphological characteristics of the MCPs were assessed using Reverse Phase Protein Microarray. Signaling nodes differentially activated in MCPs less sensitive to treatment were then pharmacologically inhibited to identify target signaling proteins putatively implicated in promoting drug resistance. RESULTS MCPs demonstrated highly heterogeneous sensitivities to osimertinib. Cell viability after treatment increased > 20% compared to the parental line in selected MCPs, whereas viability decreased by 75% in other MCPs. Reduced treatment response was detected in MCPs with higher proliferation rates, EGFR L858R expression, activation of EGFR binding partners and downstream signaling molecules, and expression of epithelial-to-mesenchymal transition markers. Levels of activation of EGFR binding partners and MCPs' proliferation rates were also associated with response to c-MET and IGFR inhibitors. CONCLUSIONS MCPs represent a suitable model system to characterize heterogeneous biomolecular behaviors in preclinical studies and identify and functionally test biological mechanisms associated with resistance to targeted therapeutics.
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Affiliation(s)
- Claire E Blanchard
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA
| | - Alison T Gomeiz
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA
| | - Kyle Avery
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA
| | - Emna El Gazzah
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA
| | - Abduljalil M Alsubaie
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA
| | - Masoumeh Sikaroodi
- Microbiome Analysis Center, George Mason University, Manassas, VA, 20110, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2TQ, UK
| | - Chelsea Ward
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA
| | - Jonathan Sanchez
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Emanuel Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Mariaelena Pierobon
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Room 2016, Manassas, VA, 20110, USA.
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA.
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2
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Li H, Han Z, Sun Y, Wang F, Hu P, Gao Y, Bai X, Peng S, Ren C, Xu X, Liu Z, Chen H, Yang Y, Bo X. CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection. Nat Commun 2024; 15:5997. [PMID: 39013885 PMCID: PMC11252405 DOI: 10.1038/s41467-024-50426-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
Cancer is rarely the straightforward consequence of an abnormality in a single gene, but rather reflects a complex interplay of many genes, represented as gene modules. Here, we leverage the recent advances of model-agnostic interpretation approach and develop CGMega, an explainable and graph attention-based deep learning framework to perform cancer gene module dissection. CGMega outperforms current approaches in cancer gene prediction, and it provides a promising approach to integrate multi-omics information. We apply CGMega to breast cancer cell line and acute myeloid leukemia (AML) patients, and we uncover the high-order gene module formed by ErbB family and tumor factors NRG1, PPM1A and DLG2. We identify 396 candidate AML genes, and observe the enrichment of either known AML genes or candidate AML genes in a single gene module. We also identify patient-specific AML genes and associated gene modules. Together, these results indicate that CGMega can be used to dissect cancer gene modules, and provide high-order mechanistic insights into cancer development and heterogeneity.
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Affiliation(s)
- Hao Li
- Academy of Military Medical Sciences, Beijing, China
| | - Zebei Han
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, China
| | - Yu Sun
- Academy of Military Medical Sciences, Beijing, China
| | - Fu Wang
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, China
| | - Pengzhen Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yuang Gao
- Department of Hematology, PLA General Hospital, the Fifth Medical Center, Beijing, China
| | - Xuemei Bai
- Academy of Military Medical Sciences, Beijing, China
| | - Shiyu Peng
- Academy of Military Medical Sciences, Beijing, China
| | - Chao Ren
- Academy of Military Medical Sciences, Beijing, China
| | - Xiang Xu
- Academy of Military Medical Sciences, Beijing, China
| | - Zeyu Liu
- Academy of Military Medical Sciences, Beijing, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing, China.
| | - Yang Yang
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, China.
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing, China.
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3
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Simsone Z, Feivalds T, Harju L, Miķelsone I, Blāķe I, Bērziņš J, Buiķis I. Morphological and Immunocytochemical Characterization of Paclitaxel-Induced Microcells in Sk-Mel-28 Melanoma Cells. Biomedicines 2024; 12:1576. [PMID: 39062149 PMCID: PMC11274385 DOI: 10.3390/biomedicines12071576] [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: 06/10/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Biomarkers, including proteins, nucleic acids, antibodies, and peptides, are essential for identifying diseases such as cancer and differentiating between healthy and abnormal cells in patients. To date, studies have shown that cancer stem cells have DNA repair mechanisms that deter the effects of medicinal treatment. Experiments with cell cultures and chemotherapy treatments of these cultures have revealed the presence of small cells, with a small amount of cytoplasm that can be intensively stained with azure eosin, called microcells. Microcells develop during sporosis from a damaged tumor macrocell. After anticancer therapy in tumor cells, a defective macrocell may produce one or more microcells. This study aims to characterize microcell morphology in melanoma cell lines. In this investigation, we characterized the population of cancer cell microcells after applying paclitaxel treatment to a Sk-Mel-28 melanoma cell line using immunocytochemical cell marker detection and fluorescent microscopy. Paclitaxel-treated cancer cells show stronger expression of stem-associated ALDH2, SOX2, and Nanog markers than untreated cells. The proliferation of nuclear antigens in cells and the synthesis of RNA in microcells indicate cell self-defense, promoting resistance to applied therapy. These findings improve our understanding of microcell behavior in melanoma, potentially informing future strategies to counteract drug resistance in cancer treatment.
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Affiliation(s)
- Zane Simsone
- Institute of Cardiology and Regenerative Medicine, The University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia; (T.F.); (J.B.); (I.B.)
| | - Tālivaldis Feivalds
- Institute of Cardiology and Regenerative Medicine, The University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia; (T.F.); (J.B.); (I.B.)
| | - Līga Harju
- Institute of Cardiology and Regenerative Medicine, The University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia; (T.F.); (J.B.); (I.B.)
| | - Indra Miķelsone
- Department of Human Physiology and Biochemistry, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia;
| | - Ilze Blāķe
- Faculty of Medicine and Life Science, The University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia;
| | - Juris Bērziņš
- Institute of Cardiology and Regenerative Medicine, The University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia; (T.F.); (J.B.); (I.B.)
| | - Indulis Buiķis
- Institute of Cardiology and Regenerative Medicine, The University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia; (T.F.); (J.B.); (I.B.)
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4
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Capp JP, Catania F, Thomas F. From genetic mosaicism to tumorigenesis through indirect genetic effects. Bioessays 2024; 46:e2300238. [PMID: 38736323 DOI: 10.1002/bies.202300238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024]
Abstract
Genetic mosaicism has long been linked to aging, and several hypotheses have been proposed to explain the potential connections between mosaicism and susceptibility to cancer. It has been proposed that mosaicism may disrupt tissue homeostasis by affecting intercellular communications and releasing microenvironmental constraints within tissues. The underlying mechanisms driving these tissue-level influences remain unidentified, however. Here, we present an evolutionary perspective on the interplay between mosaicism and cancer, suggesting that the tissue-level impacts of genetic mosaicism can be attributed to Indirect Genetic Effects (IGEs). IGEs can increase the level of cellular stochasticity and phenotypic instability among adjacent cells, thereby elevating the risk of cancer development within the tissue. Moreover, as cells experience phenotypic changes in response to challenging microenvironmental conditions, these changes can initiate a cascade of nongenetic alterations, referred to as Indirect non-Genetic Effects (InGEs), which in turn catalyze IGEs among surrounding cells. We argue that incorporating both InGEs and IGEs into our understanding of the process of oncogenic transformation could trigger a major paradigm shift in cancer research with far-reaching implications for practical applications.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Francesco Catania
- Institute of Environmental Radioactivity, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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5
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Gofrit ON, Aviv A. Predictability: A new distinguishing feature of cancer? PLoS One 2024; 19:e0305181. [PMID: 38865416 PMCID: PMC11168650 DOI: 10.1371/journal.pone.0305181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/26/2024] [Indexed: 06/14/2024] Open
Abstract
Cancer is a consequence of stochastic (mutations, genetic, and epigenetic instabilities) and deterministic (evolutionary bottlenecks) events. Stochastic events are less amenable to prediction, whereas deterministic events yield more predictable results. The relative contribution of these opposing forces determines cancer predictability, which affects the accuracy of our prognostic predictions and is critical for treatment planning. In this study, we attempted to quantify predictability. The predictability index (PI) was defined as the median overall-survival at any time point divided by the standard error at that time. Using data obtained from the SEER program, we found striking differences in the PI of different tumors. Highly predictable tumors were malignancies of the breast, thyroid, prostate, and testis (5-year PI of 3516, 1920, 1919, and 1805, respectively). Less predictable tumors were colorectal, melanoma, and bladder (5-year PI of 1264, 1197, and 760, respectively). Least predictable were pancreatic cancer and chronic myelogenous leukemia (5-year PI of 129, and 42). PI decreased during follow-up in all examined tumors and showed sex differences in some cases. Thyroid cancer was significantly more predictable in women (5-year PI of 2579 vs. 748, p = 0.00017) and bladder cancer more predictable in men (5-year PI of 723 vs. 385, p = 0.012), Predictability is a potentially new distinguishing feature of malignancy. This study sheds light on prognostic accuracy and provides insight into the relative roles of stochastic and deterministic forces during carcinogenesis.
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Affiliation(s)
- Ofer N. Gofrit
- Department of Urology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Ariel Aviv
- Department of Hematology, Ha’Emek Medical Center, Afula, Israel
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6
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Dilenko H, Bartoň Tománková K, Válková L, Hošíková B, Kolaříková M, Malina L, Bajgar R, Kolářová H. Graphene-Based Photodynamic Therapy and Overcoming Cancer Resistance Mechanisms: A Comprehensive Review. Int J Nanomedicine 2024; 19:5637-5680. [PMID: 38882538 PMCID: PMC11179671 DOI: 10.2147/ijn.s461300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/09/2024] [Indexed: 06/18/2024] Open
Abstract
Photodynamic therapy (PDT) is a non-invasive therapy that has made significant progress in treating different diseases, including cancer, by utilizing new nanotechnology products such as graphene and its derivatives. Graphene-based materials have large surface area and photothermal effects thereby making them suitable candidates for PDT or photo-active drug carriers. The remarkable photophysical properties of graphene derivates facilitate the efficient generation of reactive oxygen species (ROS) upon light irradiation, which destroys cancer cells. Surface functionalization of graphene and its materials can also enhance their biocompatibility and anticancer activity. The paper delves into the distinct roles played by graphene-based materials in PDT such as photosensitizers (PS) and drug carriers while at the same time considers how these materials could be used to circumvent cancer resistance. This will provide readers with an extensive discussion of various pathways contributing to PDT inefficiency. Consequently, this comprehensive review underscores the vital roles that graphene and its derivatives may play in emerging PDT strategies for cancer treatment and other medical purposes. With a better comprehension of the current state of research and the existing challenges, the integration of graphene-based materials in PDT holds great promise for developing targeted, effective, and personalized cancer treatments.
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Affiliation(s)
- Hanna Dilenko
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Kateřina Bartoň Tománková
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Lucie Válková
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Barbora Hošíková
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Markéta Kolaříková
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Lukáš Malina
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Robert Bajgar
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Hana Kolářová
- Department of Biophysics, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
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7
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Ramisetty S, Subbalakshmi AR, Pareek S, Mirzapoiazova T, Do D, Prabhakar D, Pisick E, Shrestha S, Achuthan S, Bhattacharya S, Malhotra J, Mohanty A, Singhal SS, Salgia R, Kulkarni P. Leveraging Cancer Phenotypic Plasticity for Novel Treatment Strategies. J Clin Med 2024; 13:3337. [PMID: 38893049 PMCID: PMC11172618 DOI: 10.3390/jcm13113337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer cells, like all other organisms, are adept at switching their phenotype to adjust to the changes in their environment. Thus, phenotypic plasticity is a quantitative trait that confers a fitness advantage to the cancer cell by altering its phenotype to suit environmental circumstances. Until recently, new traits, especially in cancer, were thought to arise due to genetic factors; however, it is now amply evident that such traits could also emerge non-genetically due to phenotypic plasticity. Furthermore, phenotypic plasticity of cancer cells contributes to phenotypic heterogeneity in the population, which is a major impediment in treating the disease. Finally, plasticity also impacts the group behavior of cancer cells, since competition and cooperation among multiple clonal groups within the population and the interactions they have with the tumor microenvironment also contribute to the evolution of drug resistance. Thus, understanding the mechanisms that cancer cells exploit to tailor their phenotypes at a systems level can aid the development of novel cancer therapeutics and treatment strategies. Here, we present our perspective on a team medicine-based approach to gain a deeper understanding of the phenomenon to develop new therapeutic strategies.
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Affiliation(s)
- Sravani Ramisetty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Ayalur Raghu Subbalakshmi
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Siddhika Pareek
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Dana Do
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Dhivya Prabhakar
- City of Hope Atlanta, 600 Celebrate Life Parkway, Newnan, GA 30265, USA;
| | - Evan Pisick
- City of Hope Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA;
| | - Sagun Shrestha
- City of Hope Phoenix, 14200 West Celebrate Life Way, Goodyear, AZ 85338, USA;
| | - Srisairam Achuthan
- Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Jyoti Malhotra
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Sharad S. Singhal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA; (S.R.); (A.R.S.); (S.P.); (T.M.); (D.D.); (J.M.); (A.M.); (S.S.S.)
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
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8
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Cheng YL, Banu MA, Zhao W, Rosenfeld SS, Canoll P, Sims PA. Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. Cell Rep 2024; 43:114139. [PMID: 38652658 PMCID: PMC11199018 DOI: 10.1016/j.celrep.2024.114139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target with roles in proliferation and invasion. Resistance to KIF11 inhibitors, which has mainly been studied in animal models, presents significant challenges. We use lineage-tracing barcodes and single-cell RNA sequencing to analyze resistance in patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lose their neural lineage identity and become mesenchymal, which is associated with poor prognosis. Conversely, cells subjected to long-term ispinesib treatment exhibit a proneural phenotype. We generate patient-derived xenografts and show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Moreover, treatment of human ex vivo GBM slices with ispinesib demonstrates phenotypic alignment with in vitro responses, underscoring the clinical relevance of our findings. Finally, using retrospective lineage tracing, we identify drugs that are synergistic with ispinesib.
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Affiliation(s)
- Yim Ling Cheng
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matei A Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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9
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Haderk F, Chou YT, Cech L, Fernández-Méndez C, Yu J, Olivas V, Meraz IM, Barbosa Rabago D, Kerr DL, Gomez C, Allegakoen DV, Guan J, Shah KN, Herrington KA, Gbenedio OM, Nanjo S, Majidi M, Tamaki W, Pourmoghadam YK, Rotow JK, McCoach CE, Riess JW, Gutkind JS, Tang TT, Post L, Huang B, Santisteban P, Goodarzi H, Bandyopadhyay S, Kuo CJ, Roose JP, Wu W, Blakely CM, Roth JA, Bivona TG. Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer. Nat Commun 2024; 15:3741. [PMID: 38702301 PMCID: PMC11068778 DOI: 10.1038/s41467-024-47423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/18/2024] [Indexed: 05/06/2024] Open
Abstract
Targeted therapy is effective in many tumor types including lung cancer, the leading cause of cancer mortality. Paradigm defining examples are targeted therapies directed against non-small cell lung cancer (NSCLC) subtypes with oncogenic alterations in EGFR, ALK and KRAS. The success of targeted therapy is limited by drug-tolerant persister cells (DTPs) which withstand and adapt to treatment and comprise the residual disease state that is typical during treatment with clinical targeted therapies. Here, we integrate studies in patient-derived and immunocompetent lung cancer models and clinical specimens obtained from patients on targeted therapy to uncover a focal adhesion kinase (FAK)-YAP signaling axis that promotes residual disease during oncogenic EGFR-, ALK-, and KRAS-targeted therapies. FAK-YAP signaling inhibition combined with the primary targeted therapy suppressed residual drug-tolerant cells and enhanced tumor responses. This study unveils a FAK-YAP signaling module that promotes residual disease in lung cancer and mechanism-based therapeutic strategies to improve tumor response.
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Affiliation(s)
- Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Yu-Ting Chou
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren Cech
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Celia Fernández-Méndez
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científícas (CSIC) y Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Johnny Yu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Victor Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Ismail M Meraz
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dora Barbosa Rabago
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Carlos Gomez
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David V Allegakoen
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Juan Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Khyati N Shah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kari A Herrington
- Center for Advanced Light Microscopy, University of California, San Francisco, San Francisco, CA, USA
| | | | - Shigeki Nanjo
- Division of Medical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Mourad Majidi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Whitney Tamaki
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yashar K Pourmoghadam
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Julia K Rotow
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Caroline E McCoach
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan W Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - J Silvio Gutkind
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Tracy T Tang
- Vivace Therapeutics, Inc., 1500 Fashion Island Blvd., Suite 102, San Mateo, CA, USA
| | - Leonard Post
- Vivace Therapeutics, Inc., 1500 Fashion Island Blvd., Suite 102, San Mateo, CA, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científícas (CSIC) y Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Sourav Bandyopadhyay
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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10
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Trnkova L, Buocikova V, Mego M, Cumova A, Burikova M, Bohac M, Miklikova S, Cihova M, Smolkova B. Epigenetic deregulation in breast cancer microenvironment: Implications for tumor progression and therapeutic strategies. Biomed Pharmacother 2024; 174:116559. [PMID: 38603889 DOI: 10.1016/j.biopha.2024.116559] [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: 12/15/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
Breast cancer comprises a substantial proportion of cancer diagnoses in women and is a primary cause of cancer-related mortality. While hormone-responsive cases generally have a favorable prognosis, the aggressive nature of triple-negative breast cancer presents challenges, with intrinsic resistance to established treatments being a persistent issue. The complexity intensifies with the emergence of acquired resistance, further complicating the management of breast cancer. Epigenetic changes, encompassing DNA methylation, histone and RNA modifications, and non-coding RNAs, are acknowledged as crucial contributors to the heterogeneity of breast cancer. The unique epigenetic landscape harbored by each cellular component within the tumor microenvironment (TME) adds great diversity to the intricate regulations which influence therapeutic responses. The TME, a sophisticated ecosystem of cellular and non-cellular elements interacting with tumor cells, establishes an immunosuppressive microenvironment and fuels processes such as tumor growth, angiogenesis, and extracellular matrix remodeling. These factors contribute to challenging conditions in cancer treatment by fostering a hypoxic environment, inducing metabolic stress, and creating physical barriers to drug delivery. This article delves into the complex connections between breast cancer treatment response, underlying epigenetic changes, and vital interactions within the TME. To restore sensitivity to treatment, it emphasizes the need for combination therapies considering epigenetic changes specific to individual members of the TME. Recognizing the pivotal role of epigenetics in drug resistance and comprehending the specificities of breast TME is essential for devising more effective therapeutic strategies. The development of reliable biomarkers for patient stratification will facilitate tailored and precise treatment approaches.
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Affiliation(s)
- Lenka Trnkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Verona Buocikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Michal Mego
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia; 2nd Department of Oncology, Comenius University, Faculty of Medicine & National Cancer Institute, Bratislava 83310, Slovakia
| | - Andrea Cumova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Monika Burikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Martin Bohac
- 2nd Department of Oncology, Comenius University, Faculty of Medicine & National Cancer Institute, Bratislava 83310, Slovakia; Regenmed Ltd., Medena 29, Bratislava 811 01, Slovakia; Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, Bratislava 811 08, Slovakia
| | - Svetlana Miklikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Marina Cihova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia.
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11
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Lamichhane A, Tavana H. Three-Dimensional Tumor Models to Study Cancer Stemness-Mediated Drug Resistance. Cell Mol Bioeng 2024; 17:107-119. [PMID: 38737455 PMCID: PMC11082110 DOI: 10.1007/s12195-024-00798-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/01/2024] [Indexed: 05/14/2024] Open
Abstract
Solid tumors often contain genetically different populations of cancer cells, stromal cells, various structural and soluble proteins, and other soluble signaling molecules. The American Cancer society estimated 1,958,310 new cancer cases and 609,820 cancer deaths in the United States in 2023. A major barrier against successful treatment of cancer patients is drug resistance. Gain of stem cell-like states by cancer cells under drug pressure or due to interactions with the tumor microenvironment is a major mechanism that renders therapies ineffective. Identifying approaches to target cancer stem cells is expected to improve treatment outcomes for patients. Most of our understanding of drug resistance and the role of cancer stemness is from monolayer cell cultures. Recent advances in cell culture technologies have enabled developing sophisticated three-dimensional tumor models that facilitate mechanistic studies of cancer drug resistance. This review summarizes the role of cancer stemness in drug resistance and highlights the various tumor models that are used to discover the underlying mechanisms and test potentially novel therapeutics.
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Affiliation(s)
- Astha Lamichhane
- Department of Biomedical Engineering, The University of Akron, Akron, OH 44325 USA
| | - Hossein Tavana
- Department of Biomedical Engineering, The University of Akron, Akron, OH 44325 USA
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12
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Babu E, Sen S. Explore & actuate: the future of personalized medicine in oncology through emerging technologies. Curr Opin Oncol 2024; 36:93-101. [PMID: 38441149 DOI: 10.1097/cco.0000000000001016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
PURPOSE OF REVIEW The future of medicine is aimed to equip the physician with tools to assess the individual health of the patient for the uniqueness of the disease that separates it from the rest. The integration of omics technologies into clinical practice, reviewed here, would open new avenues for addressing the spatial and temporal heterogeneity of cancer. The rising cancer burden patiently awaits the advent of such an approach to personalized medicine for routine clinical settings. RECENT FINDINGS To weigh the translational potential, multiple technologies were categorized based on the extractable information from the different types of samples used, to the various omic-levels of molecular information that each technology has been able to advance over the last 2 years. This review uses a multifaceted classification that helps to assess translational potential in a meaningful way toward clinical adaptation. SUMMARY The importance of distinguishing technologies based on the flow of information from exploration to actuation puts forth a framework that allows the clinicians to better adapt a chosen technology or use them in combination to enhance their goals toward personalized medicine.
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Affiliation(s)
- Erald Babu
- UM-DAE Centre for Excellence in Basic Sciences, School of Biological Sciences, University of Mumbai, Kalina Campus, Mumbai, Maharashtra, India
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13
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Lei ZN, Albadari N, Teng QX, Rahman H, Wang JQ, Wu Z, Ma D, Ambudkar SV, Wurpel JND, Pan Y, Li W, Chen ZS. ABCB1-dependent collateral sensitivity of multidrug-resistant colorectal cancer cells to the survivin inhibitor MX106-4C. Drug Resist Updat 2024; 73:101065. [PMID: 38367548 DOI: 10.1016/j.drup.2024.101065] [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: 06/01/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/19/2024]
Abstract
AIMS To investigate the collateral sensitivity (CS) of ABCB1-positive multidrug resistant (MDR) colorectal cancer cells to the survivin inhibitor MX106-4C and the mechanism. METHODS Biochemical assays (MTT, ATPase, drug accumulation/efflux, Western blot, RT-qPCR, immunofluorescence, flow cytometry) and bioinformatic analyses (mRNA-sequencing, reversed-phase protein array) were performed to investigate the hypersensitivity of ABCB1 overexpressing colorectal cancer cells to MX106-4C and the mechanisms. Synergism assay, long-term selection, and 3D tumor spheroid test were used to evaluate the anti-cancer efficacy of MX106-4C. RESULTS MX106-4C selectively killed ABCB1-positive colorectal cancer cells, which could be reversed by an ABCB1 inhibitor, knockout of ABCB1, or loss-of-function ABCB1 mutation, indicating an ABCB1 expression and function-dependent mechanism. MX106-4C's selective toxicity was associated with cell cycle arrest and apoptosis through ABCB1-dependent survivin inhibition and activation on caspases-3/7 as well as modulation on p21-CDK4/6-pRb pathway. MX106-4C had good selectivity against ABCB1-positive colorectal cancer cells and retained this in multicellular tumor spheroids. In addition, MX106-4C could exert a synergistic anti-cancer effect with doxorubicin or re-sensitize ABCB1-positive cancer cells to doxorubicin by reducing ABCB1 expression in the cell population via long-term exposure. CONCLUSIONS MX106-4C selectively kills ABCB1-positive MDR colorectal cancer cells via a novel ABCB1-dependent survivin inhibition mechanism, providing a clue for designing CS compound as an alternative strategy to overcome ABCB1-mediated colorectal cancer MDR.
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Affiliation(s)
- Zi-Ning Lei
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA; Guangdong Provincial Key Laboratory of Digestive Cancer Research, Digestive Diseases Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, PR China
| | - Najah Albadari
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Qiu-Xu Teng
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Hadiar Rahman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, MD 20892, USA
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Zhongzhi Wu
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Dejian Ma
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, MD 20892, USA
| | - John N D Wurpel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
| | - Yihang Pan
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Digestive Diseases Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, PR China.
| | - Wei Li
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
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14
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Choi S, Woo SH, Park I, Lee S, Yeo KI, Lee SH, Lee SY, Yang S, Lee G, Chang WJ, Bashir R, Kim YS, Lee SW. Cellular subpopulations identified using an ensemble average of multiple dielectrophoresis measurements. Comput Biol Med 2024; 170:108011. [PMID: 38271838 DOI: 10.1016/j.compbiomed.2024.108011] [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: 10/08/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
While the average value measurement approach can successfully analyze and predict the general behavior and biophysical properties of an isogenic cell population, it fails when significant differences among individual cells are generated in the population by intracellular changes such as the cell cycle, or different cellular responses to certain stimuli. Detecting such single-cell differences in a cell population has remained elusive. Here, we describe an easy-to-implement and generalizable platform that measures the dielectrophoretic cross-over frequency of individual cells by decreasing measurement noise with a stochastic method and computing ensemble average statistics. This platform enables multiple, real-time, label-free detection of individual cells with significant dielectric variations over time within an isogenic cell population. Using a stochastic method in combination with the platform, we distinguished cell subpopulations from a mixture of drug-untreated and -treated isogenic cells. Furthermore, we demonstrate that our platform can identify drug-treated isogenic cells with different recovery rates.
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Affiliation(s)
- Seungyeop Choi
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea; School of Biomedical Engineering, Korea University, Seoul, 02481, Republic of Korea; BK21 Four Institute of Precision Public Health, Korea University, Seoul, 02841, Republic of Korea
| | - Sung-Hun Woo
- Department of Biomedical Laboratory Science, Yonsei University, Wonju, 26493, Republic of Korea
| | - Insu Park
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biomedical Engineering, Konyang University, Daejeon, 35365, Republic of Korea
| | - Sena Lee
- Department of Precision Medicine, Wonju College of Medicine, Yonsei University, Wonju, 26426, Republic of Korea
| | - Kang In Yeo
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Sang Hyun Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Sei Young Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea; Department of Medical Informatics and Biostatistics, Graduate School, Yonsei University, Wonju, 26426, Republic of Korea
| | - Sejung Yang
- Department of Precision Medicine, Wonju College of Medicine, Yonsei University, Wonju, 26426, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Woo-Jin Chang
- Mechanical Engineering Department, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Rashid Bashir
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoon Suk Kim
- Department of Biomedical Laboratory Science, Yonsei University, Wonju, 26493, Republic of Korea.
| | - Sang Woo Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, 26493, Republic of Korea.
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15
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Mohanty A, Nam A, Srivastava S, Jones J, Lomenick B, Singhal SS, Guo L, Cho H, Li A, Behal A, Mirzapoiazova T, Massarelli E, Koczywas M, Arvanitis LD, Walser T, Villaflor V, Hamilton S, Mambetsariev I, Sattler M, Nasser MW, Jain M, Batra SK, Soldi R, Sharma S, Fakih M, Mohanty SK, Mainan A, Wu X, Chen Y, He Y, Chou TF, Roy S, Orban J, Kulkarni P, Salgia R. Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer. SCIENCE ADVANCES 2023; 9:eade3816. [PMID: 37831779 PMCID: PMC10575592 DOI: 10.1126/sciadv.ade3816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
Inherent or acquired resistance to sotorasib poses a substantialt challenge for NSCLC treatment. Here, we demonstrate that acquired resistance to sotorasib in isogenic cells correlated with increased expression of integrin β4 (ITGB4), a component of the focal adhesion complex. Silencing ITGB4 in tolerant cells improved sotorasib sensitivity, while overexpressing ITGB4 enhanced tolerance to sotorasib by supporting AKT-mTOR bypass signaling. Chronic treatment with sotorasib induced WNT expression and activated the WNT/β-catenin signaling pathway. Thus, silencing both ITGB4 and β-catenin significantly improved sotorasib sensitivity in tolerant, acquired, and inherently resistant cells. In addition, the proteasome inhibitor carfilzomib (CFZ) exhibited synergism with sotorasib by down-regulating ITGB4 and β-catenin expression. Furthermore, adagrasib phenocopies the combination effect of sotorasib and CFZ by suppressing KRAS activity and inhibiting cell cycle progression in inherently resistant cells. Overall, our findings unveil previously unrecognized nongenetic mechanisms underlying resistance to sotorasib and propose a promising treatment strategy to overcome resistance.
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Affiliation(s)
- Atish Mohanty
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Arin Nam
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Saumya Srivastava
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Jeff Jones
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sharad S. Singhal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Linlin Guo
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Hyejin Cho
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Aimin Li
- Department of Pathology, City of Hope National Medical Center, Duarte, CA 91010,USA
| | - Amita Behal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Erminia Massarelli
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Marianna Koczywas
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | | | - Tonya Walser
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Victoria Villaflor
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Stanley Hamilton
- Department of Pathology, City of Hope National Medical Center, Duarte, CA 91010,USA
| | - Isa Mambetsariev
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mohd W. Nasser
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Maneesh Jain
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Surinder K. Batra
- Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Raffaella Soldi
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, AZ 850043, USA
| | - Sunil Sharma
- Applied Cancer Research and Drug Discovery Division, Translational Genomics Research Institute (TGen) of City of Hope, Phoenix, AZ 850043, USA
| | - Marwan Fakih
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Saswat Kumar Mohanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute, City of Hope, Monrovia, CA 91016, USA
| | - Yihong Chen
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Yanan He
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - John Orban
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope National Medical Center, Duarte, CA 91010, USA
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16
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Kiweler N, Schwarz H, Nguyen A, Matschos S, Mullins C, Piée-Staffa A, Brachetti C, Roos WP, Schneider G, Linnebacher M, Brenner W, Krämer OH. The epigenetic modifier HDAC2 and the checkpoint kinase ATM determine the responses of microsatellite instable colorectal cancer cells to 5-fluorouracil. Cell Biol Toxicol 2023; 39:2401-2419. [PMID: 35608750 PMCID: PMC10547618 DOI: 10.1007/s10565-022-09731-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
The epigenetic modifier histone deacetylase-2 (HDAC2) is frequently dysregulated in colon cancer cells. Microsatellite instability (MSI), an unfaithful replication of DNA at nucleotide repeats, occurs in about 15% of human colon tumors. MSI promotes a genetic frameshift and consequently a loss of HDAC2 in up to 43% of these tumors. We show that long-term and short-term cultures of colorectal cancers with MSI contain subpopulations of cells lacking HDAC2. These can be isolated as single cell-derived, proliferating populations. Xenografted patient-derived colon cancer tissues with MSI also show variable patterns of HDAC2 expression in mice. HDAC2-positive and HDAC2-negative RKO cells respond similarly to pharmacological inhibitors of the class I HDACs HDAC1/HDAC2/HDAC3. In contrast to this similarity, HDAC2-negative and HDAC2-positive RKO cells undergo differential cell cycle arrest and apoptosis induction in response to the frequently used chemotherapeutic 5-fluorouracil, which becomes incorporated into and damages RNA and DNA. 5-fluorouracil causes an enrichment of HDAC2-negative RKO cells in vitro and in a subset of primary colorectal tumors in mice. 5-fluorouracil induces the phosphorylation of KAP1, a target of the checkpoint kinase ataxia-telangiectasia mutated (ATM), stronger in HDAC2-negative cells than in their HDAC2-positive counterparts. Pharmacological inhibition of ATM sensitizes RKO cells to cytotoxic effects of 5-fluorouracil. These findings demonstrate that HDAC2 and ATM modulate the responses of colorectal cancer cells towards 5-FU.
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Affiliation(s)
- Nicole Kiweler
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
- Present Address: Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Helena Schwarz
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Alexandra Nguyen
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Stephanie Matschos
- Department of General Surgery, Molecular Oncology and Immunotherapy, Schillingallee 35, 18057 Rostock, Germany
| | - Christina Mullins
- Department of General Surgery, Molecular Oncology and Immunotherapy, Schillingallee 35, 18057 Rostock, Germany
| | - Andrea Piée-Staffa
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Christina Brachetti
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Wynand P. Roos
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
| | - Günter Schneider
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University Munich, 81675 Munich, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Schillingallee 35, 18057 Rostock, Germany
| | - Walburgis Brenner
- Clinic for Obstetrics and Women’s Health, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Oliver H. Krämer
- Department of Toxicology, University Medical Center Mainz, 55131 Mainz, Germany
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17
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Cheng YL, Banu MA, Zhao W, Rosenfeld SS, Canoll P, Sims PA. Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557001. [PMID: 37745469 PMCID: PMC10515771 DOI: 10.1101/2023.09.09.557001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target because of its dual roles in proliferation and invasion. The clinical utility of KIF11 inhibitors has been limited by drug resistance, which has mainly been studied in animal models. We used multiplexed lineage tracing barcodes and scRNA-seq to analyze drug resistance time courses for patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lost their neural lineage identity and transitioned to a mesenchymal phenotype, which is associated with poor prognosis. In contrast, cells subjected to long-term ispinesib treatment exhibited a proneural phenotype. We generated patient-derived xenografts to show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Finally, we used lineage barcodes to nominate drug combination targets by retrospective analysis of ispinesib-resistant clones in the drug-naïve setting and identified drugs that are synergistic with ispinesib.
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Affiliation(s)
- Yim Ling Cheng
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matei A. Banu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Wenting Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Peter Canoll
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter A. Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
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18
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Gnocchi D, Nikolic D, Paparella RR, Sabbà C, Mazzocca A. Cellular Adaptation Takes Advantage of Atavistic Regression Programs during Carcinogenesis. Cancers (Basel) 2023; 15:3942. [PMID: 37568758 PMCID: PMC10416974 DOI: 10.3390/cancers15153942] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Adaptation of cancer cells to extreme microenvironmental conditions (i.e., hypoxia, high acidity, and reduced nutrient availability) contributes to cancer resilience. Furthermore, neoplastic transformation can be envisioned as an extreme adaptive response to tissue damage or chronic injury. The recent Systemic-Evolutionary Theory of the Origin of Cancer (SETOC) hypothesizes that cancer cells "revert" to "primitive" characteristics either ontogenically (embryo-like) or phylogenetically (single-celled organisms). This regression may confer robustness and maintain the disordered state of the tissue, which is a hallmark of malignancy. Changes in cancer cell metabolism during adaptation may also be the consequence of altered microenvironmental conditions, often resulting in a shift toward lactic acid fermentation. However, the mechanisms underlying the robust adaptive capacity of cancer cells remain largely unknown. In recent years, cancer cells' metabolic flexibility has received increasing attention among researchers. Here, we focus on how changes in the microenvironment can affect cancer cell energy production and drug sensitivity. Indeed, changes in the cellular microenvironment may lead to a "shift" toward "atavistic" biologic features, such as the switch from oxidative phosphorylation (OXPHOS) to lactic acid fermentation, which can also sustain drug resistance. Finally, we point out new integrative metabolism-based pharmacological approaches and potential biomarkers for early detection.
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Affiliation(s)
| | | | | | | | - Antonio Mazzocca
- Interdisciplinary Department of Medicine, University of Bari School of Medicine, Piazza G. Cesare, 11, 70124 Bari, Italy; (D.G.); (D.N.); (R.R.P.); (C.S.)
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19
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Masud MA, Kim JY, Kim E. Modeling the effect of acquired resistance on cancer therapy outcomes. Comput Biol Med 2023; 162:107035. [PMID: 37276754 DOI: 10.1016/j.compbiomed.2023.107035] [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: 02/05/2023] [Revised: 04/17/2023] [Accepted: 05/11/2023] [Indexed: 06/07/2023]
Abstract
Adaptive therapy (AT) is an evolution-based treatment strategy that exploits cell-cell competition. Acquired resistance can change the competitive nature of cancer cells in a tumor, impacting AT outcomes. We aimed to determine if adaptive therapy can still be effective with cell's acquiring resistance. We developed an agent-based model for spatial tumor growth considering three different types of acquired resistance: random genetic mutations during cell division, drug-induced reversible (plastic) phenotypic changes, and drug-induced irreversible phenotypic changes. These three resistance mechanisms lead to different spatial distributions of resistant cells. To quantify the spatial distribution, we propose an extension of Ripley's K-function, Sampled Ripley's K-function (SRKF), which calculates the non-randomness of the resistance distribution over the tumor domain. Our model predicts that the emergent spatial distribution of resistance can determine the time to progression under both adaptive and continuous therapy (CT). Notably, a high rate of random genetic mutations leads to quicker progression under AT than CT due to the emergence of many small clumps of resistant cells. Drug-induced phenotypic changes accelerate tumor progression irrespective of the treatment strategy. Low-rate switching to a sensitive state reduces the benefits of AT compared to CT. Furthermore, we also demonstrated that drug-induced resistance necessitates aggressive treatment under CT, regardless of the presence of cancer-associated fibroblasts. However, there is an optimal dose that can most effectively delay tumor relapse under AT by suppressing resistance. In conclusion, this study demonstrates that diverse resistance mechanisms can shape the distribution of resistance and thus determine the efficacy of adaptive therapy.
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Affiliation(s)
- M A Masud
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea.
| | - Jae-Young Kim
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon 34134, Republic of Korea.
| | - Eunjung Kim
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Republic of Korea.
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20
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Ingles Garces AH, Porta N, Graham TA, Banerji U. Clinical trial designs for evaluating and exploiting cancer evolution. Cancer Treat Rev 2023; 118:102583. [PMID: 37331179 DOI: 10.1016/j.ctrv.2023.102583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023]
Abstract
The evolution of drug-resistant cell subpopulations causes cancer treatment failure. Current preclinical evidence shows that it is possible to model herding of clonal evolution and collateral sensitivity where an initial treatment could favourably influence the response to a subsequent one. Novel therapy strategies exploiting this understanding are being considered, and clinical trial designs for steering cancer evolution are needed. Furthermore, preclinical evidence suggests that different subsets of drug-sensitive and resistant clones could compete between themselves for nutrients/blood supply, and clones that populate a tumour do so at the expense of other clones. Treatment paradigms based on this clinical application of exploiting cell-cell competition include intermittent dosing regimens or cycling different treatments before progression. This will require clinical trial designs different from the conventional practice of evaluating responses to individual therapy regimens. Next-generation sequencing to assess clonal dynamics longitudinally will improve current radiological assessment of clinical response/resistance and be incorporated into trials exploiting evolution. Furthermore, if understood, clonal evolution can be used to therapeutic advantage, improving patient outcomes based on a new generation of clinical trials.
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Affiliation(s)
- Alvaro H Ingles Garces
- Drug Development Unit, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, UK
| | - Nuria Porta
- Clinical Trials and Statistical Unit, The Institute of Cancer Research, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, UK
| | - Udai Banerji
- Drug Development Unit, The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, UK.
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21
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Zhu X, Zhao W, Zhou Z, Gu X. Unraveling the Drivers of Tumorigenesis in the Context of Evolution: Theoretical Models and Bioinformatics Tools. J Mol Evol 2023:10.1007/s00239-023-10117-0. [PMID: 37246992 DOI: 10.1007/s00239-023-10117-0] [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: 12/30/2022] [Accepted: 05/09/2023] [Indexed: 05/30/2023]
Abstract
Cancer originates from somatic cells that have accumulated mutations. These mutations alter the phenotype of the cells, allowing them to escape homeostatic regulation that maintains normal cell numbers. The emergence of malignancies is an evolutionary process in which the random accumulation of somatic mutations and sequential selection of dominant clones cause cancer cells to proliferate. The development of technologies such as high-throughput sequencing has provided a powerful means to measure subclonal evolutionary dynamics across space and time. Here, we review the patterns that may be observed in cancer evolution and the methods available for quantifying the evolutionary dynamics of cancer. An improved understanding of the evolutionary trajectories of cancer will enable us to explore the molecular mechanism of tumorigenesis and to design tailored treatment strategies.
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Affiliation(s)
- Xunuo Zhu
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenyi Zhao
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China.
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China.
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
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22
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Liu H, Fan Z, Lin J, Yang Y, Ran T, Chen H. The recent progress of deep-learning-based in silico prediction of drug combination. Drug Discov Today 2023:103625. [PMID: 37236526 DOI: 10.1016/j.drudis.2023.103625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/24/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
Drug combination therapy has become a common strategy for the treatment of complex diseases. There is an urgent need for computational methods to efficiently identify appropriate drug combinations owing to the high cost of experimental screening. In recent years, deep learning has been widely used in the field of drug discovery. Here, we provide a comprehensive review on deep-learning-based drug combination prediction algorithms from multiple aspects. Current studies highlight the flexibility of this technology in integrating multimodal data and the ability to achieve state-of-art performance; it is expected that deep-learning-based prediction of drug combinations should play an important part in future drug discovery.
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Affiliation(s)
- Haoyang Liu
- Department of Drug and Vaccine Research, Guangzhou Laboratory, Guangzhou 513000, China; College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhiguang Fan
- Department of Drug and Vaccine Research, Guangzhou Laboratory, Guangzhou 513000, China; School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China
| | - Jie Lin
- Department of Drug and Vaccine Research, Guangzhou Laboratory, Guangzhou 513000, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China.
| | - Ting Ran
- Department of Drug and Vaccine Research, Guangzhou Laboratory, Guangzhou 513000, China.
| | - Hongming Chen
- Department of Drug and Vaccine Research, Guangzhou Laboratory, Guangzhou 513000, China.
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23
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Masud MA, Kim JY, Kim E. Effective dose window for containing tumor burden under tolerable level. NPJ Syst Biol Appl 2023; 9:17. [PMID: 37221258 DOI: 10.1038/s41540-023-00279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
A maximum-tolerated dose (MTD) reduces the drug-sensitive cell population, though it may result in the competitive release of drug resistance. Alternative treatment strategies such as adaptive therapy (AT) or dose modulation aim to impose competitive stress on drug-resistant cell populations by maintaining a sufficient number of drug-sensitive cells. However, given the heterogeneous treatment response and tolerable tumor burden level of individual patients, determining an effective dose that can fine-tune competitive stress remains challenging. This study presents a mathematical model-driven approach that determines the plausible existence of an effective dose window (EDW) as a range of doses that conserve sufficient sensitive cells while maintaining the tumor volume below a threshold tolerable tumor volume (TTV). We use a mathematical model that explains intratumor cell competition. Analyzing the model, we derive an EDW determined by TTV and the competitive strength. By applying a fixed endpoint optimal control model, we determine the minimal dose to contain cancer at a TTV. As a proof of concept, we study the existence of EDW for a small cohort of melanoma patients by fitting the model to longitudinal tumor response data. We performed identifiability analysis, and for the patients with uniquely identifiable parameters, we deduced patient-specific EDW and minimal dose. The tumor volume for a patient could be theoretically contained at the TTV either using continuous dose or AT strategy with doses belonging to EDW. Further, we conclude that the lower bound of the EDW approximates the minimum effective dose (MED) for containing tumor volume at the TTV.
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Affiliation(s)
- M A Masud
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
| | - Jae-Young Kim
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eunjung Kim
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea.
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24
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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: 8] [Impact Index Per Article: 8.0] [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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25
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Vinogradov AE, Anatskaya OV. Systemic Alterations of Cancer Cells and Their Boost by Polyploidization: Unicellular Attractor (UCA) Model. Int J Mol Sci 2023; 24:ijms24076196. [PMID: 37047167 PMCID: PMC10094663 DOI: 10.3390/ijms24076196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Using meta-analyses, we introduce a unicellular attractor (UCA) model integrating essential features of the ‘atavistic reversal’, ‘cancer attractor’, ‘somatic mutation’, ‘genome chaos’, and ‘tissue organization field’ theories. The ‘atavistic reversal’ theory is taken as a keystone. We propose a possible mechanism of this reversal, its refinement called ‘gradual atavism’, and evidence for the ‘serial atavism’ model. We showed the gradual core-to-periphery evolutionary growth of the human interactome resulting in the higher protein interaction density and global interactome centrality in the UC center. In addition, we revealed that UC genes are more actively expressed even in normal cells. The modeling of random walk along protein interaction trajectories demonstrated that random alterations in cellular networks, caused by genetic and epigenetic changes, can result in a further gradual activation of the UC center. These changes can be induced and accelerated by cellular stress that additionally activates UC genes (especially during cell proliferation), because the genes involved in cellular stress response and cell cycle are mostly of UC origin. The functional enrichment analysis showed that cancer cells demonstrate the hyperactivation of energetics and the suppression of multicellular genes involved in communication with the extracellular environment (especially immune surveillance). Collectively, these events can unleash selfish cell behavior aimed at survival at all means. All these changes are boosted by polyploidization. The UCA model may facilitate an understanding of oncogenesis and promote the development of therapeutic strategies.
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26
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Brown A, Pan Q, Fan L, Indersie E, Tian C, Timchenko N, Li L, Hansen BS, Tan H, Lu M, Peng J, Pruett-Miller SM, Yu J, Cairo S, Zhu L. Ribonucleotide reductase subunit switching in hepatoblastoma drug response and relapse. Commun Biol 2023; 6:249. [PMID: 36882565 PMCID: PMC9992519 DOI: 10.1038/s42003-023-04630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Abstract
Prognosis of children with high-risk hepatoblastoma (HB), the most common pediatric liver cancer, remains poor. In this study, we found ribonucleotide reductase (RNR) subunit M2 (RRM2) was one of the key genes supporting cell proliferation in high-risk HB. While standard chemotherapies could effectively suppress RRM2 in HB cells, they induced a significant upregulation of the other RNR M2 subunit, RRM2B. Computational analysis revealed distinct signaling networks RRM2 and RRM2B were involved in HB patient tumors, with RRM2 supporting cell proliferation and RRM2B participating heavily in stress response pathways. Indeed, RRM2B upregulation in chemotherapy-treated HB cells promoted cell survival and subsequent relapse, during which RRM2B was gradually replaced back by RRM2. Combining an RRM2 inhibitor with chemotherapy showed an effective delaying of HB tumor relapse in vivo. Overall, our study revealed the distinct roles of the two RNR M2 subunits and their dynamic switching during HB cell proliferation and stress response.
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Affiliation(s)
- Anthony Brown
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qingfei Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Fan
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Cheng Tian
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nikolai Timchenko
- Department of Surgery, Cincinnati Children's Hospital Medical Center and Department of Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Liyuan Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Baranda S Hansen
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Meifen Lu
- Center for Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Liqin Zhu
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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27
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Hastings JF, Latham SL, Kamili A, Wheatley MS, Han JZ, Wong-Erasmus M, Phimmachanh M, Nobis M, Pantarelli C, Cadell AL, O’Donnell YE, Leong KH, Lynn S, Geng FS, Cui L, Yan S, Achinger-Kawecka J, Stirzaker C, Norris MD, Haber M, Trahair TN, Speleman F, De Preter K, Cowley MJ, Bogdanovic O, Timpson P, Cox TR, Kolch W, Fletcher JI, Fey D, Croucher DR. Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma. SCIENCE ADVANCES 2023; 9:eabp8314. [PMID: 36867694 PMCID: PMC9984174 DOI: 10.1126/sciadv.abp8314] [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: 02/28/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Gene expression noise is known to promote stochastic drug resistance through the elevated expression of individual genes in rare cancer cells. However, we now demonstrate that chemoresistant neuroblastoma cells emerge at a much higher frequency when the influence of noise is integrated across multiple components of an apoptotic signaling network. Using a JNK activity biosensor with longitudinal high-content and in vivo intravital imaging, we identify a population of stochastic, JNK-impaired, chemoresistant cells that exist because of noise within this signaling network. Furthermore, we reveal that the memory of this initially random state is retained following chemotherapy treatment across a series of in vitro, in vivo, and patient models. Using matched PDX models established at diagnosis and relapse from individual patients, we show that HDAC inhibitor priming cannot erase the memory of this resistant state within relapsed neuroblastomas but improves response in the first-line setting by restoring drug-induced JNK activity within the chemoresistant population of treatment-naïve tumors.
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Affiliation(s)
- Jordan F. Hastings
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Sharissa L. Latham
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Alvin Kamili
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Madeleine S. Wheatley
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Jeremy Z. R. Han
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Marie Wong-Erasmus
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Monica Phimmachanh
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Max Nobis
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Chiara Pantarelli
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Antonia L. Cadell
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Yolande E. I. O’Donnell
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - King Ho Leong
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Sophie Lynn
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Fan-Suo Geng
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Lujing Cui
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Sabrina Yan
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Joanna Achinger-Kawecka
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Clare Stirzaker
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Murray D. Norris
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Michelle Haber
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Mark J. Cowley
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Ozren Bogdanovic
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Paul Timpson
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Thomas R. Cox
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jamie I. Fletcher
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Dirk Fey
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - David R. Croucher
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
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Shlyakhtina Y, Bloechl B, Portal MM. BdLT-Seq as a barcode decay-based method to unravel lineage-linked transcriptome plasticity. Nat Commun 2023; 14:1085. [PMID: 36841849 PMCID: PMC9968323 DOI: 10.1038/s41467-023-36744-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
Cell plasticity is a core biological process underlying a myriad of molecular and cellular events taking place throughout organismal development and evolution. It has been postulated that cellular systems thrive to balance the organization of meta-stable states underlying this phenomenon, thereby maintaining a degree of populational homeostasis compatible with an ever-changing environment and, thus, life. Notably, albeit circumstantial evidence has been gathered in favour of the latter conceptual framework, a direct observation of meta-state dynamics and the biological consequences of such a process in generating non-genetic clonal diversity and divergent phenotypic output remains largely unexplored. To fill this void, here we develop a lineage-tracing technology termed Barcode decay Lineage Tracing-Seq. BdLT-Seq is based on episome-encoded molecular identifiers that, supported by the dynamic decay of the tracing information upon cell division, ascribe directionality to a cell lineage tree whilst directly coupling non-genetic molecular features to phenotypes in comparable genomic landscapes. We show that cell transcriptome states are both inherited, and dynamically reshaped following constrained rules encoded within the cell lineage in basal growth conditions, upon oncogene activation and throughout the process of reversible resistance to therapeutic cues thus adjusting phenotypic output leading to intra-clonal non-genetic diversity.
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Affiliation(s)
- Yelyzaveta Shlyakhtina
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, SK10 4TG, Manchester, UK
| | - Bianca Bloechl
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, SK10 4TG, Manchester, UK
| | - Maximiliano M Portal
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, SK10 4TG, Manchester, UK.
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Al-Hamaly MA, Turner LT, Rivera-Martinez A, Rodriguez A, Blackburn JS. Zebrafish Cancer Avatars: A Translational Platform for Analyzing Tumor Heterogeneity and Predicting Patient Outcomes. Int J Mol Sci 2023; 24:2288. [PMID: 36768609 PMCID: PMC9916713 DOI: 10.3390/ijms24032288] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The increasing number of available anti-cancer drugs presents a challenge for oncologists, who must choose the most effective treatment for the patient. Precision cancer medicine relies on matching a drug with a tumor's molecular profile to optimize the therapeutic benefit. However, current precision medicine approaches do not fully account for intra-tumoral heterogeneity. Different mutation profiles and cell behaviors within a single heterogeneous tumor can significantly impact therapy response and patient outcomes. Patient-derived avatar models recapitulate a patient's tumor in an animal or dish and provide the means to functionally assess heterogeneity's impact on drug response. Mouse xenograft and organoid avatars are well-established, but the time required to generate these models is not practical for clinical decision-making. Zebrafish are emerging as a time-efficient and cost-effective cancer avatar model. In this review, we highlight recent developments in zebrafish cancer avatar models and discuss the unique features of zebrafish that make them ideal for the interrogation of cancer heterogeneity and as part of precision cancer medicine pipelines.
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Affiliation(s)
- Majd A. Al-Hamaly
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40356, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Logan T. Turner
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40356, USA
| | | | - Analiz Rodriguez
- Department of Neurosurgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jessica S. Blackburn
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40356, USA
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30
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Brown A, Pan Q, Fan L, Indersie E, Tian C, Timchenko N, Li L, Hansen BS, Tan H, Lu M, Peng J, Pruett-Miller SM, Yu J, Cairo S, Zhu L. Ribonucleotide Reductase Subunit Switching in Hepatoblastoma Drug Response and Relapse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023. [PMID: 36747774 PMCID: PMC9900781 DOI: 10.1101/2023.01.24.525404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Prognosis of children with high-risk hepatoblastoma (HB), the most common pediatric liver cancer, remains poor. In this study, we found ribonucleotide reductase (RNR) subunit M2 ( RRM2 ) was one of the key genes supporting cell proliferation in high-risk HB. While standard chemotherapies could effectively suppress RRM2 in HB cells, they induced a significant upregulation of the other RNR M2 subunit, RRM2B . Computational analysis revealed distinct signaling networks RRM2 and RRM2B were involved in HB patient tumors, with RRM2 supporting cell proliferation and RRM2B participating heavily in stress response pathways. Indeed, RRM2B upregulation in chemotherapy-treated HB cells promoted cell survival and subsequent relapse, during which RRM2B was gradually replaced back by RRM2. Combining an RRM2 inhibitor with chemotherapy showed an effective delaying of HB tumor relapse in vivo. Overall, our study revealed the distinct roles of the two RNR M2 subunits and their dynamic switching during HB cell proliferation and stress response.
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Ramisetty S, Kulkarni P, Bhattacharya S, Nam A, Singhal SS, Guo L, Mirzapoiazova T, Mambetsariev B, Mittan S, Malhotra J, Pisick E, Subbiah S, Rajurkar S, Massarelli E, Salgia R, Mohanty A. A Systems Biology Approach for Addressing Cisplatin Resistance in Non-Small Cell Lung Cancer. J Clin Med 2023; 12:jcm12020599. [PMID: 36675528 PMCID: PMC9861808 DOI: 10.3390/jcm12020599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Translational research in medicine, defined as the transfer of knowledge and discovery from the basic sciences to the clinic, is typically achieved through interactions between members across scientific disciplines to overcome the traditional silos within the community. Thus, translational medicine underscores 'Team Medicine', the partnership between basic science researchers and clinicians focused on addressing a specific goal in medicine. Here, we highlight this concept from a City of Hope perspective. Using cisplatin resistance in non-small cell lung cancer (NSCLC) as a paradigm, we describe how basic research scientists, clinical research scientists, and medical oncologists, in true 'Team Science' spirit, addressed cisplatin resistance in NSCLC and identified a previously approved compound that is able to alleviate cisplatin resistance in NSCLC. Furthermore, we discuss how a 'Team Medicine' approach can help to elucidate the mechanisms of innate and acquired resistance in NSCLC and develop alternative strategies to overcome drug resistance.
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Affiliation(s)
- Sravani Ramisetty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Supriyo Bhattacharya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, 1500 Duarte Rd, Duarte, CA 91010, USA
| | - Arin Nam
- Department of Pathology, University of California, La Jolla, San Diego, CA 92093, USA
| | - Sharad S. Singhal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Linlin Guo
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Bolot Mambetsariev
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Sandeep Mittan
- Montefiore Medical Center, The University Hospital for Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Jyoti Malhotra
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1000 FivePoint, Irvine, CA 92618, USA
| | - Evan Pisick
- Cancer Treatment Centers of America (CTCA) Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1250 S. Sunset Ave., Suite 303, West Covina, CA 91790, USA
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1100 San Bernardino Road, Suite 1100, Upland, CA 91786, USA
| | - Erminia Massarelli
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
- Correspondence:
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Buss JH, Lenz LS, Pereira LC, Torgo D, Marcolin J, Begnini KR, Lenz G. The role of mitosis in generating fitness heterogeneity. J Cell Sci 2023; 136:286224. [PMID: 36594556 DOI: 10.1242/jcs.260103] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 11/25/2022] [Indexed: 01/04/2023] Open
Abstract
Cancer cells have heterogeneous fitness, and this heterogeneity stems from genetic and epigenetic sources. Here, we sought to assess the contribution of asymmetric mitosis (AM) and time on the variability of fitness in sister cells. Around one quarter of sisters had differences in fitness, assessed as the intermitotic time (IMT), from 330 to 510 min. Phenotypes related to fitness, such as ERK activity (herein referring to ERK1 and ERK2, also known as MAPK3 and MAPK1, respectively), DNA damage and nuclear morphological phenotypes were also asymmetric at mitosis or turned asymmetric over the course of the cell cycle. The ERK activity of mother cell was found to influence the ERK activity and the IMT of the daughter cells, and cells with ERK asymmetry at mitosis produced more offspring with AMs, suggesting heritability of the AM phenotype for ERK activity. Our findings demonstrate how variabilities in sister cells can be generated, contributing to the phenotype heterogeneities in tumor cells.
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Affiliation(s)
- Julieti Huch Buss
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
| | - Luana Suéling Lenz
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
| | - Luiza Cherobini Pereira
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
| | - Daphne Torgo
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
| | - Júlia Marcolin
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
| | - Karine Rech Begnini
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
| | - Guido Lenz
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil.,Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS 91509-900, Brazil
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Hanes R, Ayuda-Durán P, Rønneberg L, Nakken S, Hovig E, Zucknick M, Enserink JM. screenwerk: a modular tool for the design and analysis of drug combination screens. Bioinformatics 2022; 39:6961189. [PMID: 36573326 PMCID: PMC9825784 DOI: 10.1093/bioinformatics/btac840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/14/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022] Open
Abstract
MOTIVATION There is a rapidly growing interest in high-throughput drug combination screening to identify synergizing drug interactions for treatment of various maladies, such as cancer and infectious disease. This creates the need for pipelines that can be used to design such screens, perform quality control on the data and generate data files that can be analyzed by synergy-finding bioinformatics applications. RESULTS screenwerk is an open-source, end-to-end modular tool available as an R-package for the design and analysis of drug combination screens. The tool allows for a customized build of pipelines through its modularity and provides a flexible approach to quality control and data analysis. screenwerk is adaptable to various experimental requirements with an emphasis on precision medicine. It can be coupled to other R packages, such as bayesynergy, to identify synergistic and antagonistic drug interactions in cell lines or patient samples. screenwerk is scalable and provides a complete solution for setting up drug sensitivity screens, read raw measurements and consolidate different datasets, perform various types of quality control and analyze, report and visualize the results of drug sensitivity screens. AVAILABILITY AND IMPLEMENTATION The R-package and technical documentation is available at https://github.com/Enserink-lab/screenwerk; the R source code is publicly available at https://github.com/Enserink-lab/screenwerk under GNU General Public License v3.0; bayesynergy is accessible at https://github.com/ocbe-uio/bayesynergy. Selected modules are available through Galaxy, an open-source platform for FAIR data analysis at https://oncotools.elixir.no. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Robert Hanes
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379 Oslo, Norway,Centre for Cancer Cell Reprogramming, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway,Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379 Oslo, Norway,Centre for Cancer Cell Reprogramming, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Leiv Rønneberg
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, 0317 Oslo, Norway,MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Sigve Nakken
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway,Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo 0379, Norway,Department of Informatics, Centre for Bioinformatics, University of Oslo, Oslo 0372, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo 0379, Norway,Department of Informatics, Centre for Bioinformatics, University of Oslo, Oslo 0372, Norway
| | - Manuela Zucknick
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, 0317 Oslo, Norway
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Acquired drug resistance interferes with the susceptibility of prostate cancer cells to metabolic stress. Cell Mol Biol Lett 2022; 27:100. [PMCID: PMC9673456 DOI: 10.1186/s11658-022-00400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/28/2022] [Indexed: 11/19/2022] Open
Abstract
Background Metformin is an inhibitor of oxidative phosphorylation that displays an array of anticancer activities. The interference of metformin with the activity of multi-drug resistance systems in cancer cells has been reported. However, the consequences of the acquired chemoresistance for the adaptative responses of cancer cells to metformin-induced stress and for their phenotypic evolution remain unaddressed. Methods Using a range of phenotypic and metabolic assays, we assessed the sensitivity of human prostate cancer PC-3 and DU145 cells, and their drug-resistant lineages (PC-3_DCX20 and DU145_DCX20), to combined docetaxel/metformin stress. Their adaptation responses have been assessed, in particular the shifts in their metabolic profile and invasiveness. Results Metformin increased the sensitivity of PC-3 wild-type (WT) cells to docetaxel, as illustrated by the attenuation of their motility, proliferation, and viability after the combined drug application. These effects correlated with the accumulation of energy carriers (NAD(P)H and ATP) and with the inactivation of ABC drug transporters in docetaxel/metformin-treated PC-3 WT cells. Both PC-3 WT and PC-3_DCX20 reacted to metformin with the Warburg effect; however, PC-3_DCX20 cells were considerably less susceptible to the cytostatic/misbalancing effects of metformin. Concomitantly, an epithelial–mesenchymal transition and Cx43 upregulation was seen in these cells, but not in other more docetaxel/metformin-sensitive DU145_DCX20 populations. Stronger cytostatic effects of the combined fenofibrate/docetaxel treatment confirmed that the fine-tuning of the balance between energy supply and expenditure determines cellular welfare under metabolic stress. Conclusions Collectively, our data identify the mechanisms that underlie the limited potential of metformin for the chemotherapy of drug-resistant tumors. Metformin can enhance the sensitivity of cancer cells to chemotherapy by inducing their metabolic decoupling/imbalance. However, the acquired chemoresistance of cancer cells impairs this effect, facilitates cellular adaptation to metabolic stress, and prompts the invasive front formation. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00400-1.
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Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. Nat Commun 2022; 13:6918. [PMID: 36376301 PMCID: PMC9663587 DOI: 10.1038/s41467-022-34536-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput measurement of cells perturbed using libraries of small molecules, gene knockouts, or different microenvironmental factors is a key step in functional genomics and pre-clinical drug discovery. However, it remains difficult to perform accurate single-cell assays in 384-well plates, limiting many studies to well-average measurements (e.g., CellTiter-Glo®). Here we describe a public domain Dye Drop method that uses sequential density displacement and microscopy to perform multi-step assays on living cells. We use Dye Drop cell viability and DNA replication assays followed by immunofluorescence imaging to collect single-cell dose-response data for 67 investigational and clinical-grade small molecules in 58 breast cancer cell lines. By separating the cytostatic and cytotoxic effects of drugs computationally, we uncover unexpected relationships between the two. Dye Drop is rapid, reproducible, customizable, and compatible with manual or automated laboratory equipment. Dye Drop improves the tradeoff between data content and cost, enabling the collection of information-rich perturbagen-response datasets.
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36
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Warzecha KW, Pudełek M, Catapano J, Madeja Z, Czyż J. Long-Term Fenofibrate Treatment Stimulates the Phenotypic Microevolution of Prostate Cancer Cells In Vitro. Pharmaceuticals (Basel) 2022; 15:1320. [PMID: 36355492 PMCID: PMC9694160 DOI: 10.3390/ph15111320] [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: 09/19/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 08/30/2023] Open
Abstract
Fenofibrate is a widely used anti-hyperlipidemic agonist of peroxisome proliferator-activated receptor alpha (PPARα). As a metabolic blocker, fenofibrate interferes with cancer promotion/progression via its misbalancing effects on cellular metabolism. However, the consequences of its long-term application for patients with diagnosed drug-resistant cancers are unknown. We addressed this point by tracing the phenotypic microevolution of naïve and drug-resistant prostate cancer PC3_DCX20 cells that underwent a long-term exposition to 10 μM and 50 μM fenofibrate. Their resistance to fenofibrate, metabolic profile and invasive phenotype were estimated in the control conditions and under fenofibrate-induced stress. Apparently, drug efflux systems are not effective against the cytostatic FF action. However, wtPC3 and PC3_DCX20 cells that survived the long-term 50 μM fenofibrate treatment gave rise to lineages that displayed an increased proliferation rate, lower motility in the control conditions and enhanced fenofibrate resistance. Attenuated fenofibrate bioavailability modified the pattern of PC3 microevolution, as illustrated by phenotypic differences between wtPC3/PC3_DCX20 lineages propagated in the presence of 50 μM and 10 μM fenofibrate. Collectively, our observations indicate that fenofibrate acts as a selective factor that affects prostate cancer microevolution. We also pinpoint potential consequences of long-term exposition of prostate cancer patients to metabolic blockers.
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Affiliation(s)
| | | | | | | | - Jarosław Czyż
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Cracow, Poland
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Addressing Drug Resistance in Cancer: A Team Medicine Approach. J Clin Med 2022; 11:jcm11195701. [PMID: 36233569 PMCID: PMC9572909 DOI: 10.3390/jcm11195701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 12/04/2022] Open
Abstract
Drug resistance remains one of the major impediments to treating cancer. Although many patients respond well initially, resistance to therapy typically ensues. Several confounding factors appear to contribute to this challenge. Here, we first discuss some of the challenges associated with drug resistance. We then discuss how a ‘Team Medicine’ approach, involving an interdisciplinary team of basic scientists working together with clinicians, has uncovered new therapeutic strategies. These strategies, referred to as intermittent or ‘adaptive’ therapy, which are based on eco-evolutionary principles, have met with remarkable success in potentially precluding or delaying the emergence of drug resistance in several cancers. Incorporating such treatment strategies into clinical protocols could potentially enhance the precision of delivering personalized medicine to patients. Furthermore, reaching out to patients in the network of hospitals affiliated with leading academic centers could help them benefit from such innovative treatment options. Finally, lowering the dose of the drug and its frequency (because of intermittent rather than continuous therapy) can also have a significant impact on lowering the toxicity and undesirable side effects of the drugs while lowering the financial burden carried by the patient and insurance providers.
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Novel epigenetic therapeutic strategies and targets in cancer. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166552. [PMID: 36126898 DOI: 10.1016/j.bbadis.2022.166552] [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: 06/14/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022]
Abstract
The critical role of dysregulated epigenetic pathways in cancer genesis, development, and therapy has typically been established as a result of scientific and technical innovations in next generation sequencing. RNA interference, histone modification, DNA methylation and chromatin remodelling are epigenetic processes that control gene expression without causing mutations in the DNA. Although epigenetic abnormalities are thought to be a symptom of cell tumorigenesis and malignant events that impact tumor growth and drug resistance, physicians believe that related processes might be a key therapeutic target for cancer treatment and prevention due to the reversible nature of these processes. A plethora of novel strategies for addressing epigenetics in cancer therapy for immuno-oncological complications are currently available - ranging from basic treatment to epigenetic editing. - and they will be the subject of this comprehensive review. In this review, we cover most of the advancements made in the field of targeting epigenetics with special emphasis on microbiology, plasma science, biophysics, pharmacology, molecular biology, phytochemistry, and nanoscience.
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Zhao W, Gu X, Chen S, Wu J, Zhou Z. MODIG: Integrating Multi-Omics and Multi-Dimensional Gene Network for Cancer Driver Gene Identification based on Graph Attention Network Model. Bioinformatics 2022; 38:4901-4907. [PMID: 36094338 DOI: 10.1093/bioinformatics/btac622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/07/2022] [Accepted: 09/10/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Identifying genes that play a causal role in cancer evolution remains one of the biggest challenges in cancer biology. With the accumulation of high-throughput multi-omics data over decades, it becomes a great challenge to effectively integrate these data into the identification of cancer driver genes. RESULTS Here, we propose MODIG, a graph attention network (GAT)-based framework to identify cancer driver genes by combining multi-omics pan-cancer data (mutations, copy number variants, gene expression, and methylation levels) with multi-dimensional gene networks. First, we established diverse types of gene relationship maps based on protein-protein interactions (PPI), gene sequence similarity, KEGG pathway co-occurrence, gene co-expression patterns, and Gene Ontology (GO). Then, we constructed a multi-dimensional gene network consisting of approximately 20,000 genes as nodes and five types of gene associations as multiplex edges. We applied a GAT to model within-dimension interactions to generate a gene representation for each dimension based on this graph. Moreover, we introduced a joint learning module to fuse multiple dimension-specific representations to generate general gene representations. Finally, we used the obtained gene representation to perform a semi-supervised driver gene identification task. The experiment results show that MODIG outperforms the baseline models in terms of area under precision-recall curves (AUPR) and area under the receiver operating characteristic curves (AUROC). AVAILABILITY The MODIG program is available at https://github.com/zjupgx/modig. The code and data underlying this article are also available on Zenodo, at https://doi.org/10.5281/zenodo.7057241. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenyi Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- Second Affiliated Hospital School of Medicine, and School of Public Health, Zhejiang University, Hangzhou, 310058, China.,Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, China.,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China
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Cárdenas SD, Reznik CJ, Ranaweera R, Song F, Chung CH, Fertig EJ, Gevertz JL. Model-informed experimental design recommendations for distinguishing intrinsic and acquired targeted therapeutic resistance in head and neck cancer. NPJ Syst Biol Appl 2022; 8:32. [PMID: 36075912 PMCID: PMC9458753 DOI: 10.1038/s41540-022-00244-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/05/2022] [Indexed: 11/09/2022] Open
Abstract
The promise of precision medicine has been limited by the pervasive resistance to many targeted therapies for cancer. Inferring the timing (i.e., pre-existing or acquired) and mechanism (i.e., drug-induced) of such resistance is crucial for designing effective new therapeutics. This paper studies cetuximab resistance in head and neck squamous cell carcinoma (HNSCC) using tumor volume data obtained from patient-derived tumor xenografts. We ask if resistance mechanisms can be determined from this data alone, and if not, what data would be needed to deduce the underlying mode(s) of resistance. To answer these questions, we propose a family of mathematical models, with each member of the family assuming a different timing and mechanism of resistance. We present a method for fitting these models to individual volumetric data, and utilize model selection and parameter sensitivity analyses to ask: which member(s) of the family of models best describes HNSCC response to cetuximab, and what does that tell us about the timing and mechanisms driving resistance? We find that along with time-course volumetric data to a single dose of cetuximab, the initial resistance fraction and, in some instances, dose escalation volumetric data are required to distinguish among the family of models and thereby infer the mechanisms of resistance. These findings can inform future experimental design so that we can best leverage the synergy of wet laboratory experimentation and mathematical modeling in the study of novel targeted cancer therapeutics.
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Affiliation(s)
- Santiago D Cárdenas
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, NJ, USA
| | - Constance J Reznik
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, NJ, USA.,Datacor, Inc., Florham Park, NJ, USA
| | - Ruchira Ranaweera
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Feifei Song
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Elana J Fertig
- Convergence Institute, Department of Oncology, Department of Biomedical Engineering, Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA.
| | - Jana L Gevertz
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, NJ, USA.
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41
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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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In Vitro Characterization of Renal Drug Transporter Activity in Kidney Cancer. Int J Mol Sci 2022; 23:ijms231710177. [PMID: 36077583 PMCID: PMC9456511 DOI: 10.3390/ijms231710177] [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: 08/10/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The activity of drug transporters is central to the secretory function of the kidneys and a defining feature of renal proximal tubule epithelial cells (RPTECs). The expression, regulation, and function of these membrane-bound proteins is well understood under normal renal physiological conditions. However, the impact of drug transporters on the pathophysiology of kidney cancer is still elusive. In the present study, we employed different renal cell carcinoma (RCC) cell lines and a prototypical non-malignant RPTEC cell line to characterize the activity, expression, and potential regulatory mechanisms of relevant renal drug transporters in RCC in vitro. An analysis of the uptake and efflux activity, the expression of drug transporters, and the evaluation of cisplatin cytotoxicity under the effects of methylation or epidermal growth factor receptor (EGFR) inhibition showed that the RCC cells retained substantial drug transport activity. In RCC cells, P-glycoprotein was localized in the nucleus and its pharmacological inhibition enhanced cisplatin toxicity in non-malignant RPTECs. On the other hand, methylation inhibition enhanced cisplatin toxicity by upregulating the organic cation uptake activity in RCC cells. Differential effects of methylation and EGFR were observed in transporter expression, showing regulatory heterogeneity in these cells. Interestingly, the non-malignant RPTEC cell line that was used lacked the machinery responsible for organic cation transport, which reiterates the functional losses that renal cells undergo in vitro.
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Achuthan S, Chatterjee R, Kotnala S, Mohanty A, Bhattacharya S, Salgia R, Kulkarni P. Leveraging deep learning algorithms for synthetic data generation to design and analyze biological networks. J Biosci 2022. [DOI: 10.1007/s12038-022-00278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Ní Leathlobhair M, Lenski RE. Population genetics of clonally transmissible cancers. Nat Ecol Evol 2022; 6:1077-1089. [PMID: 35879542 DOI: 10.1038/s41559-022-01790-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
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Affiliation(s)
- Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland.
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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45
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Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer. NPJ Syst Biol Appl 2022; 8:20. [PMID: 35715421 PMCID: PMC9206019 DOI: 10.1038/s41540-022-00230-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/25/2022] [Indexed: 02/01/2023] Open
Abstract
The molecular underpinnings of acquired resistance to carboplatin are poorly understood and often inconsistent between in vitro modeling studies. After sequential treatment cycles, multiple isogenic clones reached similar levels of resistance, but significant transcriptional heterogeneity. Gene-expression based virtual synchronization of 26,772 single cells from 2 treatment steps and 4 resistant clones was used to evaluate the activity of Hallmark gene sets in proliferative (P) and quiescent (Q) phases. Two behaviors were associated with resistance: (1) broad repression in the P phase observed in all clones in early resistant steps and (2) prevalent induction in Q phase observed in the late treatment step of one clone. Furthermore, the induction of IFNα response in P phase or Wnt-signaling in Q phase were observed in distinct resistant clones. These observations suggest a model of resistance hysteresis, where functional alterations of the P and Q phase states affect the dynamics of the successive transitions between drug exposure and recovery, and prompts for a precise monitoring of single-cell states to develop more effective schedules for, or combination of, chemotherapy treatments.
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GDF15 Is an Eribulin Response Biomarker also Required for Survival of DTP Breast Cancer Cells. Cancers (Basel) 2022; 14:cancers14102562. [PMID: 35626166 PMCID: PMC9139899 DOI: 10.3390/cancers14102562] [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: 04/15/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Drug tolerant persister (DTP) cells are a unique, small sub-population of cancer cells that maintain viability under anti-cancer cytotoxic treatments. These cells enter into a reversible drug-tolerant state, which is believed to be the root of tumor recurrence. Therefore, there is a great need to find novel ways to monitor and eliminate DTP cells. We have identified the secretion of GDF15 as a response biomarker of eribulin treatment, as well as a specific biomarker of DTP cells in breast cancer. GDF15 expression is low or absent in cells sensitive to eribulin, strongly upregulated during response to the drug, and then downregulated when stable resistance is ultimately established. We have also shown that GDF15 plays a direct role in the survival of DTP cells. Thus, targeting GDF15 could help eradicate DTP cells and block the onset of stable acquired resistance. Most importantly, our data suggest that the combination of eribulin plus a GDF15 neutralizing antibody might be beneficial in the treatment of breast cancer. Abstract Drug tolerant persister (DTP) cells enter into a reversible slow-cycling state after drug treatment. We performed proteomic characterization of the breast cancer (BC) DTP cell secretome after eribulin treatment. We showed that the growth differentiation factor 15 (GDF15) is a protein significantly over-secreted upon eribulin treatment. The biomarker potential of GDF15 was confirmed in 3D-cell culture models using BC cells lines and PDXs, as well as in a TNBC in vivo model. We also found that GDF15 is required for survival of DTP cells. Direct participation of GDF15 and its receptor GFRAL in eribulin-induction of DTPs was established by the enhanced cell killing of DTPs by eribulin seen under GDF15 and GFRAL loss of function assays. Finally, we showed that combination therapy of eribulin plus an anti-GDF15 antibody kills BC-DTP cells. Our results suggest that targeting GDF15 may help eradicate DTP cells and block the onset of acquired resistance.
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Gutierrez C, Vilas CK, Wu CJ, Al'Khafaji AM. Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer. Front Immunol 2022; 13:859032. [PMID: 35603167 PMCID: PMC9120583 DOI: 10.3389/fimmu.2022.859032] [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: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
The therapeutic landscape across many cancers has dramatically improved since the introduction of potent targeted agents and immunotherapy. Nonetheless, success of these approaches is too often challenged by the emergence of therapeutic resistance, fueled by intratumoral heterogeneity and the immense evolutionary capacity inherent to cancers. To date, therapeutic strategies have attempted to outpace the evolutionary tempo of cancer but frequently fail, resulting in lack of tumor response and/or relapse. This realization motivates the development of novel therapeutic approaches which constrain evolutionary capacity by reducing the degree of intratumoral heterogeneity prior to treatment. Systematic development of such approaches first requires the ability to comprehensively characterize heterogeneous populations over the course of a perturbation, such as cancer treatment. Within this context, recent advances in functionalized lineage tracing approaches now afford the opportunity to efficiently measure multimodal features of clones within a tumor at single cell resolution, enabling the linkage of these features to clonal fitness over the course of tumor progression and treatment. Collectively, these measurements provide insights into the dynamic and heterogeneous nature of tumors and can thus guide the design of homogenization strategies which aim to funnel heterogeneous cancer cells into known, targetable phenotypic states. We anticipate the development of homogenization therapeutic strategies to better allow for cancer eradication and improved clinical outcomes.
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Affiliation(s)
- Catherine Gutierrez
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Caroline K Vilas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, United States
| | - Catherine J Wu
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
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Saunus JM, De Luca XM, Northwood K, Raghavendra A, Hasson A, McCart Reed AE, Lim M, Lal S, Vargas AC, Kutasovic JR, Dalley AJ, Miranda M, Kalaw E, Kalita-de Croft P, Gresshoff I, Al-Ejeh F, Gee JMW, Ormandy C, Khanna KK, Beesley J, Chenevix-Trench G, Green AR, Rakha EA, Ellis IO, Nicolau DV, Simpson PT, Lakhani SR. Epigenome erosion and SOX10 drive neural crest phenotypic mimicry in triple-negative breast cancer. NPJ Breast Cancer 2022; 8:57. [PMID: 35501337 PMCID: PMC9061835 DOI: 10.1038/s41523-022-00425-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 04/05/2022] [Indexed: 12/20/2022] Open
Abstract
Intratumoral heterogeneity is caused by genomic instability and phenotypic plasticity, but how these features co-evolve remains unclear. SOX10 is a neural crest stem cell (NCSC) specifier and candidate mediator of phenotypic plasticity in cancer. We investigated its relevance in breast cancer by immunophenotyping 21 normal breast and 1860 tumour samples. Nuclear SOX10 was detected in normal mammary luminal progenitor cells, the histogenic origin of most TNBCs. In tumours, nuclear SOX10 was almost exclusive to TNBC, and predicted poorer outcome amongst cross-sectional (p = 0.0015, hazard ratio 2.02, n = 224) and metaplastic (p = 0.04, n = 66) cases. To understand SOX10’s influence over the transcriptome during the transition from normal to malignant states, we performed a systems-level analysis of co-expression data, de-noising the networks with an eigen-decomposition method. This identified a core module in SOX10’s normal mammary epithelial network that becomes rewired to NCSC genes in TNBC. Crucially, this reprogramming was proportional to genome-wide promoter methylation loss, particularly at lineage-specifying CpG-island shores. We propose that the progressive, genome-wide methylation loss in TNBC simulates more primitive epigenome architecture, making cells vulnerable to SOX10-driven reprogramming. This study demonstrates potential utility for SOX10 as a prognostic biomarker in TNBC and provides new insights about developmental phenotypic mimicry—a major contributor to intratumoral heterogeneity.
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49
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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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50
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Abstract
Drug resistance and metastasis—the major complications in cancer—both entail adaptation of cancer cells to stress, whether a drug or a lethal new environment. Intriguingly, these adaptive processes share similar features that cannot be explained by a pure Darwinian scheme, including dormancy, increased heterogeneity, and stress-induced plasticity. Here, we propose that learning theory offers a framework to explain these features and may shed light on these two intricate processes. In this framework, learning is performed at the single-cell level, by stress-driven exploratory trial-and-error. Such a process is not contingent on pre-existing pathways but on a random search for a state that diminishes the stress. We review underlying mechanisms that may support this search, and show by using a learning model that such exploratory learning is feasible in a high-dimensional system as the cell. At the population level, we view the tissue as a network of exploring agents that communicate, restraining cancer formation in health. In this view, disease results from the breakdown of homeostasis between cellular exploratory drive and tissue homeostasis.
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Affiliation(s)
- Aseel Shomar
- Department of Chemical Engineering, Israel Institute of Technology, Haifa 32000, Israel
- Network Biology Research Laboratory, Israel Institute of Technology, Haifa 32000, Israel
| | - Omri Barak
- Network Biology Research Laboratory, Israel Institute of Technology, Haifa 32000, Israel
- Rappaport Faculty of Medicine Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Naama Brenner
- Department of Chemical Engineering, Israel Institute of Technology, Haifa 32000, Israel
- Network Biology Research Laboratory, Israel Institute of Technology, Haifa 32000, Israel
- Corresponding author
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