1
|
Druzhkova I, Nikonova E, Ignatova N, Koryakina I, Zyuzin M, Mozherov A, Kozlov D, Krylov D, Kuznetsova D, Lisitsa U, Shcheslavskiy V, Shirshin EA, Zagaynova E, Shirmanova M. Effect of Collagen Matrix on Doxorubicin Distribution and Cancer Cells' Response to Treatment in 3D Tumor Model. Cancers (Basel) 2022; 14:cancers14225487. [PMID: 36428580 PMCID: PMC9688511 DOI: 10.3390/cancers14225487] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
The extracellular matrix (ECM) plays an important role in regulation of many aspects of tumor growth and response to therapies. However, the specifics of the interaction of chemotherapeutic agents with cancer cells in the presence of collagen, the major component of ECM, is still poorly investigated. In this study, we explored distribution of doxorubicin (DOX) and its effects on cancer cells' metabolism in the presence of collagen with different structures in 3D models. For this, a combination of second harmonic generation imaging of collagen and multiphoton fluorescence microscopy of DOX, and metabolic cofactor NAD(P)H was used. It was found that collagen slowed down the diffusion of DOX and thus decreased the cellular drug uptake. Besides nuclei, DOX also targeted mitochondria leading to inhibition of oxidative phosphorylation, which was more pronounced in the cells growing in the absence of collagen. As a result, the cells in collagen displayed better viability upon treatment with DOX. Taken together, our data illustrate that tumor collagen contributes to heterogeneous and sub-optimal response to DOX and highlight the challenges in improving drug delivery and efficacy.
Collapse
Affiliation(s)
- Irina Druzhkova
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
- Correspondence:
| | - Elena Nikonova
- Lomonosov Moscow State University, 119991 Moscow, Russia
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
| | - Nadezhda Ignatova
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| | - Irina Koryakina
- School of Physics and Engineering, ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia
| | - Mikhail Zyuzin
- School of Physics and Engineering, ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia
| | - Artem Mozherov
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| | - Dmitriy Kozlov
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| | - Dmitry Krylov
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| | - Daria Kuznetsova
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
- Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Uliyana Lisitsa
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| | - Vladislav Shcheslavskiy
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| | - Evgeny A. Shirshin
- Lomonosov Moscow State University, 119991 Moscow, Russia
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
| | - Elena Zagaynova
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
- Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Marina Shirmanova
- Research Institute of Experimental Oncology and Biotechnology, Privolzhsky Research Medical University, 603005 Nizhny Novgorod, Russia
| |
Collapse
|
2
|
Druzhkova I, Nikonova E, Ignatova N, Koryakina I, Zyuzin M, Mozherov A, Kozlov D, Krylov D, Kuznetsova D, Lisitsa U, Shcheslavskiy V, Shirshin EA, Zagaynova E, Shirmanova M. Effect of Collagen Matrix on Doxorubicin Distribution and Cancer Cells’ Response to Treatment in 3D Tumor Model. Cancers (Basel) 2022; 14:5487. [DOI: https:/doi.org/10.3390/cancers14225487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023] Open
Abstract
The extracellular matrix (ECM) plays an important role in regulation of many aspects of tumor growth and response to therapies. However, the specifics of the interaction of chemotherapeutic agents with cancer cells in the presence of collagen, the major component of ECM, is still poorly investigated. In this study, we explored distribution of doxorubicin (DOX) and its effects on cancer cells’ metabolism in the presence of collagen with different structures in 3D models. For this, a combination of second harmonic generation imaging of collagen and multiphoton fluorescence microscopy of DOX, and metabolic cofactor NAD(P)H was used. It was found that collagen slowed down the diffusion of DOX and thus decreased the cellular drug uptake. Besides nuclei, DOX also targeted mitochondria leading to inhibition of oxidative phosphorylation, which was more pronounced in the cells growing in the absence of collagen. As a result, the cells in collagen displayed better viability upon treatment with DOX. Taken together, our data illustrate that tumor collagen contributes to heterogeneous and sub-optimal response to DOX and highlight the challenges in improving drug delivery and efficacy.
Collapse
|
3
|
Dornfeld K, Bjork J, Folkert G, Skildum A, Wallace KB. Mitochondrial activities play a pivotal role in regulating cell cycle in response to doxorubicin. CELL CYCLE (GEORGETOWN, TEX.) 2021; 20:1067-1079. [PMID: 33978554 DOI: 10.1080/15384101.2021.1919839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Doxorubicin induces both DNA damage and metabolic interference. How these effects interact to modulate cellular toxicity is not completely understood but important given the widespread use of doxorubicin in cancer treatment. This study tests the hypothesis that cell cycle arrest and survival are affected by distinct mitochondrial activities during doxorubicin exposure.Parental and mutant S. cerevisiae strains deficient in selected genes with mitochondrial function were treated with doxorubicin and assayed for changes in proliferation rates, cell survival and cell cycle arrest kinetics. Mitochondrial DNA content was estimated using quantitative PCR. Mitochondrial function was assessed by measuring oxygen consumption with and without an uncoupler.Parental cells growing in a non-fermentable carbon source medium and mutants lacking mitochondria and grown in glucose medium both show abrupt cell cycle and proliferation arrest during doxorubicin exposure compared to parental cells grown in glucose. Mitochondrial DNA increases during doxorubicin exposure in S. cerevisiae and in human breast cancer cells. Yeast strains deficient in TCA cycle activity or electron transport both show more abrupt cell cycle arrest than parental cells when exposed to doxorubicin. Concurrent treatment with the mitochondrial uncoupler dinitrophenol facilitates cell cycle progression and proliferation during doxorubicin exposure.Doxorubicin exposure induces mitochondrial DNA synthesis with TCA cycle and oxidative phosphorylation activity having opposing effects on cell proliferation, survival and cell cycle kinetics. TCA cycle activity provides biosynthetic substrates to support cell cycle progression and cell proliferation while electron transport and oxidative phosphorylation facilitate cell cycle arrest and possibly increased cytotoxicity.
Collapse
Affiliation(s)
- Ken Dornfeld
- Department of Radiation Oncology, Essentia Health, Duluth, MN, USA.,Department of Biomedical Science, University of Minnesota Medical School, Duluth Campus, USA
| | - James Bjork
- Department of Biomedical Science, University of Minnesota Medical School, Duluth Campus, USA
| | - Gavin Folkert
- Department of Biomedical Science, University of Minnesota Medical School, Duluth Campus, USA
| | - Andrew Skildum
- Department of Biomedical Science, University of Minnesota Medical School, Duluth Campus, USA.,Masonic Cancer Center, University of Minnesota, USA
| | - Kendall B Wallace
- Department of Biomedical Science, University of Minnesota Medical School, Duluth Campus, USA.,Masonic Cancer Center, University of Minnesota, USA
| |
Collapse
|
4
|
Karabekmez ME, Taymaz-Nikerel H, Eraslan S, Kirdar B. Time-dependent re-organization of biological processes by the analysis of the dynamic transcriptional response of yeast cells to doxorubicin. Mol Omics 2021; 17:572-582. [PMID: 34095940 DOI: 10.1039/d1mo00046b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Doxorubicin is an efficient chemotherapeutic reagent in the treatment of a variety of cancers. However, its underlying molecular mechanism is not fully understood and several severe side effects limit its application. In this study, the dynamic transcriptomic response of Saccharomyces cerevisiae cells to a doxorubicin pulse in a chemostat system was investigated to reveal the underlying molecular mechanism of this drug. The clustering of differentially and significantly expressed genes (DEGs) indicated that the response of yeast cells to doxorubicin is time dependent and may be classified as short-term, mid-term and long-term responses. The cells have started to reorganize their response after the first minute following the injection of the pulse. A modified version of Weighted Gene Co-expression Network Analysis (WGCNA) was used to cluster the positively correlated co-expression profiles, and functional enrichment analysis of these clusters was carried out. DNA replication and DNA repair processes were significantly affected and induced 60 minutes after exposure to doxorubicin. The response to oxidative stress was not identified as a significant term. A transcriptional re-organization of the metabolic pathways seems to be an early event and persists afterwards. The present study reveals for the first time that the RNA surveillance pathway, which is a post-transcriptional regulatory pathway, may be implicated in the short-term reaction of yeast cells to doxorubicin. Integration with regulome revealed the dynamic re-organization of the transcriptomic landscape. Fhl1p, Mbp1p, and Mcm1p were identified as primary regulatory factors responsible for tuning the differentially expressed genes.
Collapse
Affiliation(s)
| | - Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, 34060 Eyup, Istanbul, Turkey
| | - Serpil Eraslan
- Koç University Hospital, Diagnosis Centre for Genetic Disorders, Topkapı, Istanbul, Turkey
| | - Betul Kirdar
- Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey.
| |
Collapse
|
5
|
Santos SM, Laflin S, Broadway A, Burnet C, Hartheimer J, Rodgers J, Smith DL, Hartman JL. High-resolution yeast quiescence profiling in human-like media reveals complex influences of auxotrophy and nutrient availability. GeroScience 2020; 43:941-964. [PMID: 33015753 PMCID: PMC8110628 DOI: 10.1007/s11357-020-00265-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
Yeast cells survive in stationary phase culture by entering quiescence, which is measured by colony-forming capacity upon nutrient re-exposure. Yeast chronological lifespan (CLS) studies, employing the comprehensive collection of gene knockout strains, have correlated weakly between independent laboratories, which is hypothesized to reflect differential interaction between the deleted genes, auxotrophy, media composition, and other assay conditions influencing quiescence. This hypothesis was investigated by high-throughput quiescence profiling of the parental prototrophic strain, from which the gene deletion strain libraries were constructed, and all possible auxotrophic allele combinations in that background. Defined media resembling human cell culture media promoted long-term quiescence and was used to assess effects of glucose, ammonium sulfate, auxotrophic nutrient availability, target of rapamycin signaling, and replication stress. Frequent, high-replicate measurements of colony-forming capacity from cultures aged past 60 days provided profiles of quiescence phenomena such as gasping and hormesis. Media acidification was assayed in parallel to assess correlation. Influences of leucine, methionine, glucose, and ammonium sulfate metabolism were clarified, and a role for lysine metabolism newly characterized, while histidine and uracil perturbations had less impact. Interactions occurred between glucose, ammonium sulfate, auxotrophy, auxotrophic nutrient limitation, aeration, TOR signaling, and/or replication stress. Weak correlation existed between media acidification and maintenance of quiescence. In summary, experimental factors, uncontrolled across previous genome-wide yeast CLS studies, influence quiescence and interact extensively, revealing quiescence as a complex metabolic and developmental process that should be studied in a prototrophic context, omitting ammonium sulfate from defined media, and employing highly replicable protocols.
Collapse
Affiliation(s)
- Sean M Santos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Samantha Laflin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Audrie Broadway
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cosby Burnet
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joline Hartheimer
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John Rodgers
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel L Smith
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John L Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| |
Collapse
|
6
|
A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. Genes (Basel) 2019; 10:genes10100770. [PMID: 31575041 PMCID: PMC6826991 DOI: 10.3390/genes10100770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug–gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct antitumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the Saccharomyces cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug–gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug–gene interaction specific to cytarabine was less enriched in gene ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-gene ontology (GO)-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast–human homologs with correlated differential gene expression and drug efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
Collapse
|