1
|
Wang M, Scott JG, Vladimirsky A. Threshold-awareness in adaptive cancer therapy. PLoS Comput Biol 2024; 20:e1012165. [PMID: 38875286 PMCID: PMC11210878 DOI: 10.1371/journal.pcbi.1012165] [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: 04/28/2023] [Revised: 06/27/2024] [Accepted: 05/09/2024] [Indexed: 06/16/2024] Open
Abstract
Although adaptive cancer therapy shows promise in integrating evolutionary dynamics into treatment scheduling, the stochastic nature of cancer evolution has seldom been taken into account. Various sources of random perturbations can impact the evolution of heterogeneous tumors, making performance metrics of any treatment policy random as well. In this paper, we propose an efficient method for selecting optimal adaptive treatment policies under randomly evolving tumor dynamics. The goal is to improve the cumulative "cost" of treatment, a combination of the total amount of drugs used and the total treatment time. As this cost also becomes random in any stochastic setting, we maximize the probability of reaching the treatment goals (tumor stabilization or eradication) without exceeding a pre-specified cost threshold (or a "budget"). We use a novel Stochastic Optimal Control formulation and Dynamic Programming to find such "threshold-aware" optimal treatment policies. Our approach enables an efficient algorithm to compute these policies for a range of threshold values simultaneously. Compared to treatment plans shown to be optimal in a deterministic setting, the new "threshold-aware" policies significantly improve the chances of the therapy succeeding under the budget, which is correlated with a lower general drug usage. We illustrate this method using two specific examples, but our approach is far more general and provides a new tool for optimizing adaptive therapies based on a broad range of stochastic cancer models.
Collapse
Affiliation(s)
- MingYi Wang
- Center for Applied Mathematics, Cornell University, Ithaca, New York, United States of America
| | - Jacob G. Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Alexander Vladimirsky
- Department of Mathematics and Center for Applied Mathematics, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
2
|
Kerek Á, Török B, Laczkó L, Somogyi Z, Kardos G, Bányai K, Kaszab E, Bali K, Jerzsele Á. In Vitro Microevolution and Co-Selection Assessment of Amoxicillin and Cefotaxime Impact on Escherichia coli Resistance Development. Antibiotics (Basel) 2024; 13:247. [PMID: 38534682 DOI: 10.3390/antibiotics13030247] [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: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
The global spread of antimicrobial resistance has become a prominent issue in both veterinary and public health in the 21st century. The extensive use of amoxicillin, a beta-lactam antibiotic, and consequent resistance development are particularly alarming in food-producing animals, with a focus on the swine and poultry sectors. Another beta-lactam, cefotaxime, is widely utilized in human medicine, where the escalating resistance to third- and fourth-generation cephalosporins is a major concern. The aim of this study was to simulate the development of phenotypic and genotypic resistance to beta-lactam antibiotics, focusing on amoxicillin and cefotaxime. The investigation of the minimal inhibitory concentrations (MIC) of antibiotics was performed at 1×, 10×, 100×, and 1000× concentrations using the modified microbial evolution and growth arena (MEGA-plate) method. Our results indicate that amoxicillin significantly increased the MIC values of several tested antibiotics, except for oxytetracycline and florfenicol. In the case of cefotaxime, this increase was observed in all classes. A total of 44 antimicrobial resistance genes were identified in all samples. Chromosomal point mutations, particularly concerning cefotaxime, revealed numerous complex mutations, deletions, insertions, and single nucleotide polymorphisms (SNPs) that were not experienced in the case of amoxicillin. The findings suggest that, regarding amoxicillin, the point mutation of the acrB gene could explain the observed MIC value increases due to the heightened activity of the acrAB-tolC efflux pump system. However, under the influence of cefotaxime, more intricate processes occurred, including complex amino acid substitutions in the ampC gene promoter region, increased enzyme production induced by amino acid substitutions and SNPs, as well as mutations in the acrR and robA repressor genes that heightened the activity of the acrAB-tolC efflux pump system. These changes may contribute to the significant MIC increases observed for all tested antibiotics. The results underscore the importance of understanding cross-resistance development between individual drugs when choosing clinical alternative drugs. The point mutations in the mdtB and emrR genes may also contribute to the increased activity of the mdtABC-tolC and emrAB-tolC pump systems against all tested antibiotics. The exceptionally high mutation rate induced by cephalosporins justifies further investigations to clarify the exact mechanism behind.
Collapse
Affiliation(s)
- Ádám Kerek
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
| | - Bence Török
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
| | - Levente Laczkó
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Zoltán Somogyi
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
| | - Gábor Kardos
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- National Public Health Center, Albert Flórián út 2-6, H-1097 Budapest, Hungary
- Department of Gerontology, Faculty of Health Sciences, University of Debrecen, Sóstói út 2-4, H-4400 Nyíregyháza, Hungary
| | - Krisztián Bányai
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary
| | - Eszter Kaszab
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary
| | - Krisztina Bali
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary
| | - Ákos Jerzsele
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
| |
Collapse
|
3
|
Crozier D, Gray JM, Maltas JA, Bonomo RA, Burke ZDC, Card KJ, Scott JG. The evolution of diverse antimicrobial responses in vancomycin-intermediate Staphylococcus aureus and its therapeutic implications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.30.569373. [PMID: 38077036 PMCID: PMC10705500 DOI: 10.1101/2023.11.30.569373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Staphylococcus aureus causes endocarditis, osteomyelitis, and bacteremia. Clinicians often prescribe vancomycin as an empiric therapy to account for methicillin-resistant S. aureus (MRSA) and narrow treatment based on culture susceptibility results. However, these results reflect a single time point before empiric treatment and represent a limited subset of the total bacterial population within the patient. Thus, while they may indicate that the infection is susceptible to a particular drug, this recommendation may no longer be accurate during therapy. Here, we addressed how antibiotic susceptibility changes over time by accounting for evolution. We evolved 18 methicillin-susceptible S. aureus (MSSA) populations under increasing vancomycin concentrations until they reached intermediate resistance levels. Sequencing revealed parallel mutations that affect cell membrane stress response and cell-wall biosynthesis. The populations exhibited repeated cross-resistance to daptomycin and varied responses to meropenem, gentamicin, and nafcillin. We accounted for this variability by deriving likelihood estimates that express a population's probability of exhibiting a drug response following vancomycin treatment. Our results suggest antistaphylococcal penicillins are preferable first-line treatments for MSSA infections but also highlight the inherent uncertainty that evolution poses to effective therapies. Infections may take varied evolutionary paths; therefore, considering evolution as a probabilistic process should inform our therapeutic choices.
Collapse
|
4
|
Baygin RC, Yilmaz KC, Acar A. Characterization of dabrafenib-induced drug insensitivity via cellular barcoding and collateral sensitivity to second-line therapeutics. Sci Rep 2024; 14:286. [PMID: 38167959 PMCID: PMC10762103 DOI: 10.1038/s41598-023-50443-3] [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: 05/14/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Drug insensitivity is arguably one of the biggest challenges in cancer therapeutics. Although effective therapeutic solutions in cancer are limited due to the emergence of drug insensitivity, exploiting evolutionary understanding in this context can provide potential second-line therapeutics sensitizing the drug insensitive populations. Targeted therapeutic agent dabrafenib is used to treat CRC patients with BRAF V600E genotype and insensitivity to dabrafenib is often observed. Understanding underlying clonal architecture of dabrafenib-induced drug insensitivity and identification of potential second-line therapeutics that could sensitize dabrafenib insensitive populations remain to be elucidated. For this purpose, we utilized cellular barcoding technology to decipher dabrafenib-induced clonal evolution in BRAF V600E mutant HT-29 cells. This approach revealed the detection of both pre-existing and de novo barcodes with increased frequencies as a result of dabrafenib insensitivity. Furthermore, our longitudinal monitoring of drug insensitivity based on barcode detection from floating DNA within used medium enabled to identify temporal dynamics of pre-existing and de novo barcodes in relation to dabrafenib insensitivity in HT-29 cells. Moreover, whole-exome sequencing analysis exhibited possible somatic CNVs and SNVs contributing to dabrafenib insensitivity in HT-29 cells. Last, collateral drug sensitivity testing demonstrated oxaliplatin and capecitabine, alone or in combination, as successful second-like therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells. Overall, our findings demonstrate clonal dynamics of dabrafenib-insensitivity in HT-29 cells. In addition, oxaliplatin and capecitabine, alone or in combination, were successful second-line therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells.
Collapse
Affiliation(s)
- Rana Can Baygin
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Kubra Celikbas Yilmaz
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey.
| |
Collapse
|
5
|
Lozano‐Huntelman NA, Bullivant A, Chacon‐Barahona J, Valencia A, Ida N, Zhou A, Kalhori P, Bello G, Xue C, Boyd S, Kremer C, Yeh PJ. The evolution of resistance to synergistic multi-drug combinations is more complex than evolving resistance to each individual drug component. Evol Appl 2023; 16:1901-1920. [PMID: 38143903 PMCID: PMC10739078 DOI: 10.1111/eva.13608] [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: 11/05/2021] [Revised: 06/26/2023] [Accepted: 10/04/2023] [Indexed: 12/26/2023] Open
Abstract
Multidrug antibiotic resistance is an urgent public health concern. Multiple strategies have been suggested to alleviate this problem, including the use of antibiotic combinations and cyclic therapies. We examine how adaptation to (1) combinations of drugs affects resistance to individual drugs, and to (2) individual drugs alters responses to drug combinations. To evaluate this, we evolved multiple strains of drug resistant Staphylococcus epidermidis in the lab. We show that evolving resistance to four highly synergistic combinations does not result in cross-resistance to all of their components. Likewise, prior resistance to one antibiotic in a combination does not guarantee survival when exposed to the combination. We also identify four 3-step and four 2-step treatments that inhibit bacterial growth and confer collateral sensitivity with each step, impeding the development of multidrug resistance. This study highlights the importance of considering higher-order drug combinations in sequential therapies and how antibiotic interactions can influence the evolutionary trajectory of bacterial populations.
Collapse
Affiliation(s)
| | - Austin Bullivant
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Jonathan Chacon‐Barahona
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Alondra Valencia
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Nick Ida
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - April Zhou
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Pooneh Kalhori
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Gladys Bello
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Carolyn Xue
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Sada Boyd
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Colin Kremer
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
| | - Pamela J. Yeh
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCaliforniaUSA
- Santa Fe InstituteSanta FeNew MexicoUSA
| |
Collapse
|
6
|
Mandt REK, Luth MR, Tye MA, Mazitschek R, Ottilie S, Winzeler EA, Lafuente-Monasterio MJ, Gamo FJ, Wirth DF, Lukens AK. Diverse evolutionary pathways challenge the use of collateral sensitivity as a strategy to suppress resistance. eLife 2023; 12:e85023. [PMID: 37737220 PMCID: PMC10695565 DOI: 10.7554/elife.85023] [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: 11/18/2022] [Accepted: 09/21/2023] [Indexed: 09/23/2023] Open
Abstract
Drug resistance remains a major obstacle to malaria control and eradication efforts, necessitating the development of novel therapeutic strategies to treat this disease. Drug combinations based on collateral sensitivity, wherein resistance to one drug causes increased sensitivity to the partner drug, have been proposed as an evolutionary strategy to suppress the emergence of resistance in pathogen populations. In this study, we explore collateral sensitivity between compounds targeting the Plasmodium dihydroorotate dehydrogenase (DHODH). We profiled the cross-resistance and collateral sensitivity phenotypes of several DHODH mutant lines to a diverse panel of DHODH inhibitors. We focus on one compound, TCMDC-125334, which was active against all mutant lines tested, including the DHODH C276Y line, which arose in selections with the clinical candidate DSM265. In six selections with TCMDC-125334, the most common mechanism of resistance to this compound was copy number variation of the dhodh locus, although we did identify one mutation, DHODH I263S, which conferred resistance to TCMDC-125334 but not DSM265. We found that selection of the DHODH C276Y mutant with TCMDC-125334 yielded additional genetic changes in the dhodh locus. These double mutant parasites exhibited decreased sensitivity to TCMDC-125334 and were highly resistant to DSM265. Finally, we tested whether collateral sensitivity could be exploited to suppress the emergence of resistance in the context of combination treatment by exposing wildtype parasites to both DSM265 and TCMDC-125334 simultaneously. This selected for parasites with a DHODH V532A mutation which were cross-resistant to both compounds and were as fit as the wildtype parent in vitro. The emergence of these cross-resistant, evolutionarily fit parasites highlights the mutational flexibility of the DHODH enzyme.
Collapse
Affiliation(s)
- Rebecca EK Mandt
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Madeline R Luth
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Mark A Tye
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
- Harvard Graduate School of Arts and SciencesCambridgeUnited States
| | - Ralph Mazitschek
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Center for Systems Biology, Massachusetts General HospitalBostonUnited States
| | - Sabine Ottilie
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Elizabeth A Winzeler
- Division of Host Pathogen Systems and Therapeutics, Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
- Skaggs School of Pharmaceutical Sciences, University of California, San DiegoLa JollaUnited States
| | | | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKlineMadridSpain
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Infectious Disease and Microbiome Program, The Broad InstituteCambridgeUnited States
| |
Collapse
|
7
|
Danisik N, Yilmaz KC, Acar A. Identification of collateral sensitivity and evolutionary landscape of chemotherapy-induced drug resistance using cellular barcoding technology. Front Pharmacol 2023; 14:1178489. [PMID: 37497108 PMCID: PMC10366361 DOI: 10.3389/fphar.2023.1178489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
Background: One of the most significant challenges impeding cancer treatment effectiveness is drug resistance. Combining evolutionary understanding with drug resistance can pave the way for the identification of second-line drug options that can overcome drug resistance. Although capecitabine and irinotecan are commonly used therapeutic agents in the treatment of CRC patients, resistance to these agents is common. The underlying clonal dynamics of resistance to these agents using high-resolution barcode technology and identification of effective second-line drugs in this context remain unclear. Methods and materials: Caco-2 and HT-29 cell lines were barcoded, and then capecitabine and irinotecan resistant derivatives of these cell lines were established. The frequencies of barcodes from resistant cell lines and harvested medium, longitudinally, were determined. Collateral drug sensitivity testing was carried out on resistant Caco-2 and HT-29 cell lines using single agents or drug combinations. The SyngeryFinder tool was used to analyse drug combination testing. Results: In Caco-2 and HT-29 cell lines, barcode frequency measurements revealed clonal dynamics of capecitabine and irinotecan formed by both pre-existing and de novo barcodes, indicating the presence of polyclonal drug resistance. The temporal dynamics of clonal evolution in Caco-2 and HT-29 cell lines were demonstrated by longitudinal analysis of pre-existing and de novo barcodes from harvested medium. In Caco-2 and HT-29 cell lines, collateral drug sensitivity revealed a number of drugs that were effective alone and in combination. Conclusion: The use of barcoding technology reveals the clonal dynamics of chemotherapy-induced drug resistance not only from harvested cell populations, but also from longitudinal sampling throughout the course of clonal evolution. Second-line drugs that sensitize drug-resistant CRC cell lines are identified through collateral drug testing.
Collapse
|
8
|
Corzo Parada L, Urueña C, Leal-García E, Barreto A, Ballesteros-Ramírez R, Rodríguez-Pardo V, Fiorentino S. Doxorubicin Activity Is Modulated by Traditional Herbal Extracts in a 2D and 3D Multicellular Sphere Model of Leukemia. Pharmaceutics 2023; 15:1690. [PMID: 37376139 DOI: 10.3390/pharmaceutics15061690] [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: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The modulation of the tumor microenvironment by natural products may play a significant role in the response of tumor cells to chemotherapy. In this study, we evaluated the effect of extracts derived from P2Et (Caesalpinia spinosa) and Anamú-SC (Petiveria alliacea) plants, previously studied by our group, on the viability and ROS levels in the K562 cell line (Pgp- and Pgp+), endothelial cells (ECs, Eahy.926 cell line) and mesenchymal stem cells (MSC) cultured in 2D and 3D. The results show that: (a) the two botanical extracts are selective on tumor cells compared to doxorubicin (DX), (b) cytotoxicity is independent of the modulation of intracellular ROS for plant extracts, unlike DX, (c) the interaction with DX can be influenced by chemical complexity and the expression of Pgp, (d) the 3D culture shows a greater sensitivity of the tumor cells to chemotherapy, in co-treatment with the extracts. In conclusion, the effect of the extracts on the viability of leukemia cells was modified in multicellular spheroids with MSC and EC, suggesting that the in vitro evaluation of these interactions can contribute to the comprehension of the pharmacodynamics of the botanical drugs.
Collapse
Affiliation(s)
- Laura Corzo Parada
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Claudia Urueña
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Efraín Leal-García
- Departamento de Ortopedia y Traumatología, Facultad de Medicina, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
| | - Alfonso Barreto
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Ricardo Ballesteros-Ramírez
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Viviana Rodríguez-Pardo
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Susana Fiorentino
- Grupo de Inmunobiología y Biología Celular, Science Faculty, Department of Microbiology, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
- Departamento de Ortopedia y Traumatología, Facultad de Medicina, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá 110231, Colombia
| |
Collapse
|
9
|
Scarborough JA, Eschrich SA, Torres-Roca J, Dhawan A, Scott JG. Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature. NPJ Precis Oncol 2023; 7:38. [PMID: 37076665 PMCID: PMC10115855 DOI: 10.1038/s41698-023-00375-y] [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: 09/30/2022] [Accepted: 03/21/2023] [Indexed: 04/21/2023] Open
Abstract
Precision medicine offers remarkable potential for the treatment of cancer, but is largely focused on tumors that harbor actionable mutations. Gene expression signatures can expand the scope of precision medicine by predicting response to traditional (cytotoxic) chemotherapy agents without relying on changes in mutational status. We present a new signature extraction method, inspired by the principle of convergent phenotypes, which states that tumors with disparate genetic backgrounds may evolve similar phenotypes independently. This evolutionary-informed method can be utilized to produce consensus signatures predictive of response to over 200 chemotherapeutic drugs found in the Genomics of Drug Sensitivity in Cancer (GDSC) Database. Here, we demonstrate its use by extracting the Cisplatin Response Signature (CisSig). We show that this signature can predict cisplatin response within carcinoma-based cell lines from the GDSC database, and expression of the signatures aligns with clinical trends seen in independent datasets of tumor samples from The Cancer Genome Atlas (TCGA) and Total Cancer Care (TCC) database. Finally, we demonstrate preliminary validation of CisSig for use in muscle-invasive bladder cancer, predicting overall survival in a small cohort of patients who undergo cisplatin-containing chemotherapy. This methodology can be used to produce robust signatures that, with further clinical validation, may be used for the prediction of traditional chemotherapeutic response, dramatically increasing the reach of personalized medicine in cancer.
Collapse
Affiliation(s)
- Jessica A Scarborough
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Steven A Eschrich
- Biostatistics and Bioinformatics Program, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Andrew Dhawan
- Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Jacob G Scott
- Systems Biology and Bioinformatics Department, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
| |
Collapse
|
10
|
Lin-Rahardja K, Weaver DT, Scarborough JA, Scott JG. Evolution-Informed Strategies for Combating Drug Resistance in Cancer. Int J Mol Sci 2023; 24:6738. [PMID: 37047714 PMCID: PMC10095117 DOI: 10.3390/ijms24076738] [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: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
The ever-changing nature of cancer poses the most difficult challenge oncologists face today. Cancer's remarkable adaptability has inspired many to work toward understanding the evolutionary dynamics that underlie this disease in hopes of learning new ways to fight it. Eco-evolutionary dynamics of a tumor are not accounted for in most standard treatment regimens, but exploiting them would help us combat treatment-resistant effectively. Here, we outline several notable efforts to exploit these dynamics and circumvent drug resistance in cancer.
Collapse
Affiliation(s)
- Kristi Lin-Rahardja
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Davis T. Weaver
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jessica A. Scarborough
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jacob G. Scott
- Systems Biology & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Translational Hematology & Oncology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44106, USA
| |
Collapse
|
11
|
Bassil CF, Anderson GR, Mayro B, Askin KN, Winter PS, Gruber S, Hall TM, Hoj JP, Cerda-Smith C, Hutchinson HM, Killarney ST, Singleton KR, Qin L, Jubien-Girard K, Favreau C, Martin AR, Robert G, Benhida R, Auberger P, Pendergast AM, Lonard DM, Puissant A, Wood KC. MCB-613 exploits a collateral sensitivity in drug resistant EGFR-mutant non-small cell lung cancer through covalent inhibition of KEAP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524094. [PMID: 36711936 PMCID: PMC9882253 DOI: 10.1101/2023.01.17.524094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Targeted therapies have revolutionized cancer chemotherapy. Unfortunately, most patients develop multifocal resistance to these drugs within a matter of months. Here, we used a high-throughput phenotypic small molecule screen to identify MCB-613 as a compound that selectively targets EGFR-mutant, EGFR inhibitor-resistant non-small cell lung cancer (NSCLC) cells harboring diverse resistance mechanisms. Subsequent proteomic and functional genomic screens involving MCB-613 identified its target in this context to be KEAP1, revealing that this gene is selectively essential in the setting of EGFR inhibitor resistance. In-depth molecular characterization demonstrated that (1) MCB-613 binds KEAP1 covalently; (2) a single molecule of MCB-613 is capable of bridging two KEAP1 monomers together; and, (3) this modification interferes with the degradation of canonical KEAP1 substrates such as NRF2. Surprisingly, NRF2 knockout sensitizes cells to MCB-613, suggesting that the drug functions through modulation of an alternative KEAP1 substrate. Together, these findings advance MCB-613 as a new tool for exploiting the selective essentiality of KEAP1 in drug-resistant, EGFR-mutant NSCLC cells.
Collapse
Affiliation(s)
| | - Gray R Anderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Benjamin Mayro
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Kayleigh N Askin
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Peter S Winter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Samuel Gruber
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Tierney M Hall
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Jacob P Hoj
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Haley M Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Shane T Killarney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Li Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Kévin Jubien-Girard
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
| | | | - Anthony R Martin
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
- IBMM, Université de Montpellier, ENSCM, CNRS, Montpellier, France
| | | | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR 7272 - 06108 Nice, France
- Chemical & Biochemical Sciences Green-Process Engineering (CBS) Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Benguerir, Morocco
| | | | | | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Alexandre Puissant
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Paris, France
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| |
Collapse
|
12
|
Silibinin Overcomes EMT-Driven Lung Cancer Resistance to New-Generation ALK Inhibitors. Cancers (Basel) 2022; 14:cancers14246101. [PMID: 36551587 PMCID: PMC9777025 DOI: 10.3390/cancers14246101] [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: 11/06/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) may drive the escape of ALK-rearranged non-small-cell lung cancer (NSCLC) tumors from ALK-tyrosine kinase inhibitors (TKIs). We investigated whether first-generation ALK-TKI therapy-induced EMT promotes cross-resistance to new-generation ALK-TKIs and whether this could be circumvented by the flavonolignan silibinin, an EMT inhibitor. ALK-rearranged NSCLC cells acquiring a bona fide EMT phenotype upon chronic exposure to the first-generation ALK-TKI crizotinib exhibited increased resistance to second-generation brigatinib and were fully refractory to third-generation lorlatinib. Such cross-resistance to new-generation ALK-TKIs, which was partially recapitulated upon chronic TGFβ stimulation, was less pronounced in ALK-rearranged NSCLC cells solely acquiring a partial/hybrid E/M transition state. Silibinin overcame EMT-induced resistance to brigatinib and lorlatinib and restored their efficacy involving the transforming growth factor-beta (TGFβ)/SMAD signaling pathway. Silibinin deactivated TGFβ-regulated SMAD2/3 phosphorylation and suppressed the transcriptional activation of genes under the control of SMAD binding elements. Computational modeling studies and kinase binding assays predicted a targeted inhibitory binding of silibinin to the ATP-binding pocket of TGFβ type-1 receptor 1 (TGFBR1) and TGFBR2 but solely at the two-digit micromolar range. A secretome profiling confirmed the ability of silibinin to normalize the augmented release of TGFβ into the extracellular fluid of ALK-TKIs-resistant NSCLC cells and reduce constitutive and inducible SMAD2/3 phosphorylation occurring in the presence of ALK-TKIs. In summary, the ab initio plasticity along the EMT spectrum may explain the propensity of ALK-rearranged NSCLC cells to acquire resistance to new-generation ALK-TKIs, a phenomenon that could be abrogated by the silibinin-driven attenuation of the TGFβ/SMAD signaling axis in mesenchymal ALK-rearranged NSCLC cells.
Collapse
|
13
|
Singh N, Romick-Rosendale L, Watanabe-Chailland M, Privette Vinnedge LM, Komurov K. Drug resistance mechanisms create targetable proteostatic vulnerabilities in Her2+ breast cancers. PLoS One 2022; 17:e0256788. [PMID: 36480552 PMCID: PMC9731458 DOI: 10.1371/journal.pone.0256788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
Oncogenic kinase inhibitors show short-lived responses in the clinic due to high rate of acquired resistance. We previously showed that pharmacologically exploiting oncogene-induced proteotoxic stress can be a viable alternative to oncogene-targeted therapy. Here, we performed extensive analyses of the transcriptomic, metabolomic and proteostatic perturbations during the course of treatment of Her2+ breast cancer cells with a Her2 inhibitor covering the drug response, resistance, relapse and drug withdrawal phases. We found that acute Her2 inhibition, in addition to blocking mitogenic signaling, leads to significant decline in the glucose uptake, and shutdown of glycolysis and of global protein synthesis. During prolonged therapy, compensatory overexpression of Her3 allows for the reactivation of mitogenic signaling pathways, but fails to re-engage the glucose uptake and glycolysis, resulting in proteotoxic ER stress, which maintains the protein synthesis block and growth inhibition. Her3-mediated cell proliferation under ER stress during prolonged Her2 inhibition is enabled due to the overexpression of the eIF2 phosphatase GADD34, which uncouples protein synthesis block from the ER stress response to allow for active cell growth. We show that this imbalance in the mitogenic and proteostatic signaling created during the acquired resistance to anti-Her2 therapy imposes a specific vulnerability to the inhibition of the endoplasmic reticulum quality control machinery. The latter is more pronounced in the drug withdrawal phase, where the de-inhibition of Her2 creates an acute surge in the downstream signaling pathways and exacerbates the proteostatic imbalance. Therefore, the acquired resistance mechanisms to oncogenic kinase inhibitors may create secondary vulnerabilities that could be exploited in the clinic.
Collapse
Affiliation(s)
- Navneet Singh
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Lindsey Romick-Rosendale
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Miki Watanabe-Chailland
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Lisa M. Privette Vinnedge
- Division of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Kakajan Komurov
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
| |
Collapse
|
14
|
Loria R, Vici P, Di Lisa FS, Soddu S, Maugeri-Saccà M, Bon G. Cross-Resistance Among Sequential Cancer Therapeutics: An Emerging Issue. Front Oncol 2022; 12:877380. [PMID: 35814399 PMCID: PMC9259985 DOI: 10.3389/fonc.2022.877380] [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: 02/16/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Over the past two decades, cancer treatment has benefited from having a significant increase in the number of targeted drugs approved by the United States Food and Drug Administration. With the introduction of targeted therapy, a great shift towards a new era has taken place that is characterized by reduced cytotoxicity and improved clinical outcomes compared to traditional chemotherapeutic drugs. At present, targeted therapies and other systemic anti-cancer therapies available (immunotherapy, cytotoxic, endocrine therapies and others) are used alone or in combination in different settings (neoadjuvant, adjuvant, and metastatic). As a result, it is not uncommon for patients affected by an advanced malignancy to receive subsequent anti-cancer therapies. In this challenging complexity of cancer treatment, the clinical pathways of real-life patients are often not as direct as predicted by standard guidelines and clinical trials, and cross-resistance among sequential anti-cancer therapies represents an emerging issue. In this review, we summarize the main cross-resistance events described in the diverse tumor types and provide insight into the molecular mechanisms involved in this process. We also discuss the current challenges and provide perspectives for the research and development of strategies to overcome cross-resistance and proceed towards a personalized approach.
Collapse
Affiliation(s)
- Rossella Loria
- Cellular Network and Molecular Therapeutic Target Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Patrizia Vici
- Unit of Phase IV Trials, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesca Sofia Di Lisa
- Unit of Phase IV Trials, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- Medical Oncology A, Department of Radiological, Oncological, and Anatomo-Pathological Sciences, Umberto I University Hospital, University Sapienza, Rome, Italy
| | - Silvia Soddu
- Cellular Network and Molecular Therapeutic Target Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Marcello Maugeri-Saccà
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Bon
- Cellular Network and Molecular Therapeutic Target Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- *Correspondence: Giulia Bon,
| |
Collapse
|
15
|
Dalin S, Grauman-Boss B, Lauffenburger DA, Hemann MT. Collateral responses to classical cytotoxic chemotherapies are heterogeneous and sensitivities are sparse. Sci Rep 2022; 12:5453. [PMID: 35361803 PMCID: PMC8971507 DOI: 10.1038/s41598-022-09319-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/14/2022] [Indexed: 11/09/2022] Open
Abstract
Chemotherapy resistance is a major obstacle to curing cancer patients. Combination drug regimens have shown promise as a method to overcome resistance; however, to date only some cancers have been cured with this method. Collateral sensitivity-the phenomenon whereby resistance to one drug is co-occurrent with sensitivity to a second drug-has been gaining traction as a promising new concept to guide rational design of combination regimens. Here we evolved over 100 subclones of the Eµ-Myc; p19ARF-/- cell line to be resistant to one of four classical chemotherapy agents: doxorubicin, vincristine, paclitaxel, and cisplatin. We then surveyed collateral responses to acquisition of resistance to these agents. Although numerous collateral sensitivities have been documented for antibiotics and targeted cancer therapies, we observed only one collateral sensitivity: half of cell lines that acquired resistance to paclitaxel also acquired a collateral sensitivity to verapamil. However, we found that the mechanism of this collateral sensitivity was unrelated to the mechanism of paclitaxel resistance. Interestingly, we observed heterogeneity in the phenotypic response to acquisition of resistance to most of the drugs we tested, most notably for paclitaxel, suggesting the existence of multiple different states of resistance. Surprisingly, this phenotypic heterogeneity in paclitaxel resistant cell lines was unrelated to transcriptomic heterogeneity among those cell lines. These features of phenotypic and transcriptomic heterogeneity must be taken into account in future studies of treated tumor subclones and in design of chemotherapy combinations.
Collapse
Affiliation(s)
- Simona Dalin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Beatrice Grauman-Boss
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Douglas A Lauffenburger
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Room: 16-343, Cambridge, MA, 02139, USA.
| | - Michael T Hemann
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
16
|
Howard GR, Jost TA, Yankeelov TE, Brock A. Quantification of long-term doxorubicin response dynamics in breast cancer cell lines to direct treatment schedules. PLoS Comput Biol 2022; 18:e1009104. [PMID: 35358172 PMCID: PMC9004764 DOI: 10.1371/journal.pcbi.1009104] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 04/12/2022] [Accepted: 02/07/2022] [Indexed: 01/05/2023] Open
Abstract
While acquired chemoresistance is recognized as a key challenge to treating many types of cancer, the dynamics with which drug sensitivity changes after exposure are poorly characterized. Most chemotherapeutic regimens call for repeated dosing at regular intervals, and if drug sensitivity changes on a similar time scale then the treatment interval could be optimized to improve treatment performance. Theoretical work suggests that such optimal schedules exist, but experimental confirmation has been obstructed by the difficulty of deconvolving the simultaneous processes of death, adaptation, and regrowth taking place in cancer cell populations. Here we present a method of optimizing drug schedules in vitro through iterative application of experimentally calibrated models, and demonstrate its ability to characterize dynamic changes in sensitivity to the chemotherapeutic doxorubicin in three breast cancer cell lines subjected to treatment schedules varying in concentration, interval between pulse treatments, and number of sequential pulse treatments. Cell populations are monitored longitudinally through automated imaging for 600–800 hours, and this data is used to calibrate a family of cancer growth models, each consisting of a system of ordinary differential equations, derived from the bi-exponential model which characterizes resistant and sensitive subpopulations. We identify a model incorporating both a period of growth arrest in surviving cells and a delay in the death of chemosensitive cells which outperforms the original bi-exponential growth model in Akaike Information Criterion based model selection, and use the calibrated model to quantify the performance of each drug schedule. We find that the inter-treatment interval is a key variable in determining the performance of sequential dosing schedules and identify an optimal retreatment time for each cell line which extends regrowth time by 40%-239%, demonstrating that the time scale of changes in chemosensitivity following doxorubicin exposure allows optimization of drug scheduling by varying this inter-treatment interval. Acquired chemoresistance is a common cause of treatment failure in cancer. The scheduling of a multi-dose course of chemotherapeutic treatment may influence the dynamics of acquired chemoresistance, and drug schedule optimization may increase the duration of effectiveness of a particular chemotherapeutic agent for a particular patient. Here we present a method for experimentally optimizing an in vitro drug schedule through iterative rounds of experimentation and computational analysis, and demonstrate the method’s ability to improve the performance of doxorubicin treatment in three breast carcinoma cell lines. Specifically, we find that the interval between drug exposures can be optimized while holding drug concentration and number of treatments constant, suggesting that this may be a key variable to explore in future drug schedule optimization efforts. We further use this method’s model calibration and selection process to extract information about the underlying biology of the doxorubicin response, and find that the incorporation of delays on both cell death and regrowth are necessary for accurate parameterization of cell growth data.
Collapse
Affiliation(s)
- Grant R. Howard
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Tyler A. Jost
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
| | - Thomas E. Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Oncology, The University of Texas at Austin, Austin, Texas, United States of America
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas, United States of America
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
| |
Collapse
|
17
|
Yin Q, Li P, Wang P, Zhang Z, Liu Q, Sun Z, Li W, Ma L, Wang X. Alectinib Together with Intracranial Therapies Improved Survival Outcomes in Untreated ALK-Positive Patients with Non-Small-Cell Lung Cancer and Symptomatic and Synchronic Brain Metastases: A Retrospective Study. Onco Targets Ther 2022; 14:5533-5542. [PMID: 35002258 PMCID: PMC8722687 DOI: 10.2147/ott.s345439] [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: 10/20/2021] [Accepted: 12/17/2021] [Indexed: 12/23/2022] Open
Abstract
Purpose The performance of alectinib and crizotinib in untreated anaplastic lymphoma kinase (ALK)-positive patients with non-small-cell lung cancer (NSCLC) and symptomatic and synchronic brain metastases is largely unknown. This retrospective study assessed the effectiveness of alectinib and crizotinib, together with intracranial therapies in a cohort of these patients. Patients and Methods This study included 34 previously untreated ALK-positive NSCLC patients with three or fewer intracranial metastases. Of these patients, 13 received oral alectinib 600 mg twice daily, and 21 received oral crizotinib 250 mg twice daily, until progressive disease, unacceptable toxicity, or death. All intracranial metastases were treated with craniotomy, CyberKnife, or both. Results Median overall progression-free survival (PFS) was 32.8 months (95% CI 24.4–41.2 months) in patients treated with alectinib and 8.0 months (95% CI 7.3–8.7 months) in patients treated with crizotinib. Median PFS of brain lesions was not yet reached with alectinib (95% CI 30.1 months–not estimated) and was 8.5 months (95% CI 7.2–12.3 months) with crizotinib. Median PFS of lung lesions was 38.5 months (95% CI 27.5–49.5 months) with alectinib and 9.2 months (95% CI 7.4–11.0 months) with crizotinib. Median overall survival was not yet reached with alectinib (95% CI 31.0 months–not estimated) and 30.3 months (95% CI 27.3–37.1 months) with crizotinib. Conclusion Compared with crizotinib, alectinib showed superior efficacy and lower toxicity in the treatment of ALK-positive patients with NSCLC and symptomatic and synchronic brain metastases. The inclusion of intracranial therapies such as craniotomy or CyberKnife further improved the brain PFS and overall survival of these patients.
Collapse
Affiliation(s)
- Qiang Yin
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Peng Li
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Peng Wang
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Zhen Zhang
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Qun Liu
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Zengfeng Sun
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Wenliang Li
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Li Ma
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Xiaoguang Wang
- Department of Neurosurgery, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| |
Collapse
|
18
|
AIM and Evolutionary Theory. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
19
|
Weaver DT, Pishas KI, Williamson D, Scarborough J, Lessnick SL, Dhawan A, Scott JG. Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma. PLoS Comput Biol 2021; 17:e1008755. [PMID: 34662337 PMCID: PMC8601628 DOI: 10.1371/journal.pcbi.1008755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 11/18/2021] [Accepted: 09/20/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNA (miRNA)-based therapies are an emerging class of targeted therapeutics with many potential applications. Ewing Sarcoma patients could benefit dramatically from personalized miRNA therapy due to inter-patient heterogeneity and a lack of druggable (to this point) targets. However, because of the broad effects miRNAs may have on different cells and tissues, trials of miRNA therapies have struggled due to severe toxicity and unanticipated immune response. In order to overcome this hurdle, a network science-based approach is well-equipped to evaluate and identify miRNA candidates and combinations of candidates for the repression of key oncogenic targets while avoiding repression of essential housekeeping genes. We first characterized 6 Ewing sarcoma cell lines using mRNA sequencing. We then estimated a measure of tumor state, which we term network potential, based on both the mRNA gene expression and the underlying protein-protein interaction network in the tumor. Next, we ranked mRNA targets based on their contribution to network potential. We then identified miRNAs and combinations of miRNAs that preferentially act to repress mRNA targets with the greatest influence on network potential. Our analysis identified TRIM25, APP, ELAV1, RNF4, and HNRNPL as ideal mRNA targets for Ewing sarcoma therapy. Using predicted miRNA-mRNA target mappings, we identified miR-3613-3p, let-7a-3p, miR-300, miR-424-5p, and let-7b-3p as candidate optimal miRNAs for preferential repression of these targets. Ultimately, our work, as exemplified in the case of Ewing sarcoma, describes a novel pipeline by which personalized miRNA cocktails can be designed to maximally perturb gene networks contributing to cancer progression.
Collapse
Affiliation(s)
- Davis T. Weaver
- Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio, United States of America
| | | | - Drew Williamson
- Department of Pathology, Brigham & Women’s Hospital, Boston, Massachusetts, United States of America
| | - Jessica Scarborough
- Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio, United States of America
| | | | - Andrew Dhawan
- Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio, United States of America
- Division of Neurology, Cleveland Clinic, Cleveland, Ohio, United States of America
- * E-mail: (AD); (JGS)
| | - Jacob G. Scott
- Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Translational Hematology Oncology Research, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Physics, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (AD); (JGS)
| |
Collapse
|
20
|
Yoon N, Krishnan N, Scott J. Theoretical modeling of collaterally sensitive drug cycles: shaping heterogeneity to allow adaptive therapy. J Math Biol 2021; 83:47. [PMID: 34632539 DOI: 10.1007/s00285-021-01671-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 07/15/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022]
Abstract
In previous work, we focused on the optimal therapeutic strategy with a pair of drugs which are collaterally sensitive to each other, that is, a situation in which evolution of resistance to one drug induces sensitivity to the other, and vice versa. Yoona (Bull Math Biol 8:1-34,Yoon et al. 2018) Here, we have extended this exploration to the optimal strategy with a collaterally sensitive drug sequence of an arbitrary length, N. To explore this, we have developed a dynamical model of sequential drug therapies with N drugs. In this model, tumor cells are classified as one of N subpopulations represented as [Formula: see text]. Each subpopulation, [Formula: see text], is resistant to '[Formula: see text]' and each subpopulation, [Formula: see text] (or [Formula: see text], if [Formula: see text]), is sensitive to it, so that [Formula: see text] increases under '[Formula: see text]' as it is resistant to it, and after drug-switching, decreases under '[Formula: see text]' as it is sensitive to that drug(s). Similar to our previous work examining optimal therapy with two drugs, we found that there is an initial period of time in which the tumor is 'shaped' into a specific makeup of each subpopulation, at which time all the drugs are equally effective ([Formula: see text]). After this shaping period, all the drugs are quickly switched with duration relative to their efficacy in order to maintain each subpopulation, consistent with the ideas underlying adaptive therapy. West(Canver Res 80(7):578-589Gatenby et al. 2009) and Gatenby (Cancer Res 67(11):4894-4903West et al. 2020). Additionally, we have developed methodologies to administer the optimal regimen under clinical or experimental situations in which no drug parameters and limited information of trackable populations data (all the subpopulations or only total population) are known. The therapy simulation based on these methodologies showed consistency with the theoretical effect of optimal therapy .
Collapse
Affiliation(s)
- Nara Yoon
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Department of Mathematics and Computer Science, Adelphi University, Garden City, NY, USA
| | - Nikhil Krishnan
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA.
| |
Collapse
|
21
|
Anderson PM, Scott J, Parsai S, Zahler S, Worley S, Shrikanthan S, Subbiah V, Murphy E. 223-Radium for metastatic osteosarcoma: combination therapy with other agents and external beam radiotherapy. ESMO Open 2021; 5:S2059-7029(20)30059-4. [PMID: 32303572 PMCID: PMC7199915 DOI: 10.1136/esmoopen-2019-000635] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/31/2022] Open
Abstract
Background Bone-seeking radiopharmaceuticals can deposit radiation selectively to some osteosarcoma tumours because of the bone-forming nature of this cancer. Objectives This is the first report of using 223-radium, an alpha-emitting calcium analogue with a high therapeutic index, in combination therapy with other agents in 15 patients with metastatic osteoblastic osteosarcoma. Methods Candidates for alpha-radiotherapy if 99mTc-MDP bone scan had avid bone-forming lesions and no therapy of higher priority (eg, definitive surgery). Monthly 223-radium infusions (1.49 μCi/kg or 55.13 kBq/kg) were given. Results The median infusion number was three and the average time to progression was 4.3 months for this cohort receiving 223-radium+other agents. Agents provided during 223-radium included (1) drugs to reduce skeletal complications: monthly denosumab (n=13) or zolendronate (n=1); (2) agents with antivascular endothelial growth factor activity, pazopanib (n=8) or sorafenib (n=1), (3) alkylating agents: oral cyclophosphamide (n=1) or ifosfamide, given as a 14-day continuous infusion (n=1, two cycles), (4) high-dose methotrexate (n=1), pegylated liposomal doxorubicin (n=1); and (5) two other combinations: nivolumab and everolimus (n=1) and rapamycin and auranofin (n=1). Radiation therapy, including stereotactic body radiotherapy (SBRT), was also given to 11 patients concurrently with 223-radium (n=2), after 223-radium completion (n=3), or both concurrently and then sequentially for other sites (n=6). After 223-radium infusions, patients without RT had a median overall survival of 4.3 months compared with those with SBRT and/or RT, who had a median overall survival of 13.5 months. Conclusion Although only 1/15 of patients with osteoblastic osteosarcoma still remain alive after 223-radium, overall survival
Collapse
Affiliation(s)
- Pete M Anderson
- Pediatric Hematology/Oncology/BMT, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jacob Scott
- Radiation Oncology and Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shireen Parsai
- Radiation Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stacey Zahler
- Pediatric Hematology/Oncology and BMT, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sarah Worley
- Quantative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | | | | | - Erin Murphy
- Radiation Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| |
Collapse
|
22
|
Chemotherapy confers a conserved secondary tolerance to EGFR inhibition via AXL-mediated signaling bypass. Sci Rep 2021; 11:8016. [PMID: 33850249 PMCID: PMC8044124 DOI: 10.1038/s41598-021-87599-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/31/2021] [Indexed: 02/01/2023] Open
Abstract
Drug resistance remains the major culprit of therapy failure in disseminated cancers. Simultaneous resistance to multiple, chemically different drugs feeds this failure resulting in cancer relapse. Here, we investigate co-resistance signatures shared between antimitotic drugs (AMDs) and inhibitors of receptor tyrosine kinases (RTKs) to probe mechanisms of secondary resistance. We map co-resistance ranks in multiple drug pairs and identified a more widespread occurrence of co-resistance to the EGFR-tyrosine kinase inhibitor (TKI) gefitinib in hundreds of cancer cell lines resistant to at least 11 AMDs. By surveying different parameters of genomic alterations, we find that the two RTKs EGFR and AXL displayed similar alteration and expression signatures. Using acquired paclitaxel and epothilone B resistance as first-line AMD failure models, we show that a stable collateral resistance to gefitinib can be relayed by entering a dynamic, drug-tolerant persister state where AXL acts as bypass signal. Delayed AXL degradation rendered this persistence to become stably resistant. We probed this degradation process using a new EGFR-TKI candidate YD and demonstrated that AXL bypass-driven collateral resistance can be suppressed pharmacologically. The findings emphasize that AXL bypass track is employed by chemoresistant cancer cells upon EGFR inhibition to enter a persister state and evolve resistance to EGFR-TKIs.
Collapse
|
23
|
The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics. PLoS Comput Biol 2021; 17:e1008702. [PMID: 33577569 PMCID: PMC7906468 DOI: 10.1371/journal.pcbi.1008702] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 02/25/2021] [Accepted: 01/14/2021] [Indexed: 11/19/2022] Open
Abstract
Intratumour heterogeneity is increasingly recognized as a frequent problem for cancer treatment as it allows for the evolution of resistance against treatment. While cancer genotyping becomes more and more established and allows to determine the genetic heterogeneity, less is known about the phenotypic heterogeneity among cancer cells. We investigate how phenotypic differences can impact the efficiency of therapy options that select on this diversity, compared to therapy options that are independent of the phenotype. We employ the ecological concept of trait distributions and characterize the cancer cell population as a collection of subpopulations that differ in their growth rate. We show in a deterministic model that growth rate-dependent treatment types alter the trait distribution of the cell population, resulting in a delayed relapse compared to a growth rate-independent treatment. Whether the cancer cell population goes extinct or relapse occurs is determined by stochastic dynamics, which we investigate using a stochastic model. Again, we find that relapse is delayed for the growth rate-dependent treatment type, albeit an increased relapse probability, suggesting that slowly growing subpopulations are shielded from extinction. Sequential application of growth rate-dependent and growth rate-independent treatment types can largely increase treatment efficiency and delay relapse. Interestingly, even longer intervals between decisions to change the treatment type may achieve close-to-optimal efficiencies and relapse times. Monitoring patients at regular check-ups may thus provide the temporally resolved guidance to tailor treatments to the changing cancer cell trait distribution and allow clinicians to cope with this dynamic heterogeneity. The individual cells within a cancer cell population are not all equal. The heterogeneity among them can strongly affect disease progression and treatment success. Recent diagnostic advances allow measuring how the characteristics of this heterogeneity change over time. To match these advances, we developed deterministic and stochastic trait-based models that capture important characteristics of the intratumour heterogeneity and allow to evaluate different treatment types that either do or do not interact with this heterogeneity. We focus on growth rate as the decisive characteristic of the intratumour heterogeneity. We find that by shifting the trait distribution of the cancer cell population, the growth rate-dependent treatment delays an eventual relapse compared to the growth rate-independent treatment. As a downside, however, we observe a refuge effect where slower-growing subpopulations are less affected by the growth rate-dependent treatment, which may decrease the likelihood of successful therapy. We find that navigating along this trade-off may be achieved by sequentially combining both treatment types, which agrees qualitatively with current clinical practice. Interestingly, even rather large intervals between treatment changes allow for close-to-optimal treatment results, which again hints towards a practical applicability.
Collapse
|
24
|
Araujo A, Cook LM, Frieling JS, Tan W, Copland JA, Kohli M, Gupta S, Dhillon J, Pow-Sang J, Lynch CC, Basanta D. Quantification and Optimization of Standard-of-Care Therapy to Delay the Emergence of Resistant Bone Metastatic Prostate Cancer. Cancers (Basel) 2021; 13:677. [PMID: 33567529 PMCID: PMC7915310 DOI: 10.3390/cancers13040677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Bone metastatic prostate cancer (BMPCa), despite the initial responsiveness to androgen deprivation therapy (ADT), inevitably becomes resistant. Recent clinical trials with upfront treatment of ADT combined with chemotherapy or novel hormonal therapies (NHTs) have extended overall patient survival. These results indicate that there is significant potential for the optimization of standard-of-care therapies to delay the emergence of progressive metastatic disease. METHODS Here, we used data extracted from human bone metastatic biopsies pre- and post-abiraterone acetate/prednisone to generate a mathematical model of bone metastatic prostate cancer that can unravel the treatment impact on disease progression. Intra-tumor heterogeneity in regard to ADT and chemotherapy resistance was derived from biopsy data at a cellular level, permitting the model to track the dynamics of resistant phenotypes in response to treatment from biological first-principles without relying on data fitting. These cellular data were mathematically correlated with a clinical proxy for tumor burden, utilizing prostate-specific antigen (PSA) production as an example. RESULTS Using this correlation, our model recapitulated the individual patient response to applied treatments in a separate and independent cohort of patients (n = 24), and was able to estimate the initial resistance to the ADT of each patient. Combined with an intervention-decision algorithm informed by patient-specific prediction of initial resistance, we propose to optimize the sequence of treatments for each patient with the goal of delaying the evolution of resistant disease and limit cancer cell growth, offering evidence for an improvement against retrospective data. CONCLUSIONS Our results show how minimal but widely available patient information can be used to model and track the progression of BMPCa in real time, offering a clinically relevant insight into the patient-specific evolutionary dynamics of the disease and suggesting new therapeutic options for intervention. TRIAL REGISTRATION NCT # 01953640. FUNDING Funded by an NCI U01 (NCI) U01CA202958-01 and a Moffitt Team Science Award. CCL and DB were partly funded by an NCI PSON U01 (U01CA244101). AA was partly funded by a Department of Defense Prostate Cancer Research Program (W81XWH-15-1-0184) fellowship. LC was partly funded by a postdoctoral fellowship (PF-13-175-01-CSM) from the American Cancer Society.
Collapse
Affiliation(s)
- Arturo Araujo
- Integrated Mathematical Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
- School of Arts, University of Roehampton, London SW15 5PU, UK
- Department of Computer Science, University College London, London WC1E 6BT, UK
| | - Leah M. Cook
- Fred & Pamela Buffett Cancer Center, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Jeremy S. Frieling
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
| | - Winston Tan
- Department of Medical Oncology Mayo Clinic, Jacksonville, FL 32224, USA;
| | | | - Manish Kohli
- Division of Medical Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84122, USA;
| | - Shilpa Gupta
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Jasreman Dhillon
- Genitourinary Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (J.D.); (J.P.-S.)
| | - Julio Pow-Sang
- Genitourinary Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (J.D.); (J.P.-S.)
| | - Conor C. Lynch
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
- Genitourinary Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (J.D.); (J.P.-S.)
| | - David Basanta
- Integrated Mathematical Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
- Genitourinary Oncology Department, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (J.D.); (J.P.-S.)
| |
Collapse
|
25
|
AIM and Evolutionary Theory. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_41-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
26
|
Maltas J, McNally DM, Wood KB. Evolution in alternating environments with tunable interlandscape correlations. Evolution 2021; 75:10-24. [PMID: 33206376 PMCID: PMC8246403 DOI: 10.1111/evo.14121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 10/15/2020] [Indexed: 11/29/2022]
Abstract
Natural populations are often exposed to temporally varying environments. Evolutionary dynamics in varying environments have been extensively studied, although understanding the effects of varying selection pressures remains challenging. Here, we investigate how cycling between a pair of statistically related fitness landscapes affects the evolved fitness of an asexually reproducing population. We construct pairs of fitness landscapes that share global fitness features but are correlated with one another in a tunable way, resulting in landscape pairs with specific correlations. We find that switching between these landscape pairs, depending on the ruggedness of the landscape and the interlandscape correlation, can either increase or decrease steady-state fitness relative to evolution in single environments. In addition, we show that switching between rugged landscapes often selects for increased fitness in both landscapes, even in situations where the landscapes themselves are anticorrelated. We demonstrate that positively correlated landscapes often possess a shared maximum in both landscapes that allows the population to step through sub-optimal local fitness maxima that often trap single landscape evolution trajectories. Finally, we demonstrate that switching between anticorrelated paired landscapes leads to ergodic-like dynamics where each genotype is populated with nonzero probability, dramatically lowering the steady-state fitness in comparison to single landscape evolution.
Collapse
Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | | | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
- Department of Physics, University of Michigan, Ann Arbor, MI 4810
| |
Collapse
|
27
|
Cunningham J, Thuijsman F, Peeters R, Viossat Y, Brown J, Gatenby R, Staňková K. Optimal control to reach eco-evolutionary stability in metastatic castrate-resistant prostate cancer. PLoS One 2020; 15:e0243386. [PMID: 33290430 PMCID: PMC7723267 DOI: 10.1371/journal.pone.0243386] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/19/2020] [Indexed: 12/16/2022] Open
Abstract
In the absence of curative therapies, treatment of metastatic castrate-resistant prostate cancer (mCRPC) using currently available drugs can be improved by integrating evolutionary principles that govern proliferation of resistant subpopulations into current treatment protocols. Here we develop what is coined as an 'evolutionary stable therapy', within the context of the mathematical model that has been used to inform the first adaptive therapy clinical trial of mCRPC. The objective of this therapy is to maintain a stable polymorphic tumor heterogeneity of sensitive and resistant cells to therapy in order to prolong treatment efficacy and progression free survival. Optimal control analysis shows that an increasing dose titration protocol, a very common clinical dosing process, can achieve tumor stabilization for a wide range of potential initial tumor compositions and volumes. Furthermore, larger tumor volumes may counter intuitively be more likely to be stabilized if sensitive cells dominate the tumor composition at time of initial treatment, suggesting a delay of initial treatment could prove beneficial. While it remains uncertain if metastatic disease in humans has the properties that allow it to be truly stabilized, the benefits of a dose titration protocol warrant additional pre-clinical and clinical investigations.
Collapse
Affiliation(s)
- Jessica Cunningham
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Frank Thuijsman
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Ralf Peeters
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Yannick Viossat
- CEREMADE, Université Paris-Dauphine, Université PSL, Paris, France
| | - Joel Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Robert Gatenby
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Department of Diagnostic Imaging and Interventional Radiology, Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Kateřina Staňková
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
- Delft Institute of Applied Mathematics, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
28
|
Ilan Y, Spigelman Z. Establishing patient-tailored variability-based paradigms for anti-cancer therapy: Using the inherent trajectories which underlie cancer for overcoming drug resistance. Cancer Treat Res Commun 2020; 25:100240. [PMID: 33246316 DOI: 10.1016/j.ctarc.2020.100240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/30/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Drug resistance is a major obstacle for successful therapy of many malignancies and is affecting the loss of response to chemotherapy and immunotherapy. Tumor-related compensatory adaptation mechanisms contribute to the development of drug resistance. Variability is inherent to biological systems and altered patterns of variability are associated with disease conditions. The marked intra and inter patient tumor heterogeneity, and the diverse mechanism contributing to drug resistance in different subjects, which may change over time even in the same patient, necessitate the development of personalized dynamic approaches for overcoming drug resistance. Altered dosing regimens, the potential role of chronotherapy, and drug holidays are effective in cancer therapy and immunotherapy. In the present review we describe the difficulty of overcoming drug resistance in a dynamic system and present the use of the inherent trajectories which underlie cancer development for building therapeutic regimens which can overcome resistance. The establishment of a platform wherein patient-tailored variability signatures are used for overcoming resistance for ensuing long term sustainable improved responses is presented.
Collapse
Affiliation(s)
- Yaron Ilan
- Department of Medicine, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
| | - Zachary Spigelman
- Department of Hematology and Oncology, Lahey Hospital and Beth Israel Medical Center, MA, USA
| |
Collapse
|
29
|
Yates JWT, Mistry H. Clone Wars: Quantitatively Understanding Cancer Drug Resistance. JCO Clin Cancer Inform 2020; 4:938-946. [PMID: 33112660 DOI: 10.1200/cci.20.00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A key aim of early clinical development for new cancer treatments is to detect the potential for efficacy early and to identify a safe therapeutic dose to take forward to phase II. Because of this need, researchers have sought to build mathematical models linking initial radiologic tumor response, often assessed after 6 to 8 weeks of treatment, with overall survival. However, there has been mixed success of this approach in the literature. We argue that evolutionary selection pressure should be considered to interpret these early efficacy signals and so optimize cancer therapy.
Collapse
Affiliation(s)
| | - Hitesh Mistry
- Division of Pharmacy and Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
30
|
Pisa R, Kapoor TM. Chemical strategies to overcome resistance against targeted anticancer therapeutics. Nat Chem Biol 2020; 16:817-825. [PMID: 32694636 DOI: 10.1038/s41589-020-0596-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Emergence of resistance is a major factor limiting the efficacy of molecularly targeted anticancer drugs. Understanding the specific mutations, or other genetic or cellular changes, that confer drug resistance can help in the development of therapeutic strategies with improved efficacies. Here, we outline recent progress in understanding chemotype-specific mechanisms of resistance and present chemical strategies, such as designing drugs with distinct binding modes or using proteolysis targeting chimeras, to overcome resistance. We also discuss how targeting multiple binding sites with bifunctional inhibitors or identifying collateral sensitivity profiles can be exploited to limit the emergence of resistance. Finally, we highlight how incorporating analyses of resistance early in drug development can help with the design and evaluation of therapeutics that can have long-term benefits for patients.
Collapse
Affiliation(s)
- Rudolf Pisa
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
31
|
Identifying States of Collateral Sensitivity during the Evolution of Therapeutic Resistance in Ewing's Sarcoma. iScience 2020; 23:101293. [PMID: 32623338 PMCID: PMC7334607 DOI: 10.1016/j.isci.2020.101293] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/06/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Advances in the treatment of Ewing's sarcoma (EWS) are desperately needed, particularly in the case of metastatic disease. A deeper understanding of collateral sensitivity, where the evolution of therapeutic resistance to one drug aligns with sensitivity to another drug, may improve our ability to effectively target this disease. For the first time in a solid tumor, we produced a temporal collateral sensitivity map that demonstrates the evolution of collateral sensitivity and resistance in EWS. We found that the evolution of collateral resistance was predictable with some drugs but had significant variation in response to other drugs. Using this map of temporal collateral sensitivity in EWS, we can see that the path toward collateral sensitivity is not always repeatable, nor is there always a clear trajectory toward resistance or sensitivity. Identifying transcriptomic changes that accompany these states of transient collateral sensitivity could improve treatment planning for patients with EWS. Ewing's sarcoma cell lines were evolved to become resistant to standard chemotherapy A temporal collateral sensitivity map shows response to alternative drugs over time Collateral drug response is repeatable in some instances and stochastic in others Differential gene expression elucidates potential biomarkers of drug response
Collapse
|
32
|
Grolmusz VK, Chen J, Emond R, Cosgrove PA, Pflieger L, Nath A, Moos PJ, Bild AH. Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells in a cell line model. Cancer Cell Int 2020; 20:253. [PMID: 32565737 PMCID: PMC7301982 DOI: 10.1186/s12935-020-01337-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022] Open
Abstract
Background CDK4/6 inhibitors such as ribociclib are becoming widely used targeted therapies in hormone-receptor-positive (HR+) human epidermal growth factor receptor 2-negative (HER2-) breast cancer. However, cancers can advance due to drug resistance, a problem in which tumor heterogeneity and evolution are key features. Methods Ribociclib-resistant HR+/HER2- CAMA-1 breast cancer cells were generated through long-term ribociclib treatment. Characterization of sensitive and resistant cells were performed using RNA sequencing and whole exome sequencing. Lentiviral labeling with different fluorescent proteins enabled us to track the proliferation of sensitive and resistant cells under different treatments in a heterogeneous, 3D spheroid coculture system using imaging microscopy and flow cytometry. Results Transcriptional profiling of sensitive and resistant cells revealed the downregulation of the G2/M checkpoint in the resistant cells. Exploiting this acquired vulnerability; resistant cells exhibited collateral sensitivity for the Wee-1 inhibitor, adavosertib (AZD1775). The combination of ribociclib and adavosertib achieved additional antiproliferative effect exclusively in the cocultures compared to monocultures, while decreasing the selection for resistant cells. Conclusions Our results suggest that optimal antiproliferative effects in heterogeneous cancers can be achieved via an integrative therapeutic approach targeting sensitive and resistant cancer cell populations within a tumor, respectively.
Collapse
Affiliation(s)
- Vince Kornél Grolmusz
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Jinfeng Chen
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Rena Emond
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Patrick A Cosgrove
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Lance Pflieger
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Aritro Nath
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| | - Philip J Moos
- Department of Pharmacology and Toxicology, University of Utah, 30 S 2000 East, Salt Lake City, UT 84112 USA
| | - Andrea H Bild
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute, City of Hope National Medical Center, 1218 S Fifth Ave, Monrovia, CA 91016 USA
| |
Collapse
|
33
|
Vander Velde R, Yoon N, Marusyk V, Durmaz A, Dhawan A, Miroshnychenko D, Lozano-Peral D, Desai B, Balynska O, Poleszhuk J, Kenian L, Teng M, Abazeed M, Mian O, Tan AC, Haura E, Scott J, Marusyk A. Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures. Nat Commun 2020; 11:2393. [PMID: 32409712 PMCID: PMC7224215 DOI: 10.1038/s41467-020-16212-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/17/2020] [Indexed: 12/21/2022] Open
Abstract
Despite high initial efficacy, targeted therapies eventually fail in advanced cancers, as tumors develop resistance and relapse. In contrast to the substantial body of research on the molecular mechanisms of resistance, understanding of how resistance evolves remains limited. Using an experimental model of ALK positive NSCLC, we explored the evolution of resistance to different clinical ALK inhibitors. We found that resistance can originate from heterogeneous, weakly resistant subpopulations with variable sensitivity to different ALK inhibitors. Instead of the commonly assumed stochastic single hit (epi) mutational transition, or drug-induced reprogramming, we found evidence for a hybrid scenario involving the gradual, multifactorial adaptation to the inhibitors through acquisition of multiple cooperating genetic and epigenetic adaptive changes. Additionally, we found that during this adaptation tumor cells might present unique, temporally restricted collateral sensitivities, absent in therapy naïve or fully resistant cells, suggesting the potential for new therapeutic interventions, directed against evolving resistance. Acquired resistance to cancer therapies reflects the ability of cancers to adapt to therapy-imposed selective pressures. Here, the authors elucidate the dynamics of developing resistance to ALK inhibitors in an ALK+ lung cancer cell line showing that resistance originates from drug-specific tolerant cancer cells and it develops as a gradual adaptation.
Collapse
Affiliation(s)
- Robert Vander Velde
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Nara Yoon
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Viktoriya Marusyk
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA.,Systems Biology and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Andrew Dhawan
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Daria Miroshnychenko
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Diego Lozano-Peral
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA.,Supercomputer and Bioinnovation Center, University of Málaga, Málaga, Spain
| | - Bina Desai
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA.,University of South Florida Cancer Biology PhD Program, Tampa, FL, USA
| | - Olena Balynska
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Jan Poleszhuk
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Warsaw, Poland
| | - Liu Kenian
- Department of Pathology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Mingxiang Teng
- Department of Biostatistic and Bioinformatics, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Mohamed Abazeed
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Omar Mian
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Aik Choon Tan
- Department of Biostatistic and Bioinformatics, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Eric Haura
- Department of Thoracic Oncology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA
| | - Jacob Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA. .,Systems Biology and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Andriy Marusyk
- Department of Cancer Physiology, H Lee Moffitt Cancer Centre and Research Institute, Tampa, FL, USA. .,Department of Molecular Medicine, University of South Florida, Tampa, FL, USA.
| |
Collapse
|
34
|
Maltas J, Krasnick B, Wood KB. Using Selection by Nonantibiotic Stressors to Sensitize Bacteria to Antibiotics. Mol Biol Evol 2020; 37:1394-1406. [PMID: 31851309 PMCID: PMC7182213 DOI: 10.1093/molbev/msz303] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Evolutionary adaptation of bacteria to nonantibiotic selective forces, such as osmotic stress, has been previously associated with increased antibiotic resistance, but much less is known about potentially sensitizing effects of nonantibiotic stressors. In this study, we use laboratory evolution to investigate adaptation of Enterococcus faecalis, an opportunistic bacterial pathogen, to a broad collection of environmental agents, ranging from antibiotics and biocides to extreme pH and osmotic stress. We find that nonantibiotic selection frequently leads to increased sensitivity to other conditions, including multiple antibiotics. Using population sequencing and whole-genome sequencing of single isolates from the evolved populations, we identify multiple mutations in genes previously linked with resistance to the selecting conditions, including genes corresponding to known drug targets or multidrug efflux systems previously tied to collateral sensitivity. Finally, we hypothesized based on the measured sensitivity profiles that sequential rounds of antibiotic and nonantibiotic selection may lead to hypersensitive populations by harnessing the orthogonal collateral effects of particular pairs of selective forces. To test this hypothesis, we show experimentally that populations evolved to a sequence of linezolid (an oxazolidinone antibiotic) and sodium benzoate (a common preservative) exhibit increased sensitivity to more stressors than adaptation to either condition alone. The results demonstrate how sequential adaptation to drug and nondrug environments can be used to sensitize bacteria to antibiotics and highlight new potential strategies for exploiting shared constraints governing adaptation to diverse environmental challenges.
Collapse
Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, MI
| | - Brian Krasnick
- Department of Biophysics, University of Michigan, Ann Arbor, MI
| | - Kevin B Wood
- Department of Biophysics, University of Michigan, Ann Arbor, MI
- Department of Physics, University of Michigan, Ann Arbor, MI
| |
Collapse
|
35
|
Lima NC, Atkinson E, Bunney TD, Katan M, Huang PH. Targeting the Src Pathway Enhances the Efficacy of Selective FGFR Inhibitors in Urothelial Cancers with FGFR3 Alterations. Int J Mol Sci 2020; 21:E3214. [PMID: 32370101 PMCID: PMC7246793 DOI: 10.3390/ijms21093214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Selective FGFR inhibitors such as infigratinib (BGJ398) and erdafitinib (JNJ-42756493) have been evaluated in clinical trials for cancers with FGFR3 molecular alterations, particularly in urothelial carcinoma patients. However, a substantial proportion of these patients (up to 50%) display intrinsic resistance to these drugs and receive minimal clinical benefit. There is thus an unmet need for alternative therapeutic strategies to overcome primary resistance to selective FGFR inhibitors. In this study, we demonstrate that cells expressing cancer-associated activating FGFR3 mutants and the FGFR3-TACC3 fusion showed primary resistance to infigratinib in long-term colony formation assays in both NIH-3T3 and urothelial carcinoma models. We find that expression of these FGFR3 molecular alterations resulted in elevated constitutive Src activation compared to wildtype FGFR3 and that cells co-opted this pathway as a means to achieve intrinsic resistance to infigratinib. Targeting the Src pathway with low doses of the kinase inhibitor dasatinib synergistically sensitized multiple urothelial carcinoma lines harbouring endogenous FGFR3 alterations to infigratinib. Our data provide preclinical rationale that supports the use of dasatinib in combination with selective FGFR inhibitors as a means to overcome intrinsic drug resistance in the salvage therapy setting in urothelial cancer patients with FGFR3 molecular alterations.
Collapse
Affiliation(s)
- Nadia Carvalho Lima
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (N.C.L.); (E.A.)
| | - Eliza Atkinson
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (N.C.L.); (E.A.)
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK; (T.D.B.); (M.K.)
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK; (T.D.B.); (M.K.)
| | - Paul H. Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; (N.C.L.); (E.A.)
| |
Collapse
|
36
|
Celecoxib Prevents Doxorubicin-Induced Multidrug Resistance in Canine and Mouse Lymphoma Cell Lines. Cancers (Basel) 2020; 12:cancers12051117. [PMID: 32365663 PMCID: PMC7280963 DOI: 10.3390/cancers12051117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 11/30/2022] Open
Abstract
Background: Treatment of malignancies is still a major challenge in human and canine cancer, mostly due to the emergence of multidrug resistance (MDR). One of the main contributors of MDR is the overexpression P-glycoprotein (Pgp), which recognizes and extrudes various chemotherapeutics from cancer cells. Methods: To study mechanisms underlying the development of drug resistance, we established an in vitro treatment protocol to rapidly induce Pgp-mediated MDR in cancer cells. Based on a clinical observation showing that a 33-day-long, unplanned drug holiday can reverse the MDR phenotype of a canine diffuse large B-cell lymphoma patient, our aim was to use the established assay to prevent the emergence of drug resistance in the early stages of treatment. Results: We showed that an in vitro drug holiday results in the decrease of Pgp expression in MDR cell lines. Surprisingly, celecoxib, a known COX-2 inhibitor, prevented the emergence of drug-induced MDR in murine and canine lymphoma cell lines. Conclusions: Our findings suggest that celecoxib could significantly improve the efficiency of chemotherapy by preventing the development of MDR in B-cell lymphoma.
Collapse
|
37
|
Nichol D, Robertson-Tessi M, Anderson ARA, Jeavons P. Model genotype-phenotype mappings and the algorithmic structure of evolution. J R Soc Interface 2019; 16:20190332. [PMID: 31690233 PMCID: PMC6893500 DOI: 10.1098/rsif.2019.0332] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/04/2019] [Indexed: 12/13/2022] Open
Abstract
Cancers are complex dynamic systems that undergo evolution and selection. Personalized medicine approaches in the clinic increasingly rely on predictions of tumour response to one or more therapies; these predictions are complicated by the inevitable evolution of the tumour. Despite enormous amounts of data on the mutational status of cancers and numerous therapies developed in recent decades to target these mutations, many of these treatments fail after a time due to the development of resistance in the tumour. The emergence of these resistant phenotypes is not easily predicted from genomic data, since the relationship between genotypes and phenotypes, termed the genotype-phenotype (GP) mapping, is neither injective nor functional. We present a review of models of this mapping within a generalized evolutionary framework that takes into account the relation between genotype, phenotype, environment and fitness. Different modelling approaches are described and compared, and many evolutionary results are shown to be conserved across studies despite using different underlying model systems. In addition, several areas for future work that remain understudied are identified, including plasticity and bet-hedging. The GP-mapping provides a pathway for understanding the potential routes of evolution taken by cancers, which will be necessary knowledge for improving personalized therapies.
Collapse
Affiliation(s)
- Daniel Nichol
- Department of Computer Science, University of Oxford, Oxford, UK
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alexander R. A. Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Peter Jeavons
- Department of Computer Science, University of Oxford, Oxford, UK
| |
Collapse
|
38
|
Barbosa C, Römhild R, Rosenstiel P, Schulenburg H. Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa. eLife 2019; 8:e51481. [PMID: 31658946 PMCID: PMC6881144 DOI: 10.7554/elife.51481] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/21/2019] [Indexed: 12/27/2022] Open
Abstract
Evolution is at the core of the impending antibiotic crisis. Sustainable therapy must thus account for the adaptive potential of pathogens. One option is to exploit evolutionary trade-offs, like collateral sensitivity, where evolved resistance to one antibiotic causes hypersensitivity to another one. To date, the evolutionary stability and thus clinical utility of this trade-off is unclear. We performed a critical experimental test on this key requirement, using evolution experiments with Pseudomonas aeruginosa, and identified three main outcomes: (i) bacteria commonly failed to counter hypersensitivity and went extinct; (ii) hypersensitivity sometimes converted into multidrug resistance; and (iii) resistance gains frequently caused re-sensitization to the previous drug, thereby maintaining the trade-off. Drug order affected the evolutionary outcome, most likely due to variation in the effect size of collateral sensitivity, epistasis among adaptive mutations, and fitness costs. Our finding of robust genetic trade-offs and drug-order effects can guide design of evolution-informed antibiotic therapy.
Collapse
Affiliation(s)
- Camilo Barbosa
- Department of Evolutionary Ecology and GeneticsUniversity of KielKielGermany
| | - Roderich Römhild
- Department of Evolutionary Ecology and GeneticsUniversity of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | | | - Hinrich Schulenburg
- Department of Evolutionary Ecology and GeneticsUniversity of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| |
Collapse
|
39
|
Maltas J, Wood KB. Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance. PLoS Biol 2019; 17:e3000515. [PMID: 31652256 PMCID: PMC6834293 DOI: 10.1371/journal.pbio.3000515] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 11/06/2019] [Accepted: 10/07/2019] [Indexed: 11/19/2022] Open
Abstract
Evolved resistance to one antibiotic may be associated with "collateral" sensitivity to other drugs. Here, we provide an extensive quantitative characterization of collateral effects in Enterococcus faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are pervasive but difficult to predict because independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity as well as markedly different fitness costs. Using whole-genome sequencing of evolved populations, we identified mutations in a number of known resistance determinants, including mutations in several genes previously linked with collateral sensitivity in other species. Although phenotypic drug sensitivity profiles show significant diversity, they cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. To exploit the statistical structure in these resistance profiles, we develop a simple mathematical model based on a stochastic control process and use it to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. The approach reveals a new conceptual strategy for mitigating resistance by balancing short-term inhibition of pathogen growth with infrequent use of drugs intended to steer pathogen populations to a more vulnerable future state. Experiments in laboratory populations confirm that model-inspired sequences of four drugs reduce growth and slow adaptation relative to naive protocols involving the drugs alone, in pairwise cycles, or in a four-drug uniform cycle.
Collapse
Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| |
Collapse
|
40
|
Santos-Lopez A, Marshall CW, Scribner MR, Snyder DJ, Cooper VS. Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle. eLife 2019; 8:47612. [PMID: 31516122 PMCID: PMC6814407 DOI: 10.7554/elife.47612] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/13/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial populations vary in their stress tolerance and population structure depending upon whether growth occurs in well-mixed or structured environments. We hypothesized that evolution in biofilms would generate greater genetic diversity than well-mixed environments and lead to different pathways of antibiotic resistance. We used experimental evolution and whole genome sequencing to test how the biofilm lifestyle influenced the rate, genetic mechanisms, and pleiotropic effects of resistance to ciprofloxacin in Acinetobacter baumannii populations. Both evolutionary dynamics and the identities of mutations differed between lifestyle. Planktonic populations experienced selective sweeps of mutations including the primary topoisomerase drug targets, whereas biofilm-adapted populations acquired mutations in regulators of efflux pumps. An overall trade-off between fitness and resistance level emerged, wherein biofilm-adapted clones were less resistant than planktonic but more fit in the absence of drug. However, biofilm populations developed collateral sensitivity to cephalosporins, demonstrating the clinical relevance of lifestyle on the evolution of resistance. A bacterium known as Acinetobacter baumannii causes serious lung infections in people with weakened immune systems. These illnesses are becoming more common largely because A. baumannii is increasingly developing resistance to antibiotics. Inside the airways, individual A. baumannii cells can stick together and coat themselves in a slimy substance to form a structure called biofilm, which physically protects bacteria from antibiotics. This may be one of the reasons why it is often harder to treat bacterial infections associated with biofilms. Another possibility is that bacteria may evolve differently in biofilms compared with cells living independently. For example, A. baumannii may colonize several regions of the lungs during an infection, leading to distinct groups of bacteria that experience different conditions and evolve separately. Each population may therefore respond differently to an antibiotic. In contrast, bacteria living independently in a well-mixed population – such as in the bloodstream of their host – would be more likely to all evolve in the same way. Santos-Lopez, Marshall et al. tested this theory by exposing populations of A. baumannii that lived either independently or in biofilms to increasing levels of an antibiotic called ciprofloxacin. The genetic information of these cells was examined as the populations were evolving, and the bacteria were also put in contact with other types of antibiotics. The analyses revealed that bacteria in well-mixed populations shared the same limited number of mutations: these gave the bacteria high levels of resistance to the antibiotic’s primary target, an enzyme involved in DNA processes. The bacteria had also become resistant to other classes of antibiotics. In contrast, the bacteria in biofilm populations evolved to be more genetically diverse, exhibiting different types of mutations that helped the cells to pump out the drug. These bacteria were less resistant to ciprofloxacin and more sensitive to other types of antibiotics. Further experiments looked into the fitness of the bacteria – their ability to survive, reproduce and compete with each other. High levels of antibiotic resistance came with lower fitness: biofilm bacteria had evolved to become being fitter than those from well-mixed population. Even in the absence of drugs, these populations were in fact fitter than the original cells. Overall, understanding how the lifestyles of bacteria affect the way they respond to drugs may help researchers to develop new approaches that limit the spread of antibiotic resistance and improve treatment.
Collapse
Affiliation(s)
- Alfonso Santos-Lopez
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Christopher W Marshall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Michelle R Scribner
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Daniel J Snyder
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States.,Microbial Genome Sequencing Center, University of Pittsburgh, Pittsburgh, United States
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States.,Microbial Genome Sequencing Center, University of Pittsburgh, Pittsburgh, United States
| |
Collapse
|
41
|
Goldman A, Khiste S, Freinkman E, Dhawan A, Majumder B, Mondal J, Pinkerton AB, Eton E, Medhi R, Chandrasekar V, Rahman MM, Ichimura T, Gopinath KS, Majumder P, Kohandel M, Sengupta S. Targeting tumor phenotypic plasticity and metabolic remodeling in adaptive cross-drug tolerance. Sci Signal 2019; 12:12/595/eaas8779. [PMID: 31431543 DOI: 10.1126/scisignal.aas8779] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metastable phenotypic state transitions in cancer cells can lead to the development of transient adaptive resistance or tolerance to chemotherapy. Here, we report that the acquisition of a phenotype marked by increased abundance of CD44 (CD44Hi) by breast cancer cells as a tolerance response to routinely used cytotoxic drugs, such as taxanes, activated a metabolic switch that conferred tolerance against unrelated standard-of-care chemotherapeutic agents, such as anthracyclines. We characterized the sequence of molecular events that connected the induced CD44Hi phenotype to increased activity of both the glycolytic and oxidative pathways and glucose flux through the pentose phosphate pathway (PPP). When given in a specific order, a combination of taxanes, anthracyclines, and inhibitors of glucose-6-phosphate dehydrogenase (G6PD), an enzyme involved in glucose metabolism, improved survival in mouse models of breast cancer. The same sequence of the three-drug combination reduced the viability of patient breast tumor samples in an explant system. Our findings highlight a convergence between phenotypic and metabolic state transitions that confers a survival advantage to cancer cells against clinically used drug combinations. Pharmacologically targeting this convergence could overcome cross-drug tolerance and could emerge as a new paradigm in the treatment of cancer.
Collapse
Affiliation(s)
- Aaron Goldman
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. .,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Mitra Biotech, Integrative Immuno-Oncology Center, Woburn, MA 01801, USA
| | - Sachin Khiste
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Elizaveta Freinkman
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Andrew Dhawan
- School of Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Biswanath Majumder
- Mitra Biotech, Integrative Immuno-Oncology Center, Woburn, MA 01801, USA.,Mitra Biotech, 7, Service Road, Pragathi Nagar, Electronic City, Bengaluru, Karnataka 560100, India
| | - Jayanta Mondal
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Elliot Eton
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ragini Medhi
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vineethkrishna Chandrasekar
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - M Mamunur Rahman
- Medical and Biological Laboratories International, Woburn, MA 01801, USA
| | - Takaharu Ichimura
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kodaganur S Gopinath
- Department of Surgical Oncology, HCG Bangalore Institute of Oncology Specialty Center, Bengaluru, Karnataka 560027, India
| | - Pradip Majumder
- Mitra Biotech, Integrative Immuno-Oncology Center, Woburn, MA 01801, USA
| | - Mohammad Kohandel
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Shiladitya Sengupta
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. .,Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.,Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.,Dana Farber Cancer Institute, Boston, MA 02115, USA
| |
Collapse
|
42
|
Apjok G, Boross G, Nyerges Á, Fekete G, Lázár V, Papp B, Pál C, Csörgő B. Limited Evolutionary Conservation of the Phenotypic Effects of Antibiotic Resistance Mutations. Mol Biol Evol 2019; 36:1601-1611. [PMID: 31058961 PMCID: PMC6657729 DOI: 10.1093/molbev/msz109] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Multidrug-resistant clinical isolates are common in certain pathogens, but rare in others. This pattern may be due to the fact that mutations shaping resistance have species-specific effects. To investigate this issue, we transferred a range of resistance-conferring mutations and a full resistance gene into Escherichia coli and closely related bacteria. We found that resistance mutations in one bacterial species frequently provide no resistance, in fact even yielding drug hypersensitivity in close relatives. In depth analysis of a key gene involved in aminoglycoside resistance (trkH) indicated that preexisting mutations in other genes-intergenic epistasis-underlie such extreme differences in mutational effects between species. Finally, reconstruction of adaptive landscapes under multiple antibiotic stresses revealed that mutations frequently provide multidrug resistance or elevated drug susceptibility (i.e., collateral sensitivity) only with certain combinations of other resistance mutations. We conclude that resistance and collateral sensitivity are contingent upon the genetic makeup of the bacterial population, and such contingency could shape the long-term fate of resistant bacteria. These results underlie the importance of species-specific treatment strategies.
Collapse
Affiliation(s)
- Gábor Apjok
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Gábor Boross
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Department of Biology, Stanford University, Stanford, CA
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Viktória Lázár
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Technion – Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
| |
Collapse
|
43
|
Tokutomi N, Moyret‐Lalle C, Puisieux A, Sugano S, Martinez P. Quantifying local malignant adaptation in tissue-specific evolutionary trajectories by harnessing cancer's repeatability at the genetic level. Evol Appl 2019; 12:1062-1075. [PMID: 31080515 PMCID: PMC6503823 DOI: 10.1111/eva.12781] [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: 09/04/2018] [Revised: 12/03/2018] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
Cancer is a potentially lethal disease, in which patients with nearly identical genetic backgrounds can develop a similar pathology through distinct combinations of genetic alterations. We aimed to reconstruct the evolutionary process underlying tumour initiation, using the combination of convergence and discrepancies observed across 2,742 cancer genomes from nine tumour types. We developed a framework using the repeatability of cancer development to score the local malignant adaptation (LMA) of genetic clones, as their potential to malignantly progress and invade their environment of origin. Using this framework, we found that premalignant skin and colorectal lesions appeared specifically adapted to their local environment, yet insufficiently for full cancerous transformation. We found that metastatic clones were more adapted to the site of origin than to the invaded tissue, suggesting that genetics may be more important for local progression than for the invasion of distant organs. In addition, we used network analyses to investigate evolutionary properties at the system-level, highlighting that different dynamics of malignant progression can be modelled by such a framework in tumour-type-specific fashion. We find that occurrence-based methods can be used to specifically recapitulate the process of cancer initiation and progression, as well as to evaluate the adaptation of genetic clones to given environments. The repeatability observed in the evolution of most tumour types could therefore be harnessed to better predict the trajectories likely to be taken by tumours and preneoplastic lesions in the future.
Collapse
Affiliation(s)
- Natsuki Tokutomi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoTokyoJapan
| | - Caroline Moyret‐Lalle
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Alain Puisieux
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoTokyoJapan
| | - Pierre Martinez
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| |
Collapse
|
44
|
Kaznatcheev A, Peacock J, Basanta D, Marusyk A, Scott JG. Fibroblasts and alectinib switch the evolutionary games played by non-small cell lung cancer. Nat Ecol Evol 2019; 3:450-456. [PMID: 30778184 PMCID: PMC6467526 DOI: 10.1038/s41559-018-0768-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/22/2018] [Indexed: 01/22/2023]
Abstract
Heterogeneity in strategies for survival and proliferation among the cells which constitute a tumour is a driving force behind the evolution of resistance to cancer therapy. The rules mapping the tumour’s strategy distribution to the fitness of individual strategies can be represented as an evolutionary game. We develop a game assay to measure effective evolutionary games in co-cultures of non-small cell lung cancer cells which are sensitive and resistant to the anaplastic lymphoma kinase inhibitor Alectinib. The games are not only quantitatively different between different environments, but targeted therapy and cancer associated fibroblasts qualitatively switch the type of game being played by the in-vitro population from Leader to Deadlock. This observation provides empirical confirmation of a central theoretical postulate of evolutionary game theory in oncology: we can treat not only the player, but also the game. Although we concentrate on measuring games played by cancer cells, the measurement methodology we develop can be used to advance the study of games in other microscopic systems by providing a quantitative description of non-cell-autonomous effects.
Collapse
Affiliation(s)
- Artem Kaznatcheev
- Department of Computer Science, University of Oxford, Oxford, UK. .,Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA.
| | - Jeffrey Peacock
- Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - David Basanta
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL, USA.
| | - Jacob G Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA. .,Department of Radiation Oncology, Cleveland Clinic, Cleveland, OH, USA.
| |
Collapse
|
45
|
Antibiotic collateral sensitivity is contingent on the repeatability of evolution. Nat Commun 2019; 10:334. [PMID: 30659188 PMCID: PMC6338734 DOI: 10.1038/s41467-018-08098-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/13/2018] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance represents a growing health crisis that necessitates the immediate discovery of novel treatment strategies. One such strategy is the identification of collateral sensitivities, wherein evolution under a first drug induces susceptibility to a second. Here, we report that sequential drug regimens derived from in vitro evolution experiments may have overstated therapeutic benefit, predicting a collaterally sensitive response where cross-resistance ultimately occurs. We quantify the likelihood of this phenomenon by use of a mathematical model parametrised with combinatorially complete fitness landscapes for Escherichia coli. Through experimental evolution we then verify that a second drug can indeed stochastically exhibit either increased susceptibility or increased resistance when following a first. Genetic divergence is confirmed as the driver of this differential response through targeted and whole genome sequencing. Taken together, these results highlight that the success of evolutionarily-informed therapies is predicated on a rigorous probabilistic understanding of the contingencies that arise during the evolution of drug resistance. The evolution of resistance to an antibiotic can render bacteria more susceptible, or more resistant, to a second antibiotic. Here, Nichol et al. provide evidence that the final outcome can be fairly stochastic and depends on the shape of the evolutionary fitness landscape.
Collapse
|
46
|
Taylor J, Bebawy M. Proteins Regulating Microvesicle Biogenesis and Multidrug Resistance in Cancer. Proteomics 2019; 19:e1800165. [PMID: 30520565 DOI: 10.1002/pmic.201800165] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/02/2018] [Indexed: 01/01/2023]
Abstract
Microvesicles (MV) are emerging as important mediators of intercellular communication. While MVs are important signaling vectors for many physiological processes, they are also implicated in cancer pathology and progression. Cellular activation is perhaps the most widely reported initiator of MV biogenesis, however, the precise mechanism remains undefined. Uncovering the proteins involved in regulating MV biogenesis is of interest given their role in the dissemination of deleterious cancer traits. MVs shed from drug-resistant cancer cells transfer multidrug resistance (MDR) proteins to drug-sensitive cells and confer the MDR phenotype in a matter of hours. MDR is attributed to the overexpression of ABC transporters, primarily P-glycoprotein and MRP1. Their expression and functionality is dependent on a number of proteins. In particular, FERM domain proteins have been implicated in supporting the functionality of efflux transporters in drug-resistant cells and in recipient cells during intercellular transfer by vesicles. Herein, the most recent research on the proteins involved in MV biogenesis and in the dissemination of MV-mediated MDR are discussed. Attention is drawn to unanswered questions in the literature that may prove to be of benefit in ongoing efforts to improve clinical response to chemotherapy and circumventing MDR.
Collapse
Affiliation(s)
- Jack Taylor
- Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney, Sydney, Australia
| | - Mary Bebawy
- Discipline of Pharmacy, Graduate School of Health, The University of Technology Sydney, Sydney, Australia
| |
Collapse
|
47
|
Fernández A. Drug-based cancer therapy to overcome immune resistance by steering tumor evolution. Expert Opin Drug Discov 2018; 14:5-8. [PMID: 30486683 DOI: 10.1080/17460441.2019.1550066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ariel Fernández
- a Ariel Fernandez Innovation, Pharmaceutical Consultancy , Buenos Aires.,b CONICET- Argentine National Research Council , Buenos Aires.,c Chemistry Institute , INQUISUR/UNS/CONICET , Bahia Blanca , Argentina
| |
Collapse
|
48
|
Ancistrolikokine I and further 5,8′-coupled naphthylisoquinoline alkaloids from the Congolese liana Ancistrocladus likoko and their cytotoxic activities against drug-sensitive and multidrug resistant human leukemia cells. Fitoterapia 2018; 129:114-125. [DOI: 10.1016/j.fitote.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/12/2018] [Accepted: 06/14/2018] [Indexed: 11/19/2022]
|
49
|
Vargas R, Gopal P, Kuzmishin GB, DeBernardo R, Koyfman SA, Jha BK, Mian OY, Scott J, Adams DJ, Peacock CD, Abazeed ME. Case study: patient-derived clear cell adenocarcinoma xenograft model longitudinally predicts treatment response. NPJ Precis Oncol 2018; 2:14. [PMID: 30202792 PMCID: PMC6041303 DOI: 10.1038/s41698-018-0060-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 01/06/2023] Open
Abstract
There has been little progress in the use of patient-derived xenografts (PDX) to guide individual therapeutic strategies. In part, this can be attributed to the operational challenges of effecting successful engraftment and testing multiple candidate drugs in a clinically workable timeframe. It also remains unclear whether the ancestral tumor will evolve along similar evolutionary trajectories in its human and rodent hosts in response to similar selective pressures (i.e., drugs). Herein, we combine a metastatic clear cell adenocarcinoma PDX with a timely 3 mouse x 1 drug experimental design, followed by a co-clinical trial to longitudinally guide a patient's care. Using this approach, we accurately predict response to first- and second-line therapies in so far as tumor response in mice correlated with the patient's clinical response to first-line therapy (gemcitabine/nivolumab), development of resistance and response to second-line therapy (paclitaxel/neratinib) before these events were observed in the patient. Treatment resistance to first-line therapy in the PDX is coincident with biologically relevant changes in gene and gene set expression, including upregulation of phase I/II drug metabolism (CYP2C18, UGT2A, and ATP2A1) and DNA interstrand cross-link repair (i.e., XPA, FANCE, FANCG, and FANCL) genes. A total of 5.3% of our engrafted PDX collection is established within 2 weeks of implantation, suggesting our experimental designs can be broadened to other cancers. These findings could have significant implications for PDX-based avatars of aggressive human cancers.
Collapse
Affiliation(s)
- Roberto Vargas
- 1Gynecologic Oncology Division, Women's Health Institute, Cleveland Clinic, 9500 Euclid Avenue/A8, Cleveland, OH 44195 USA
| | - Priyanka Gopal
- 2Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St/NE6-258, Cleveland, OH 44195 USA
| | - Gwendolyn B Kuzmishin
- 2Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St/NE6-258, Cleveland, OH 44195 USA
| | - Robert DeBernardo
- 1Gynecologic Oncology Division, Women's Health Institute, Cleveland Clinic, 9500 Euclid Avenue/A8, Cleveland, OH 44195 USA
| | - Shlomo A Koyfman
- 3Department of Radiation Oncology, Cleveland Clinic, 9500 Euclid Avenue/CA-60, Cleveland, OH 44195 USA
| | - Babal K Jha
- 2Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St/NE6-258, Cleveland, OH 44195 USA
| | - Omar Y Mian
- 2Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St/NE6-258, Cleveland, OH 44195 USA.,3Department of Radiation Oncology, Cleveland Clinic, 9500 Euclid Avenue/CA-60, Cleveland, OH 44195 USA
| | - Jacob Scott
- 2Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St/NE6-258, Cleveland, OH 44195 USA.,3Department of Radiation Oncology, Cleveland Clinic, 9500 Euclid Avenue/CA-60, Cleveland, OH 44195 USA
| | - Drew J Adams
- 4Department of Genetics, Case Western Reserve University, 2109 Adelbert Road/BRB, Cleveland, OH 44106 USA
| | - Craig D Peacock
- 2Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St/NE6-258, Cleveland, OH 44195 USA
| | - Mohamed E Abazeed
- 2Department of Translational Hematology Oncology Research, Cleveland Clinic, 2111 East 96th St/NE6-258, Cleveland, OH 44195 USA.,3Department of Radiation Oncology, Cleveland Clinic, 9500 Euclid Avenue/CA-60, Cleveland, OH 44195 USA
| |
Collapse
|
50
|
Pogrebniak KL, Curtis C. Harnessing Tumor Evolution to Circumvent Resistance. Trends Genet 2018; 34:639-651. [PMID: 29903534 DOI: 10.1016/j.tig.2018.05.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 02/08/2023]
Abstract
High-throughput sequencing can be used to measure changes in tumor composition across space and time. Specifically, comparisons of pre- and post-treatment samples can reveal the underlying clonal dynamics and resistance mechanisms. Here, we discuss evidence for distinct modes of tumor evolution and their implications for therapeutic strategies. In addition, we consider the utility of spatial tissue sampling schemes, single-cell analysis, and circulating tumor DNA to track tumor evolution and the emergence of resistance, as well as approaches that seek to forestall resistance by targeting tumor evolution. Ultimately, characterization of the (epi)genomic, transcriptomic, and phenotypic changes that occur during tumor progression coupled with computational and mathematical modeling of tumor evolutionary dynamics may inform personalized treatment strategies.
Collapse
Affiliation(s)
- Katherine L Pogrebniak
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; http://med.stanford.edu/curtislab.html
| | - Christina Curtis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; http://med.stanford.edu/curtislab.html.
| |
Collapse
|