1
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Bastos RS, de Aguiar CPO, Cruz JN, Ramos RS, Kimani NM, de Souza JSN, Chaves MH, de Freitas HF, Pita SSR, dos Santos CBR. Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis. Int J Mol Sci 2024; 25:6715. [PMID: 38928422 PMCID: PMC11204165 DOI: 10.3390/ijms25126715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
This study investigated the potential of selected compounds as inhibitors of SARS-CoV-2 Mpro through pharmacokinetic and toxicological analyses, molecular docking, and molecular dynamics simulations. In silico molecular docking simulations revealed promising ligands with favorable binding affinities for Mpro, ranging from -6.2 to -9.5 kcal/mol. Moreover, molecular dynamics simulations demonstrated the stability of protein-ligand complexes over 200 ns, maintaining protein secondary structures. MM-PBSA analysis revealed favorable interactions between ligands and Mpro, with negative binding energy values. Hydrogen bond formation capacity during molecular dynamics was confirmed, indicating consistent interactions with Mpro catalytic residues. Based on these findings, selected ligands show promise for future studies in developing COVID-19 treatments.
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Affiliation(s)
- Ruan S. Bastos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Christiane P. O. de Aguiar
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Ryan S. Ramos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Njogu M. Kimani
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya
| | - João S. N. de Souza
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Mariana H. Chaves
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil
| | - Humberto F. de Freitas
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil; (H.F.d.F.); (S.S.R.P.)
| | - Samuel S. R. Pita
- Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil; (H.F.d.F.); (S.S.R.P.)
| | - Cleydson B. R. dos Santos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
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2
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Shaw I, Boafo GF, Ali YS, Liu Y, Mlambo R, Tan S, Chen C. Advancements and prospects of lipid-based nanoparticles: dual frontiers in cancer treatment and vaccine development. J Microencapsul 2024; 41:226-254. [PMID: 38560994 DOI: 10.1080/02652048.2024.2326091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
Cancer is a complex heterogeneous disease that poses a significant public health challenge. In recent years, lipid-based nanoparticles (LBNPs) have expanded drug delivery and vaccine development options owing to their adaptable, non-toxic, tuneable physicochemical properties, versatile surface functionalisation, and biocompatibility. LBNPs are tiny artificial structures composed of lipid-like materials that can be engineered to encapsulate and deliver therapeutic agents with pinpoint accuracy. They have been widely explored in oncology; however, our understanding of their pharmacological mechanisms, effects of their composition, charge, and size on cellular uptake, tumour penetration, and how they can be utilised to develop cancer vaccines is still limited. Hence, we reviewed LBNPs' unique characteristics, biochemical features, and tumour-targeting mechanisms. Furthermore, we examined their ability to enhance cancer therapies and their potential contribution in developing anticancer vaccines. We critically analysed their advantages and challenges impeding swift advancements in oncology and highlighted promising avenues for future research.
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Affiliation(s)
- Ibrahim Shaw
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - George Frimpong Boafo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Yimer Seid Ali
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, People's Republic of China
- Department of Pharmacy, College of Medicine and Health Science, Wollo University, Dessie, Ethiopia
| | - Yang Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Ronald Mlambo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, People's Republic of China
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3
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Póti Á, Szüts D, Vermezovic J. Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa. Nucleic Acids Res 2024; 52:1779-1792. [PMID: 38180823 PMCID: PMC10899757 DOI: 10.1093/nar/gkad1250] [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: 10/03/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
Planarians are organisms with a unique capacity to regenerate any part of their body. New tissues are generated in a process that requires many swift cell divisions. How costly is this process to an animal in terms of mutational load remains unknown. Using whole genome sequencing, we defined the mutational profile of the process of regeneration in the planarian species Schmidtea polychroa. We assembled de novo the genome of S. polychroa and analyzed mutations in animals that have undergone regeneration. We observed a threefold increase in the number of mutations and an altered mutational spectrum. High allele frequencies of subclonal mutations in regenerated animals suggested that most of the cells in the regenerated animal were descendants of a small number of stem cells with high expansion potential. We provide, for the first time, the draft genome assembly of S. polychroa, an estimation of the germline mutation rate for a planarian species and the mutational spectrum of the regeneration process of a living organism.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Jelena Vermezovic
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
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4
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Fischer MM, Blüthgen N. On minimising tumoural growth under treatment resistance. J Theor Biol 2024; 579:111716. [PMID: 38135033 DOI: 10.1016/j.jtbi.2023.111716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Drug resistance is a major challenge for curative cancer treatment, representing the main reason of death in patients. Evolutionary biology suggests pauses between treatment rounds as a way to delay or even avoid resistance emergence. Indeed, this approach has already shown promising preclinical and early clinical results, and stimulated the development of mathematical models for finding optimal treatment protocols. Due to their complexity, however, these models do not lend themself to a rigorous mathematical analysis, hence so far clinical recommendations generally relied on numerical simulations and ad-hoc heuristics. Here, we derive two mathematical models describing tumour growth under genetic and epigenetic treatment resistance, respectively, which are simple enough for a complete analytical investigation. First, we find key differences in response to treatment protocols between the two modes of resistance. Second, we identify the optimal treatment protocol which leads to the largest possible tumour shrinkage rate. Third, we fit the "epigenetic model" to previously published xenograft experiment data, finding excellent agreement, underscoring the biological validity of our approach. Finally, we use the fitted model to calculate the optimal treatment protocol for this specific experiment, which we demonstrate to cause curative treatment, making it superior to previous approaches which generally aimed at stabilising tumour burden. Overall, our approach underscores the usefulness of simple mathematical models and their analytical examination, and we anticipate our findings to guide future preclinical and, ultimately, clinical research in optimising treatment regimes.
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Affiliation(s)
- Matthias M Fischer
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, 10115 Berlin, Germany.
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5
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Damoiseaux D, Amant F, Beijnen JH, Barnett S, Veal GJ, Huitema ADR, Dorlo TPC. Physiologically-based pharmacokinetic model to predict doxorubicin and paclitaxel exposure in infants through breast milk. CPT Pharmacometrics Syst Pharmacol 2023; 12:1931-1944. [PMID: 37798909 PMCID: PMC10725259 DOI: 10.1002/psp4.13043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Limited information is available concerning infant exposure and safety when breastfed by mothers receiving chemotherapy. Whereas defining distribution to breast milk is important to infer drug exposure, infant pharmacokinetics also determine to what extent the infant will be exposed to potential toxic effects. We aimed to assess the impact of chemotherapy containing breast milk on infants by predicting systemic and local (intestinal) exposure of paclitaxel and doxorubicin in infants through breast milk using a physiologically-based pharmacokinetic (PBPK) approach. Whole-body PBPK models of i.v. paclitaxel and doxorubicin were extended from the literature, with an oral absorption component to enable predictions in infants receiving paclitaxel or doxorubicin-containing breast milk. For safety considerations, worst-case scenarios were explored. Finally, paclitaxel and doxorubicin exposures in plasma and intestinal tissue of infants following feeding of breast milk from paclitaxel- or doxorubicin-treated mothers were simulated and breast milk discarding strategies were evaluated. The upper 95th percentile of the predicted peak concentrations in peripheral venous blood were 3.48 and 0.74 nM (0.4%-1.7% and 0.1%-1.8% of on-treatment) for paclitaxel and doxorubicin, respectively. Intestinal exposure reached peak concentrations of 1.0 and 140 μM for paclitaxel and doxorubicin, respectively. Discarding breast milk for the first 3 days after maternal chemotherapy administration reduced systemic and tissue exposures even further, to over 90% and 80% for paclitaxel and doxorubicin, respectively. PBPK simulations of chemotherapy exposure in infants after breastfeeding with chemotherapy containing breast milk suggest that particularly local gastrointestinal adverse events should be monitored, whereas systemic adverse events are not expected.
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Affiliation(s)
- David Damoiseaux
- Department of Pharmacy and PharmacologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Frédéric Amant
- Department of GynecologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Gynecologic OncologyUZ LeuvenLeuvenBelgium
| | - Jos H. Beijnen
- Department of Pharmacy and PharmacologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Utrecht Institute of Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Shelby Barnett
- Newcastle University Centre for CancerNewcastle UniversityNewcastle upon TyneUK
| | - Gareth J. Veal
- Newcastle University Centre for CancerNewcastle UniversityNewcastle upon TyneUK
| | - Alwin D. R. Huitema
- Department of Pharmacy and PharmacologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Department of PharmacologyPrincess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Department of Clinical Pharmacy, University Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Thomas P. C. Dorlo
- Department of Pharmacy and PharmacologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Department of PharmacyUppsala UniversityUppsalaSweden
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6
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Lózsa R, Németh E, Gervai JZ, Márkus BG, Kollarics S, Gyüre Z, Tóth J, Simon F, Szüts D. DNA mismatch repair protects the genome from oxygen-induced replicative mutagenesis. Nucleic Acids Res 2023; 51:11040-11055. [PMID: 37791890 PMCID: PMC10639081 DOI: 10.1093/nar/gkad775] [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: 05/16/2023] [Revised: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
DNA mismatch repair (MMR) corrects mismatched DNA bases arising from multiple sources including polymerase errors and base damage. By detecting spontaneous mutagenesis using whole genome sequencing of cultured MMR deficient human cell lines, we show that a primary role of MMR is the repair of oxygen-induced mismatches. We found an approximately twofold higher mutation rate in MSH6 deficient DLD-1 cells or MHL1 deficient HCT116 cells exposed to atmospheric conditions as opposed to mild hypoxia, which correlated with oxidant levels measured using electron paramagnetic resonance spectroscopy. The oxygen-induced mutations were dominated by T to C base substitutions and single T deletions found primarily on the lagging strand. A broad sequence context preference, dependence on replication timing and a lack of transcriptional strand bias further suggested that oxygen-induced mutations arise from polymerase errors rather than oxidative base damage. We defined separate low and high oxygen-specific MMR deficiency mutation signatures common to the two cell lines and showed that the effect of oxygen is observable in MMR deficient cancer genomes, where it best correlates with the contribution of mutation signature SBS21. Our results imply that MMR corrects oxygen-induced genomic mismatches introduced by a replicative process in proliferating cells.
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Affiliation(s)
- Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Bence G Márkus
- Stavropoulos Center for Complex Quantum Matter, Department of Physics and Astronomy, University of Notre Dame, Notre Dame, IN 46556, USA
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Sándor Kollarics
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, H-1085 Budapest, Hungary
- Turbine Simulated Cell Technologies, H-1027 Budapest, Hungary
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Ferenc Simon
- Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
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7
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Li J, Stenberg S, Yue JX, Mikhalev E, Thompson D, Warringer J, Liti G. Genome instability footprint under rapamycin and hydroxyurea treatments. PLoS Genet 2023; 19:e1011012. [PMID: 37931001 PMCID: PMC10653606 DOI: 10.1371/journal.pgen.1011012] [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: 10/04/2023] [Revised: 11/16/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The mutational processes dictating the accumulation of mutations in genomes are shaped by genetic background, environment and their interactions. Accurate quantification of mutation rates and spectra under drugs has important implications in disease treatment. Here, we used whole-genome sequencing and time-resolved growth phenotyping of yeast mutation accumulation lines to give a detailed view of the mutagenic effects of rapamycin and hydroxyurea on the genome and cell growth. Mutation rates depended on the genetic backgrounds but were only marginally affected by rapamycin. As a remarkable exception, rapamycin treatment was associated with frequent chromosome XII amplifications, which compensated for rapamycin induced rDNA repeat contraction on this chromosome and served to maintain rDNA content homeostasis and fitness. In hydroxyurea, a wide range of mutation rates were elevated regardless of the genetic backgrounds, with a particularly high occurrence of aneuploidy that associated with dramatic fitness loss. Hydroxyurea also induced a high T-to-G and low C-to-A transversion rate that reversed the common G/C-to-A/T bias in yeast and gave rise to a broad range of structural variants, including mtDNA deletions. The hydroxyurea mutation footprint was consistent with the activation of error-prone DNA polymerase activities and non-homologues end joining repair pathways. Taken together, our study provides an in-depth view of mutation rates and signatures in rapamycin and hydroxyurea and their impact on cell fitness, which brings insights for assessing their chronic effects on genome integrity.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Simon Stenberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | | | - Dawn Thompson
- Ginkgo Bioworks, Boston, Massachusetts, United States of America
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gianni Liti
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
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Emori C, Boucher Z, Bolcun-Filas E. CHEK2 signaling is the key regulator of oocyte survival after chemotherapy. SCIENCE ADVANCES 2023; 9:eadg0898. [PMID: 37862420 PMCID: PMC10588956 DOI: 10.1126/sciadv.adg0898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/06/2023] [Indexed: 10/22/2023]
Abstract
Cancer treatments can damage the ovarian follicle reserve, leading to primary ovarian insufficiency and infertility among survivors. Checkpoint kinase 2 (CHEK2) deficiency prevents elimination of oocytes in primordial follicles in female mice exposed to radiation and preserves their ovarian function and fertility. Here, we demonstrate that CHEK2 also coordinates the elimination of oocytes after exposure to standard-of-care chemotherapy drugs. CHEK2 activates two downstream targets-TAp63 and p53-which direct oocyte elimination. CHEK2 knockout or pharmacological inhibition preserved ovarian follicle reserve after radiation and chemotherapy. However, the lack of specificity for CHEK2 among available inhibitors limits their potential for clinical development. These findings demonstrate that CHEK2 is a master regulator of the ovarian cellular response to damage caused by radiation and chemotherapy and warrant the development of selective inhibitors specific to CHEK2 as a potential avenue for ovario-protective treatments.
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Affiliation(s)
- Chihiro Emori
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 5650871, Japan
| | - Zachary Boucher
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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9
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Ratnayaka-Gamage ND, Alesi LR, Zerafa N, Stringer JM, Hutt KJ. Xrcc5/KU80 is not required for the survival or activation of prophase-arrested oocytes in primordial follicles. Front Endocrinol (Lausanne) 2023; 14:1268009. [PMID: 37900135 PMCID: PMC10603181 DOI: 10.3389/fendo.2023.1268009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction The non-growing, meiotically-arrested oocytes housed within primordial follicles are exquisitely sensitive to genotoxic insults from endogenous and exogenous sources. Even a single DNA double-strand break (DSB) can trigger oocyte apoptosis, which can lead to accelerated depletion of the ovarian reserve, early loss of fertility and menopause. Therefore, repair of DNA damage is important for preserving the quality of oocytes to sustain fertility across the reproductive lifespan. This study aimed to evaluate the role of KU80 (encoded by the XRCC5 gene) - an essential component of the non-homologous end joining (NHEJ) pathway - in the repair of oocyte DNA DSBs during reproductive ageing, and following insult caused by the DNA-damaging chemotherapies cyclophosphamide and cisplatin. Methods To investigate the importance of KU80 following endogenous and exogenous DNA damage, ovaries from conditional oocyte-specific Xrcc5 knockout (Xrcc5 cKO) and wildtype (WT) mice that were aged or exposed to DNA damage-inducing chemotherapy were compared. Ovarian follicles and oocytes were quantified, morphologically assessed and analysed via immunohistochemistry for markers of DNA damage and apoptosis. In addition, chemotherapy exposed mice were superovulated, and the numbers and quality of mature metaphase- II (MII) oocytes were assessed. Results The number of healthy follicles, atretic (dying) follicles, and corpora lutea were similar in Xrcc5 cKO and WT mice at PN50, PN200 and PN300. Additionally, primordial follicle number and ovulation rates were similar in young adult Xrcc5 cKO and WT mice following treatment with cyclophosphamide (75mg/kg), cisplatin (4mg/kg), or vehicle control (saline). Furthermore, KU80 was not essential for the repair of exogenously induced DNA damage in primordial follicle oocytes. Discussion These data indicate that KU80 is not required for maintenance of the ovarian reserve, follicle development, or ovulation during maternal ageing. Similarly, this study also indicates that KU80 is not required for the repair of exogenously induced DSBs in the prophase-arrested oocytes of primordial follicles.
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Affiliation(s)
| | | | | | | | - Karla J. Hutt
- *Correspondence: Jessica M. Stringer, ; Karla J. Hutt,
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10
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Yang K, Halima A, Chan TA. Antigen presentation in cancer - mechanisms and clinical implications for immunotherapy. Nat Rev Clin Oncol 2023; 20:604-623. [PMID: 37328642 DOI: 10.1038/s41571-023-00789-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
Over the past decade, the emergence of effective immunotherapies has revolutionized the clinical management of many types of cancers. However, long-term durable tumour control is only achieved in a fraction of patients who receive these therapies. Understanding the mechanisms underlying clinical response and resistance to treatment is therefore essential to expanding the level of clinical benefit obtained from immunotherapies. In this Review, we describe the molecular mechanisms of antigen processing and presentation in tumours and their clinical consequences. We examine how various aspects of the antigen-presentation machinery (APM) shape tumour immunity. In particular, we discuss genomic variants in HLA alleles and other APM components, highlighting their influence on the immunopeptidomes of both malignant cells and immune cells. Understanding the APM, how it is regulated and how it changes in tumour cells is crucial for determining which patients will respond to immunotherapy and why some patients develop resistance. We focus on recently discovered molecular and genomic alterations that drive the clinical outcomes of patients receiving immune-checkpoint inhibitors. An improved understanding of how these variables mediate tumour-immune interactions is expected to guide the more precise administration of immunotherapies and reveal potentially promising directions for the development of new immunotherapeutic approaches.
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Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Ahmed Halima
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA.
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA.
- National Center for Regenerative Medicine, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Cleveland, OH, USA.
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11
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Gyüre Z, Póti Á, Németh E, Szikriszt B, Lózsa R, Krawczyk M, Richardson AL, Szüts D. Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase ζ and PRIMPOL. Cell Rep 2023; 42:112887. [PMID: 37498746 DOI: 10.1016/j.celrep.2023.112887] [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: 03/17/2023] [Revised: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL-/- cells. Small deletions in short repeats appear in REV1-/-PCNAK164R/K164R double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1-/- and REV3L-/- mutants, and chromosomal instability is detectable in REV1-/-PRIMPOL-/- cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.
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Affiliation(s)
- Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, 1085 Budapest, Hungary; Turbine Simulated Cell Technologies, 1027 Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Michał Krawczyk
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; National Laboratory for Drug Research and Development, 1117 Budapest, Hungary.
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12
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Kaur P, Nagar S, Mehta R, Sahadeo K, Vancura A. Hydroxyurea and inactivation of checkpoint kinase MEC1 inhibit transcription termination and pre-mRNA cleavage at polyadenylation sites in budding yeast. Sci Rep 2023; 13:13106. [PMID: 37567961 PMCID: PMC10421882 DOI: 10.1038/s41598-023-40294-3] [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: 02/16/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023] Open
Abstract
The DNA damage response (DDR) is an evolutionarily conserved process essential for cell survival. The transcription changes triggered by DDR depend on the nature of DNA damage, activation of checkpoint kinases, and the stage of cell cycle. The transcription changes can be localized and affect only damaged DNA, but they can be also global and affect genes that are not damaged. While the purpose of localized transcription inhibition is to avoid transcription of damaged genes and make DNA accessible for repair, the purpose and mechanisms of global transcription inhibition of undamaged genes are less well understood. We show here that a brief cell treatment with hydroxyurea (HU) globally inhibits RNA synthesis and transcription by RNA polymerase I, II, and III (RNAPI, RNAPII, and RNAPIII). HU reduces efficiency of transcription termination and inhibits pre-mRNA cleavage at the polyadenylation (pA) sites, destabilizes mRNAs, and shortens poly(A) tails of mRNAs, indicating defects in pre-mRNA 3' end processing. Inactivation of the checkpoint kinase Mec1p downregulates the efficiency of transcription termination and reduces the efficiency of pre-mRNAs clevage at the pA sites, suggesting the involvement of DNA damage checkpoint in transcription termination and pre-mRNA 3' end processing.
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Affiliation(s)
- Pritpal Kaur
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Shreya Nagar
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Riddhi Mehta
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Kyle Sahadeo
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA
| | - Ales Vancura
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.
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13
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Christensen IB, Abrahamsen M, Ribas L, Buch‐Larsen K, Marina D, Andersson M, Larsen S, Schwarz P, Dela F, Gillberg L. Peripheral blood mononuclear cells exhibit increased mitochondrial respiration after adjuvant chemo- and radiotherapy for early breast cancer. Cancer Med 2023; 12:16985-16996. [PMID: 37439084 PMCID: PMC10501284 DOI: 10.1002/cam4.6333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/20/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Adjuvant chemo- and radiotherapy cause cellular damage to tumorous and healthy dividing cells. Chemotherapy has been shown to cause mitochondrial respiratory dysfunction in non-tumorous tissues, but the effects on human peripheral blood mononuclear cells (PBMCs) remain unknown. AIM We aimed to investigate mitochondrial respiration of PBMCs before and after adjuvant chemo- and radiotherapy in postmenopausal patients with early breast cancer (EBC) and relate these to metabolic parameters of the patients. METHODS Twenty-three postmenopausal women diagnosed with EBC were examined before and shortly after chemotherapy with (n = 18) or without (n = 5) radiotherapy. Respiration (O2 flux per million PBMCs) was assessed by high-resolution respirometry of intact and permeabilized PBMCs. Clinical metabolic characteristics and mitochondrial DNA (mtDNA) content of PBMCs (mtDN relative to nuclear DNA) were furthermore assessed. RESULTS Respiration of intact and permeabilized PBMCs from EBC patients significantly increased with adjuvant chemo- and radiotherapy (p = 6 × 10-5 and p = 1 × 10-7 , respectively). The oxygen flux attributed to specific mitochondrial complexes and respiratory states increased by 17-43% compared to before therapy initiation. Similarly, PBMC mtDNA content increased by 40% (p = 0.002). Leukocytes (p = 0.0001), hemoglobin (p = 0.0003), and HDL cholesterol (p = 0.003) concentrations decreased whereas triglyceride (p = 0.01) and LDL (p = 0.02) concentrations increased after treatment suggesting a worsened metabolic state. None of the metabolic parameters or the mtDNA content of PBMCs correlated significantly with PBMC respiration. CONCLUSION This study shows that mitochondrial respiration and mtDNA content in circulating PBMCs increase after adjuvant chemo- and radiotherapy in postmenopausal patients with EBC. Besides the increased mtDNA content, a shift in PBMC subpopulation proportions towards cells relying on oxidative phosphorylation, who may be less sensitive to chemotherapy, might influence the increased mitochondrial respiration observed iafter chemotherapy.
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Affiliation(s)
| | | | - Lucas Ribas
- Xlab, Department of Biomedical SciencesUniversity of CopenhagenCopenhagenDenmark
| | | | - Djordje Marina
- Department of EndocrinologyRigshospitaletCopenhagenDenmark
| | | | - Steen Larsen
- Xlab, Department of Biomedical SciencesUniversity of CopenhagenCopenhagenDenmark
- Clinical Research CentreMedical University of BialystokBialystokPoland
| | - Peter Schwarz
- Department of EndocrinologyRigshospitaletCopenhagenDenmark
- Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Flemming Dela
- Xlab, Department of Biomedical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of GeriatricsBispebjerg University HospitalCopenhagenDenmark
| | - Linn Gillberg
- Xlab, Department of Biomedical SciencesUniversity of CopenhagenCopenhagenDenmark
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14
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Casimir L, Zimmer S, Racine-Brassard F, Goudreau F, Jacques PÉ, Maréchal A. Chronic treatment with ATR and CHK1 inhibitors does not substantially increase the mutational burden of human cells. Mutat Res 2023; 827:111834. [PMID: 37531716 DOI: 10.1016/j.mrfmmm.2023.111834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023]
Abstract
DNA replication stress (RS) entails the frequent slow down and arrest of replication forks by a variety of conditions that hinder accurate and processive genome duplication. Elevated RS leads to genome instability, replication catastrophe and eventually cell death. RS is particularly prevalent in cancer cells and its exacerbation to unsustainable levels by chemotherapeutic agents remains a cornerstone of cancer treatments. The adverse consequences of RS are normally prevented by the ATR and CHK1 checkpoint kinases that stabilize stressed forks, suppress origin firing and promote cell cycle arrest when replication is perturbed. Specific inhibitors of these kinases have been developed and shown to potentiate RS and cell death in multiple in vitro cancer settings. Ongoing clinical trials are now probing their efficacy against various cancer types, either as single agents or in combination with mainstay chemotherapeutics. Despite their promise as valuable additions to the anti-cancer pharmacopoeia, we still lack a genome-wide view of the potential mutagenicity of these new drugs. To investigate this question, we performed chronic long-term treatments of TP53-depleted human cancer cells with ATR and CHK1 inhibitors (ATRi, AZD6738/ceralasertib and CHK1i, MK8776/SCH-900776). ATR or CHK1 inhibition did not significantly increase the mutational burden of cells, nor generate specific mutational signatures. Indeed, no notable changes in the numbers of base substitutions, short insertions/deletions and larger scale rearrangements were observed despite induction of replication-associated DNA breaks during treatments. Interestingly, ATR inhibition did induce a slight increase in closely-spaced mutations, a feature previously attributed to translesion synthesis DNA polymerases. The results suggest that ATRi and CHK1i do not have substantial mutagenic effects in vitro when used as standalone agents.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Félix Goudreau
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke J1K 2R1, QC, Canada; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke J1K 2R1, QC, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke J1H 5N3, QC, Canada.
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15
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Ding Y, Xiu H, Zhang Y, Ke M, Lin L, Yan H, Hu P, Xiao M, He X, Zhang T. Learning and Investigation of the Role of Angiotensin-Converting Enzyme in Radiotherapy for Nasopharyngeal Carcinoma. Biomedicines 2023; 11:1581. [PMID: 37371679 DOI: 10.3390/biomedicines11061581] [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: 04/09/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Ionizing radiation (IR) is an important treatment for nasopharyngeal carcinoma (NPC) that mainly kills tumor cells by producing large amounts of reactive oxygen species (ROS). Intracellular ROS levels affect the sensitivity of tumor cells to IR. Recently, angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin-converting enzyme (ACE) have been found to affect the intracellular levels of ROS. Therefore, we performed a health informatics assessment of ACE in the TCGA database. We explored the effect of ACE in NPC cells. We found that either knockdown of ACE or inhibition of ACE by enalaprilat could decrease ROS levels in NPC cells. Furthermore, knockdown of ACE or inhibition of ACE by enalaprilat could reduce IR-induced ROS levels. ACE knockdown or inhibition reduced IR-induced DNA damage and apoptosis. ACE overexpression increased the level of ROS in NPC cells and further increased sensitivity to IR. These findings indicate that ACE influences the effect of IR by regulating the level of ROS in NPC cells.
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Affiliation(s)
- Yanan Ding
- Department of Otolaryngology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
| | - Huanhuan Xiu
- Department of Anesthesiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510062, China
| | - Yanling Zhang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Miaola Ke
- Department of Blood Transfusion, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Letao Lin
- Minimally Invasive Interventional Division, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Huzheng Yan
- Department of Interventional Radiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Pan Hu
- Minimally Invasive Interventional Division, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Meigui Xiao
- Minimally Invasive Interventional Division, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xu He
- Interventional Medical Center, Zhuhai People's Hospital, Zhuhai 519050, China
| | - Tao Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
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16
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Anand J, Chiou L, Sciandra C, Zhang X, Hong J, Wu D, Zhou P, Vaziri C. Roles of trans-lesion synthesis (TLS) DNA polymerases in tumorigenesis and cancer therapy. NAR Cancer 2023; 5:zcad005. [PMID: 36755961 PMCID: PMC9900426 DOI: 10.1093/narcan/zcad005] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/10/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
DNA damage tolerance and mutagenesis are hallmarks and enabling characteristics of neoplastic cells that drive tumorigenesis and allow cancer cells to resist therapy. The 'Y-family' trans-lesion synthesis (TLS) DNA polymerases enable cells to replicate damaged genomes, thereby conferring DNA damage tolerance. Moreover, Y-family DNA polymerases are inherently error-prone and cause mutations. Therefore, TLS DNA polymerases are potential mediators of important tumorigenic phenotypes. The skin cancer-propensity syndrome xeroderma pigmentosum-variant (XPV) results from defects in the Y-family DNA Polymerase Pol eta (Polη) and compensatory deployment of alternative inappropriate DNA polymerases. However, the extent to which dysregulated TLS contributes to the underlying etiology of other human cancers is unclear. Here we consider the broad impact of TLS polymerases on tumorigenesis and cancer therapy. We survey the ways in which TLS DNA polymerases are pathologically altered in cancer. We summarize evidence that TLS polymerases shape cancer genomes, and review studies implicating dysregulated TLS as a driver of carcinogenesis. Because many cancer treatment regimens comprise DNA-damaging agents, pharmacological inhibition of TLS is an attractive strategy for sensitizing tumors to genotoxic therapies. Therefore, we discuss the pharmacological tractability of the TLS pathway and summarize recent progress on development of TLS inhibitors for therapeutic purposes.
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Affiliation(s)
- Jay Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lilly Chiou
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carly Sciandra
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xingyuan Zhang
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
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17
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Khan M, Du K, Ai M, Wang B, Lin J, Ren A, Chen C, Huang Z, Qiu W, Yuan Y, Tian Y. PD-L1 expression as biomarker of efficacy of PD-1/PD-L1 checkpoint inhibitors in metastatic triple negative breast cancer: A systematic review and meta-analysis. Front Immunol 2023; 14:1060308. [PMID: 36949944 PMCID: PMC10027008 DOI: 10.3389/fimmu.2023.1060308] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
Background Inhibitors of programmed cell death 1 (PD-1)/programmed cell death ligand 1(PD-L1) checkpoint have been approved for metastatic triple negative breast cancer (mTNBC) in patients positive for PD-L1 expression. Negative results from the recent phase III trials (IMPassion131 and IMPassion132) have raises questions on the efficacy of PD-1/PD-L1 checkpoint inhibitors and the predictive value of PD-L1 expression. Here we attempt to systematically analyze the biomarker value of PD-L1 expression for predicting the response of PD-1/PD-L1 checkpoint inhibitors in mTNBC. Materials and methods PubMed database was searched until Dec 2021 for studies evaluating PD-1/PD-L1 checkpoint inhibitors plus/minus chemotherapy in mTNBC. Outcome of interest included objective response rate (ORR), progression-free survival (PFS), and overall survival (OS). Review Manager (RevMan) version 5.4. was used for data-analysis. Results In total, 20 clinical trials comprising 3962 mTNBC patients (ICT: 2665 (67%); CT: 1297 (33%) were included in this study. Overall ORR was 22% (95%CI, 14-30%) and significant improvement was observed for PD-L1+ patients (ORR 1.78 [95%CI, 1.45-2.19], p<0.00001) as compared to PD-L1- cohort. Pooled outcome also indicated a significant 1-year PFS and 2-year OS advantage for patients with PD-L1 expression (1-year PFS: ORR 1.39 [95%CI, 1.04-1.85], p=0.02; I2 = 0%; 2-year OS: (ORR 2.47 [95%CI, 1.30-4.69], p=0.006; I2 = 63%). Subgroup analysis indicated that PD-L1 expression can successfully predict tumor response and 2-year OS benefit in mTNBC patients regardless of the type of investigating agent, line of treatment administration, and to some extent the type of treatment. Biomarker ability of PD-L1 expression to predict 1-year PFS was slightly better with pembrolizumab (p=0.09) than atezolizumab (p=0.18), and significantly better when treatment was administered in the first-line setting (OR 1.38 [95%CI, 1.02-1.87], p=0.04) and chemotherapy was added (OR 1.38 [95%CI, 1.02-1.86], p=0.03). Immune-related toxicity of any grade and grade≥3 was 39% (95%CI, 26%-52%) and 10% (95%CI, 8%-13%), respectively. Conclusions PD-L1 expression can predict objective response rate and 2-year OS in mTNBC patients receiving PD-1/PD-L1 checkpoint inhibitors. One-year PFS is also predicted in selected patients. PD-L1 expression can be a useful biomarker of efficacy of PD-1/PD-L1 checkpoint inhibitors in mTNBC.
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Affiliation(s)
- Muhammad Khan
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Kunpeng Du
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Meiling Ai
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Baiyao Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jie Lin
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Anbang Ren
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Chengcong Chen
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Zhong Huang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Wenze Qiu
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yawei Yuan
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Yunhong Tian, ; Yawei Yuan,
| | - Yunhong Tian
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Yunhong Tian, ; Yawei Yuan,
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18
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Thol K, Pawlik P, McGranahan N. Therapy sculpts the complex interplay between cancer and the immune system during tumour evolution. Genome Med 2022; 14:137. [PMID: 36476325 PMCID: PMC9730559 DOI: 10.1186/s13073-022-01138-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer development is an evolutionary process. A key selection pressure is exerted by therapy, one of the few players in cancer evolution that can be controlled. As such, an understanding of how treatment acts to sculpt the tumour and its microenvironment and how this influences a tumour's subsequent evolutionary trajectory is critical. In this review, we examine cancer evolution and intra-tumour heterogeneity in the context of therapy. We focus on how radiotherapy, chemotherapy and immunotherapy shape both tumour development and the environment in which tumours evolve and how resistance can develop or be selected for during treatment.
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Affiliation(s)
- Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Piotr Pawlik
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
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19
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Attili A, Scifoni E, Tommasino F. Modelling the HPRT-gene mutation induction of particle beams: systematic in vitro data collection, analysis and microdosimetric kinetic model implementation. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac8c80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/24/2022] [Indexed: 11/11/2022]
Abstract
Abstract
Objective. Since the early years, particle therapy treatments have been associated with concerns for late toxicities, especially secondary cancer risk (SCR). Nowadays, this concern is related to patients for whom long-term survival is expected (e.g. breast cancer, lymphoma, paediatrics). In the aim to contribute to this research, we present a dedicated statistical and modelling analysis aiming at improving our understanding of the RBE for mutation induction (
RBE
M
˜
) for different particle species. Approach. We built a new database based on a systematic collection of RBE data for mutation assays of the gene encoding for the purine salvage enzyme hypoxanthine-guanine phosphoribosyltransferase from literature (105 entries, distributed among 3 cell lines and 16 particle species). The data were employed to perform statistical and modelling analysis. For the latter, we adapted the microdosimetric kinetic model (MKM) to describe the mutagenesis in analogy to lethal lesion induction. Main results. Correlation analysis between RBE for survival (RBES) and
RBE
M
˜
reveals significant correlation between these two quantities (ρ = 0.86, p < 0.05). The correlation gets stronger when looking at subsets of data based on cell line and particle species. We also show that the MKM can be successfully employed to describe
RBE
M
˜
,
obtaining comparably good agreement with the experimental data. Remarkably, to improve the agreement with experimental data the MKM requires, consistently in all the analysed cases, a reduced domain size for the description of mutation induction compared to that adopted for survival. Significance. We were able to show that RBES and
RBE
M
˜
are strongly related quantities. We also showed for the first time that the MKM could be successfully applied to the description of mutation induction, representing an endpoint different from the more traditional cell killing. In analogy to the RBES,
RBE
M
˜
can be implemented into treatment planning system evaluations.
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20
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Kumari S, Sharma S, Advani D, Khosla A, Kumar P, Ambasta RK. Unboxing the molecular modalities of mutagens in cancer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62111-62159. [PMID: 34611806 PMCID: PMC8492102 DOI: 10.1007/s11356-021-16726-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 04/16/2023]
Abstract
The etiology of the majority of human cancers is associated with a myriad of environmental causes, including physical, chemical, and biological factors. DNA damage induced by such mutagens is the initial step in the process of carcinogenesis resulting in the accumulation of mutations. Mutational events are considered the major triggers for introducing genetic and epigenetic insults such as DNA crosslinks, single- and double-strand DNA breaks, formation of DNA adducts, mismatched bases, modification in histones, DNA methylation, and microRNA alterations. However, DNA repair mechanisms are devoted to protect the DNA to ensure genetic stability, any aberrations in these calibrated mechanisms provoke cancer occurrence. Comprehensive knowledge of the type of mutagens and carcinogens and the influence of these agents in DNA damage and cancer induction is crucial to develop rational anticancer strategies. This review delineated the molecular mechanism of DNA damage and the repair pathways to provide a deep understanding of the molecular basis of mutagenicity and carcinogenicity. A relationship between DNA adduct formation and cancer incidence has also been summarized. The mechanistic basis of inflammatory response and oxidative damage triggered by mutagens in tumorigenesis has also been highlighted. We elucidated the interesting interplay between DNA damage response and immune system mechanisms. We addressed the current understanding of DNA repair targeted therapies and DNA damaging chemotherapeutic agents for cancer treatment and discussed how antiviral agents, anti-inflammatory drugs, and immunotherapeutic agents combined with traditional approaches lay the foundations for future cancer therapies.
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Affiliation(s)
- Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Sudhanshu Sharma
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Dia Advani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Akanksha Khosla
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
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21
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Bernstein AP, Loloi J, Reddy R, Ramsoomair C, Campbell K, Maura F, Landgren O, Nassau D, Ibrahim E, Ramasamy R. Mutagenic effect of chemotherapy on sperm DNA and implications for family planning. Nat Rev Urol 2022; 19:511-512. [PMID: 35906486 DOI: 10.1038/s41585-022-00625-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ari P Bernstein
- Department of Urology, New York University Langone Health, New York, NY, USA
| | - Justin Loloi
- Department of Urology, Montefiore Medical Center, Bronx, NY, USA
| | - Rohit Reddy
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | | | - Francesco Maura
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ola Landgren
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Daniel Nassau
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Urology, Nicklaus Children's Hospital, Miami, FL, USA
| | - Emad Ibrahim
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ranjith Ramasamy
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, USA.
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22
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Weinstock LB, Brook JB, Molderings GJ. Efficacy and toxicity of hydroxyurea in mast cell activation syndrome patients refractory to standard medical therapy: retrospective case series. Naunyn Schmiedebergs Arch Pharmacol 2022; 395:1441-1447. [PMID: 35982335 PMCID: PMC9388361 DOI: 10.1007/s00210-022-02282-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/11/2022] [Indexed: 12/04/2022]
Abstract
Determine efficacy and adverse events (AEs) of hydroxyurea (HU) in mast cell activation syndrome (MCAS) patients who were refractory to standard medical therapy. An electronic chart review was performed to find MCAS patients who received HU in a MCAS medical practice. Diagnosis of MCAS was established on the basis of mast cell (MC) activation symptoms in ≥ 5 systems plus ≥ 1 abnormal MC mediators and/or ≥ 20 MC/high power field on duodenal biopsies. Medicines not providing significant clinical improvement prior to HU were tabulated. The following symptoms were evaluated by patients on a 0–10 scale prior to and at the study conclusion: bone pain, abdominal pain, diarrhea, bloating, and nausea. Safety labs were obtained on a regular basis. Twenty out of three hundred ten (8.4%) MCAS patients received HU. Patients included 22 females, average age 42.4 years. Dysautonomia was present in 60%. An average of 10.6 (SD 1.7, range 8–13) medications were used prior to adding HU to various concomitant medications. Average dose of HU was 634 mg. In 20 patients who continued therapy for ≥ 2 months, there was statistically significant reduction of bone pain, abdominal pain, diarrhea, bloating, and nausea. Fourteen patients noted prolonged success with therapy. Six patients stopped HU within 6 weeks owing to AEs. Four patients treated ≥ 2 months had AEs and 2 led to HU cessation. All AEs were reversible. Refractory MCAS patients showed clear significant improvement in bone pain and gastrointestinal symptoms on HU. Systematic monitoring was effective in preventing the occurrence of severe HU-induced adverse events.
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Affiliation(s)
- Leonard B Weinstock
- Clinical Medicine, Department of Medicine, Washington University School of Medicine, President, Specialists in Gastroenterology, 11525 Olde Cabin Road, St. Louis, MO, 63141, USA
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23
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Abstract
The evolutionary history of hepatobiliary cancers is embedded in their genomes. By analysing their catalogue of somatic mutations and the DNA sequence context in which they occur, it is possible to infer the mechanisms underpinning tumorigenesis. These mutational signatures reflect the exogenous and endogenous origins of genetic damage as well as the capacity of hepatobiliary cells to repair and replicate DNA. Genomic analysis of thousands of patients with hepatobiliary cancers has highlighted the diversity of mutagenic processes active in these malignancies, highlighting a prominent source of the inter-cancer-type, inter-patient, intertumour and intratumoural heterogeneity that is observed clinically. However, a substantial proportion of mutational signatures detected in hepatocellular carcinoma and biliary tract cancer remain of unknown cause, emphasizing the important contribution of processes yet to be identified. Exploiting mutational signatures to retrospectively understand hepatobiliary carcinogenesis could advance preventative management of these aggressive tumours as well as potentially predict treatment response and guide the development of therapies targeting tumour evolution.
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24
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Levatić J, Salvadores M, Fuster-Tormo F, Supek F. Mutational signatures are markers of drug sensitivity of cancer cells. Nat Commun 2022; 13:2926. [PMID: 35614096 PMCID: PMC9132939 DOI: 10.1038/s41467-022-30582-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Genomic analyses have revealed mutational footprints associated with DNA maintenance gone awry, or with mutagen exposures. Because cancer therapeutics often target DNA synthesis or repair, we asked if mutational signatures make useful markers of drug sensitivity. We detect mutational signatures in cancer cell line exomes (where matched healthy tissues are not available) by adjusting for the confounding germline mutation spectra across ancestries. We identify robust associations between various mutational signatures and drug activity across cancer cell lines; these are as numerous as associations with established genetic markers such as driver gene alterations. Signatures of prior exposures to DNA damaging agents – including chemotherapy – tend to associate with drug resistance, while signatures of deficiencies in DNA repair tend to predict sensitivity towards particular therapeutics. Replication analyses across independent drug and CRISPR genetic screening data sets reveal hundreds of robust associations, which are provided as a resource for drug repurposing guided by mutational signature markers. Mutational signatures can reveal the impact of mutagenic processes in cancer, including exposure to therapy. Here, the authors develop an approach that can accurately predict drug responses in cancer using mutational signatures while simultaneously correcting for germline variants with an ancestry matching procedure.
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Affiliation(s)
- Jurica Levatić
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Marina Salvadores
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Francisco Fuster-Tormo
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain.,MDS Group, Josep Carreras Leukaemia Research Institute, Ctra de Can Ruti, Camí de les Escoles s/n, 08916, Badalona, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, C/ Baldiri Reixac 10, 08028, Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010, Barcelona, Spain.
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25
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Gutierrez C, Vilas CK, Wu CJ, Al'Khafaji AM. Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer. Front Immunol 2022; 13:859032. [PMID: 35603167 PMCID: PMC9120583 DOI: 10.3389/fimmu.2022.859032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
The therapeutic landscape across many cancers has dramatically improved since the introduction of potent targeted agents and immunotherapy. Nonetheless, success of these approaches is too often challenged by the emergence of therapeutic resistance, fueled by intratumoral heterogeneity and the immense evolutionary capacity inherent to cancers. To date, therapeutic strategies have attempted to outpace the evolutionary tempo of cancer but frequently fail, resulting in lack of tumor response and/or relapse. This realization motivates the development of novel therapeutic approaches which constrain evolutionary capacity by reducing the degree of intratumoral heterogeneity prior to treatment. Systematic development of such approaches first requires the ability to comprehensively characterize heterogeneous populations over the course of a perturbation, such as cancer treatment. Within this context, recent advances in functionalized lineage tracing approaches now afford the opportunity to efficiently measure multimodal features of clones within a tumor at single cell resolution, enabling the linkage of these features to clonal fitness over the course of tumor progression and treatment. Collectively, these measurements provide insights into the dynamic and heterogeneous nature of tumors and can thus guide the design of homogenization strategies which aim to funnel heterogeneous cancer cells into known, targetable phenotypic states. We anticipate the development of homogenization therapeutic strategies to better allow for cancer eradication and improved clinical outcomes.
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Affiliation(s)
- Catherine Gutierrez
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Caroline K Vilas
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, United States
| | - Catherine J Wu
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
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26
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The interplay between anticancer challenges and the microbial communities from the gut. Eur J Clin Microbiol Infect Dis 2022; 41:691-711. [PMID: 35353280 DOI: 10.1007/s10096-022-04435-2] [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: 12/22/2021] [Accepted: 03/15/2022] [Indexed: 11/03/2022]
Abstract
Cancer being an increasing burden on human health, the use of anticancer drugs has risen over the last decades. The physiological effects of these drugs are not only perceived by the host's cells but also by the microbial cells it harbors as commensals, notably the gut microbiota. Since the early '50 s, the cytotoxicity of anticancer chemotherapy was evaluated on bacteria revealing some antimicrobial activities that result in an established perturbation of the gut microbiota. This perturbation can affect the host's health through dysbiosis, which can lead to multiple complications, but has also been shown to have a direct effect on the treatment efficiency.We, therefore, conducted a review of literature focusing on this triangular relationship involving the microbial communities from the gut, the host's disease, and the anticancer treatment. We focused specifically on the antimicrobial effects of anticancer chemotherapy, their impact on mutagenesis in bacteria, and the perspectives of using bacteria-based tools to help in the diagnostic and treatment of cancer.
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27
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DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
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Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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28
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Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy. Clin Sci (Lond) 2022; 136:383-404. [PMID: 35274136 PMCID: PMC8919091 DOI: 10.1042/cs20210682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/02/2022] [Accepted: 02/28/2022] [Indexed: 12/15/2022]
Abstract
Genome sequencing can be used to detect DNA repair failures in tumors and learn about underlying mechanisms. Here, we synthesize findings from genomic studies that examined deficiencies of the DNA mismatch repair (MMR) pathway. The impairment of MMR results in genome-wide hypermutation and in the ‘microsatellite instability’ (MSI) phenotype—occurrence of indel mutations at short tandem repeat (microsatellite) loci. The MSI status of tumors was traditionally assessed by molecular testing of a selected set of MS loci or by measuring MMR protein expression levels. Today, genomic data can provide a more complete picture of the consequences on genomic instability. Multiple computational studies examined somatic mutation distributions that result from failed DNA repair pathways in tumors. These include analyzing the commonly studied trinucleotide mutational spectra of single-nucleotide variants (SNVs), as well as of other features such as indels, structural variants, mutation clusters and regional mutation rate redistribution. The identified mutation patterns can be used to rigorously measure prevalence of MMR failures across cancer types, and potentially to subcategorize the MMR deficiencies. Diverse data sources, genomic and pre-genomic, from human and from experimental models, suggest there are different ways in which MMR can fail, and/or that the cell-type or genetic background may result in different types of MMR mutational patterns. The spectrum of MMR failures may direct cancer evolution, generating particular sets of driver mutations. Moreover, MMR affects outcomes of therapy by DNA damaging drugs, antimetabolites, nonsense-mediated mRNA decay (NMD) inhibitors, and immunotherapy by promoting either resistance or sensitivity, depending on the type of therapy.
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29
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Singh SK, Mukerjee A, Gupta P, Kumar Tripathi A. Evaluation of Antigenotoxic Effect of Cinnamon Oil and Usnic Acid Blended Nanoemulsion on Swiss Albino Mice. BIONANOSCIENCE 2022. [DOI: 10.1007/s12668-021-00902-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Póti Á, Szikriszt B, Gervai JZ, Chen D, Szüts D. Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis. PLoS Genet 2022; 18:e1010051. [PMID: 35130276 PMCID: PMC8870599 DOI: 10.1371/journal.pgen.1010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/24/2022] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
Translesion DNA synthesis (TLS) is a fundamental damage bypass pathway that utilises specialised polymerases with relaxed template specificity to achieve replication through damaged DNA. Misinsertions by low fidelity TLS polymerases may introduce additional mutations on undamaged DNA near the original lesion site, which we termed collateral mutations. In this study, we used whole genome sequencing datasets of chicken DT40 and several human cell lines to obtain evidence for collateral mutagenesis in higher eukaryotes. We found that cisplatin and UVC radiation frequently induce close mutation pairs within 25 base pairs that consist of an adduct-associated primary and a downstream collateral mutation, and genetically linked their formation to TLS activity involving PCNA ubiquitylation and polymerase κ. PCNA ubiquitylation was also indispensable for close mutation pairs observed amongst spontaneously arising base substitutions in cell lines with disrupted homologous recombination. Collateral mutation pairs were also found in melanoma genomes with evidence of UV exposure. We showed that collateral mutations frequently copy the upstream base, and extracted a base substitution signature that describes collateral mutagenesis in the presented dataset regardless of the primary mutagenic process. Using this mutation signature, we showed that collateral mutagenesis creates approximately 10–20% of non-paired substitutions as well, underscoring the importance of the process. DNA base substitutions are the most common form of genomic mutations, formed both spontaneously and in response to environmental mutagens. One of the main mechanisms of base substitution mutagenesis is translesion synthesis, a process that relies on specialised DNA polymerases to replicate damaged DNA templates. In addition to incorrect base insertions at the site of lesions in the template, translesion polymerases may also generate ‘collateral’ mutations away from the lesion due to their lower accuracy in selecting the correct incoming nucleotide. In this study, we surveyed the whole genome sequence of experimental cell clones to examine the extent and genetic dependence of collateral mutagenesis in higher eukaryotes. Looking for close mutation pairs, we found that collateral mutations frequently occur near primary lesions generated by cisplatin or ultraviolet radiation in chicken and human cells, but are restricted to a short distance of approximately 25 base pairs. By analysing their sequence context, we showed that collateral mutations can also occur near correctly bypassed primary lesions and may be responsible for a considerable proportion of all base substitution mutations.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- * E-mail:
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31
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Brady SW, Gout AM, Zhang J. Therapeutic and prognostic insights from the analysis of cancer mutational signatures. Trends Genet 2022; 38:194-208. [PMID: 34483003 PMCID: PMC8752466 DOI: 10.1016/j.tig.2021.08.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The somatic mutations in each cancer genome are caused by multiple mutational processes, each of which leaves a characteristic imprint (or 'signature'), potentially caused by specific etiologies or exposures. Deconvolution of these signatures offers a glimpse into the evolutionary history of individual tumors. Recent work has shown that mutational signatures may also yield therapeutic and prognostic insights, including the identification of cell-intrinsic signatures as biomarkers of drug response and prognosis. For example, mutational signatures indicating homologous recombination deficiency are associated with poly(ADP)-ribose polymerase (PARP) inhibitor sensitivity, whereas APOBEC-associated signatures are associated with ataxia telangiectasia and Rad3-related kinase (ATR) inhibitor sensitivity. Furthermore, therapy-induced mutational signatures implicated in cancer progression have also been uncovered, including the identification of thiopurine-induced TP53 mutations in leukemia. In this review, we explore the various ways mutational signatures can reveal new therapeutic and prognostic insights, thus extending their traditional role in identifying disease etiology.
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Affiliation(s)
- Samuel W Brady
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Alexander M Gout
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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32
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Chen D, Gervai JZ, Póti Á, Németh E, Szeltner Z, Szikriszt B, Gyüre Z, Zámborszky J, Ceccon M, d'Adda di Fagagna F, Szallasi Z, Richardson AL, Szüts D. BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1. Nat Commun 2022; 13:226. [PMID: 35017534 PMCID: PMC8752635 DOI: 10.1038/s41467-021-27872-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/15/2021] [Indexed: 12/25/2022] Open
Abstract
Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The inactivation of 53BP1 in BRCA1 mutant cells markedly reduces TLS-specific mutagenesis, and rescues the deficiency of template switch-mediated gene conversions in the immunoglobulin V locus of BRCA1 mutant chicken DT40 cells. 53BP1 also promotes TLS in human cellular extracts in vitro. Our results show that HR deficiency-specific mutagenesis is largely caused by TLS, and suggest a function for 53BP1 in regulating the choice between TLS and error-free template switching in replicative DNA damage bypass.
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Affiliation(s)
- Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, Budapest, H-1085, Hungary
| | - Judit Zámborszky
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Marta Ceccon
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital and Harvard Medical School, Boston, MA, 02215, USA
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, H-1092, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.
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33
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Development of a G2/M arrest high-throughput screening method identifies potent radiosensitizers. Transl Oncol 2022; 16:101336. [PMID: 34986454 PMCID: PMC8732089 DOI: 10.1016/j.tranon.2021.101336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022] Open
Abstract
Radiation is a powerful tool used to control tumor growth and induce an immune response; however, it is limited by damage to surrounding tissue and adverse effects such skin irritation. Breast cancer patients in particular may endure radiation dermatitis, and potentially lymphedema, after a course of radiotherapy. Radio-sensitizing small molecule drugs may enable lower effective doses of both radiation and chemotherapy to minimize toxicity to healthy tissue. In this study, we identified a novel high-throughput method for screening radiosensitizers by image analysis of nuclear size and cell cycle. In vitro assays were performed on cancer cells lines to assess combined therapeutic and radiation effects. In vivo, radiation in combination with proflavine hemisulfate led to enhanced efficacy demonstrated by improved tumor volume control in mice bearing syngeneic breast tumors. This study provides a proof of concept for utilizing G2/M stall as a predictor of radiosensitization and is the first report of a flavin acting as an X-ray radiation enhancer in a breast cancer mouse model.
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34
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Li X, Thirumalai D. A mathematical model for phenotypic heterogeneity in breast cancer with implications for therapeutic strategies. J R Soc Interface 2022; 19:20210803. [PMID: 35078336 PMCID: PMC8790361 DOI: 10.1098/rsif.2021.0803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Inevitably, almost all cancer patients develop resistance to targeted therapy. Intratumour heterogeneity is a major cause of drug resistance. Mathematical models that explain experiments quantitatively are useful in understanding the origin of intratumour heterogeneity, which then could be used to explore scenarios for efficacious therapy. Here, we develop a mathematical model to investigate intratumour heterogeneity in breast cancer by exploiting the observation that HER2+ and HER2- cells could divide symmetrically or asymmetrically. Our predictions for the evolution of cell fractions are in quantitative agreement with single-cell experiments. Remarkably, the colony size of HER2+ cells emerging from a single HER2- cell (or vice versa), which occurs in about four cell doublings, also agrees with experimental results, without tweaking any parameter in the model. The theory explains experimental data on the responses of breast tumours under different treatment protocols. We then used the model to predict that, not only the order of two drugs, but also the treatment period for each drug and the tumour cell plasticity could be manipulated to improve the treatment efficacy. Mathematical models, when integrated with data on patients, make possible exploration of a broad range of parameters readily, which might provide insights in devising effective therapies.
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Affiliation(s)
- Xin Li
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
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35
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Long MJC, Ly P, Aye Y. Still no Rest for the Reductases: Ribonucleotide Reductase (RNR) Structure and Function: An Update. Subcell Biochem 2022; 99:155-197. [PMID: 36151376 DOI: 10.1007/978-3-031-00793-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herein we present a multidisciplinary discussion of ribonucleotide reductase (RNR), the essential enzyme uniquely responsible for conversion of ribonucleotides to deoxyribonucleotides. This chapter primarily presents an overview of this multifaceted and complex enzyme, covering RNR's role in enzymology, biochemistry, medicinal chemistry, and cell biology. It further focuses on RNR from mammals, whose interesting and often conflicting roles in health and disease are coming more into focus. We present pitfalls that we think have not always been dealt with by researchers in each area and further seek to unite some of the field-specific observations surrounding this enzyme. Our work is thus not intended to cover any one topic in extreme detail, but rather give what we consider to be the necessary broad grounding to understand this critical enzyme holistically. Although this is an approach we have advocated in many different areas of scientific research, there is arguably no other single enzyme that embodies the need for such broad study than RNR. Thus, we submit that RNR itself is a paradigm of interdisciplinary research that is of interest from the perspective of the generalist and the specialist alike. We hope that the discussions herein will thus be helpful to not only those wanting to tackle RNR-specific problems, but also those working on similar interdisciplinary projects centering around other enzymes.
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Affiliation(s)
- Marcus J C Long
- University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Biochemistry, UNIL, Epalinges, Switzerland
| | - Phillippe Ly
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- EPFL SB ISIC LEAGO, Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- EPFL SB ISIC LEAGO, Lausanne, Switzerland.
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36
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Kato G, Mitome H, Shigematsu S, Utsunomiya A, Shimasaki M, Sasaki Y, Maki T, Yamamoto H, Tanabe T, Funahashi T, Hatae N, Hidaka N, Tanaka M, Akira K. Degradation and inactivation efficacy of ozone water for antineoplastic drugs in hospital settings. J Oncol Pharm Pract 2021; 28:1781-1789. [PMID: 34709082 DOI: 10.1177/10781552211042525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Occupational exposure to antineoplastic drugs in hospital settings is recognized to be hazardous, and as such environmental decontamination including degradation and inactivation of such drugs is recommended. To data, although various agents such as oxidants have been reported to be useful for decontamination, simpler, safer, and more convenient methods are required. In this study, the degradation and inactivation efficacy of ozone water, which has newly been introduced for decontamination of antineoplastic drugs in spills, was investigated for formulations of gemcitabine, irinotecan, and paclitaxel. METHODS Antineoplastic formulations (medicinal ingredient: ∼1.5 μmol) were mixed with 50 mL of ozone water (>4 mg/L). The reactions were monitored by high-performance liquid chromatography, and the degradation mixtures were analyzed by 1H nuclear magnetic resonance spectroscopy in order to obtain the structural information of the degradation products. The formulations of gemcitabine and irinotecan and those degradation mixtures were evaluated for their mutagenicity using the Ames test and cytotoxicity against human cancer cells. RESULTS gemcitabine and irinotecan were found to be readily degraded by the ozone treatment, and their active sites were suggested to be degraded. In contrast, paclitaxel was hard to be decomposed, possibly owing to the consumption of ozone by the polyoxyethylene castor oil added as a pharmaceutical additive of the formulation. No significant mutagenic changes of Salmonella typhimurium strains used for the Ames test were observed for the samples within the concentration ranges examined. The ozone treatment showed obvious increases in cell viability for gemcitabine formulation, and mild increases for irinotecan formulation. CONCLUSIONS Ozone water was shown to be effective as a decomposition agent for the antineoplastic drug formulations examined, although the efficacy depends on the chemical structures of the drugs and the pharmaceutical additives. It was also suggested that ozone treatment has a tendency to decrease the toxicity of the antineoplastic drug formulations. As such, further studies are required in order to clarify the effects and application limitations of ozone water.
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Affiliation(s)
- Ginjiro Kato
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
| | - Hidemichi Mitome
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
| | - Saki Shigematsu
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
| | - Aya Utsunomiya
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
| | - Miho Shimasaki
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
| | - Yuta Sasaki
- Division of Pharmacy, 68286National Hospital Organization Shikoku Cancer Center Japan
| | - Tsuneo Maki
- Division of Pharmacy, 68286National Hospital Organization Shikoku Cancer Center Japan
| | - Hiroshi Yamamoto
- Division of Pharmacy, 68286National Hospital Organization Shikoku Cancer Center Japan
| | - Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
| | - Tatsuya Funahashi
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
| | - Noriyuki Hatae
- Faculty of Pharmaceutical Sciences, 68348Yokohama University of Pharmacy, Japan
| | - Noriaki Hidaka
- Division of Pharmacy, 89456Ehime University Hospital, Japan
| | - Mamoru Tanaka
- Division of Pharmacy, 89456Ehime University Hospital, Japan
| | - Kazuki Akira
- Laboratory of Pharmaceutical Analytical Chemistry, College of Pharmaceutical Sciences, 12694Matsuyama University, Japan
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Martínez-Gregorio H, Rojas-Jiménez E, Mejía-Gómez JC, Díaz-Velásquez C, Quezada-Urban R, Vallejo-Lecuona F, de la Cruz-Montoya A, Porras-Reyes FI, Pérez-Sánchez VM, Maldonado-Martínez HA, Robles-Estrada M, Bargalló-Rocha E, Cabrera-Galeana P, Ramos-Ramírez M, Chirino YI, Alonso Herrera L, Terrazas LI, Frecha C, Oliver J, Perdomo S, Vaca-Paniagua F. The Evolution of Clinically Aggressive Triple-Negative Breast Cancer Shows a Large Mutational Diversity and Early Metastasis to Lymph Nodes. Cancers (Basel) 2021; 13:5091. [PMID: 34680239 PMCID: PMC8534164 DOI: 10.3390/cancers13205091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
In triple-negative breast cancer (TNBC), only 30% of patients treated with neoadjuvant chemotherapy achieve a pathological complete response after treatment and more than 90% die due to metastasis formation. The diverse clinical responses and metastatic developments are attributed to extensive intrapatient genetic heterogeneity and tumor evolution acting on this neoplasm. In this work, we aimed to evaluate genomic alterations and tumor evolution in TNBC patients with aggressive disease. We sequenced the whole exome of 16 lesions from four patients who did not respond to therapy, and took several follow-up samples, including samples from tumors before and after treatment, as well as from the lymph nodes and skin metastases. We found substantial intrapatient genetic heterogeneity, with a variable tumor mutational composition. Early truncal events were MCL1 amplifications. Metastatic lesions had deletions in RB1 and PTEN, along with TERT, AKT2, and CCNE1 amplifications. Mutational signatures 06 and 12 were mainly detected in skin metastases and lymph nodes. According to phylogenetic analysis, the lymph node metastases occurred at an early stage of TNBC development. Finally, each patient had three to eight candidate driving mutations for targeted treatments. This study delves into the genomic complexity and the phylogenetic and evolutionary development of aggressive TNBC, supporting early metastatic development, and identifies specific genetic alterations associated with a response to targeted therapies.
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Affiliation(s)
- Héctor Martínez-Gregorio
- Posgrado en Ciencias Biológicas de la Universidad Nacional Autonóma de Mexico, Facultad de Estudios Superiores Iztacala, UNAM, Mexico City 54090, Mexico;
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Ernesto Rojas-Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Javier César Mejía-Gómez
- Division of Breast Cancer, Department of Medical Oncology, Mt. Sinai Hospital, University of Toronto, Toronto, ON M5G 1X5, Canada;
| | - Clara Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
| | - Rosalía Quezada-Urban
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Fernando Vallejo-Lecuona
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Aldo de la Cruz-Montoya
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Fany Iris Porras-Reyes
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Víctor Manuel Pérez-Sánchez
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Héctor Aquiles Maldonado-Martínez
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | | | - Enrique Bargalló-Rocha
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Paula Cabrera-Galeana
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Maritza Ramos-Ramírez
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Yolanda Irasema Chirino
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Luis Alonso Herrera
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
- Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas—Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Cecilia Frecha
- Unidad de Producción Celular del Hospital Regional Universitario de Málaga—IBIMA—Málaga, 29010 Málaga, Spain;
| | - Javier Oliver
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, 29010 Málaga, Spain;
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), 150 Cours Albert Thomas, 69372 Lyon, France;
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
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Koh G, Degasperi A, Zou X, Momen S, Nik-Zainal S. Mutational signatures: emerging concepts, caveats and clinical applications. Nat Rev Cancer 2021; 21:619-637. [PMID: 34316057 DOI: 10.1038/s41568-021-00377-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/08/2021] [Indexed: 02/05/2023]
Abstract
Whole-genome sequencing has brought the cancer genomics community into new territory. Thanks to the sheer power provided by the thousands of mutations present in each patient's cancer, we have been able to discern generic patterns of mutations, termed 'mutational signatures', that arise during tumorigenesis. These mutational signatures provide new insights into the causes of individual cancers, revealing both endogenous and exogenous factors that have influenced cancer development. This Review brings readers up to date in a field that is expanding in computational, experimental and clinical directions. We focus on recent conceptual advances, underscoring some of the caveats associated with using the mutational signature frameworks and highlighting the latest experimental insights. We conclude by bringing attention to areas that are likely to see advancements in clinical applications.
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Affiliation(s)
- Gene Koh
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Xueqing Zou
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Sophie Momen
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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Pich O, Cortes-Bullich A, Muiños F, Pratcorona M, Gonzalez-Perez A, Lopez-Bigas N. The evolution of hematopoietic cells under cancer therapy. Nat Commun 2021; 12:4803. [PMID: 34376657 PMCID: PMC8355079 DOI: 10.1038/s41467-021-24858-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/29/2021] [Indexed: 02/08/2023] Open
Abstract
Chemotherapies may increase mutagenesis of healthy cells and change the selective pressures in tissues, thus influencing their evolution. However, their contributions to the mutation burden and clonal expansions of healthy somatic tissues are not clear. Here, exploiting the mutational footprint of some chemotherapies, we explore their influence on the evolution of hematopoietic cells. Cells of Acute Myeloid Leukemia (AML) secondary to treatment with platinum-based drugs show the mutational footprint of these drugs, indicating that non-malignant blood cells receive chemotherapy mutations. No trace of the 5-fluorouracil (5FU) mutational signature is found in AMLs secondary to exposure to 5FU, suggesting that cells establishing the leukemia could be quiescent during treatment. Using the platinum-based mutational signature as a barcode, we determine that the clonal expansion originating the secondary AMLs begins after the start of the cytotoxic treatment. Its absence in clonal hematopoiesis cases is consistent with the start of the clonal expansion predating the exposure to platinum-based drugs.
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Affiliation(s)
- Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Albert Cortes-Bullich
- Hematology and Hemotherapy Department, Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Pratcorona
- Hematology and Hemotherapy Department, Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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Zhou S, Hill CS, Sarkar S, Tse LV, Woodburn BMD, Schinazi RF, Sheahan TP, Baric RS, Heise MT, Swanstrom R. β-d-N4-hydroxycytidine Inhibits SARS-CoV-2 Through Lethal Mutagenesis But Is Also Mutagenic To Mammalian Cells. J Infect Dis 2021; 224:415-419. [PMID: 33961695 PMCID: PMC8136050 DOI: 10.1093/infdis/jiab247] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
Mutagenic ribonucleosides can act as broad-based antiviral agents. They are metabolized to the active ribonucleoside triphosphate form and concentrate in genomes of RNA viruses during viral replication. β-d-N4-hydroxycytidine (NHC, initial metabolite of molnupiravir) is >100-fold more active than ribavirin or favipiravir against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with antiviral activity correlated to the level of mutagenesis in virion RNA. However, NHC also displays host mutational activity in an animal cell culture assay, consistent with RNA and DNA precursors sharing a common intermediate of a ribonucleoside diphosphate. These results indicate highly active mutagenic ribonucleosides may hold risk for the host.
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Affiliation(s)
- Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Collin S Hill
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Blaide M D Woodburn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raymond F Schinazi
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Activation of DNA Damage Tolerance Pathways May Improve Immunotherapy of Mesothelioma. Cancers (Basel) 2021; 13:cancers13133211. [PMID: 34199066 PMCID: PMC8269013 DOI: 10.3390/cancers13133211] [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: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 12/20/2022] Open
Abstract
Immunotherapy based on two checkpoint inhibitors (ICI), programmed cell death 1 (PD-1, Nivolumab) and cytotoxic T-lymphocyte 4 (CTLA-4, Ipilimumab), has provided a significant improvement in overall survival for malignant mesothelioma (MM). Despite this major breakthrough, the median overall survival of patients treated with the two ICIs only reached 18.1 months vs. 14 months in standard chemotherapy. With an objective response rate of 40%, only a subset of patients benefits from immunotherapy. A critical step in the success of immunotherapy is the presentation of tumor-derived peptides by the major histocompatibility complex I (MHC-I) of tumor cells. These neoantigens are potentially immunogenic and trigger immune responses orchestrated by cytotoxic cells. In MM, tumor development is nevertheless characterized by a low mutation rate despite major structural chromosomal rearrangements driving oncogenesis (BAP1, NF2, CDKN2AB). In this opinion, we propose to investigate an approach based on the mechanisms of the DNA damage tolerance (DDT) pathways to increase the frequency of non-synonymous mutations. The idea is to transiently activate the error-prone DDT in order to generate neoantigens while preserving a fully competent antitumor immune response.
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Hawkins CJ, Miles MA. Mutagenic Consequences of Sublethal Cell Death Signaling. Int J Mol Sci 2021; 22:ijms22116144. [PMID: 34200309 PMCID: PMC8201051 DOI: 10.3390/ijms22116144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 02/06/2023] Open
Abstract
Many human cancers exhibit defects in key DNA damage response elements that can render tumors insensitive to the cell death-promoting properties of DNA-damaging therapies. Using agents that directly induce apoptosis by targeting apoptotic components, rather than relying on DNA damage to indirectly stimulate apoptosis of cancer cells, may overcome classical blocks exploited by cancer cells to evade apoptotic cell death. However, there is increasing evidence that cells surviving sublethal exposure to classical apoptotic signaling may recover with newly acquired genomic changes which may have oncogenic potential, and so could theoretically spur the development of subsequent cancers in cured patients. Encouragingly, cells surviving sublethal necroptotic signaling did not acquire mutations, suggesting that necroptosis-inducing anti-cancer drugs may be less likely to trigger therapy-related cancers. We are yet to develop effective direct inducers of other cell death pathways, and as such, data regarding the consequences of cells surviving sublethal stimulation of those pathways are still emerging. This review details the currently known mutagenic consequences of cells surviving different cell death signaling pathways, with implications for potential oncogenic transformation. Understanding the mechanisms of mutagenesis associated (or not) with various cell death pathways will guide us in the development of future therapeutics to minimize therapy-related side effects associated with DNA damage.
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Affiliation(s)
- Christine J. Hawkins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia;
| | - Mark A. Miles
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia;
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
- Correspondence:
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Szikriszt B, Póti Á, Németh E, Kanu N, Swanton C, Szüts D. A comparative analysis of the mutagenicity of platinum-containing chemotherapeutic agents reveals direct and indirect mutagenic mechanisms. Mutagenesis 2021; 36:75-86. [PMID: 33502495 PMCID: PMC8081379 DOI: 10.1093/mutage/geab005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Platinum-based drugs are a mainstay of cancer chemotherapy. However, their mutagenic effect can increase tumour heterogeneity, contribute to the evolution of treatment resistance and also induce secondary malignancies. We coupled whole genome sequencing with phenotypic investigations on two cell line models to compare the magnitude and examine the mechanism of mutagenicity of cisplatin, carboplatin and oxaliplatin. Cisplatin induced significantly more base substitution mutations than carboplatin or oxaliplatin when used at equitoxic concentrations on human TK6 or chicken DT40 cells, and also induced the highest number of short insertions and deletions. The analysis of base substitution spectra revealed that all three tested platinum drugs elicit both a direct mutagenic effect at purine dinucleotides, and an indirect effect of accelerating endogenous mutagenic processes, whereas the direct mutagenic effect appeared to correlate with the level of DNA damage caused as assessed through histone H2AX phosphorylation and single-cell agarose gel electrophoresis, the indirect mutagenic effects were equal. The different mutagenicity and DNA-damaging effect of equitoxic platinum drug treatments suggest that DNA damage independent mechanisms significantly contribute to their cytotoxicity. Thus, the comparatively high mutagenicity of cisplatin should be taken into account in the design of chemotherapeutic regimens.
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Affiliation(s)
- Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nnennaya Kanu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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Melo Bisneto AVD, Oliveira LCD, Silva Fernandes A, Silva LS, Véras JH, Cardoso CG, E Silva CR, de Moraes Filho AV, Carneiro CC, Chen-Chen L. Recombinogenic, genotoxic, and cytotoxic effects of azathioprine using in vivo assays. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2021; 84:261-271. [PMID: 33372579 DOI: 10.1080/15287394.2020.1864692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Azathioprine (Aza) is a purine antimetabolite immunosuppressant that is widely employed for immunosuppressive therapy in post-transplant recipients or patients with autoimmune diseases. Chronic use of immunosuppressants might produce several side effects, including a high rate of neoplasms in these patients. Considering that genotoxic effects are associated with an increased risk of developing cancer, the aim of this study was to examine the recombinogenic, genotoxic, and cytotoxic effects of Aza using Somatic Mutation and Recombination Test (SMART) in Drosophila melanogaster, as well as comet and micronucleus assays in mouse bone marrow cells. Further, the adverse effects of Aza were determined in mouse hepatic and renal tissues using histopathological analysis. Data demonstrated that Aza induced significant increased genotoxicity in D. melanogaster and mouse bone marrow cells at all concentrations tested. Homologous recombination was the predominant genotoxic event noted for the first time to be initiated by Aza in SMART. In histopathological analysis, Aza did not show any marked toxic activity in mouse hepatic and renal tissues. Therefore, the high rate of neoplasms reported in patients with long-term use of Aza may be attributed, at least partially, to the genotoxic action of this drug.
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Affiliation(s)
- A V D Melo Bisneto
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
| | - L C D Oliveira
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
| | - A Silva Fernandes
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
| | - L S Silva
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
| | - J H Véras
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
| | - C G Cardoso
- Department of Morphology, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
| | - Carolina R E Silva
- Department of Morphology, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
| | - A V de Moraes Filho
- Institute of Health Sciences, Alfredo Nasser University, Aparecida de Goiânia, Brazil
| | - C C Carneiro
- Institute of Health Sciences, Universidade Paulista, Campus Flamboyant, Goiânia, Brazil
| | - L Chen-Chen
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Campus Samambaia, Federal University of Goiás, Goiânia, Brazil
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45
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Pan B, Kaldhone PR, Alund AW, Du H, Guo X, Yan J, Chen Y, Zhou T, Robison TW, Chen T. Mutagenicity of silver nanoparticles evaluated using whole-genome sequencing in mouse lymphoma cells. Nanotoxicology 2021; 15:418-432. [PMID: 33710943 DOI: 10.1080/17435390.2021.1894614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The increasing medical and food applications of silver nanoparticles (AgNPs) raise concerns about their safety, including the potential health consequences of human exposure. Previous studies found that AgNPs were negative in the Ames test due to both their microbicidal activity and the inability of nanoparticles to penetrate bacterial cell walls. Thus, the mutagenicity of AgNPs is still not completely clear, though they do induce chromosome damage, as suggested by many previous genotoxicity studies. In this study, whole-genome sequencing (WGS) was used to analyze the mutagenicity of AgNPs in mouse lymphoma cells expanded from single-cell clones. The cells were treated with AgNPs, 4-nitroquinolone-1-oxide (4-NQO) as the positive control, and vehicle controls. Both AgNPs and 4-NQO significantly increased mutation frequencies over their concurrent controls by 1.12-fold and 4.89-fold with mutation rates at 4-fold and 130-fold, respectively. AgNP-induced mutations mainly occurred at G:C sites with G:C > T:A transversions, G:C > A:T transitions, and deletions as the most commonly observed mutations. AgNPs also induced higher fold changes in tandem mutations. The results suggest that the WGS mutation assay conducted here can detect the low-level mutagenicity of AgNPs, providing substantial support for the use of the WGS method as a possible alternative assay with respect to the mutagenic assessment of nanomaterials.
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Affiliation(s)
- Bohu Pan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Pravin R Kaldhone
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Alexander W Alund
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Hua Du
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Tong Zhou
- Center for Veterinary Medicine, Food and Drug Administration, Rockville, MD, USA
| | - Timothy W Robison
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
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Ware RE, Dertinger SD. Absence of hydroxyurea-induced mutational effects supports higher utilisation for the treatment of sickle cell anaemia. Br J Haematol 2021; 194:252-266. [PMID: 33570176 DOI: 10.1111/bjh.17323] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022]
Abstract
Hydroxyurea (hydroxycarbamide) is approved for treating both children and adults with sickle cell anaemia (SCA). Fetal haemoglobin (HbF) induction is the primary treatment response, along with improved anaemia, reduced haemolysis, myelosuppression and decreased endothelial inflammation. Hydroxyurea has proven clinical efficacy for SCA - treatment significantly reduces disease manifestations and prolongs survival. Despite these recognised benefits, long-standing concerns regarding the risks of mutagenic and potentially carcinogenic drug exposure have hampered efforts for broad hydroxyurea use in SCA, although these are based largely on outdated experimental models and treatment experiences with myeloproliferative neoplasms. Consequently, many patients with SCA are not receiving this highly effective disease-modifying therapy. In this review, we describe the concept of genotoxicity and its laboratory measurements, summarise hydroxyurea-associated data from both preclinical and clinical studies, and discuss carcinogenic potential. The genotoxicity results clearly demonstrate that hydroxyurea does not directly bind DNA and is not mutagenic. Rather, its genotoxic effects are limited to indirect clastogenicity occurring in select cell types, and only when high dose and time thresholds are exceeded. This absence of mutagenic activity is consistent with the observed lack of any compelling carcinogenic potential. Since hydroxyurea therapy for SCA carries minimal carcinogenic risks, the current drug labelling should be modified accordingly, and prescribing practices should be broadened to allow better access and increased utilisation of this highly effective drug.
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Affiliation(s)
- Russell E Ware
- Division of Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Global Health Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Cheng K, Nair NU, Lee JS, Ruppin E. Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity. SCIENCE ADVANCES 2021; 7:eabc2100. [PMID: 33523837 PMCID: PMC7775773 DOI: 10.1126/sciadv.abc2100] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/10/2020] [Indexed: 05/30/2023]
Abstract
Various characteristics of cancers exhibit tissue specificity, including lifetime cancer risk, onset age, and cancer driver genes. Previously, the large variation in cancer risk across human tissues was found to strongly correlate with the number of stem cell divisions and abnormal DNA methylation levels. Here, we study the role of synthetic lethality in cancer risk. Analyzing normal tissue transcriptomics data in the Genotype-Tissue Expression project, we quantify the extent of co-inactivation of cancer synthetic lethal (cSL) gene pairs and find that normal tissues with more down-regulated cSL gene pairs have lower and delayed cancer risk. Consistently, more cSL gene pairs become up-regulated in cells treated by carcinogens and throughout premalignant stages in vivo. We also show that the tissue specificity of numerous tumor suppressor genes is associated with the expression of their cSL partner genes across normal tissues. Overall, our findings support the possible role of synthetic lethality in tumorigenesis.
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Affiliation(s)
- Kuoyuan Cheng
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joo Sang Lee
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
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Babu G, Chaudhuri P, Rajappa M, Biswas M, Sansar B, Rajegowda C, Radhakrishnan A, Advani J, Tewary B, Radhakrishnan P, Thiyagarajan S, Chatterjee A, Upadhayaya RS, Majumder PK. JAK-STAT inhibitor as a potential therapeutic opportunity in AML patients resistant to cytarabine and epigenetic therapy. Cancer Biol Ther 2020; 22:66-78. [PMID: 33356802 DOI: 10.1080/15384047.2020.1831371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The prognosis of AML is generally poor, with 5-year survival rate of 25%. There has been substantial progress in identification of new therapeutic targets, along with approval of at least three targeted therapies for AML in recent years. Nevertheless, treatment has largely remained unchanged over couple of decades, with ~40% patients not achieving remission. AML is a highly heterogenous disease and there is a need for a preclinical platform to understand the heterogeneity and tumor microenvironment that can guide therapy selection. In this study, we employed an ex vivo tumor explant model to study tumor microenvironment and to select a treatment course for AML patients. Our data reveal dysregulation of DNA methyltransferase (DNMT) and histone deacetylase (HDAC) in a subset of AML patients. Based on this observation, epigenetic modulators azacitidine and panobinostat alone and in combination, were evaluated as treatment regimens in cytarabine refractory tumors. More than 50% of the treated samples showed response to the combination therapy. In order to explore alternate treatment modalities for tumors refractory to these epigenetic modulators, TCGA data analysis was done which revealed increased expression and hypomethylation of IFNGR1/2, suggesting activation of JAK/STAT pathway in AML. This was further interrogated ex vivo, with p-STAT3 expression in patients' samples. Fedratinib, a JAK/STAT inhibitor was evaluated and 78% tumor efficacy response was achieved. Taken together, our data indicate that ex vivo platform derived from patient samples is capable in guiding optimal therapy selection for various classes of drugs including identification of novel targeted therapies.
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Affiliation(s)
- Govind Babu
- Department of Medical Oncology, Kidwai Memorial Institute of Oncology , Bengaluru, India
| | | | - Manoj Rajappa
- Departments of Cancer Biology, Mitra Biotech , Woburn, Massachusetts, USA
| | - Manjusha Biswas
- Molecular Pathology, Mitra Biotech , Woburn, Massachusetts, USA
| | - Bipinesh Sansar
- Department of Medical Oncology, Kidwai Memorial Institute of Oncology , Bengaluru, India
| | - Chethan Rajegowda
- Department of Medical Oncology, Kidwai Memorial Institute of Oncology , Bengaluru, India
| | | | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park , Bangalore, India
| | - Biplab Tewary
- Departments of Cancer Biology, Mitra Biotech , Woburn, Massachusetts, USA
| | | | | | - Aditi Chatterjee
- Departments of Cancer Biology, Mitra Biotech , Woburn, Massachusetts, USA
| | | | - Pradip K Majumder
- Departments of Cancer Biology, Mitra Biotech , Woburn, Massachusetts, USA.,Ohm Oncology, Austin, TX, USA
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Anthony EJ, Bolitho EM, Bridgewater HE, Carter OWL, Donnelly JM, Imberti C, Lant EC, Lermyte F, Needham RJ, Palau M, Sadler PJ, Shi H, Wang FX, Zhang WY, Zhang Z. Metallodrugs are unique: opportunities and challenges of discovery and development. Chem Sci 2020; 11:12888-12917. [PMID: 34123239 PMCID: PMC8163330 DOI: 10.1039/d0sc04082g] [Citation(s) in RCA: 318] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Metals play vital roles in nutrients and medicines and provide chemical functionalities that are not accessible to purely organic compounds. At least 10 metals are essential for human life and about 46 other non-essential metals (including radionuclides) are also used in drug therapies and diagnostic agents. These include platinum drugs (in 50% of cancer chemotherapies), lithium (bipolar disorders), silver (antimicrobials), and bismuth (broad-spectrum antibiotics). While the quest for novel and better drugs is now as urgent as ever, drug discovery and development pipelines established for organic drugs and based on target identification and high-throughput screening of compound libraries are less effective when applied to metallodrugs. Metallodrugs are often prodrugs which undergo activation by ligand substitution or redox reactions, and are multi-targeting, all of which need to be considered when establishing structure-activity relationships. We focus on early-stage in vitro drug discovery, highlighting the challenges of evaluating anticancer, antimicrobial and antiviral metallo-pharmacophores in cultured cells, and identifying their targets. We highlight advances in the application of metal-specific techniques that can assist the preclinical development, including synchrotron X-ray spectro(micro)scopy, luminescence, and mass spectrometry-based methods, combined with proteomic and genomic (metallomic) approaches. A deeper understanding of the behavior of metals and metallodrugs in biological systems is not only key to the design of novel agents with unique mechanisms of action, but also to new understanding of clinically-established drugs.
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Affiliation(s)
- Elizabeth J Anthony
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Elizabeth M Bolitho
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Hannah E Bridgewater
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Oliver W L Carter
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Jane M Donnelly
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Cinzia Imberti
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Edward C Lant
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Frederik Lermyte
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Russell J Needham
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Marta Palau
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Huayun Shi
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Fang-Xin Wang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Wen-Ying Zhang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Zijin Zhang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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50
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Preexisting or therapy-induced mutations in relapsed acute lymphoblastic leukemia? Blood 2020; 136:2233-2235. [PMID: 32603411 DOI: 10.1182/blood.2020005258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/15/2020] [Indexed: 11/20/2022] Open
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