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Nussinov R, Yavuz BR, Jang H. Anticancer drugs: How to select small molecule combinations? Trends Pharmacol Sci 2024; 45:503-519. [PMID: 38782689 PMCID: PMC11162304 DOI: 10.1016/j.tips.2024.04.012] [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: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Small molecules are at the forefront of anticancer therapies. Successive treatments with single molecules incur drug resistance, calling for combination. Here, we explore the tough choices oncologists face - not just which drugs to use but also the best treatment plans, based on factors such as target proteins, pathways, and gene expression. We consider the reality of cancer's disruption of normal cellular processes, highlighting why it's crucial to understand the ins and outs of current treatment methods. The discussion on using combination drug therapies to target multiple pathways sheds light on a promising approach while also acknowledging the hurdles that come with it, such as dealing with pathway crosstalk. We review options and provide examples and the mechanistic basis, altogether providing the first comprehensive guide to combinatorial therapy selection.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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2
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Nussinov R, Jang H. Direct K-Ras Inhibitors to Treat Cancers: Progress, New Insights, and Approaches to Treat Resistance. Annu Rev Pharmacol Toxicol 2024; 64:231-253. [PMID: 37524384 DOI: 10.1146/annurev-pharmtox-022823-113946] [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] [Indexed: 08/02/2023]
Abstract
Here we discuss approaches to K-Ras inhibition and drug resistance scenarios. A breakthrough offered a covalent drug against K-RasG12C. Subsequent innovations harnessed same-allele drug combinations, as well as cotargeting K-RasG12C with a companion drug to upstream regulators or downstream kinases. However, primary, adaptive, and acquired resistance inevitably emerge. The preexisting mutation load can explain how even exceedingly rare mutations with unobservable effects can promote drug resistance, seeding growth of insensitive cell clones, and proliferation. Statistics confirm the expectation that most resistance-related mutations are in cis, pointing to the high probability of cooperative, same-allele effects. In addition to targeted Ras inhibitors and drug combinations, bifunctional molecules and innovative tri-complex inhibitors to target Ras mutants are also under development. Since the identities and potential contributions of preexisting and evolving mutations are unknown, selecting a pharmacologic combination is taxing. Collectively, our broad review outlines considerations and provides new insights into pharmacology and resistance.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
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3
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Selves J, de Castro E Gloria H, Brunac AC, Saffi J, Guimbaud R, Brousset P, Hoffmann JS. Exploring the basis of heterogeneity of cancer aggressiveness among the mutated POLE variants. Life Sci Alliance 2024; 7:e202302290. [PMID: 37891003 PMCID: PMC10610022 DOI: 10.26508/lsa.202302290] [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: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Germline pathogenic variants in the exonuclease domain of the replicative DNA polymerase Pol ε encoded by the POLE gene, predispose essentially to colorectal and endometrial tumors by inducing an ultramutator phenotype. It is still unclear whether all the POLE alterations influence similar strength tumorigenesis, immune microenvironment, and treatment response. In this review, we summarize the current understanding of the mechanisms and consequences of POLE mutations in human malignancies; we highlight the heterogeneity of mutation rate and cancer aggressiveness among POLE variants, propose some mechanistic basis underlining such heterogeneity, and discuss novel considerations for the choice and efficacy of therapies of POLE tumors.
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Affiliation(s)
- Janick Selves
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
| | - Helena de Castro E Gloria
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Anne-Cécile Brunac
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Rosine Guimbaud
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
- Department of Digestive Surgery, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Pierre Brousset
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
| | - Jean-Sébastien Hoffmann
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
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4
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Fessart D, Robert J. [Mechanisms of cancer drug resistance]. Bull Cancer 2024; 111:37-50. [PMID: 37679207 DOI: 10.1016/j.bulcan.2023.07.001] [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: 03/31/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 09/09/2023]
Abstract
Despite decades of research into the molecular mechanisms of cancer and the development of new treatments, drug resistance persists as a major problem. This is in part due to the heterogeneity of cancer, including the diversity of tumor cell lineage and cell plasticity, the spectrum of somatic mutations, the complexity of microenvironments, and immunosuppressive characteristic, then necessitating the use of many different therapeutic approaches. We summarize here the biological causes of resistance, thus offering new perspectives for tackle drug resistance.
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Affiliation(s)
- Delphine Fessart
- ARTiSt lab, Université de Bordeaux, Inserm U1312 BRIC, 33000 Bordeaux, France.
| | - Jacques Robert
- ARTiSt lab, Université de Bordeaux, Inserm U1312 BRIC, 33000 Bordeaux, France
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Bahnassy S, Stires H, Jin L, Tam S, Mobin D, Balachandran M, Podar M, McCoy MD, Beckman RA, Riggins RB. Unraveling Vulnerabilities in Endocrine Therapy-Resistant HER2+/ER+ Breast Cancer. Endocrinology 2023; 164:bqad159. [PMID: 37897495 PMCID: PMC10651073 DOI: 10.1210/endocr/bqad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/01/2023] [Accepted: 10/26/2023] [Indexed: 10/30/2023]
Abstract
Breast tumors overexpressing human epidermal growth factor receptor (HER2) confer intrinsic resistance to endocrine therapy (ET), and patients with HER2/estrogen receptor-positive (HER2+/ER+) breast cancer (BCa) are less responsive to ET than HER2-/ER+. However, real-world evidence reveals that a large subset of patients with HER2+/ER+ receive ET as monotherapy, positioning this treatment pattern as a clinical challenge. In the present study, we developed and characterized 2 in vitro models of ET-resistant (ETR) HER2+/ER+ BCa to identify possible therapeutic vulnerabilities. To mimic ETR to aromatase inhibitors (AIs), we developed 2 long-term estrogen deprivation (LTED) cell lines from BT-474 (BT474) and MDA-MB-361 (MM361). Growth assays, PAM50 subtyping, and genomic and transcriptomic analyses, followed by validation and functional studies, were used to identify targetable differences between ET-responsive parental and ETR-LTED HER2+/ER+ cells. Compared to their parental cells, MM361 LTEDs grew faster, lost ER, and increased HER2 expression, whereas BT474 LTEDs grew slower and maintained ER and HER2 expression. Both LTED variants had reduced responsiveness to fulvestrant. Whole-genome sequencing of aggressive MM361 LTEDs identified mutations in genes encoding transcription factors and chromatin modifiers. Single-cell RNA sequencing demonstrated a shift towards non-luminal phenotypes, and revealed metabolic remodeling of MM361 LTEDs, with upregulated lipid metabolism and ferroptosis-associated antioxidant genes, including GPX4. Combining a GPX4 inhibitor with anti-HER2 agents induced significant cell death in both MM361 and BT474 LTEDs. The BT474 and MM361 AI-resistant models capture distinct phenotypes of HER2+/ER+ BCa and identify altered lipid metabolism and ferroptosis remodeling as vulnerabilities of this type of ETR BCa.
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Affiliation(s)
- Shaymaa Bahnassy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | | | - Lu Jin
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Stanley Tam
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Dua Mobin
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Manasi Balachandran
- Department of Medicine, University of Tennessee Medical Center, Knoxville, TN 37920, USA
| | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Matthew D McCoy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Robert A Beckman
- Department of Oncology and of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC 20007, USA
- Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Rebecca B Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
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6
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Bahnassy S, Stires H, Jin L, Tam S, Mobin D, Balachandran M, Podar M, McCoy MD, Beckman RA, Riggins RB. Unraveling Vulnerabilities in Endocrine Therapy-Resistant HER2+/ER+ Breast Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554116. [PMID: 37662291 PMCID: PMC10473676 DOI: 10.1101/2023.08.21.554116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Breast tumors overexpressing human epidermal growth factor receptor (HER2) confer intrinsic resistance to endocrine therapy (ET), and patients with HER2/ estrogen receptor-positive (HER2+/HR+) breast cancer (BCa) are less responsive to ET than HER2-/ER+. However, real-world evidence reveals that a large subset of HER2+/ER+ patients receive ET as monotherapy, positioning this treatment pattern as a clinical challenge. In the present study, we developed and characterized two distinct in vitro models of ET-resistant (ETR) HER2+/ER+ BCa to identify possible therapeutic vulnerabilities. Methods To mimic ETR to aromatase inhibitors (AI), we developed two long-term estrogen-deprived (LTED) cell lines from BT-474 (BT474) and MDA-MB-361 (MM361). Growth assays, PAM50 molecular subtyping, genomic and transcriptomic analyses, followed by validation and functional studies, were used to identify targetable differences between ET-responsive parental and ETR-LTED HER2+/ER+ cells. Results Compared to their parental cells, MM361 LTEDs grew faster, lost ER, and increased HER2 expression, whereas BT474 LTEDs grew slower and maintained ER and HER2 expression. Both LTED variants had reduced responsiveness to fulvestrant. Whole-genome sequencing of the more aggressive MM361 LTED model system identified exonic mutations in genes encoding transcription factors and chromatin modifiers. Single-cell RNA sequencing demonstrated a shift towards non-luminal phenotypes, and revealed metabolic remodeling of MM361 LTEDs, with upregulated lipid metabolism and antioxidant genes associated with ferroptosis, including GPX4. Combining the GPX4 inhibitor RSL3 with anti-HER2 agents induced significant cell death in both the MM361 and BT474 LTEDs. Conclusions The BT474 and MM361 AI-resistant models capture distinct phenotypes of HER2+/ER+ BCa and identify altered lipid metabolism and ferroptosis remodeling as vulnerabilities of this type of ETR BCa.
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Affiliation(s)
- Shaymaa Bahnassy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | | | - Lu Jin
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Stanley Tam
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Dua Mobin
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Manasi Balachandran
- Department of Medicine, University of Tennessee Medical Center, Knoxville, TN
| | | | - Matthew D. McCoy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Robert A. Beckman
- Departments of Oncology and of Biostatistics, Bioinformatics, and Biomathematics, Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Rebecca B. Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
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Derbal Y. Cell Adaptive Fitness and Cancer Evolutionary Dynamics. Cancer Inform 2023; 22:11769351231154679. [PMID: 36860424 PMCID: PMC9969436 DOI: 10.1177/11769351231154679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/17/2023] [Indexed: 02/26/2023] Open
Abstract
Genome instability of cancer cells translates into increased entropy and lower information processing capacity, leading to metabolic reprograming toward higher energy states, presumed to be aligned with a cancer growth imperative. Dubbed as the cell adaptive fitness, the proposition postulates that the coupling between cell signaling and metabolism constrains cancer evolutionary dynamics along trajectories privileged by the maintenance of metabolic sufficiency for survival. In particular, the conjecture postulates that clonal expansion becomes restricted when genetic alterations induce a sufficiently high level of disorder, that is, high entropy, in the regulatory signaling network, abrogating as a result the ability of cancer cells to successfully replicate, leading to a stage of clonal stagnation. The proposition is analyzed in the context of an in-silico model of tumor evolutionary dynamics to illustrate how cell-inherent adaptive fitness may predictably constrain clonal evolution of tumors, which would have significant implications for the design of adaptive cancer therapies.
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Affiliation(s)
- Youcef Derbal
- Youcef Derbal, Ted Rogers School of
Information Technology Management, Toronto Metropolitan University, 350 Victoria
Street, Toronto, ON M5B 2K3, Canada.
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8
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Beckman RA, Makohon-Moore AP, Puzanov I. Intratumoral and Microenvironmental Heterogeneity in Patient Outcome Prediction. JCO Precis Oncol 2023; 7:e2200698. [PMID: 36848610 PMCID: PMC10309571 DOI: 10.1200/po.22.00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 03/01/2023] Open
Affiliation(s)
- Robert A. Beckman
- Departments of Oncology and of Biostatistics, Bioinformatics, and Biomathematics, Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Alvin P. Makohon-Moore
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC
| | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY
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9
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Niu Y, Yang W, Qian H, Sun Y. Intracellular and extracellular factors of colorectal cancer liver metastasis: a pivotal perplex to be fully elucidated. Cancer Cell Int 2022; 22:341. [DOI: 10.1186/s12935-022-02766-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractMetastasis is the leading cause of death in colorectal cancer (CRC) patients, and the liver is the most common site of metastasis. Tumor cell metastasis can be thought of as an invasion-metastasis cascade and metastatic organotropism is thought to be a process that relies on the intrinsic properties of tumor cells and their interactions with molecules and cells in the microenvironment. Many studies have provided new insights into the molecular mechanism and contributing factors involved in CRC liver metastasis for a better understanding of the organ-specific metastasis process. The purpose of this review is to summarize the theories that explain CRC liver metastasis at multiple molecular dimensions (including genetic and non-genetic factors), as well as the main factors that cause CRC liver metastasis. Many findings suggest that metastasis may occur earlier than expected and with specific organ-anchoring property. The emergence of potential metastatic clones, the timing of dissemination, and the distinct routes of metastasis have been explained by genomic studies. The main force of CRC liver metastasis is also thought to be epigenetic alterations and dynamic phenotypic traits. Furthermore, we review key extrinsic factors that influence CRC cell metastasis and liver tropisms, such as pre-niches, tumor stromal cells, adhesion molecules, and immune/inflammatory responses in the tumor microenvironment. In addition, biomarkers associated with early diagnosis, prognosis, and recurrence of liver metastasis from CRC are summarized to enlighten potential clinical practice, including some markers that can be used as therapeutic targets to provide new perspectives for the treatment strategies of CRC liver metastasis.
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Xu L, Zhang J, Sun J, Hou K, Yang C, Guo Y, Liu X, Kalvakolanu DV, Zhang L, Guo B. Epigenetic regulation of cancer stem cells: Shedding light on the refractory/relapsed cancers. Biochem Pharmacol 2022; 202:115110. [PMID: 35640714 DOI: 10.1016/j.bcp.2022.115110] [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: 03/31/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023]
Abstract
The resistance to drugs, ability to enter quiescence and generate heterogeneous cancer cells, and enhancement of aggressiveness, make cancer stem cells (CSCs) integral part of tumor progression, metastasis and recurrence after treatment. The epigenetic modification machinery is crucial for the viability of CSCs and evolution of aggressive forms of a tumor. These mechanisms can also be targeted by specific drugs, providing a promising approach for blocking CSCs. In this review, we summarize the epigenetic regulatory mechanisms in CSCs which contribute to drug resistance, quiescence and tumor heterogeneity. We also discuss the drugs that can potentially target these processes and data from experimental and clinical studies.
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Affiliation(s)
- Libo Xu
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, PR China; Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Jinghua Zhang
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Jicheng Sun
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Kunlin Hou
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Chenxin Yang
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Ying Guo
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Xiaorui Liu
- Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China
| | - Dhan V Kalvakolanu
- Greenebaum NCI Comprehensive Cancer Center, Department of Microbiology and Immunology, University of Maryland School Medicine, Baltimore, MD, USA
| | - Ling Zhang
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, PR China; Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, PR China.
| | - Baofeng Guo
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, PR China.
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Angaroni F, Guidi A, Ascolani G, d'Onofrio A, Antoniotti M, Graudenzi A. J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinformatics 2022; 23:269. [PMID: 35804300 PMCID: PMC9270769 DOI: 10.1186/s12859-022-04779-8] [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: 02/23/2022] [Accepted: 06/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background The combined effects of biological variability and measurement-related errors on cancer sequencing data remain largely unexplored. However, the spatio-temporal simulation of multi-cellular systems provides a powerful instrument to address this issue. In particular, efficient algorithmic frameworks are needed to overcome the harsh trade-off between scalability and expressivity, so to allow one to simulate both realistic cancer evolution scenarios and the related sequencing experiments, which can then be used to benchmark downstream bioinformatics methods. Result We introduce a Julia package for SPAtial Cancer Evolution (J-SPACE), which allows one to model and simulate a broad set of experimental scenarios, phenomenological rules and sequencing settings.Specifically, J-SPACE simulates the spatial dynamics of cells as a continuous-time multi-type birth-death stochastic process on a arbitrary graph, employing different rules of interaction and an optimised Gillespie algorithm. The evolutionary dynamics of genomic alterations (single-nucleotide variants and indels) is simulated either under the Infinite Sites Assumption or several different substitution models, including one based on mutational signatures. After mimicking the spatial sampling of tumour cells, J-SPACE returns the related phylogenetic model, and allows one to generate synthetic reads from several Next-Generation Sequencing (NGS) platforms, via the ART read simulator. The results are finally returned in standard FASTA, FASTQ, SAM, ALN and Newick file formats. Conclusion J-SPACE is designed to efficiently simulate the heterogeneous behaviour of a large number of cancer cells and produces a rich set of outputs. Our framework is useful to investigate the emergent spatial dynamics of cancer subpopulations, as well as to assess the impact of incomplete sampling and of experiment-specific errors. Importantly, the output of J-SPACE is designed to allow the performance assessment of downstream bioinformatics pipelines processing NGS data. J-SPACE is freely available at: https://github.com/BIMIB-DISCo/J-Space.jl.
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Affiliation(s)
- Fabrizio Angaroni
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy.
| | - Alessandro Guidi
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy
| | - Gianluca Ascolani
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy
| | - Alberto d'Onofrio
- Department of Mathematics and Geosciences, Univ. of Trieste, Trieste, Italy
| | - Marco Antoniotti
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Milan, Italy
| | - Alex Graudenzi
- Dept. of Informatics, Systems and Communication, Univ. of Milan-Bicocca, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Milan, Italy.,Inst. of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Segrate, Italy
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12
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Chan HT, Chin YM, Low SK. Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges. Cancers (Basel) 2022; 14:3275. [PMID: 35805046 PMCID: PMC9265547 DOI: 10.3390/cancers14133275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a 'plasma first' or 'tissue first' approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the 'right assay for the right patient at the right time'.
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Affiliation(s)
- Hiu Ting Chan
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
| | - Yoon Ming Chin
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
- Cancer Precision Medicine, Inc., Kawasaki 213-0012, Japan
| | - Siew-Kee Low
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
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13
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De quelques théories de l’oncogenèse. Bull Cancer 2022; 109:742-747. [DOI: 10.1016/j.bulcan.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/23/2022]
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14
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Cheng P, Lan Y, Liao J, Zhao E, Yan H, Xu L, A S, Ping Y, Xu J. Systematic investigation of the prognostic impact of clonal status of somatic mutations across multiple cancer types. Genomics 2022; 114:110412. [PMID: 35714828 DOI: 10.1016/j.ygeno.2022.110412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/15/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022]
Abstract
Tumors are genetically heterogeneous and many mutations are actually present in subclonal populations. The clonal status of mutations is valuable for accurate prognosis, clinical management. The aim of this study was to identify the clonal status of somatic mutations and systematically evaluate their prognostic values across various cancer types. We totally identified 227 clonal and 432 subclonal mutations contributed to prognosis and demonstrated the importance of clonal status in improving mutation-related clinical guidance. We further developed a customized multi-step approach to identify gene-specific prognostic patterns of clonal status at pan-cancer level and found some cancer-specific prognostic patterns. The 'subclonal-dependent risk' subpattern was one of the most common subpatterns, it usually accompanied by high genomic in-stability and high extent of intra-tumor heterogeneity and could be used to improve the accuracy of prognostic analysis. Our results revealed the importance of clonal status, especially subclonal mutation in clinical survival.
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Affiliation(s)
- Peng Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jianlong Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Erjie Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Suru A
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
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15
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van den Bosch T, Vermeulen L, Miedema DM. Quantitative models for the inference of intratumor heterogeneity. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2022. [DOI: 10.1002/cso2.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology Center for Experimental and Molecular Medicine Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism Amsterdam University Medical Centers Amsterdam The Netherlands
- Oncode Institute Amsterdam The Netherlands
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16
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Arabyarmohammadi S, Leo P, Viswanathan VS, Janowczyk A, Corredor G, Fu P, Meyerson H, Metheny L, Madabhushi A. Machine Learning to Predict Risk of Relapse Using Cytologic Image Markers in Patients With Acute Myeloid Leukemia Posthematopoietic Cell Transplantation. JCO Clin Cancer Inform 2022; 6:e2100156. [PMID: 35522898 PMCID: PMC9126529 DOI: 10.1200/cci.21.00156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/28/2022] [Accepted: 03/08/2022] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Allogenic hematopoietic stem-cell transplant (HCT) is a curative therapy for acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Relapse post-HCT is the most common cause of treatment failure and is associated with a poor prognosis. Pathologist-based visual assessment of aspirate images and the manual myeloblast counting have shown to be predictive of relapse post-HCT. However, this approach is time-intensive and subjective. The premise of this study was to explore whether computer-extracted morphology and texture features from myeloblasts' chromatin patterns could help predict relapse and prognosticate relapse-free survival (RFS) after HCT. MATERIALS AND METHODS In this study, Wright-Giemsa-stained post-HCT aspirate images were collected from 92 patients with AML/MDS who were randomly assigned into a training set (St = 52) and a validation set (Sv = 40). First, a deep learning-based model was developed to segment myeloblasts. A total of 214 texture and shape descriptors were then extracted from the segmented myeloblasts on aspirate slide images. A risk score on the basis of texture features of myeloblast chromatin patterns was generated by using the least absolute shrinkage and selection operator with a Cox regression model. RESULTS The risk score was associated with RFS in St (hazard ratio = 2.38; 95% CI, 1.4 to 3.95; P = .0008) and Sv (hazard ratio = 1.57; 95% CI, 1.01 to 2.45; P = .044). We also demonstrate that this resulting signature was predictive of AML relapse with an area under the receiver operating characteristic curve of 0.71 within Sv. All the relevant code is available at GitHub. CONCLUSION The texture features extracted from chromatin patterns of myeloblasts can predict post-HCT relapse and prognosticate RFS of patients with AML/MDS.
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Affiliation(s)
- Sara Arabyarmohammadi
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH
| | - Patrick Leo
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH
| | | | - Andrew Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH
- Lausanne University Hospital, Precision Oncology Center, Vaud, Switzerland
| | - German Corredor
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH
| | - Pingfu Fu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Howard Meyerson
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Leland Metheny
- Department of Hematology and Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH
- Louis Stokes Veterans Administration Medical Center, Cleveland, OH
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17
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Vakil V, Trappe W. Drug-Resistant Cancer Treatment Strategies Based on the Dynamics of Clonal Evolution and PKPD Modeling of Drug Combinations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1603-1614. [PMID: 33326383 DOI: 10.1109/tcbb.2020.3045315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A method for determining a dosage strategy is proposed to combat drug resistance in tumor progression. The method is based on a dynamic model for the clonal evolution of cancerous cells and considers the Pharmacokinetic/Pharmacodynamic (PKPD) modeling of combination therapy. The proposed mathematical representation models the dynamic and kinetic effects of multiple drugs on the number of cells while considering potential mutations and assuming that no cross-resistance arises. An optimization problem is then proposed to minimize the total number of cancerous cells in a finite treatment period given a limited number of treatments. The dosage schedule, including the amount of each drug to be administered and the timing, is found by solving the optimization problem. This treatment schedule is constrained to achieve a target minimum effectiveness, while also ensuring that the concentration of the drugs, individually and totally, does not exceed a prescribed toxicity threshold. The proposed optimization problem is represented as a Complementary Geometric Programming (CGP) problem. The results show that the solution of the optimization problem for combination therapy is the dosing schedule that leads to tumor eradication at the end of the treatment period. The results also investigate the tumor dynamics for all mutation types when undergoing treatment, showing that single drug therapies can fail to combat the emergence of resistance, while optimized combination therapies can reduce the amount of all mutation types during the course of treatment, thereby combating resistance.
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18
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Accurate Detection of Subclonal Variants in Paired Diagnosis-Relapse Acute Myeloid Leukemia Samples by Next Generation Duplex Sequencing. Leuk Res 2022; 115:106822. [PMID: 35303493 PMCID: PMC9014797 DOI: 10.1016/j.leukres.2022.106822] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/22/2022] [Accepted: 03/07/2022] [Indexed: 11/22/2022]
Abstract
Mutations characterize diverse human cancers; there is a positive correlation between elevated mutation frequency and tumor progression. One exception is acute myeloid leukemia (AML), which has few clonal single nucleotide mutations. We used highly sensitive and accurate Duplex Sequencing (DS) to show now that AML, in addition, has an extensive repertoire of variants with low allele frequencies, < 1%, which is below the accurate detection limit of most other sequencing methodologies. The subclonal variants are unique to each individual and change in composition, frequency, and sequence context from diagnosis to relapse. Their functional significance is apparent by the observation that many are known variants and cluster within functionally important protein domains. Subclones provide a reservoir of variants that could expand and contribute to the development of drug resistance and relapse. In accord, we accurately identified subclonal variants in AML driver genes NRAS and RUNX1 at allele frequencies between 0.1% and 0.3% at diagnosis, which expanded to comprise a major fraction (14-53%) of the blast population at relapse. Early and accurate detection of subclonal variants with low allele frequency thus offers the opportunity for early intervention, prior to detection of clinical relapse, to improve disease outcome and enhance patient survival.
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19
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Salazar R, Arbeithuber B, Ivankovic M, Heinzl M, Moura S, Hartl I, Mair T, Lahnsteiner A, Ebner T, Shebl O, Pröll J, Tiemann-Boege I. Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing. Genome Res 2022; 32:499-511. [PMID: 35210354 PMCID: PMC8896467 DOI: 10.1101/gr.275695.121] [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: 04/26/2021] [Accepted: 01/14/2022] [Indexed: 11/25/2022]
Abstract
De novo mutations (DNMs) are important players in heritable diseases and evolution. Of particular interest are highly recurrent DNMs associated with congenital disorders that have been described as selfish mutations expanding in the male germline, thus becoming more frequent with age. Here, we have adapted duplex sequencing (DS), an ultradeep sequencing method that renders sequence information on both DNA strands; thus, one mutation can be reliably called in millions of sequenced bases. With DS, we examined ∼4.5 kb of the FGFR3 coding region in sperm DNA from older and younger donors. We identified sites with variant allele frequencies (VAFs) of 10-4 to 10-5, with an overall mutation frequency of the region of ∼6 × 10-7 Some of the substitutions are recurrent and are found at a higher VAF in older donors than in younger ones or are found exclusively in older donors. Also, older donors harbor more mutations associated with congenital disorders. Other mutations are present in both age groups, suggesting that these might result from a different mechanism (e.g., postzygotic mosaicism). We also observe that independent of age, the frequency and deleteriousness of the mutational spectra are more similar to COSMIC than to gnomAD variants. Our approach is an important strategy to identify mutations that could be associated with a gain of function of the receptor tyrosine kinase activity, with unexplored consequences in a society with delayed fatherhood.
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Affiliation(s)
- Renato Salazar
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | | | - Maja Ivankovic
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Monika Heinzl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Sofia Moura
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Ingrid Hartl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria 4020
| | | | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Kepler University Hospital, Linz, Austria 4020
| | - Omar Shebl
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Kepler University Hospital, Linz, Austria 4020
| | - Johannes Pröll
- Center for Medical Research, Faculty of Medicine, Johannes Kepler University, Linz, Austria 4020
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20
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Lin Y, Pan X, Chen Z, Lin S, Shen Z, Chen S. Prognostic value and immune infiltration of novel signatures in colon cancer microenvironment. Cancer Cell Int 2021; 21:679. [PMID: 34922547 PMCID: PMC8684099 DOI: 10.1186/s12935-021-02342-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background Growing evidence has shown that the prognosis for colon cancer depends on changes in microenvironment. The purpose of this study was to elucidate the prognostic value of long noncoding RNAs (lncRNAs) related to immune microenvironment (IM) in colon cancer. Methods Single sample gene set enrichment analysis (ssGSEA) was used to identify the subtypes of colon cancer based on the immune genomes of 29 immune signatures. Cox regression analysis identified a lncRNA signatures associated with immune infiltration. The Tumor Immune Estimation Resource database was used to analyze immune cell content. Results Colon cancer samples were divided into three subtypes by unsupervised cluster analysis. Cox regression analysis identified an immune infiltration-related 5-lncRNA signature. This signature combined with clinical factors can effectively improve the predictive ability for the overall survival (OS) of colon cancer. At the same time, we found that the expression of H19 affects the content of B cells and macrophages in the microenvironment of colon cancer and affects the prognosis of colon cancer. Finally, we constructed the H19 regulatory network and further analyzed the possible mechanisms. We found that knocking down the expression of H19 can significantly inhibit the expression of CCND1 and VEGFA. At the same time, the immunohistochemical assay found that the expression of CCND1 and VEGFA protein was significantly positively correlated with the infiltration of M2 type macrophages. Conclusion The findings may help to formulate clinical strategies and understand the underlying mechanisms of H19 regulation. H19 may be a biomarker for targeted treatment of colon cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02342-8.
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Affiliation(s)
- Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China
| | - Xiaoxian Pan
- Department of Radiotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zhihua Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Suyong Lin
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China.
| | - Shaoqin Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China.
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21
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Wang J, Zhang Y, Liu X, Liu H. Is the Fixed Periodic Treatment Effective for the Tumor System without Complete Information? Cancer Manag Res 2021; 13:8915-8928. [PMID: 34876854 PMCID: PMC8643150 DOI: 10.2147/cmar.s339787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022] Open
Abstract
Objective The treatment plans designed with the guidance of the mathematical model and adaptive strategy can trap tumor subpopulations in a periodic and controllable loop. But this process requires detailed information about the tumor system, which is difficult to obtain. Therefore, we wondered whether the fixed periodic treatment plans designed with the typical values of population parameters could be applied to a similar tumor system without complete information. Methods A binary tumor system constructed by an EGFR-mutant and a KRAS-mutant cell line was used to explore the applicability of the fixed periodic treatment plans. The dynamics of this system were described by combining the Lotka-Volterra model with the framework of the nonlinear mixed-effects model. The typical values of population parameters were used to design the plans, and the robust plans were screened through parameter variation. These screened plans were examined their applicability in animal experiments and simulations. Results In animal experiments where system parameters vary from -30% to 30%, the "osimertinib administration, withdrawal, FK866 administration and withdrawal" plan can trap subpopulations of the system in periodic cycles. In simulation, when there was an unknown resistant subpopulation, the screened fixed periodic treatment plans can still delay the evolution of resistance. The median outcomes of screened plans were better than conventional sequential treatment in most cases. There was no significant difference between the outcomes of the screened plan with median stability and the optimal therapy. The evolutionary trajectories of these two plans were similar. Conclusion According to the results, these fixed periodic plans should be tried in treatment even the information of the tumor system was incomplete.
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Affiliation(s)
- Jiali Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.,Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Yixuan Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.,Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Xiaoquan Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.,Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Haochen Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.,Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
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22
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Nussinov R, Tsai CJ, Jang H. Anticancer drug resistance: An update and perspective. Drug Resist Updat 2021; 59:100796. [PMID: 34953682 PMCID: PMC8810687 DOI: 10.1016/j.drup.2021.100796] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022]
Abstract
Driver mutations promote initiation and progression of cancer. Pharmacological treatment can inhibit the action of the mutant protein; however, drug resistance almost invariably emerges. Multiple studies revealed that cancer drug resistance is based upon a plethora of distinct mechanisms. Drug resistance mutations can occur in the same protein or in different proteins; as well as in the same pathway or in parallel pathways, bypassing the intercepted signaling. The dilemma that the clinical oncologist is facing is that not all the genomic alterations as well as alterations in the tumor microenvironment that facilitate cancer cell proliferation are known, and neither are the alterations that are likely to promote metastasis. For example, the common KRasG12C driver mutation emerges in different cancers. Most occur in NSCLC, but some occur, albeit to a lower extent, in colorectal cancer and pancreatic ductal carcinoma. The responses to KRasG12C inhibitors are variable and fall into three categories, (i) new point mutations in KRas, or multiple copies of KRAS G12C which lead to higher expression level of the mutant protein; (ii) mutations in genes other than KRAS; (iii) original cancer transitioning to other cancer(s). Resistance to adagrasib, an experimental antitumor agent exerting its cytotoxic effect as a covalent inhibitor of the G12C KRas, indicated that half of the cases present multiple KRas mutations as well as allele amplification. Redundant or parallel pathways included MET amplification; emerging driver mutations in NRAS, BRAF, MAP2K1, and RET; gene fusion events in ALK, RET, BRAF, RAF1, and FGFR3; and loss-of-function mutations in NF1 and PTEN tumor suppressors. In the current review we discuss the molecular mechanisms underlying drug resistance while focusing on those emerging to common targeted cancer drivers. We also address questions of why cancers with a common driver mutation are unlikely to evolve a common drug resistance mechanism, and whether one can predict the likely mechanisms that the tumor cell may develop. These vastly important and tantalizing questions in drug discovery, and broadly in precision medicine, are the focus of our present review. We end with our perspective, which calls for target combinations to be selected and prioritized with the help of the emerging massive compute power which enables artificial intelligence, and the increased gathering of data to overcome its insatiable needs.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD, 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD, 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD, 21702, USA
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23
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Yeoh Y, Low TY, Abu N, Lee PY. Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance. PeerJ 2021; 9:e12338. [PMID: 34733591 PMCID: PMC8544255 DOI: 10.7717/peerj.12338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.
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Affiliation(s)
- Yeelon Yeoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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24
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Poon GYP, Watson CJ, Fisher DS, Blundell JR. Synonymous mutations reveal genome-wide levels of positive selection in healthy tissues. Nat Genet 2021; 53:1597-1605. [PMID: 34737428 DOI: 10.1038/s41588-021-00957-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Genetic alterations under positive selection in healthy tissues have implications for cancer risk. However, total levels of positive selection across the genome remain unknown. Passenger mutations are influenced by all driver mutations, regardless of type or location in the genome. Therefore, the total number of passengers can be used to estimate the total number of drivers-including unidentified drivers outside of cancer genes that are traditionally missed. Here we analyze the variant allele frequency spectrum of synonymous mutations from healthy blood and esophagus to quantify levels of missing positive selection. In blood, we find that only 30% of passengers can be explained by single-nucleotide variants in driver genes, suggesting high levels of positive selection for mutations elsewhere in the genome. In contrast, more than half of all passengers in the esophagus can be explained by just the two driver genes NOTCH1 and TP53, suggesting little positive selection elsewhere.
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Affiliation(s)
- Gladys Y P Poon
- Early Detection Programme, CRUK Cambridge Cancer Centre, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
| | - Caroline J Watson
- Early Detection Programme, CRUK Cambridge Cancer Centre, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Daniel S Fisher
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Jamie R Blundell
- Early Detection Programme, CRUK Cambridge Cancer Centre, University of Cambridge, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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25
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He S, Schein A, Sarsani V, Flaherty P. A BAYESIAN NONPARAMETRIC MODEL FOR INFERRING SUBCLONAL POPULATIONS FROM STRUCTURED DNA SEQUENCING DATA. Ann Appl Stat 2021; 15:925-951. [PMID: 34262633 DOI: 10.1214/20-aoas1434] [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: 11/19/2022]
Abstract
There are distinguishing features or "hallmarks" of cancer that are found across tumors, individuals, and types of cancer, and these hallmarks can be driven by specific genetic mutations. Yet, within a single tumor there is often extensive genetic heterogeneity as evidenced by single-cell and bulk DNA sequencing data. The goal of this work is to jointly infer the underlying genotypes of tumor subpopulations and the distribution of those subpopulations in individual tumors by integrating single-cell and bulk sequencing data. Understanding the genetic composition of the tumor at the time of treatment is important in the personalized design of targeted therapeutic combinations and monitoring for possible recurrence after treatment. We propose a hierarchical Dirichlet process mixture model that incorporates the correlation structure induced by a structured sampling arrangement and we show that this model improves the quality of inference. We develop a representation of the hierarchical Dirichlet process prior as a Gamma-Poisson hierarchy and we use this representation to derive a fast Gibbs sampling inference algorithm using the augment-and-marginalize method. Experiments with simulation data show that our model outperforms standard numerical and statistical methods for decomposing admixed count data. Analyses of real acute lymphoblastic leukemia cancer sequencing dataset shows that our model improves upon state-of-the-art bioinformatic methods. An interpretation of the results of our model on this real dataset reveals co-mutated loci across samples.
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Affiliation(s)
- Shai He
- Department of Mathematics and Statistics, University of Massachusetts Amherst
| | | | - Vishal Sarsani
- Department of Mathematics and Statistics, University of Massachusetts Amherst
| | - Patrick Flaherty
- Department of Mathematics and Statistics, University of Massachusetts Amherst
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26
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Abstract
Choosing and optimizing treatment strategies for cancer requires
capturing its complex dynamics sufficiently well for understanding but
without being overwhelmed. Mathematical models are essential to
achieve this understanding, and we discuss the challenge of choosing
the right level of complexity to address the full range of tumor
complexity from growth, the generation of tumor heterogeneity, and
interactions within tumors and with treatments and the tumor
microenvironment. We discuss the differences between conceptual and
descriptive models, and compare the use of predator-prey models,
evolutionary game theory, and dynamic precision medicine approaches in
the face of uncertainty about mechanisms and parameter values.
Although there is of course no one-size-fits-all approach, we conclude
that broad and flexible thinking about cancer, based on combined
modeling approaches, will play a key role in finding creative and
improved treatments.
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Affiliation(s)
- Robert A Beckman
- Departments of Oncology and Biostatistics, Bioinformatics, & Biomathematics, Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, 12231Georgetown University Medical Center, Washington, DC, USA
| | - Irina Kareva
- Mathematical and Computational Sciences Center, School of Human Evolution and Social Change, 7864Arizona State University, Tempe, AZ, USA
| | - Frederick R Adler
- School of Biological Sciences, 415772University of Utah, Salt Lake City, UT, USA.,Department of Mathematics, 415772University of Utah, Salt Lake City, UT, USA
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27
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Banerjee S, Zhang X, Kuang S, Wang J, Li L, Fan G, Luo Y, Sun S, Han P, Wu Q, Yang S, Ji X, Li Y, Deng L, Tian X, Wang Z, Zhang Y, Wu K, Zhu S, Bolund L, Yang H, Xu X, Liu J, Lu Y, Liu X. Comparative analysis of clonal evolution among patients with right- and left-sided colon and rectal cancer. iScience 2021; 24:102718. [PMID: 34258553 PMCID: PMC8254024 DOI: 10.1016/j.isci.2021.102718] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/21/2020] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
Tumor multiregion sequencing reveals intratumor heterogeneity (ITH) and clonal evolution playing a key role in tumor progression and metastases. Large-scale high-depth multiregional sequencing of colorectal cancer, comparative analysis among patients with right-sided colon cancer (RCC), left-sided colon cancer (LCC), and rectal cancer (RC), as well as the study of lymph node metastasis (LN) with extranodal tumor deposits (ENTDs) from evolutionary perspective remain weakly explored. Here, we recruited 68 patients with RCC (18), LCC (20), and RC (30). We performed high-depth whole-exome sequencing of 206 tumor regions including 176 primary tumors, 19 LN, and 11 ENTD samples. Our results showed ITH with a Darwinian pattern of evolution and the evolution pattern of LCC and RC was more complex and divergent than RCC. Genetic and evolutionary evidences found that both LN and ENTD originated from different clones. Moreover, ENTD was a distinct entity from LN and evolved later.
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Affiliation(s)
- Santasree Banerjee
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xianxiang Zhang
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shan Kuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jigang Wang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Lei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yonglun Luo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Peng Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Qingyao Wu
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shujian Yang
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaobin Ji
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Yong Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Li Deng
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaofen Tian
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhiwei Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lars Bolund
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Junnian Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yun Lu
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China.,Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao University, Qingdao, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
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28
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Baudoin NC, Bloomfield M. Karyotype Aberrations in Action: The Evolution of Cancer Genomes and the Tumor Microenvironment. Genes (Basel) 2021; 12:558. [PMID: 33921421 PMCID: PMC8068843 DOI: 10.3390/genes12040558] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer is a disease of cellular evolution. For this cellular evolution to take place, a population of cells must contain functional heterogeneity and an assessment of this heterogeneity in the form of natural selection. Cancer cells from advanced malignancies are genomically and functionally very different compared to the healthy cells from which they evolved. Genomic alterations include aneuploidy (numerical and structural changes in chromosome content) and polyploidy (e.g., whole genome doubling), which can have considerable effects on cell physiology and phenotype. Likewise, conditions in the tumor microenvironment are spatially heterogeneous and vastly different than in healthy tissues, resulting in a number of environmental niches that play important roles in driving the evolution of tumor cells. While a number of studies have documented abnormal conditions of the tumor microenvironment and the cellular consequences of aneuploidy and polyploidy, a thorough overview of the interplay between karyotypically abnormal cells and the tissue and tumor microenvironments is not available. Here, we examine the evidence for how this interaction may unfold during tumor evolution. We describe a bidirectional interplay in which aneuploid and polyploid cells alter and shape the microenvironment in which they and their progeny reside; in turn, this microenvironment modulates the rate of genesis for new karyotype aberrations and selects for cells that are most fit under a given condition. We conclude by discussing the importance of this interaction for tumor evolution and the possibility of leveraging our understanding of this interplay for cancer therapy.
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Affiliation(s)
- Nicolaas C. Baudoin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Biological Sciences and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mathew Bloomfield
- Department of Biological Sciences and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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29
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Oberndorfer F, Moling S, Hagelkruys LA, Grimm C, Polterauer S, Sturdza A, Aust S, Reinthaller A, Müllauer L, Schwameis R. Risk Reclassification of Patients with Endometrial Cancer Based on Tumor Molecular Profiling: First Real World Data. J Pers Med 2021; 11:jpm11010048. [PMID: 33467460 PMCID: PMC7830511 DOI: 10.3390/jpm11010048] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Recently, guidelines for endometrial cancer (EC) were released that guide treatment decisions according to the tumors’ molecular profiles. To date, no real-world data regarding the clinical feasibility of molecular profiling have been released. This retrospective, monocentric study investigated the clinical feasibility of molecular profiling and its potential impact on treatment decisions. Tumor specimens underwent molecular profiling (testing for genetic alterations, (immune-)histological examination of lymphovascular space invasion (LVSI), and L1CAM) as part of the clinical routine and were classified according to the European Society for Medical Oncology (ESMO) classification system and to an integrated molecular risk stratification. Shifts between risk groups and potential treatment alterations are described. A total of 60 cases were included, of which twelve were excluded (20%), and eight of the remaining 48 were not characterized (drop-out rate of 16.7%). Molecular profiling revealed 4, 6, 25, and 5 patients with DNA polymerase-epsilon mutation, microsatellite instability, no specific molecular profile, and TP53 mutation, respectively. Three patients had substantial LVSI, and four patients showed high L1CAM expression. Molecular profiling took a median of 18.5 days. Substantial shifts occurred between the classification systems: four patients were upstaged, and 19 patients were downstaged. Molecular profiling of EC specimens is feasible in a daily routine, and new risk classification systems will change treatment decisions substantially.
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Affiliation(s)
- Felicitas Oberndorfer
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria; (F.O.); (L.A.H.); (L.M.)
| | - Sarah Moling
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (S.M.); (S.P.); (S.A.); (A.R.); (R.S.)
| | - Leonie Annika Hagelkruys
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria; (F.O.); (L.A.H.); (L.M.)
| | - Christoph Grimm
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (S.M.); (S.P.); (S.A.); (A.R.); (R.S.)
- Karl Landsteiner Institute for General Gynecology and Experimental Gynecologic Oncology, 1090 Vienna, Austria
- Correspondence: ; Tel.: +43-1-40400-29150
| | - Stephan Polterauer
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (S.M.); (S.P.); (S.A.); (A.R.); (R.S.)
- Karl Landsteiner Institute for General Gynecology and Experimental Gynecologic Oncology, 1090 Vienna, Austria
| | - Alina Sturdza
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
| | - Stefanie Aust
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (S.M.); (S.P.); (S.A.); (A.R.); (R.S.)
| | - Alexander Reinthaller
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (S.M.); (S.P.); (S.A.); (A.R.); (R.S.)
- Karl Landsteiner Institute for General Gynecology and Experimental Gynecologic Oncology, 1090 Vienna, Austria
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria; (F.O.); (L.A.H.); (L.M.)
| | - Richard Schwameis
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria; (S.M.); (S.P.); (S.A.); (A.R.); (R.S.)
- Karl Landsteiner Institute for General Gynecology and Experimental Gynecologic Oncology, 1090 Vienna, Austria
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30
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Aguadé-Gorgorió G, Solé R. Tumour neoantigen heterogeneity thresholds provide a time window for combination immunotherapy. J R Soc Interface 2020; 17:20200736. [PMID: 33109023 DOI: 10.1098/rsif.2020.0736] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Following the advent of cancer immunotherapy, increasing insight has been gained on the role of mutational load and neoantigens as key ingredients in T cell recognition of malignancies. However, not all highly mutational tumours react to immune therapies, and initial success is often followed by eventual relapse. Heterogeneity in the neoantigen landscape of a tumour might be key in the failure of immune surveillance. In this work, we present a mathematical framework to describe how neoantigen distributions shape the immune response. The model predicts the existence of an antigen diversity threshold level beyond which T cells fail at controlling heterogeneous tumours. Incorporating this diversity marker adds predictive value to antigen load for two cohorts of anti-CTLA-4 treated melanoma patients. Furthermore, our analytical approach indicates rapid increases in epitope heterogeneity in early malignancy growth following immune escape. We propose a combination therapy scheme that takes advantage of preexisting resistance to a targeted agent. The model indicates that the selective sweep for a resistant subclone reduces neoantigen heterogeneity, and we postulate the existence of a time window before tumour relapse where checkpoint blockade immunotherapy can become more effective.
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Affiliation(s)
- Guim Aguadé-Gorgorió
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva (CSIC-UPF), Psg Maritim Barceloneta, 37, 08003 Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva (CSIC-UPF), Psg Maritim Barceloneta, 37, 08003 Barcelona, Spain.,Santa Fe Institute, 399 Hyde Park Road, Santa Fe NM 87501, USA
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31
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Clarke R, Kraikivski P, Jones BC, Sevigny CM, Sengupta S, Wang Y. A systems biology approach to discovering pathway signaling dysregulation in metastasis. Cancer Metastasis Rev 2020; 39:903-918. [PMID: 32776157 PMCID: PMC7487029 DOI: 10.1007/s10555-020-09921-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023]
Abstract
Total metastatic burden is the primary cause of death for many cancer patients. While the process of metastasis has been studied widely, much remains to be understood. Moreover, few agents have been developed that specifically target the major steps of the metastatic cascade. Many individual genes and pathways have been implicated in metastasis but a holistic view of how these interact and cooperate to regulate and execute the process remains somewhat rudimentary. It is unclear whether all of the signaling features that regulate and execute metastasis are yet fully understood. Novel features of a complex system such as metastasis can often be discovered by taking a systems-based approach. We introduce the concepts of systems modeling and define some of the central challenges facing the application of a multidisciplinary systems-based approach to understanding metastasis and finding actionable targets therein. These challenges include appreciating the unique properties of the high-dimensional omics data often used for modeling, limitations in knowledge of the system (metastasis), tumor heterogeneity and sampling bias, and some of the issues key to understanding critical features of molecular signaling in the context of metastasis. We also provide a brief introduction to integrative modeling that focuses on both the nodes and edges of molecular signaling networks. Finally, we offer some observations on future directions as they relate to developing a systems-based model of the metastatic cascade.
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Affiliation(s)
- Robert Clarke
- Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA.
- Hormel Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Austin, MN, 55912, USA.
| | - Pavel Kraikivski
- Academy of Integrated Science, Division of Systems Biology, Virginia Polytechnic and State University, Blacksburg, VA, 24061, USA
| | - Brandon C Jones
- Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Catherine M Sevigny
- Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Surojeet Sengupta
- Department of Oncology, Georgetown University Medical Center, 3970 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Yue Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, 22203, USA
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32
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Mastrogamvraki N, Zaravinos A. Signatures of co-deregulated genes and their transcriptional regulators in colorectal cancer. NPJ Syst Biol Appl 2020; 6:23. [PMID: 32737302 PMCID: PMC7395738 DOI: 10.1038/s41540-020-00144-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
The deregulated genes in colorectal cancer (CRC) vary significantly across different studies. Thus, a systems biology approach is needed to identify the co-deregulated genes (co-DEGs), explore their molecular networks, and spot the major hub proteins within these networks. We reanalyzed 19 GEO gene expression profiles to identify and annotate CRC versus normal signatures, single-gene perturbation, and single-drug perturbation signatures. We identified the co-DEGs across different studies, their upstream regulating kinases and transcription factors (TFs). Connectivity Map was used to identify likely repurposing drugs against CRC within each group. The functional changes of the co-upregulated genes in the first category were mainly associated with negative regulation of transforming growth factor β production and glomerular epithelial cell differentiation; whereas the co-downregulated genes were enriched in cotranslational protein targeting to the membrane. We identified 17 hub proteins across the co-upregulated genes and 18 hub proteins across the co-downregulated genes, composed of well-known TFs (MYC, TCF3, PML) and kinases (CSNK2A1, CDK1/4, MAPK14), and validated most of them using GEPIA2 and HPA, but also through two signature gene lists composed of the co-up and co-downregulated genes. We further identified a list of repurposing drugs that can potentially target the co-DEGs in CRC, including camptothecin, neostigmine bromide, emetine, remoxipride, cephaeline, thioridazine, and omeprazole. Similar analyses were performed in the co-DEG signatures in single-gene or drug perturbation experiments in CRC. MYC, PML, CDKs, CSNK2A1, and MAPKs were common hub proteins among all studies. Overall, we identified the critical genes in CRC and we propose repurposing drugs that could be used against them.
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Affiliation(s)
- Natalia Mastrogamvraki
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516, Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Basic Medical Sciences, College of Medicine, Member of QU Health, Qatar University, Doha, Qatar.
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33
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Beckman RA, Loeb LA. Rare Mutations in Cancer Drug Resistance and Implications for Therapy. Clin Pharmacol Ther 2020; 108:437-439. [PMID: 32648584 PMCID: PMC7484911 DOI: 10.1002/cpt.1938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Robert A Beckman
- Departments of Oncology and of Biostatistics, Bioinformatics, and Biomathematics, Lombardi Comprehensive Cancer Center and Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Lawrence A Loeb
- Departments of Pathology and Biochemistry, University of Washington School of Medicine, Seattle, Washington, USA
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