1
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Hu C, Huang C, Hsu M, Chien H, Wu P, Chen Y, Jeng Y, Tang S, Chung M, Shen C, Chang M, Chang Y, Tien Y, Lee W. Oncogenic KRAS, Mucin 4, and Activin A-Mediated Fibroblast Activation Cooperate for PanIN Initiation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301240. [PMID: 37964407 PMCID: PMC10754145 DOI: 10.1002/advs.202301240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/22/2023] [Indexed: 11/16/2023]
Abstract
Over 90% of patients with pancreatic ductal adenocarcinoma (PDAC) have oncogenic KRAS mutations. Nevertheless, mutated KRAS alone is insufficient to initiate pancreatic intraepithelial neoplasia (PanIN), the precursor of PDAC. The identities of the other factors/events required to drive PanIN formation remain elusive. Here, optic-clear 3D histology is used to analyze entire pancreases of 2-week-old Pdx1-Cre; LSL-KrasG12D/+ (KC) mice to detect the earliest emergence of PanIN and observed that the occurrence is independent of physical location. Instead, it is found that the earliest PanINs overexpress Muc4 and associate with αSMA+ fibroblasts in both transgenic mice and human specimens. Mechanistically, KrasG12D/+ pancreatic cells upregulate Muc4 through genetic alterations to increase proliferation and fibroblast recruitments via Activin A secretion and consequently enhance cell transformation for PanIN formation. Inhibition of Activin A signaling using Follistatin (FST) diminishes early PanIN-associated fibroblast recruitment, effectively curtailing PanIN initiation and growth in KC mice. These findings emphasize the vital role of interactions between oncogenic KrasG12D/+ -driven genetic alterations and induced microenvironmental changes in PanIN initiation, suggesting potential avenues for early PDAC diagnostic and management approaches.
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Affiliation(s)
- Chun‐Mei Hu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Chien‐Chang Huang
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
- Biomedical Translation Research CenterAcademia SinicaTaipei11529Taiwan
| | - Min‐Fen Hsu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Hung‐Jen Chien
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Pei‐Jung Wu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Yi‐Ing Chen
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Yung‐Ming Jeng
- Department of PathologyNational Taiwan University HospitalTaipei10041Taiwan
- Graduate Institute of Pathology, College of MedicineNational Taiwan UniversityTaipei10041Taiwan
| | - Shiue‐Cheng Tang
- Department of Medical ScienceNational Tsing Hua UniversityHsinchu30013Taiwan
| | - Mei‐Hsin Chung
- Department of PathologyNational Taiwan University Hospital−Hsinchu BranchHsinchu30331Taiwan
| | - Chia‐Ning Shen
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
- Biomedical Translation Research CenterAcademia SinicaTaipei11529Taiwan
| | - Ming‐Chu Chang
- Department of Internal MedicineNational Taiwan University HospitalTaipei10041Taiwan
| | - Yu‐Ting Chang
- Department of Internal MedicineNational Taiwan University HospitalTaipei10041Taiwan
| | - Yu‐Wen Tien
- Department of SurgeryNational Taiwan University HospitalTaipei10041Taiwan
| | - Wen‐Hwa Lee
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
- Drug Development CenterChina Medical UniversityTaichung40402Taiwan
- Department of Biological ChemistryUniversity of CaliforniaIrvineCA92697USA
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2
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Huang M, Ma J, An G, Ye X. Unravelling cancer subtype-specific driver genes in single-cell transcriptomics data with CSDGI. PLoS Comput Biol 2023; 19:e1011450. [PMID: 38096269 PMCID: PMC10754467 DOI: 10.1371/journal.pcbi.1011450] [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: 08/22/2023] [Revised: 12/28/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023] Open
Abstract
Cancer is known as a heterogeneous disease. Cancer driver genes (CDGs) need to be inferred for understanding tumor heterogeneity in cancer. However, the existing computational methods have identified many common CDGs. A key challenge exploring cancer progression is to infer cancer subtype-specific driver genes (CSDGs), which provides guidane for the diagnosis, treatment and prognosis of cancer. The significant advancements in single-cell RNA-sequencing (scRNA-seq) technologies have opened up new possibilities for studying human cancers at the individual cell level. In this study, we develop a novel unsupervised method, CSDGI (Cancer Subtype-specific Driver Gene Inference), which applies Encoder-Decoder-Framework consisting of low-rank residual neural networks to inferring driver genes corresponding to potential cancer subtypes at the single-cell level. To infer CSDGs, we apply CSDGI to the tumor single-cell transcriptomics data. To filter the redundant genes before driver gene inference, we perform the differential expression genes (DEGs). The experimental results demonstrate CSDGI is effective to infer driver genes that are cancer subtype-specific. Functional and disease enrichment analysis shows these inferred CSDGs indicate the key biological processes and disease pathways. CSDGI is the first method to explore cancer driver genes at the cancer subtype level. We believe that it can be a useful method to understand the mechanisms of cell transformation driving tumours.
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Affiliation(s)
- Meng Huang
- Department of Automation, Xiamen University, Xiamen, China
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Jiangtao Ma
- Department of Automation, Xiamen University, Xiamen, China
- School of Engineering, Dali University, Dali, Yunnan, China
| | - Guangqi An
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
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3
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Nejati-Koshki K, Roberts CT, Babaei G, Rastegar M. The Epigenetic Reader Methyl-CpG-Binding Protein 2 (MeCP2) Is an Emerging Oncogene in Cancer Biology. Cancers (Basel) 2023; 15:2683. [PMID: 37345019 DOI: 10.3390/cancers15102683] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/23/2023] Open
Abstract
Epigenetic mechanisms are gene regulatory processes that control gene expression and cellular identity. Epigenetic factors include the "writers", "readers", and "erasers" of epigenetic modifications such as DNA methylation. Accordingly, the nuclear protein Methyl-CpG-Binding Protein 2 (MeCP2) is a reader of DNA methylation with key roles in cellular identity and function. Research studies have linked altered DNA methylation, deregulation of MeCP2 levels, or MECP2 gene mutations to different types of human disease. Due to the high expression level of MeCP2 in the brain, many studies have focused on its role in neurological and neurodevelopmental disorders. However, it is becoming increasingly apparent that MeCP2 also participates in the tumorigenesis of different types of human cancer, with potential oncogenic properties. It is well documented that aberrant epigenetic regulation such as altered DNA methylation may lead to cancer and the process of tumorigenesis. However, direct involvement of MeCP2 with that of human cancer was not fully investigated until lately. In recent years, a multitude of research studies from independent groups have explored the molecular mechanisms involving MeCP2 in a vast array of human cancers that focus on the oncogenic characteristics of MeCP2. Here, we provide an overview of the proposed role of MeCP2 as an emerging oncogene in different types of human cancer.
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Affiliation(s)
- Kazem Nejati-Koshki
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil 85991-56189, Iran
| | - Chris-Tiann Roberts
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Ghader Babaei
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia 57157-89400, Iran
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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4
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Reilly L, Seddighi S, Singleton AB, Cookson MR, Ward ME, Qi YA. Variant biomarker discovery using mass spectrometry-based proteogenomics. FRONTIERS IN AGING 2023; 4:1191993. [PMID: 37168844 PMCID: PMC10165118 DOI: 10.3389/fragi.2023.1191993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
Genomic diversity plays critical roles in risk of disease pathogenesis and diagnosis. While genomic variants-including single nucleotide variants, frameshift variants, and mis-splicing isoforms-are commonly detected at the DNA or RNA level, their translated variant protein or polypeptide products are ultimately the functional units of the associated disease. These products are often released in biofluids and could be leveraged for clinical diagnosis and patient stratification. Recent emergence of integrated analysis of genomics with mass spectrometry-based proteomics for biomarker discovery, also known as proteogenomics, have significantly advanced the understanding disease risk variants, precise medicine, and biomarker discovery. In this review, we discuss variant proteins in the context of cancers and neurodegenerative diseases, outline current and emerging proteogenomic approaches for biomarker discovery, and provide a comprehensive proteogenomic strategy for detection of putative biomarker candidates in human biospecimens. This strategy can be implemented for proteogenomic studies in any field of enquiry. Our review timely addresses the need of biomarkers for aging related diseases.
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Affiliation(s)
- Luke Reilly
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sahba Seddighi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Yue A. Qi
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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5
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Vitorino JD, Costa PM. After a Century of Research into Environmental Mutagens and Carcinogens, Where Do We Stand? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1040. [PMID: 36673796 PMCID: PMC9859577 DOI: 10.3390/ijerph20021040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Cancer is one of the longest-known human diseases, yet only in recent times have we begun to perceive that the percentage of neoplasms caused by environmental factors, lifestyle and chemicals, is likely underestimated. The first medical reports associating cancer with pollutants like tars appeared by the early 20th century, but despite initial evidence relating oncogenesis and chromosomal alterations, only after the structure of DNA had been elucidated in the 1950s have genetic disorders been fully perceived as cause. This led to a growing interest in genotoxic and mutagenic pollutants. Even though we are now familiar with a range of environmental carcinogens spanning between aromatic hydrocarbons and asbestos to radionuclides and forms of carbon nanomaterials, establishing causal networks between pollutants and cancer remains cumbersome. In most part, this is due to the complexity of toxicant matrices, unknown modes-of-action of chemicals or their mixtures, the widening array of novel pollutants plus difficulties in subtracting background effects from true aetiology of disease. Recent advances in analytical chemistry, high-throughput toxicology, next-generation sequencing, computational biology and databases that allocate whole normal and cancer genomes, all indicate that we are on the verge of a new age of research into mechanistic 'oncotoxicology', but how can it impact risk assessment and prevention?
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Affiliation(s)
| | - Pedro M. Costa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
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6
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Mehmood S, Aslam S, Dilshad E, Ismail H, Khan AN. Transforming Diagnosis and Therapeutics Using Cancer Genomics. Cancer Treat Res 2023; 185:15-47. [PMID: 37306902 DOI: 10.1007/978-3-031-27156-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In past quarter of the century, much has been understood about the genetic variation and abnormal genes that activate cancer in humans. All the cancers somehow possess alterations in the DNA sequence of cancer cell's genome. In present, we are heading toward the era where it is possible to obtain complete genome of the cancer cells for their better diagnosis, categorization and to explore treatment options.
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Affiliation(s)
- Sabba Mehmood
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan.
| | - Shaista Aslam
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Erum Dilshad
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
| | - Hammad Ismail
- Departments of Biochemistry and Biotechnology, University of Gujrat (UOG) Gujrat, Gujrat, Pakistan
| | - Amna Naheed Khan
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
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7
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: https:/doi.org/10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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8
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: 10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
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9
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Siebenaler RF, Chugh S, Waninger JJ, Dommeti VL, Kenum C, Mody M, Gautam A, Patel N, Chu A, Bawa P, Hon J, Smith RD, Carlson H, Cao X, Tesmer JJG, Shankar S, Chinnaiyan AM. Argonaute 2 modulates EGFR-RAS signaling to promote mutant HRAS and NRAS-driven malignancies. PNAS NEXUS 2022; 1:pgac084. [PMID: 35923912 PMCID: PMC9338400 DOI: 10.1093/pnasnexus/pgac084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/26/2022] [Indexed: 02/05/2023]
Abstract
Activating mutations in RAS GTPases drive nearly 30% of all human cancers. Our prior work described an essential role for Argonaute 2 (AGO2), of the RNA-induced silencing complex, in mutant KRAS-driven cancers. Here, we identified a novel endogenous interaction between AGO2 and RAS in both wild-type (WT) and mutant HRAS/NRAS cells. This interaction was regulated through EGFR-mediated phosphorylation of Y393-AGO2, and utilizing molecular dynamic simulation, we identified a conformational change in pY393-AGO2 protein structure leading to disruption of the RAS binding site. Knockdown of AGO2 led to a profound decrease in proliferation of mutant HRAS/NRAS-driven cell lines but not WT RAS cells. These cells demonstrated oncogene-induced senescence (OIS) as evidenced by β-galactosidase staining and induction of multiple downstream senescence effectors. Mechanistically, we discovered that the senescent phenotype was mediated via induction of reactive oxygen species. Intriguingly, we further identified that loss of AGO2 promoted a novel feed forward pathway leading to inhibition of the PTP1B phosphatase and activation of EGFR-MAPK signaling, consequently resulting in OIS. Taken together, our study demonstrates that the EGFR-AGO2-RAS signaling axis is essential for maintaining mutant HRAS and NRAS-driven malignancies.
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Affiliation(s)
| | | | - Jessica J Waninger
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vijaya L Dommeti
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carson Kenum
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Malay Mody
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anudeeta Gautam
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nidhi Patel
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alec Chu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pushpinder Bawa
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer Hon
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard D Smith
- College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Heather Carlson
- College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - John J G Tesmer
- Departments of Biological Sciences and Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Sunita Shankar
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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10
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Caligola S, De Sanctis F, Canè S, Ugel S. Breaking the Immune Complexity of the Tumor Microenvironment Using Single-Cell Technologies. Front Genet 2022; 13:867880. [PMID: 35651929 PMCID: PMC9149246 DOI: 10.3389/fgene.2022.867880] [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: 02/01/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
Tumors are not a simple aggregate of transformed cells but rather a complicated ecosystem containing various components, including infiltrating immune cells, tumor-related stromal cells, endothelial cells, soluble factors, and extracellular matrix proteins. Profiling the immune contexture of this intricate framework is now mandatory to develop more effective cancer therapies and precise immunotherapeutic approaches by identifying exact targets or predictive biomarkers, respectively. Conventional technologies are limited in reaching this goal because they lack high resolution. Recent developments in single-cell technologies, such as single-cell RNA transcriptomics, mass cytometry, and multiparameter immunofluorescence, have revolutionized the cancer immunology field, capturing the heterogeneity of tumor-infiltrating immune cells and the dynamic complexity of tenets that regulate cell networks in the tumor microenvironment. In this review, we describe some of the current single-cell technologies and computational techniques applied for immune-profiling the cancer landscape and discuss future directions of how integrating multi-omics data can guide a new "precision oncology" advancement.
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Affiliation(s)
- Simone Caligola
- Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| | | | - Stefania Canè
- Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Stefano Ugel
- Immunology Section, Department of Medicine, University of Verona, Verona, Italy
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11
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Lietman CD, Johnson ML, McCormick F, Lindsay CR. More to the RAS Story: KRAS G12C Inhibition, Resistance Mechanisms, and Moving Beyond KRAS G12C. Am Soc Clin Oncol Educ Book 2022; 42:1-13. [PMID: 35561303 DOI: 10.1200/edbk_351333] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the discovery of RAS oncogenes in human tumor DNA 40 years ago, the development of effective targeted therapies directed against RAS has lagged behind those more successful advancements in the field of therapeutic tyrosine kinase inhibitors targeting other oncogenes such as EGFR, ALK, and ROS1. The discoveries that (1) malignant RAS oncogenes differ from their wild-type counterparts by only a single amino acid change and (2) covalent inhibition of the cysteine residue at codon 12 of KRASG12C in its inactive GDP-bound state resulted in effective inhibition of oncogenic RAS signaling and have catalyzed a dramatic shift in mindset toward KRAS-driven cancers. Although the development of allele-selective KRASG12C inhibitors has changed a treatment paradigm, the clinical activity of these agents is more modest than tyrosine kinase inhibitors targeting other oncogene-driven cancers. Heterogeneous resistance mechanisms generally result in the restoration of RAS/mitogen-activated protein kinase pathway signaling. Many approaches are being evaluated to overcome this resistance, with many combinatorial clinical trials ongoing. Furthermore, because KRASG12D and KRASG12V are more prevalent than KRASG12C, there remains an unmet need for additional therapeutic strategies for these patients. Thus, our current translational standing could be described as "the end of the beginning," with additional discovery and research innovation needed to address the enormous disease burden imposed by RAS-mutant cancers. Here, we describe the development of KRASG12C inhibitors, the challenges of resistance to these inhibitors, strategies to mitigate that resistance, and new approaches being taken to address other RAS-mutant cancers.
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Affiliation(s)
| | | | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
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12
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Odeniyide P, Yohe ME, Pollard K, Vaseva AV, Calizo A, Zhang L, Rodriguez FJ, Gross JM, Allen AN, Wan X, Somwar R, Schreck KC, Kessler L, Wang J, Pratilas CA. Targeting farnesylation as a novel therapeutic approach in HRAS-mutant rhabdomyosarcoma. Oncogene 2022; 41:2973-2983. [PMID: 35459782 PMCID: PMC9122815 DOI: 10.1038/s41388-022-02305-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/11/2023]
Abstract
Activating RAS mutations are found in a subset of fusion-negative rhabdomyosarcoma (RMS), and therapeutic strategies to directly target RAS in these tumors have been investigated, without clinical success to date. A potential strategy to inhibit oncogenic RAS activity is the disruption of RAS prenylation, an obligate step for RAS membrane localization and effector pathway signaling, through inhibition of farnesyltransferase (FTase). Of the major RAS family members, HRAS is uniquely dependent on FTase for prenylation, whereas NRAS and KRAS can utilize geranylgeranyl transferase as a bypass prenylation mechanism. Tumors driven by oncogenic HRAS may therefore be uniquely sensitive to FTase inhibition. To investigate the mutation-specific effects of FTase inhibition in RMS we utilized tipifarnib, a potent and selective FTase inhibitor, in in vitro and in vivo models of RMS genomically characterized for RAS mutation status. Tipifarnib reduced HRAS processing, and plasma membrane localization leading to decreased GTP-bound HRAS and decreased signaling through RAS effector pathways. In HRAS-mutant cell lines, tipifarnib reduced two-dimensional and three-dimensional cell growth, and in vivo treatment with tipifarnib resulted in tumor growth inhibition exclusively in HRAS-mutant RMS xenografts. Our data suggest that small molecule inhibition of FTase is active in HRAS-driven RMS and may represent an effective therapeutic strategy for a genomically-defined subset of patients with RMS.
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Affiliation(s)
- Patience Odeniyide
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marielle E Yohe
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kai Pollard
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Angelina V Vaseva
- The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ana Calizo
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lindy Zhang
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fausto J Rodriguez
- Department of Laboratory Medicine and Pathology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John M Gross
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy N Allen
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaolin Wan
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Romel Somwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karisa C Schreck
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jiawan Wang
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christine A Pratilas
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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13
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Désage AL, Léonce C, Swalduz A, Ortiz-Cuaran S. Targeting KRAS Mutant in Non-Small Cell Lung Cancer: Novel Insights Into Therapeutic Strategies. Front Oncol 2022; 12:796832. [PMID: 35251972 PMCID: PMC8889932 DOI: 10.3389/fonc.2022.796832] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 01/07/2022] [Indexed: 12/17/2022] Open
Abstract
Although KRAS-activating mutations represent the most common oncogenic driver in non-small cell lung cancer (NSCLC), various attempts to inhibit KRAS failed in the past decade. KRAS mutations are associated with a poor prognosis and a poor response to standard therapeutic regimen. The recent development of new therapeutic agents (i.e., adagrasib, sotorasib) that target specifically KRAS G12C in its GDP-bound state has evidenced an unprecedented success in the treatment of this subgroup of patients. Despite providing pre-clinical and clinical efficacy, several mechanisms of acquired resistance to KRAS G12C inhibitors have been reported. In this setting, combined therapeutic strategies including inhibition of either SHP2, SOS1 or downstream effectors of KRAS G12C seem particularly interesting to overcome acquired resistance. In this review, we will discuss the novel therapeutic strategies targeting KRAS G12C and promising approaches of combined therapy to overcome acquired resistance to KRAS G12C inhibitors.
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Affiliation(s)
- Anne-Laure Désage
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.,Department of Pulmonology and Thoracic Oncology, North Hospital, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Camille Léonce
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Aurélie Swalduz
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
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14
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Kwan AK, Piazza GA, Keeton AB, Leite CA. The path to the clinic: a comprehensive review on direct KRASG12C inhibitors. J Exp Clin Cancer Res 2022; 41:27. [PMID: 35045886 PMCID: PMC8767686 DOI: 10.1186/s13046-021-02225-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/16/2021] [Indexed: 02/08/2023] Open
Abstract
AbstractThe RAS oncogene is both the most frequently mutated oncogene in human cancer and the first confirmed human oncogene to be discovered in 1982. After decades of research, in 2013, the Shokat lab achieved a seminal breakthrough by showing that the activated KRAS isozyme caused by the G12C mutation in the KRAS gene can be directly inhibited via a newly unearthed switch II pocket. Building upon this groundbreaking discovery, sotorasib (AMG510) obtained approval by the United States Food and Drug Administration in 2021 to become the first therapy to directly target the KRAS oncoprotein in any KRAS-mutant cancers, particularly those harboring the KRASG12C mutation. Adagrasib (MRTX849) and other direct KRASG12C inhibitors are currently being investigated in multiple clinical trials. In this review, we delve into the path leading to the development of this novel KRAS inhibitor, starting with the discovery, structure, and function of the RAS family of oncoproteins. We then examine the clinical relevance of KRAS, especially the KRASG12C mutation in human cancer, by providing an in-depth analysis of its cancer epidemiology. Finally, we review the preclinical evidence that supported the initial development of the direct KRASG12C inhibitors and summarize the ongoing clinical trials of all direct KRASG12C inhibitors.
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15
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Feizi N, Liu Q, Murphy L, Hu P. Computational Prediction of the Pathogenic Status of Cancer-Specific Somatic Variants. Front Genet 2022; 12:805656. [PMID: 35116056 PMCID: PMC8804317 DOI: 10.3389/fgene.2021.805656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
In-silico classification of the pathogenic status of somatic variants is shown to be promising in promoting the clinical utilization of genetic tests. Majority of the available classification tools are designed based on the characteristics of germline variants or the combination of germline and somatic variants. Significance of somatic variants in cancer initiation and progression urges for development of classifiers specialized for classifying pathogenic status of cancer somatic variants based on the model trained on cancer somatic variants. We established a gold standard exclusively for cancer somatic single nucleotide variants (SNVs) collected from the catalogue of somatic mutations in cancer. We developed two support vector machine (SVM) classifiers based on genomic features of cancer somatic SNVs located in coding and non-coding regions of the genome, respectively. The SVM classifiers achieved the area under the ROC curve of 0.94 and 0.89 regarding the classification of the pathogenic status of coding and non-coding cancer somatic SNVs, respectively. Our models outperform two well-known classification tools including FATHMM-FX and CScape in classifying both coding and non-coding cancer somatic variants. Furthermore, we applied our models to predict the pathogenic status of somatic variants identified in young breast cancer patients from METABRIC and TCGA-BRCA studies. The results indicated that using the classification threshold of 0.8 our “coding” model predicted 1853 positive SNVs (out of 6,910) from the TCGA-BRCA dataset, and 500 positive SNVs (out of 1882) from the METABRIC dataset. Interestingly, through comparative survival analysis of the positive predictions from our models, we identified a young-specific pathogenic somatic variant with potential for the prognosis of early onset of breast cancer in young women.
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Affiliation(s)
- Nikta Feizi
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Qian Liu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada
| | - Leigh Murphy
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
- *Correspondence: Pingzhao Hu,
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16
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Clark-Garvey S, Kim WY. RAF1 amplification: an exemplar of MAPK pathway activation in urothelial carcinoma. J Clin Invest 2021; 131:154095. [PMID: 34779406 DOI: 10.1172/jci154095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Despite recent therapeutic gains in the treatment of advanced bladder cancer, the overall survival in patients with metastatic disease remains poor and further therapeutic discovery is needed. Advanced bladder cancer is a molecularly heterogeneous disease, and the identification of driver genetic alterations has led to effective targeted therapeutic agents, such as fibroblast growth factor receptor (FGFR) inhibitors. In this issue of the JCI, Bekele et al. identify a subtype of muscle-invasive bladder cancer (MIBC) that harbors RAF1 amplification. The authors showed that RAF1 inhibition, with pan-RAF inhibitors, and the combination of RAF1 inhibition with MEK inhibition were efficacious in preclinical models harboring RAF1 amplifications as well as in tumors with HRAS and NRAS mutations. This study highlights RAF1 amplification as a driver event in bladder cancer and establishes the central role of the MAPK pathway in bladder tumorigenesis.
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Affiliation(s)
| | - William Y Kim
- Division of Oncology, Department of Medicine.,Lineberger Comprehensive Cancer Center.,Department of Pharmacology; and.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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17
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Abbasi A, Alexandrov LB. Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures. DNA Repair (Amst) 2021; 107:103200. [PMID: 34411908 PMCID: PMC9478565 DOI: 10.1016/j.dnarep.2021.103200] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Next generation sequencing technologies (NGS) have been critical in characterizing the genomic landscape and untangling the genetic heterogeneity of human cancer. Since its advent, NGS has played a pivotal role in identifying the patterns of somatic mutations imprinted on cancer genomes and in deciphering the signatures of the mutational processes that have generated these patterns. Mutational signatures serve as phenotypic molecular footprints of exposures to environmental factors as well as deficiency and infidelity of DNA replication and repair pathways. Since the first roadmap of mutational signatures in human cancer was generated from whole-genome and whole-exome sequencing data, there has been a growing interest to extract mutational signatures from other NGS technologies such as targeted panel sequencing, RNA sequencing, single-cell sequencing, duplex sequencing, reduced representation sequencing, and long-read sequencing. Many of these technologies have their inherent sequencing biases and produce technical artifacts that can confound the extraction of reliable and interpretable mutational signatures. In this review, we highlight the relevance, limitations, and prospects of using different NGS technologies for examining mutational patterns and for deciphering mutational signatures.
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Affiliation(s)
- Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
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18
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Heppner DE, Eck MJ. A structural perspective on targeting the RTK/Ras/MAP kinase pathway in cancer. Protein Sci 2021; 30:1535-1553. [PMID: 34008902 PMCID: PMC8284588 DOI: 10.1002/pro.4125] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
Abstract
Precision oncology is premised on identifying and drugging proteins and pathways that drive tumorigenesis or are required for survival of tumor cells. Across diverse cancer types, the signaling pathway emanating from receptor tyrosine kinases on the cell surface to RAS and the MAP kinase pathway is the most frequent target of oncogenic mutations, and key proteins in this signaling axis including EGFR, SHP2, RAS, BRAF, and MEK have long been a focus in cancer drug discovery. In this review, we provide an overview of historical and recent efforts to develop inhibitors targeting these nodes with an emphasis on the role that an understanding of protein structure and regulation has played in inhibitor discovery and characterization. Beyond its well-established role in structure-based drug design, structural biology has revealed mechanisms of allosteric regulation, distinct effects of activating oncogenic mutations, and other vulnerabilities that have opened new avenues in precision cancer drug discovery.
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Affiliation(s)
- David E. Heppner
- Department of ChemistryUniversity at Buffalo, State University of New YorkBuffaloNew YorkUSA
- Department of Pharmacology and TherapeuticsRoswell Park Comprehensive Cancer CenterBuffaloNew YorkUSA
| | - Michael J. Eck
- Department of Cancer BiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMassachusettsUSA
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19
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Smith-Uffen M, Bartley N, Davies G, Best M. Motivations and barriers to pursue cancer genomic testing: A systematic review. PATIENT EDUCATION AND COUNSELING 2021; 104:1325-1334. [PMID: 33390305 DOI: 10.1016/j.pec.2020.12.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/21/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Single-gene testing is associated with psycho-social challenges for cancer patients. Genomic testing may amplify these. The aim of this study was to understand patients' motivations and barriers to pursue cancer genomic testing, to enable healthcare providers to support their patients throughout the testing process and interpretation of test results. METHODS Five databases were searched for original peer reviewed research articles published between January 2001 and September 2018 addressing motivation for genomic cancer testing. QualSyst was used to assess quality. RESULTS 182 studies were identified and 17 were included for review. Studies were heterogenous. Both somatic and germline testing were included, and 14 studies used hypothetical scenarios. 3249 participants were analyzed, aged 18 to 94. Most were female and white. The most common diagnoses were breast, ovarian, lung and colorectal cancer. Interest in testing was high. Motivations included ability to predict cancer risk, inform disease management, benefit families, and understand cancer. Barriers included concerns about cost, privacy/confidentiality, clinical utility, and psychological harm. CONCLUSIONS Despite concerns, consumers are interested in cancer genomic testing if it can provide actionable results for themselves and their families. PRACTICE IMPLICATIONS Providers must manage understanding and expectations of testing and translate genetic information into health-promoting behaviours.
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Affiliation(s)
- Megan Smith-Uffen
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
| | - Nicci Bartley
- Faculty of Science, School of Psychology, University of Sydney, Sydney, Australia
| | - Grace Davies
- Faculty of Science, School of Psychology, University of Sydney, Sydney, Australia
| | - Megan Best
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia; Faculty of Science, School of Psychology, University of Sydney, Sydney, Australia; University of Notre Dame Australia, Sydney, Australia
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20
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40 Years of RAS-A Historic Overview. Genes (Basel) 2021; 12:genes12050681. [PMID: 34062774 PMCID: PMC8147265 DOI: 10.3390/genes12050681] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
It has been over forty years since the isolation of the first human oncogene (HRAS), a crucial milestone in cancer research made possible through the combined efforts of a few selected research groups at the beginning of the 1980s. Those initial discoveries led to a quantitative leap in our understanding of cancer biology and set up the onset of the field of molecular oncology. The following four decades of RAS research have produced a huge pool of new knowledge about the RAS family of small GTPases, including how they regulate signaling pathways controlling many cellular physiological processes, or how oncogenic mutations trigger pathological conditions, including developmental syndromes or many cancer types. However, despite the extensive body of available basic knowledge, specific effective treatments for RAS-driven cancers are still lacking. Hopefully, recent advances involving the discovery of novel pockets on the RAS surface as well as highly specific small-molecule inhibitors able to block its interaction with effectors and/or activators may lead to the development of new, effective treatments for cancer. This review intends to provide a quick, summarized historical overview of the main milestones in RAS research spanning from the initial discovery of the viral RAS oncogenes in rodent tumors to the latest attempts at targeting RAS oncogenes in various human cancers.
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21
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Köhler J, Jänne PA. If Virchow and Ehrlich Had Dreamt Together: What the Future Holds for KRAS-Mutant Lung Cancer. Int J Mol Sci 2021; 22:3025. [PMID: 33809660 PMCID: PMC8002337 DOI: 10.3390/ijms22063025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 12/26/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) with Kirsten rat sarcoma (KRAS) mutations has notoriously challenged oncologists and researchers for three notable reasons: (1) the historical assumption that KRAS is "undruggable", (2) the disease heterogeneity and (3) the shaping of the tumor microenvironment by KRAS downstream effector functions. Better insights into KRAS structural biochemistry allowed researchers to develop direct KRAS(G12C) inhibitors, which have shown early signs of clinical activity in NSCLC patients and have recently led to an FDA breakthrough designation for AMG-510. Following the approval of immune checkpoint inhibitors for PDL1-positive NSCLC, this could fuel yet another major paradigm shift in the treatment of advanced lung cancer. Here, we review advances in our understanding of the biology of direct KRAS inhibition and project future opportunities and challenges of dual KRAS and immune checkpoint inhibition. This strategy is supported by preclinical models which show that KRAS(G12C) inhibitors can turn some immunologically "cold" tumors into "hot" ones and therefore could benefit patients whose tumors harbor subtype-defining STK11/LKB1 co-mutations. Forty years after the discovery of KRAS as a transforming oncogene, we are on the verge of approval of the first KRAS-targeted drug combinations, thus therapeutically unifying Paul Ehrlich's century-old "magic bullet" vision with Rudolf Virchow's cancer inflammation theory.
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Affiliation(s)
- Jens Köhler
- Dana-Farber Cancer Institute, Department of Medical Oncology, Harvard Medical School, Boston, MA 02215, USA
| | - Pasi A. Jänne
- Dana-Farber Cancer Institute, Department of Medical Oncology, Harvard Medical School, Boston, MA 02215, USA
- Belfer Center for Applied Cancer Sciences, Boston, MA 02215, USA
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22
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Ishitsuka Y, Hanaoka Y, Tanemura A, Fujimoto M. Cutaneous Squamous Cell Carcinoma in the Age of Immunotherapy. Cancers (Basel) 2021; 13:1148. [PMID: 33800195 PMCID: PMC7962464 DOI: 10.3390/cancers13051148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most prevalent skin cancer globally. Because most cSCC cases are manageable by local excision/radiotherapy and hardly become life-threatening, they are often excluded from cancer registries in most countries. Compared with cutaneous melanoma that originates from the melanin-producing, neural crest-derived epidermal resident, keratinocyte (KC)-derived cancers are influenced by the immune system with regards to their pathogenetic behaviour. Congenital or acquired immunosurveillance impairments compromise tumoricidal activity and raises cSCC incidence rates. Intriguingly, expanded applications of programmed death-1 (PD-1) blockade therapies have revealed cSCC to be one of the most amenable targets, particularly when compared with the mucosal counterparts arisen in the esophagus or the cervix. The clinical observation reminds us that cutaneous tissue has a peculiarly high immunogenicity that can evoke tumoricidal recall responses topically. Here we attempt to redefine cSCC biology and review current knowledge about cSCC from multiple viewpoints that involve epidemiology, clinicopathology, molecular genetics, molecular immunology, and developmental biology. This synthesis not only underscores the primal importance of the immune system, rather than just a mere accumulation of ultraviolet-induced mutations but also reinforces the following hypothesis: PD-1 blockade effectively restores the immunity specially allowed to exist within the fully cornified squamous epithelium, that is, the epidermis.
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Affiliation(s)
- Yosuke Ishitsuka
- Department of Dermatology Integrated Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.H.); (A.T.); (M.F.)
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23
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Fernandez-Rozadilla C, Simões AR, Lleonart ME, Carnero A, Carracedo Á. Tumor Profiling at the Service of Cancer Therapy. Front Oncol 2021; 10:595613. [PMID: 33505911 PMCID: PMC7832432 DOI: 10.3389/fonc.2020.595613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer treatment options have evolved significantly in the past few years. From the initial surgical procedures, to the latest next-generation technologies, we are now in the position to analyze and understand tumors in a one-by-one basis and use that to our advantage to provide with individualized treatment options that may increase patient survival. In this review, we will focus on how tumor profiling has evolved over the past decades to deliver more efficient and personalized treatment options, and how novel technologies can help us envisage the future of precision oncology toward a better management and, ultimately, increased survival.
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Affiliation(s)
- Ceres Fernandez-Rozadilla
- Grupo de Medicina Xenómica (USC), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Ana Rita Simões
- Grupo de Medicina Xenómica (USC), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Matilde E Lleonart
- Biomedical Research in Cancer Stem Cells, Vall d´Hebron Research Institute (VHIR), Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology, CIBERONC, Madrid, Spain
| | - Amancio Carnero
- Spanish Biomedical Research Network Centre in Oncology, CIBERONC, Madrid, Spain.,Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica (USC), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica (USC), Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
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24
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Zhang Y, Xu Y, Lu W, Ghergurovich JM, Guo L, Blair IA, Rabinowitz JD, Yang X. Upregulation of Antioxidant Capacity and Nucleotide Precursor Availability Suffices for Oncogenic Transformation. Cell Metab 2021; 33:94-109.e8. [PMID: 33159852 PMCID: PMC7846267 DOI: 10.1016/j.cmet.2020.10.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/04/2020] [Accepted: 09/30/2020] [Indexed: 12/17/2022]
Abstract
The emergence of cancer from diverse normal tissues has long been rationalized to represent a common set of fundamental processes. However, these processes are not fully defined. Here, we show that forced expression of glucose-6-phosphate dehydrogenase (G6PD) affords immortalized mouse and human cells anchorage-independent growth in vitro and tumorigenicity in animals. Mechanistically, G6PD augments the NADPH pool by stimulating NAD+ kinase-mediated NADP+ biosynthesis in addition to converting NADP+ to NADPH, bolstering antioxidant defense. G6PD also increases nucleotide precursor levels through the production of ribose and NADPH, promoting cell proliferation. Supplementation of antioxidants or nucleosides suffices to convert immortalized mouse and human cells into a tumorigenic state, and supplementation of both is required when their overlapping metabolic consequences are minimized. These results suggest that normal cells have a limited capacity for redox balance and nucleotide synthesis, and overcoming this limit might represent a key aspect of oncogenic transformation.
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Affiliation(s)
- Yang Zhang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Jonathan M Ghergurovich
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Lili Guo
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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25
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Pieczynski JN, Kee HL. "Designer babies?!" A CRISPR-based learning module for undergraduates built around the CCR5 gene. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:80-93. [PMID: 32777177 PMCID: PMC7891609 DOI: 10.1002/bmb.21395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 05/11/2023]
Abstract
CRISPR-cas technology is being incorporated into undergraduate biology curriculum through lab experiences to immerse students in modern technology that is rapidly changing the landscape of science, medicine and agriculture. We developed and implemented an educational module that introduces students to CRISPR-cas technology in a Genetic course and an Advanced Genetics course. Our primary teaching objective was to immerse students in the design, strategy, conceptual modeling, and application of CRISPR-cas technology using the current research claim of the modification of the CCR5 gene in twin girls. This also allowed us to engage students in an open conversation about the bioethical implications of heritable germline and non-heritable somatic genomic editing. We assessed student-learning outcomes and conclude that this learning module is an effective strategy for teaching undergraduates the fundamentals and application of CRISPR-cas gene editing technology and can be adapted to other genes and diseases that are currently being treated with CRISPR-cas technology.
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Affiliation(s)
- Jay N Pieczynski
- Department of Biology, Rollins College, Winter Park, Florida, USA
| | - Hooi Lynn Kee
- Department of Biology, Stetson University, DeLand, Florida, USA
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26
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Salam T, Lyngdoh RHD. Clues to the non-carcinogenicity of certain N-Nitroso compounds: Role of alkylated DNA bases. Biophys Chem 2020; 271:106539. [PMID: 33508580 DOI: 10.1016/j.bpc.2020.106539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/16/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
N-Nitroso compounds (NOC) are known for the carcinogenicity of most members. However, 13% of 332 NOC reviewed in 1984 were found to be non-carcinogenic. The non-carcinogenicity of all N-nitrosamines with even one tertiary alkyl group is notable. Clues to the lack of carcinogenicity include (a) inability to generate the reactive ultimate carcinogen which alkylates DNA bases, and (b) inability of the alkylated DNA base to mispair during DNA replication. This DFT study probes a three-stage process for the induction of mutations, including (a) N-deprotonation of O-alkylated DNA bases formed by attack of the carcinogen, (b) adoption of a conformer by the O-alkylated base conducive to mutagenic base mispairing, and (c) creation of the base mismatch involving the O-alkylated base. These three criteria are applied to the products of methylation, ethylation, isopropylation and tert-butylation at the N7-G, O6-G and O4-T sites. The N-deprotonation criterion differentiates the non-mutagenic N7-alkylguanines from the promutagenic O6-alkylguanines and O4-alkylthymines. All the O-alkylated bases except O4-tert-butylthymine are predicted as capable of adopting a conformer conducive to successful mispairing. O4-tert-butylthymine is predicted as incapable of creating a base mismatch by H-bonding with guanine, pointing to the non-mutagenic effects of tert-butylation of the O4-T site. By extrapolating to all tertiary alkyl groups, this explains why tert-alkylating N-nitrosamines are carcinogenically inactive. These results also highlight the carcinogenic role of alkylation at the O4-T site rather than at the O6-G site.
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Affiliation(s)
- Tejeshwori Salam
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - R H Duncan Lyngdoh
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India.
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27
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Martínez-Jiménez F, Muiños F, Sentís I, Deu-Pons J, Reyes-Salazar I, Arnedo-Pac C, Mularoni L, Pich O, Bonet J, Kranas H, Gonzalez-Perez A, Lopez-Bigas N. A compendium of mutational cancer driver genes. Nat Rev Cancer 2020; 20:555-572. [PMID: 32778778 DOI: 10.1038/s41568-020-0290-x] [Citation(s) in RCA: 503] [Impact Index Per Article: 125.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
A fundamental goal in cancer research is to understand the mechanisms of cell transformation. This is key to developing more efficient cancer detection methods and therapeutic approaches. One milestone towards this objective is the identification of all the genes with mutations capable of driving tumours. Since the 1970s, the list of cancer genes has been growing steadily. Because cancer driver genes are under positive selection in tumorigenesis, their observed patterns of somatic mutations across tumours in a cohort deviate from those expected from neutral mutagenesis. These deviations, which constitute signals of positive selection, may be detected by carefully designed bioinformatics methods, which have become the state of the art in the identification of driver genes. A systematic approach combining several of these signals could lead to a compendium of mutational cancer genes. In this Review, we present the Integrative OncoGenomics (IntOGen) pipeline, an implementation of such an approach to obtain the compendium of mutational cancer drivers. Its application to somatic mutations of more than 28,000 tumours of 66 cancer types reveals 568 cancer genes and points towards their mechanisms of tumorigenesis. The application of this approach to the ever-growing datasets of somatic tumour mutations will support the continuous refinement of our knowledge of the genetic basis of cancer.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Deu-Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Iker Reyes-Salazar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Pich
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jose Bonet
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hanna Kranas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 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, 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, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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28
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Sarkar A, Atay Y, Erickson AL, Arisi I, Saltini C, Kahveci T. An Efficient Algorithm for Identifying Mutated Subnetworks Associated with Survival in Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1582-1594. [PMID: 30990435 DOI: 10.1109/tcbb.2019.2911069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Protein-protein interaction (PPI) network models interconnections between protein-encoding genes. A group of proteins that perform similar functions are often connected to each other in the PPI network. The corresponding genes form pathways or functional modules. Mutation in protein-encoding genes affect behavior of pathways. This results in initiation, progression, and severity of diseases that propagates through pathways. In this work, we integrate mutation, survival information of patients, and PPI network to identify connected subnetworks associated with survival. We define the computational problem using a fitness function called log-rank statistic to score subnetworks. Log-rank statistic compares the survival between two populations. We propose a novel method, Survival Associated Mutated Subnetwork (SAMS) that adopts genetic algorithm strategy to find the connected subnetwork within the PPI network whose mutation yields highest log-rank statistic. We test on real cancer and synthetic datasets. SAMS generate solutions in negligible time while the state-of-art method in literature takes exponential time. Log-rank statistic of SAMS selected mutated subnetworks are comparable to the method. Our result genesets show significant overlap with well-known cancer driver genes derived from curated datasets and studies in literature, display high text-mining score in terms of number of citations combined with disease-specific keywords in PubMed, and identify pathways having high biological relevance.
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29
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Kelly MR, Kostyrko K, Han K, Mooney NA, Jeng EE, Spees K, Dinh PT, Abbott KL, Gwinn DM, Sweet-Cordero EA, Bassik MC, Jackson PK. Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities. Cancer Discov 2020; 10:1950-1967. [PMID: 32727735 PMCID: PMC7710624 DOI: 10.1158/2159-8290.cd-19-1274] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 06/08/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022]
Abstract
Activating mutations in RAS GTPases drive many cancers, but limited understanding of less-studied RAS interactors, and of the specific roles of different RAS interactor paralogs, continues to limit target discovery. We developed a multistage discovery and screening process to systematically identify genes conferring RAS-related susceptibilities in lung adenocarcinoma. Using affinity purification mass spectrometry, we generated a protein-protein interaction map of RAS interactors and pathway components containing hundreds of interactions. From this network, we constructed a CRISPR dual knockout library targeting 119 RAS-related genes that we screened for KRAS-dependent genetic interactions (GI). This approach identified new RAS effectors, including the adhesion controller RADIL and the endocytosis regulator RIN1, and >250 synthetic lethal GIs, including a potent KRAS-dependent interaction between RAP1GDS1 and RHOA. Many GIs link specific paralogs within and between gene families. These findings illustrate the power of multiomic approaches to uncover synthetic lethal combinations specific for hitherto untreatable cancer genotypes. SIGNIFICANCE: We establish a deep network of protein-protein and genetic interactions in the RAS pathway. Many interactions validated here demonstrate important specificities and redundancies among paralogous RAS regulators and effectors. By comparing synthetic lethal interactions across KRAS-dependent and KRAS-independent cell lines, we identify several new combination therapy targets for RAS-driven cancers.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Marcus R Kelly
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California.,Program in Cancer Biology, Stanford University School of Medicine, Stanford, California
| | - Kaja Kostyrko
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Kyuho Han
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California
| | - Edwin E Jeng
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Kaitlyn Spees
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Phuong T Dinh
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Keene L Abbott
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California
| | - Dana M Gwinn
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - E Alejandro Sweet-Cordero
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California.
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, California. .,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California. .,Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
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30
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Simatou A, Simatos G, Goulielmaki M, Spandidos DA, Baliou S, Zoumpourlis V. Historical retrospective of the SRC oncogene and new perspectives (Review). Mol Clin Oncol 2020; 13:21. [PMID: 32765869 PMCID: PMC7403812 DOI: 10.3892/mco.2020.2091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/14/2020] [Indexed: 12/15/2022] Open
Abstract
Since its first discovery as part of the Rous sarcoma virus (RSV) genome, the c-SRC (SRC) proto-oncogene has been proved a key regulator of cancer development and progression, and thus it has been highlighted as an attractive target for anti-cancer therapeutic strategies. Though the exact mechanisms of its action are still not fully understood, SRC protein mediates crucial normal cell functions, such as cell development, proliferation and survival, and its dysregulation is considered as an oncogenic signature and a driving force for cancer initiation. In the present review, we present a flashback to the history of the Src research, while focusing on the most important milestones in the field. Moreover, we investigate the proposed regulatory mechanisms and molecules that mediate its action in order to designate putative therapeutic targets and useful prognostic and/or diagnostic tools. Furthermore, we present and discuss existing therapeutic approaches that are explored in clinical settings.
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Affiliation(s)
| | - George Simatos
- First Breast Unit, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Maria Goulielmaki
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Stella Baliou
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
| | - Vassilios Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
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31
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Cancer associated fibroblast: Mediators of tumorigenesis. Matrix Biol 2020; 91-92:19-34. [PMID: 32450219 DOI: 10.1016/j.matbio.2020.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
It is well accepted that the tumor microenvironment plays a pivotal role in cancer onset, development, and progression. The majority of clinical interventions are designed to target either cancer or stroma cells. These emphases have been directed by one of two prevailing theories in the field, the Somatic Mutation Theory and the Tissue Organization Field Theory, which represent two seemingly opposing concepts. This review proposes that the two theories are mutually inclusive and should be concurrently considered for cancer treatments. Specifically, this review discusses the dynamic and reciprocal processes between stromal cells and extracellular matrices, using pancreatic cancer as an example, to demonstrate the inclusivity of the theories. Furthermore, this review highlights the functions of cancer associated fibroblasts, which represent the major stromal cell type, as important mediators of the known cancer hallmarks that the two theories attempt to explain.
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32
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Nagasaka M, Li Y, Sukari A, Ou SHI, Al-Hallak MN, Azmi AS. KRAS G12C Game of Thrones, which direct KRAS inhibitor will claim the iron throne? Cancer Treat Rev 2020; 84:101974. [PMID: 32014824 PMCID: PMC7041424 DOI: 10.1016/j.ctrv.2020.101974] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 12/11/2022]
Abstract
Mutations in Kirsten rat sarcoma viral oncogene homolog (KRAS) are among the most common aberrations in cancer, including non-small cell lung cancer (NSCLC). The lack of an ideal small molecule binding pocket in the KRAS protein and its high affinity towards the abundance of cellular guanosine triphosphate (GTP) renders the design of specific small molecule drugs challenging. Despite efforts, KRAS remains a challenging therapeutic target. Among the different known mutations; the KRASG12C (glycine 12 to cysteine) mutation has been considered potentially druggable. Several novel covalent direct inhibitors targeting KRASG12C with similar covalent binding mechanisms are now in clinical trials. Both AMG 510 from Amgen and MRTX849 from Mirati Therapeutics covalently binds to KRASG12C at the cysteine at residue 12, keeping KRASG12C in its inactive GDP-bound state and inhibiting KRAS-dependent signaling. Both inhibitors are being studied as a single agent or as combination with other targets. In addition, two novel KRAS G12C inhibitors JNJ-74699157 and LY3499446 will have entered phase 1 studies by the end of 2019. Given the rapid clinical development of 4 direct covalent KRAS G12C inhibitors within a short period of time, understanding the similarities and differences among these will be important to determine the best treatment option based on tumor specific response (NSCLC versus colorectal carcinoma), potential resistance mechanisms (i.e. anticipated acquired mutation at the cysteine 12 residue) and central nervous system (CNS) activity. Additionally, further investigation evaluating the efficacy and safety of combination therapies with agents such as immune checkpoint inhibitors will be important next steps.
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Affiliation(s)
- Misako Nagasaka
- Karmanos Cancer Institute Wayne State University, Detroit MI, USA; St. Marianna University Graduate School of Medicine, Kawasaki, Japan.
| | - Yiwei Li
- Karmanos Cancer Institute Wayne State University, Detroit MI, USA; Wayne State University, School of Medicine, Detroit MI, USA.
| | - Ammar Sukari
- Karmanos Cancer Institute Wayne State University, Detroit MI, USA.
| | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, Department of Medicine, Division of Hematology-Oncology, University of California Irvine School of Medicine, Orange, CA, USA.
| | | | - Asfar S Azmi
- Karmanos Cancer Institute Wayne State University, Detroit MI, USA; Wayne State University, School of Medicine, Detroit MI, USA.
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33
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Brennick CA, George MM, Srivastava PK, Karandikar SH. Prediction of cancer neoepitopes needs new rules. Semin Immunol 2020; 47:101387. [PMID: 31952902 DOI: 10.1016/j.smim.2020.101387] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/01/2020] [Indexed: 12/30/2022]
Abstract
Tumors are immunogenic and the non-synonymous point mutations harbored by tumors are a source of their immunogenicity. Immunologists have long been enamored by the idea of synthetic peptides corresponding to mutated epitopes (neoepitopes) as specific "vaccines" against tumors presenting those neoepitopes in context of MHC I. Tumors may harbor hundreds of point mutations and it would require effective prediction algorithms to identify candidate neoepitopes capable of eliciting potent tumor-specific CD8+ T cell responses. Our current understanding of MHC I-restricted epitopes come from the observance of CD8+ T cell responses against viral (vaccinia, lymphocytic choriomeningitis etc.) and model (chicken ovalbumin, hen egg lysozyme etc.) antigens. Measurable CD8+ T cell responses elicited by model or viral antigens are always directed against epitopes possessing strong binding affinity for the restricting MHC I alleles. Immense collective effort to develop methodologies combining genomic sequencing, bioinformatics and traditional immunological techniques to identify neoepitopes with strong binding affinity to MHC I has only yielded inaccurate prediction algorithms. Additionally, new evidence has emerged suggesting that neoepitopes, which unlike the epitopes of viral or model antigens have closely resembling wild-type counterparts, may not necessarily demonstrate strong affinity to MHC I. Our bearing need recalibration.
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Affiliation(s)
- Cory A Brennick
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
| | - Mariam M George
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
| | - Pramod K Srivastava
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
| | - Sukrut H Karandikar
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, 06030, USA.
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34
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Lim JKM, Leprivier G. The impact of oncogenic RAS on redox balance and implications for cancer development. Cell Death Dis 2019; 10:955. [PMID: 31852884 PMCID: PMC6920345 DOI: 10.1038/s41419-019-2192-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 02/07/2023]
Abstract
The RAS family of proto-oncogenes comprises HRAS, KRAS, and NRAS, which are among the most mutated genes in human cancers. The RAS family genes encode small GTPases that coordinate key signaling pathways in response to growth factors. Mutations in RAS result in a constitutively active form of the protein that supports cellular transformation and tumorigenesis. The mechanisms of oncogenic RAS-mediated transformation encompass uncontrolled proliferation and inhibition of cell death through overactivation of the RAF-MEK-ERK and the PI3K-AKT pathways, respectively. In addition, the control of redox balance by RAS has also been proposed to play a role in its oncogenic properties. However, the exact role of redox balance in mediating mutant RAS transformation is still under debate. Here, we present, on one hand, the involvement of pro-oxidant components in oncogenic RAS transformation, such as NADPH oxidases and mitochondrial reactive oxygen species, and how these promote transformation. On the other hand, we describe the contribution of antioxidant components to mutant RAS transformation, including Nrf2, glutathione biosynthesis and xCT, as well as the mechanisms by which antioxidant programs drive transformation. Finally, we aim to reconcile the seemingly opposite effects of oncogenic RAS on redox balance and discuss a model for the complementary role of both pro-oxidant and antioxidant pathways in mutant RAS-driven tumor progression.
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Affiliation(s)
- Jonathan K M Lim
- Institute for Neuropathology, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Gabriel Leprivier
- Institute for Neuropathology, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
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35
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Abstract
Oncogenic activation of RAS isoforms leads tumor initiation and progression in many types of cancers and is gaining increasing interest as target for novel therapeutic strategies. In sharp contrast with other types of cancer, the importance of RAS in breast tumorigenesis has long been undermined by the low frequency of its oncogenic mutation in human breast lesions. Nevertheless, a wealth of studies over the last years have revealed how the engagement of RAS function might be mandatory downstream varied oncogenic alterations for the progression, metastatic dissemination, and therapy resistance in breast cancers. We review herein the major studies over the last three decades which have explored the controversial role of RAS proteins and their mutation status in breast tumorigenesis and have contributed to reveal their role as supporting actors, instead of as primary cause, in breast cancer.
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Affiliation(s)
- Mirco Galiè
- Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
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36
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Pharmacogenomics, biomarker network, and allele frequencies in colorectal cancer. THE PHARMACOGENOMICS JOURNAL 2019; 20:136-158. [PMID: 31616044 DOI: 10.1038/s41397-019-0102-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is one of the leading causes of cancer death worldwide. Over the last decades, several studies have shown that tumor-related genomic alterations predict tumor prognosis, drug response, and toxicity. These observations have led to the development of several therapies based on individual genomic profiles. As part of these approaches, pharmacogenomics analyses genomic alterations which may predict an efficient therapeutic response. Studying these mutations as biomarkers for predicting drug response is of a great interest to improve precision medicine. We conduct a comprehensive review of the main pharmacogenomics biomarkers and genomic alterations affecting enzyme activity, transporter capacity, channels, and receptors; and therefore the new advances in CRC precision medicine to select the best therapeutic strategy in populations worldwide, with a focus on Latin America.
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37
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Lee J, Lee AJ, Lee JK, Park J, Kwon Y, Park S, Chun H, Ju YS, Hong D. Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures. Nucleic Acids Res 2019; 46:W102-W108. [PMID: 29790943 PMCID: PMC6030918 DOI: 10.1093/nar/gky406] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022] Open
Abstract
Somatic genome mutations occur due to combinations of various intrinsic/extrinsic mutational processes and DNA repair mechanisms. Different molecular processes frequently generate different signatures of somatic mutations in their own favored contexts. As a result, the regional somatic mutation rate is dependent on the local DNA sequence, the DNA replication/RNA transcription dynamics and epigenomic chromatin organization landscape in the genome. Here, we propose an online computational framework, termed Mutalisk, which correlates somatic mutations with various genomic, transcriptional and epigenomic features in order to understand mutational processes that contribute to the generation of the mutations. This user-friendly tool explores the presence of localized hypermutations (kataegis), dissects the spectrum of mutations into the maximum likelihood combination of known mutational signatures and associates the mutation density with numerous regulatory elements in the genome. As a result, global patterns of somatic mutations in any query sample can be efficiently screened, thus enabling a deeper understanding of various mutagenic factors. This tool will facilitate more effective downstream analyses of cancer genome sequences to elucidate the diversity of mutational processes underlying the development and clonal evolution of cancer cells. Mutalisk is freely available at http://mutalisk.org.
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Affiliation(s)
- Jongkeun Lee
- Clinical Genomics Analysis Branch, National Cancer Center, Goyang 10408, Republic of Korea
| | - Andy Jinseok Lee
- Clinical Genomics Analysis Branch, National Cancer Center, Goyang 10408, Republic of Korea
| | - June-Koo Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jongkeun Park
- Clinical Genomics Analysis Branch, National Cancer Center, Goyang 10408, Republic of Korea
| | - Youngoh Kwon
- Clinical Genomics Analysis Branch, National Cancer Center, Goyang 10408, Republic of Korea
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyonho Chun
- Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Dongwan Hong
- Clinical Genomics Analysis Branch, National Cancer Center, Goyang 10408, Republic of Korea
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Murugan AK, Grieco M, Tsuchida N. RAS mutations in human cancers: Roles in precision medicine. Semin Cancer Biol 2019; 59:23-35. [PMID: 31255772 DOI: 10.1016/j.semcancer.2019.06.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 05/13/2019] [Accepted: 06/07/2019] [Indexed: 02/07/2023]
Abstract
Ras proteins play a crucial role as a central component of the cellular networks controlling a variety of signaling pathways that regulate growth, proliferation, survival, differentiation, adhesion, cytoskeletal rearrangements and motility of a cell. Almost, 4 decades passed since Ras research was started and ras genes were originally discovered as retroviral oncogenes. Later on, mutations of the human RAS genes were linked to tumorigenesis. Genetic analyses found that RAS is one of the most deregulated oncogenes in human cancers. In this review, we summarize the pioneering works which allowed the discovery of RAS oncogenes, the finding of frequent mutations of RAS in various human cancers, the role of these mutations in tumorigenesis and mutation-activated signaling networks. We further describe the importance of RAS mutations in personalized or precision medicine particularly in molecular targeted therapy, as well as their use as diagnostic and prognostic markers as therapeutic determinants in human cancers.
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Affiliation(s)
- Avaniyapuram Kannan Murugan
- Department of Molecular Cellular Oncology and Microbiology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549 Japan.
| | - Michele Grieco
- DiSTABiF, Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, via Vivaldi 43, Caserta 81100 Italy
| | - Nobuo Tsuchida
- Department of Molecular Cellular Oncology and Microbiology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549 Japan.
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Subbarayan K, Seliger B. Tumor-dependent Effects of Proteoglycans and Various Glycosaminoglycan Synthesizing Enzymes and Sulfotransferases on Patients’ Outcome. Curr Cancer Drug Targets 2019; 19:210-221. [DOI: 10.2174/1568009618666180706165845] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/31/2018] [Accepted: 06/13/2018] [Indexed: 12/11/2022]
Abstract
Background: The small leucine-rich proteoglycans (SLRPs) biglycan (BGN) and decorin (DCN) linked with sulfated glycosaminoglycan (GAG) chains exhibit oncogenic or tumor suppressive potentials depending on the cellular context and association with GAGs. </P><P> Objective: We hypothesized that structural alterations and expression levels of BGN, DCN and their associated chondroitin sulfate (CS) polymerizing enzymes, dermatan sulfate (DS) epimerases and various sulfatases might be correlated with the tumor (sub)type and patients’ survival. </P><P> Methods: We acquired breast cancer (BC) and glioma patients’ datasets from cBioPortal and R2 Genomics. Structural alterations and the expression pattern of CS polymerizing enzymes, DS epimerases and carbohydrate sulfotransferases (CHST) were compared to that of BGN and DCN and correlated to their clinical relevance. </P><P> Results: In BC, no mutations, but amplifications (0.2 – 2.1 %) and deletions (0.05 – 0.4 %) were found in BGN, DCN and CS/DS enzymes. In contrast, missense and/or truncated mutations (0.1 – 0.5 %), but a reduced amplification rate (0 – 1.5 %) were found in glioma. When compared to BC, the structural abnormalities caused altered mRNA expression levels of BGN, DCN, GAG synthesizing enzymes and CHST. Mutations in SLPRs, CHSY1, CHST4 and CHSY3 were correlated with a poor prognosis in glioma, while lack of mutations and copy number variations in the SLRPs, CHSY3, CHST15 and DSE displayed an increased survival in BC. </P><P> Conclusion: A distinct association of BGN and DCN with CHST, CS polymerizing enzymes and DS epimerases was found in BC and glioma. Thus, a unique pattern of structural alterations and expression, which has clinical relevance, was found for PGs and GAG synthesizing enzymes and CHST in BC and glioma, which might help to identify high-risk patients and to develop personalized therapeutics.
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Affiliation(s)
- Karthikeyan Subbarayan
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, 06112 Halle/ Saale, Germany
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, 06112 Halle/ Saale, Germany
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40
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Rudd AK, Brea RJ, Devaraj NK. Amphiphile-Mediated Depalmitoylation of Proteins in Living Cells. J Am Chem Soc 2018; 140:17374-17378. [PMID: 30516377 DOI: 10.1021/jacs.8b10806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Post-translational S-palmitoylation plays a central role in protein localization, trafficking, stability, aggregation, and cell signaling. Dysregulation of palmitoylation pathways in cells can alter protein function and is the cause of several diseases. Considering the biological and clinical importance of S-palmitoylation, tools for direct, in vivo modulation of this lipid modification would be extremely valuable. Here, we describe a method for the cleavage of native S-palmitoyl groups from proteins in living cells. Using a cell permeable, cysteine-functionalized amphiphile, we demonstrate the direct depalmitoylation of cellular proteins. We show that amphiphile-mediated depalmitoylation (AMD) can effectively cleave S-palmitoyl groups from the native GTPase HRas and successfully depalmitoylate mislocalized proteins in an infantile neuronal ceroid lipofuscinosis (INCL) disease model. AMD enables direct and facile depalmitoylation of proteins in live cells and has potential therapeutic applications for diseases such as INCL, where native protein thioesterase activity is deficient.
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Affiliation(s)
- Andrew K Rudd
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Roberto J Brea
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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Damani Shah H, Saranath D, Das S, Kharkar P, Karande A. In‐silico identification of small molecules targeting H‐Ras and in‐vitro cytotoxicity with caspase‐mediated apoptosis in carcinoma cells. J Cell Biochem 2018; 120:5519-5530. [PMID: 30367521 DOI: 10.1002/jcb.27836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/14/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Hetal Damani Shah
- Department of Biological Sciences, Sunandan Divatia School of Science Narsee Monjee Institute of Management Studies (deemed‐to‐be) University Mumbai India
| | - Dhananjaya Saranath
- Department of Biological Sciences, Sunandan Divatia School of Science Narsee Monjee Institute of Management Studies (deemed‐to‐be) University Mumbai India
| | - Soma Das
- Department of Biochemistry Indian Institute of Science Bangalore India
| | - Prashant Kharkar
- Department of Pharmaceutical Chemistry Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, Narsee Monjee Institute of Management Studies (deemed‐to‐be) University Mumbai India
| | - Anjali Karande
- Department of Biochemistry Indian Institute of Science Bangalore India
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42
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Kontogeorgos G, Aninos D. Recent Aspects in the Diagnosis and Prognosis of Bladder Cancer. TUMORI JOURNAL 2018; 84:301-7. [PMID: 9678611 DOI: 10.1177/030089169808400303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epidemiologic studies have stated the progressive increase of bladder tumors during the last decades. The aim of our review is to refer to factors implicated in bladder carcinogenesis (such as activated oncogenes, growth factors and chromosomal aberrations) and to resistance to drug uptake (i.e., multidrug resistance gene and P-glycoprotein). The review also provides information of diagnostic and prognostic significance, based on DNA analysis of transitional cancer cells. In addition to cytometric data, alternative counterings for estimation of the S-phase fraction, useful in indicating the biologic behavior of bladder cancer, are presented. Knowledge of such mechanisms results in a better approach to the diagnosis, prognosis and prevention of bladder carcinomas, especially those that do not respond to systemic intravesical chemotherapy. We have tried to mention all significant factors related to the development of bladder cancer. We conclude that the progress made in understanding the pathogenesis of bladder cancer has been significant. However, more studies are needed in order to introduce and adopt reliable criteria to accurately predict the clinical behavior.
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Affiliation(s)
- G Kontogeorgos
- Department of Pathology, G. Gennimatas General Hospital of Athens, Greece.
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43
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Umstead M, Xiong J, Qi Q, Du Y, Fu H. Aurora kinase A interacts with H-Ras and potentiates Ras-MAPK signaling. Oncotarget 2018; 8:28359-28372. [PMID: 28177880 PMCID: PMC5438655 DOI: 10.18632/oncotarget.15049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/07/2017] [Indexed: 11/25/2022] Open
Abstract
In cancer, upregulated Ras promotes cellular transformation and proliferation in part through activation of oncogenic Ras-MAPK signaling. While directly inhibiting Ras has proven challenging, new insights into Ras regulation through protein-protein interactions may offer unique opportunities for therapeutic intervention. Here we report the identification and validation of Aurora kinase A (Aurora A) as a novel Ras binding protein. We demonstrate that the kinase domain of Aurora A mediates the interaction with the N-terminal domain of H-Ras. Further more, the interaction of Aurora A and H-Ras exists in a protein complex with Raf-1. We show that binding of H-Ras to Raf-1 and subsequent MAPK signaling is enhanced by Aurora A, and requires active H-Ras. Thus, the functional linkage between Aurora A and the H-Ras/Raf-1 protein complex may provide a mechanism for Aurora A's oncogenic activity through direct activation of the Ras/MAPK pathway.
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Affiliation(s)
- MaKendra Umstead
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, USA.,Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Jinglin Xiong
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, USA.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Qi Qi
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuhong Du
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Haian Fu
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, USA.,Winship Cancer Institute, Atlanta, GA, USA
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44
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Lu M, Zhan X. The crucial role of multiomic approach in cancer research and clinically relevant outcomes. EPMA J 2018; 9:77-102. [PMID: 29515689 PMCID: PMC5833337 DOI: 10.1007/s13167-018-0128-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/29/2018] [Indexed: 02/06/2023]
Abstract
Cancer with heavily economic and social burden is the hot point in the field of medical research. Some remarkable achievements have been made; however, the exact mechanisms of tumor initiation and development remain unclear. Cancer is a complex, whole-body disease that involves multiple abnormalities in the levels of DNA, RNA, protein, metabolite and medical imaging. Biological omics including genomics, transcriptomics, proteomics, metabolomics and radiomics aims to systematically understand carcinogenesis in different biological levels, which is driving the shift of cancer research paradigm from single parameter model to multi-parameter systematical model. The rapid development of various omics technologies is driving one to conveniently get multi-omics data, which accelerates predictive, preventive and personalized medicine (PPPM) practice allowing prediction of response with substantially increased accuracy, stratification of particular patients and eventual personalization of medicine. This review article describes the methodology, advances, and clinically relevant outcomes of different "omics" technologies in cancer research, and especially emphasizes the importance and scientific merit of integrating multi-omics in cancer research and clinically relevant outcomes.
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Affiliation(s)
- Miaolong Lu
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
- The State Key Laboratory of Medical Genetics, Central South University, 88 Xiangya Road, Changsha, Hunan 410008 People’s Republic of China
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Tsuchida N, Murugan AK, Grieco M. Kirsten Ras* oncogene: significance of its discovery in human cancer research. Oncotarget 2018; 7:46717-46733. [PMID: 27102293 PMCID: PMC5216832 DOI: 10.18632/oncotarget.8773] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/10/2016] [Indexed: 12/24/2022] Open
Abstract
The KRAS/ K-RAS oncogene is crucially involved in human cancer. The term "oncogene" -- i.e., a gene able to transform a normal cell into a tumor cell - was introduced in 1969, but the word was not used in the human carcinogenesis literature until much later. Transforming Kras and Hras oncogenes from the Kirsten and Harvey sarcoma viruses were not identified until the early 1980s due to the complicated structures of the viral genomes. Orthologs of these viral oncogenes were then found in transforming DNA fragments in human cancers in the form of mutated versions of the HRAS and KRAS proto-oncogenes. Thus, RAS genes were the first human oncogenes to be identified. Subsequent studies showed that mutated KRAS acted as an in vivo oncogenic driver, as indicated by studies of anti-EGFR therapy for metastatic colorectal cancers. This review addresses the historical background and experimental studies that led to the discovery of Kirsten Ras as an oncogene, the role of mutated KRAS in human carcinogenesis, and recent therapeutic studies of cancer cells with KRAS mutations.
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Affiliation(s)
- Nobuo Tsuchida
- Graduate School of Medical and Dental Sciences, Tokyo Medical Dental University, Yushima, Bunkyo-ku, Tokyo, Japan
| | | | - Michele Grieco
- DiSTABiF, Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta, Italy
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Salam T, Premila Devi S, Duncan Lyngdoh RH. Molecular criteria for mutagenesis by DNA methylation: Some computational elucidations. Mutat Res 2018; 807:10-20. [PMID: 29220701 DOI: 10.1016/j.mrfmmm.2017.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/05/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Alkylating agents and N-nitroso compounds are well-known mutagens and carcinogens which act by alkylating DNA at the nucleobase moieties. Criteria for mutagenicity through DNA alkylation include (a) absence of the Watson-Crick (N1-guanine and N3-thymine) protons, (b) rotation of the alkyl group away from the H-bonding zone, (c) configuration of the alkylated base pair close to the Watson-Crick type. This computational study brings together these three molecular criteria for the first time. Three methylated DNA bases-N7-methylguanine, O6-methylguanine and O4-methylthymine-are studied using computational chemical methods. Watson-Crick proton loss is predicted more feasible for the mutagenic O6-methylguanine and O4-methylthymine than for the non-mutagenic N7-methylguanine in agreement with the observed trend for pKa values. Attainment of a conformer conducive to mutagenesis is more feasible for O6-methylguanine than for O4-methylthymine, though the latter is more mutagenic. These methylated bases yield 9 H-bonded pairs with normal DNA bases. At biological pH, O6-methylguanine and O4-methylthymine would yield stable mutagenic pairs having Watson-Crick type configuration by H-bonded pairing with thymine and guanine respectively, while N7-methylguanine would yield a non-mutagenic pair with cytosine. The three criteria thus well differentiate the non-mutagenic N7-methylguanine from the mutagenic O6-methylguanine and O4-methylthymine in good accord with experimental observations.
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Affiliation(s)
- Tejeshwori Salam
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - S Premila Devi
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - R H Duncan Lyngdoh
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India.
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Abstract
Although there have been many recent discoveries in the molecular alterations associated with urothelial carcinoma, current understanding of this disease lags behind many other malignancies. Historically, a two-pathway model had been applied to distinguish low- and high-grade urothelial carcinoma, although significant overlap and increasing complexity of molecular alterations has been recently described. In many cases, mutations in HRAS and FGFR3 that affect the MAPK and PI3K pathways seem to be associated with noninvasive low-grade papillary tumors, whereas mutations in TP53 and RB that affect the G1-S transition of the cell cycle are associated with high-grade in situ and invasive carcinoma. However, recent large-scale analyses have identified overlap in these pathways relative to morphology, and in addition, many other variants in a wide variety of oncogenes and tumor-suppressor genes have been identified. New technologies including next-generation sequencing have enabled more detailed analysis of urothelial carcinoma, and several groups have proposed molecular classification systems based on these data, although consensus is elusive. This article reviews the current understanding of alterations affecting oncogenes and tumor-suppressor genes associated with urothelial carcinoma, and their application in the context of morphology and classification schema.
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Affiliation(s)
- James P Solomon
- Department of Pathology, University of California, San Diego, 200 West Arbor Drive, La Jolla, CA 92103, USA
| | - Donna E Hansel
- Division of Anatomic Pathology, Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093, USA.
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48
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John BA, Said N. Insights from animal models of bladder cancer: recent advances, challenges, and opportunities. Oncotarget 2017; 8:57766-57781. [PMID: 28915710 PMCID: PMC5593682 DOI: 10.18632/oncotarget.17714] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/18/2017] [Indexed: 12/16/2022] Open
Abstract
Bladder cancer (urothelial cancer of the bladder) is the most common malignancy affecting the urinary system with increasing incidence and mortality. Treatment of bladder cancer has not advanced in the past 30 years. Therefore, there is a crucial unmet need for novel therapies, especially for high grade/stage disease that can only be achieved by preclinical model systems that faithfully recapitulate the human disease. Animal models are essential elements in bladder cancer research to comprehensively study the multistep cascades of carcinogenesis, progression and metastasis. They allow for the investigation of premalignant phases of the disease that are not clinically encountered. They can be useful for identification of diagnostic and prognostic biomarkers for disease progression and for preclinical identification and validation of therapeutic targets/candidates, advancing translation of basic research to clinic. This review summarizes the latest advances in the currently available bladder cancer animal models, their translational potential, merits and demerits, and the prevalent tumor evaluation modalities. Thereby, findings from these model systems would provide valuable information that can help researchers and clinicians utilize the model that best answers their research questions.
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Affiliation(s)
- Bincy Anu John
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Neveen Said
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Department of Urology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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49
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Le Gallo M, Lozy F, Bell DW. Next-Generation Sequencing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 943:119-148. [DOI: 10.1007/978-3-319-43139-0_5] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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50
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HAMDOUN Z, EHSAN H. Aftermath of the Human Genome Project: an era of struggle and discovery. Turk J Biol 2017. [DOI: 10.3906/biy-1609-77] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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