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Jani V, Sonavane U, Joshi R. Insight into structural dynamics involved in activation mechanism of full length KRAS wild type and P-loop mutants. Heliyon 2024; 10:e36161. [PMID: 39247361 PMCID: PMC11379609 DOI: 10.1016/j.heliyon.2024.e36161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 09/10/2024] Open
Abstract
KRAS protein is known to be frequently mutated in various cancers. The most common mutations being at position 12, 13 and 61. The positions 12 and 13 form part of the phosphate binding region (P-loop) of KRAS. Owing to mutation, the protein remains in continuous active state and affects the normal cellular process. Understanding the structural changes owing to mutations in GDP-bound (inactive state) and GTP-bound (active state) may help in the design of better therapeutics. To understand the structural flexibility due to the mutations specifically located at P-loop regions (G12D, G12V and G13D), extensive molecular dynamics simulations (24 μs) have been carried for both inactive (GDP-bound) and active (GTP-bound) structures for the wild type and these mutants. The study revealed that the local structural changes at the site of mutations allosterically guide changes in distant regions of the protein through hydrogen bond and hydrophobic signalling network. The dynamic cross correlation analysis and the comparison of the correlated motions among different systems manifested that changes in SW-I, SW-II, α3 and the loop preceding α3 affects the interactions of GDP/GTP with different regions of the protein thereby affecting its hydrolysis. Further, the Markov state modelling analysis confirmed that the mutations, especially G13D imparts rigidity to structure compared to wild type and thus limiting its conformational state in either intermediate state or active state. The study suggests that along with SW-I and SW-II regions, the loop region preceding the α3 helix and α3 helix are also involved in affecting the hydrolysis of nucleotides and may be considered while designing therapeutics against KRAS.
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Affiliation(s)
- Vinod Jani
- Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India
| | - Uddhavesh Sonavane
- Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India
| | - Rajendra Joshi
- Centre for Development of Advanced Computing (C-DAC), Panchavati, Pashan, Pune, India
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2
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Parise A, Cresca S, Magistrato A. Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins. Expert Opin Drug Discov 2024:1-21. [PMID: 39105536 DOI: 10.1080/17460441.2024.2387856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
INTRODUCTION Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes. Their deregulation is linked to several diseases, making them appealing drug targets. The broad roles of small-GTPases in cellular processes and the recent approval of a covalent KRas inhibitor as an anticancer agent renewed the interest in targeting small-GTPase with small molecules. AREA COVERED This review emphasizes the role of MD simulations in elucidating small-GTPase mechanisms, assessing the impact of cancer-related variants, and discovering novel inhibitors. EXPERT OPINION The application of MD simulations to small-GTPases exemplifies the role of MD simulations in the structure-based drug design process for challenging biomolecular targets. Furthermore, AI and machine learning-enhanced MD simulations, coupled with the upcoming power of quantum computing, are promising instruments to target elusive small-GTPases mutations and splice variants. This powerful synergy will aid in developing innovative therapeutic strategies associated to small-GTPases deregulation, which could potentially be used for personalized therapies and in a tissue-agnostic manner to treat tumors with mutations in small-GTPases.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Sofia Cresca
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
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3
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Salamh S, Sayyed-Ahmad A. Investigating the effects of cysteine-118 oxidation on G12D KRas structure and dynamics: insights from MD simulations. J Biomol Struct Dyn 2024; 42:6968-6981. [PMID: 37480262 DOI: 10.1080/07391102.2023.2238080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Mutations of Ras proteins are believed to be among the most prominent causes of cancer. There is increasing evidence that the activity of Ras may be controlled by the redox state of cysteine residues located within the NKCD motif. This redox signaling is critical to both physiological and pathological processes and occurs when C118 is oxidized in a reversible manner. In this study, we used atomistic molecular dynamics simulations and Markov state models to investigate the structural and conformational effects of C118 oxidation on the oncogenic mutant KRas(G12D). While both mutants share common features and exhibit some distinct conformational states and fluctuations, we have found that the oxidized variant KRas(G12D/C118SOH) is more dynamic than the unoxidized counterpart, particularly in the switch II region. Additionally, C118 oxidation is found to alter the structure of the nucleotide-binding site and the switch regions as well as perturb the conformational equilibrium between Ras active and inactive states. These conformational preferences may alter the affinity to different effectors, resulting in selective downstream activation. Our results are anticipated to help future drug development efforts aimed at KRAS-related anticancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shimaa Salamh
- Department of Physics, Birzeit University, Birzeit, Palestine
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Bhadhadhara K, Jani V, Koulgi S, Sonavane U, Joshi R. Studying early structural changes in SOS1 mediated KRAS activation mechanism. Curr Res Struct Biol 2023; 7:100115. [PMID: 38188543 PMCID: PMC10765296 DOI: 10.1016/j.crstbi.2023.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
KRAS activation is known to be modulated by a guanine nucleotide exchange factor (GEF), namely, Son of Sevenless1 (SOS1). SOS1 facilitates the exchange of GDP to GTP thereby leading to activation of KRAS. The binding of GDP/GTP to KRAS at the REM/allosteric site of SOS1 regulates the activation of KRAS at CDC25/catalytic site by facilitating its exchange. Different aspects of the allosteric activation of KRAS through SOS1 are still being explored. To understand the SOS1 mediated activation of KRAS, molecular dynamics simulations for a total of nine SOS1 complexes (KRAS-SOS1-KRAS) were performed. These nine systems comprised different combinations of KRAS-bound nucleotides (GTP/GDP) at REM and CDC25 sites of SOS1. Various conformational and thermodynamic parameters were analyzed for these simulation systems. MMPBSA free energy analysis revealed that binding at CDC25 site of SOS1 was significantly low for GDP-bound KRAS as compared to that of GTP-bound KRAS. It was observed that presence of either GDP/GTP bound KRAS at the REM site of SOS1 affected the activation related changes in the KRAS present at CDC25 site. The conformational changes at the catalytic site of SOS1 resulting from GDP/GTP-bound KRAS at the allosteric changes may hint at KRAS activation through different pathways (slow/fast/rare). The allosteric effect on activation of KRAS at CDC25 site may be due to conformations adopted by switch-I, switch-II, beta2 regions of KRAS at REM site. The effect of structural rearrangements occurring at allosteric KRAS may have led to increased interactions between SOS1 and KRAS at both the sites. The SOS1 residues involved in these important interactions with KRAS at the REM site were R694, S732 and K735. Whereas the ones interacting with KRAS at CDC25 site were S807, W809 and K814. This may suggest the crucial role of these residues in guiding the allosteric activation of KRAS at CDC25 site. The conformational shifts observed in the switch-I, switch-II and alpha3 regions of KRAS at CDC25 site may be attributed to be a part of allosteric activation. The binding affinities, interacting residues and conformational dynamics may provide an insight into development of inhibitors targeting the SOS1 mediated KRAS activation.
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Affiliation(s)
- Kirti Bhadhadhara
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Vinod Jani
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Shruti Koulgi
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Uddhavesh Sonavane
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
| | - Rajendra Joshi
- High Performance Computing-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, 411008, India
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Khozooei S, Veerappan S, Toulany M. YB-1 activating cascades as potential targets in KRAS-mutated tumors. Strahlenther Onkol 2023; 199:1110-1127. [PMID: 37268766 DOI: 10.1007/s00066-023-02092-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/23/2023] [Indexed: 06/04/2023]
Abstract
Y‑box binding protein‑1 (YB-1) is a multifunctional protein that is highly expressed in human solid tumors of various entities. Several cellular processes, e.g. cell cycle progression, cancer stemness and DNA damage signaling that are involved in the response to chemoradiotherapy (CRT) are tightly governed by YB‑1. KRAS gene with about 30% mutations in all cancers, is considered the most commonly mutated oncogene in human cancers. Accumulating evidence indicates that oncogenic KRAS mediates CRT resistance. AKT and p90 ribosomal S6 kinase are downstream of KRAS and are the major kinases that stimulate YB‑1 phosphorylation. Thus, there is a close link between the KRAS mutation status and YB‑1 activity. In this review paper, we highlight the importance of the KRAS/YB‑1 cascade in the response of KRAS-mutated solid tumors to CRT. Likewise, the opportunities to interfere with this pathway to improve CRT outcome are discussed in light of the current literature.
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Affiliation(s)
- Shayan Khozooei
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Soundaram Veerappan
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Mahmoud Toulany
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany.
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6
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Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex. Int J Mol Sci 2022; 23:ijms232213865. [PMID: 36430338 PMCID: PMC9692486 DOI: 10.3390/ijms232213865] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
KRAS-G12D mutations are the one of most frequent oncogenic drivers in human cancers. Unfortunately, no therapeutic agent directly targeting KRAS-G12D has been clinically approved yet, with such mutated species remaining undrugged. Notably, cofactor Mg2+ is closely related to the function of small GTPases, but no investigation has been conducted yet on Mg2+ when associated with KRAS. Herein, through microsecond scale molecular dynamics simulations, we found that Mg2+ plays a crucial role in the conformational changes of the KRAS-GDP complex. We located two brand new druggable dynamic pockets exclusive to KRAS-G12D. Using the structural characteristics of these two dynamic pockets, we designed in silico the inhibitor DBD15-21-22, which can specifically and tightly target the KRAS-G12D-GDP-Mg2+ ternary complex. Overall, we provide two brand new druggable pockets located on KRAS-G12D and suitable strategies for its inhibition.
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Behairy MY, Soltan MA, Adam MS, Refaat AM, Ezz EM, Albogami S, Fayad E, Althobaiti F, Gouda AM, Sileem AE, Elfaky MA, Darwish KM, Alaa Eldeen M. Computational Analysis of Deleterious SNPs in NRAS to Assess Their Potential Correlation With Carcinogenesis. Front Genet 2022; 13:872845. [PMID: 36051694 PMCID: PMC9424727 DOI: 10.3389/fgene.2022.872845] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/03/2022] [Indexed: 12/12/2022] Open
Abstract
The NRAS gene is a well-known oncogene that acts as a major player in carcinogenesis. Mutations in the NRAS gene have been linked to multiple types of human tumors. Therefore, the identification of the most deleterious single nucleotide polymorphisms (SNPs) in the NRAS gene is necessary to understand the key factors of tumor pathogenesis and therapy. We aimed to retrieve NRAS missense SNPs and analyze them comprehensively using sequence and structure approaches to determine the most deleterious SNPs that could increase the risk of carcinogenesis. We also adopted structural biology methods and docking tools to investigate the behavior of the filtered SNPs. After retrieving missense SNPs and analyzing them using six in silico tools, 17 mutations were found to be the most deleterious mutations in NRAS. All SNPs except S145L were found to decrease NRAS stability, and all SNPs were found on highly conserved residues and important functional domains, except R164C. In addition, all mutations except G60E and S145L showed a higher binding affinity to GTP, implicating an increase in malignancy tendency. As a consequence, all other 14 mutations were expected to increase the risk of carcinogenesis, with 5 mutations (G13R, G13C, G13V, P34R, and V152F) expected to have the highest risk. Thermodynamic stability was ensured for these SNP models through molecular dynamics simulation based on trajectory analysis. Free binding affinity toward the natural substrate, GTP, was higher for these models as compared to the native NRAS protein. The Gly13 SNP proteins depict a differential conformational state that could favor nucleotide exchange and catalytic potentiality. A further application of experimental methods with all these 14 mutations could reveal new insights into the pathogenesis and management of different types of tumors.
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Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
- *Correspondence: Mohamed A. Soltan, ; Muhammad Alaa Eldeen,
| | - Mohamed S. Adam
- Department of Pharmacology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Ahmed M. Refaat
- Zoology Departmen, Faculty of Science, Minia University, El-Minia, Egypt
| | - Ehab M. Ezz
- Department of Pharmacology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sarah Albogami
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Fayez Althobaiti
- Department of Biotechnology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Ahmed M. Gouda
- Department of Pharmacy Practice, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Ashraf E. Sileem
- Department of Chest Diseases, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Mahmoud A. Elfaky
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology and Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
- *Correspondence: Mohamed A. Soltan, ; Muhammad Alaa Eldeen,
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8
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Lee KY, Enomoto M, Gebregiworgis T, Gasmi-Seabrook GMC, Ikura M, Marshall CB. Oncogenic KRAS G12D mutation promotes dimerization through a second, phosphatidylserine-dependent interface: a model for KRAS oligomerization. Chem Sci 2021; 12:12827-12837. [PMID: 34703570 PMCID: PMC8494122 DOI: 10.1039/d1sc03484g] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/04/2021] [Indexed: 12/02/2022] Open
Abstract
KRAS forms transient dimers and higher-order multimers (nanoclusters) on the plasma membrane, which drive MAPK signaling and cell proliferation. KRAS is a frequently mutated oncogene, and while it is well known that the most prevalent mutation, G12D, impairs GTP hydrolysis, thereby increasing KRAS activation, G12D has also been shown to enhance nanoclustering. Elucidating structures of dynamic KRAS assemblies on a membrane has been challenging, thus we have refined our NMR approach that uses nanodiscs to study KRAS associated with membranes. We incorporated paramagnetic relaxation enhancement (PRE) titrations and interface mutagenesis, which revealed that, in addition to the symmetric ‘α–α’ dimerization interface shared with wild-type KRAS, the G12D mutant also self-associates through an asymmetric ‘α–β’ interface. The ‘α–β’ association is dependent on the presence of phosphatidylserine lipids, consistent with previous reports that this lipid promotes KRAS self-assembly on the plasma membrane in cells. Experiments using engineered mutants to spoil each interface, together with PRE probes attached to the membrane or free in solvent, suggest that dimerization through the primary ‘α–α’ interface releases β interfaces from the membrane promoting formation of the secondary ‘α–β’ interaction, potentially initiating nanoclustering. In addition, the small molecule BI-2852 binds at a β–β interface, stabilizing a new dimer configuration that outcompetes native dimerization and blocks the effector-binding site. Our data indicate that KRAS self-association involves a delicately balanced conformational equilibrium between transient states, which is sensitive to disease-associated mutation and small molecule inhibitors. The methods developed here are applicable to biologically important transient interactions involving other membrane-associated proteins. Studies of membrane-dependent dimerization of KRAS on nanodiscs using paramagnetic NMR titrations and mutagenesis revealed a novel asymmetric ‘α–β’ interface that provides a potential mechanism for the enhanced assembly of KRAS–G12D nanoclusters.![]()
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Affiliation(s)
- Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
| | - Teklab Gebregiworgis
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
| | | | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada .,Department of Medical Biophysics, University of Toronto Toronto Ontario M5G 1L7 Canada
| | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network Toronto Ontario M5G 1L7 Canada
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Evaluation of RAS mutational status through BEAMing assay to monitor disease progression of metastatic colorectal cancer: a case report. Anticancer Drugs 2021; 31:979-982. [PMID: 32889896 DOI: 10.1097/cad.0000000000000923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Since the introduction of antiepidermal growth factor receptor (anti-EGFR) monoclonal antibodies (moAbs), the treatment of metastatic colorectal cancer (mCRC) has become crucially dependent on the mutation profile of the tumour over the last two decades. Recently, rechallenge strategy with cetuximab-based chemotherapy has demonstrated to be active in a subgroup of patients whose tumour maintained wild-type RAS and RAF status. In this setting, liquid biopsy may replace tissue sample for the identification of specific subgroups of pretreated patients that may benefit from the reintroduction of anti-EGFR moAbs. In November 2014, a 64-year-old man with IVB stage BRAF, KRAS and NRAS wild-type mCRC was admitted in our hospital. He received FOLFIRI cetuximab as first-line treatment with deep and long-lasting partial response (PR), followed by cetuximab maintenance therapy until January 2016. At the time of disease progression, FOLFIRI cetuximab regimen was reintroduced resulting in stabilization of disease and he continued with capecitabine cetuximab therapy until disease progression in October 2016. Then, the patient consecutively received FOLFOX bevacizumab, TAS-102, regorafenib and FOLFIRI followed by de Gramont maintenance treatment. Finally, he was retreated with FOLFIRI cetuximab with disease progression within 3 months and died in May 2019. During his clinical course, liquid biopsy detected two mutations: one in KRAS Cd.12 and one in NRAS Cd. 61. The longitudinal assessment of RAS status offers considerable advantages in order to avoid side effects and economic costs for ineffective treatment choices. Liquid biopsy could help better monitor the disease and provide molecularly guided treatments.
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Akram AM, Chaudhary A, Kausar H, Althobaiti F, Abbas AS, Hussain Z, Fatima N, Zafar E, Asif W, Afzal U, Yousaf Z, Zafar A, Harakeh SM, Qamer S. Analysis of RAS gene mutations in cytogenetically normal de novo acute myeloid leukemia patients reveals some novel alterations. Saudi J Biol Sci 2021; 28:3735-3740. [PMID: 34220225 PMCID: PMC8241590 DOI: 10.1016/j.sjbs.2021.04.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 11/26/2022] Open
Abstract
Rat sarcoma gene (RAS) holds great importance in pathogenesis of acute myeloid leukemia (AML). The activated mutations in Neuroblastoma rat sarcoma viral oncogene homolog (NRAS) and Kirsten rat sarcoma viral oncogene homolog (KRAS) confers proliferative and survival signals, deliberating numerous effects on overall survival and progression free survival in AML patients. In this study thirty one (31) blood samples of adult newly diagnosed AML patients were collected to identify possible incidence of mutations through amplification of KRAS (exon 1 and 2) and NRAS gene (exon 1 and 2) using polymerase chain reaction (PCR). Amplicons were then subjected to sequencing and were analyzed through Geneious Prime 2019. Five of thirty one (16.12%) patients had altered sites in either NRAS or KRAS. The NRAS mutations were observed in three AML patients (N = 3, 9.67%). A novel missense mutation NRAS-I36R (239 T > G) representing a substitution of single nucleotide basepair found in NRAS exon 1 while exon 2 was detected with heterozygous mutation NRAS-E63X (318G > T) and insertion (A), resulting in frameshift of the amino acid sequence and insertion of two nucleotide basepairs (TA) in two of the patients. KRAS mutations (N = 2, 6.45%) were found in exon 1 whereas no mutations in KRAS exon 2 were detected in our patient cohort. Mutation in KRAS Exon 1, KRAS-D30N (280G > A) was observed in two patients and one of them also had a novel heterozygous mutation KRAS-L16N (240G > C). In addition there was no statistically significant association of mutRAS gene of AML patients with several prognostic markers including age, gender, karyotyping, CD34 positivity, cytogenetic abnormalities, total leukocyte count, white blood cell count and French-American-British (FAB) classification. However, the presence of mutRAS gene were strongly associated (p = 0.001) with increased percentage of bone marrow blasts. The prevalence of mutations in correlation with clinical and hematological parameter is useful for risk stratification in AML patients.
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Affiliation(s)
- Afia Muhammad Akram
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Asma Chaudhary
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Humera Kausar
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Fayez Althobaiti
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Afshan Syed Abbas
- Department of Zoology, University of Education, Lower Mall Campus, Lahore, Pakistan
| | - Zawar Hussain
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Naz Fatima
- Molecular Biology Laboratory, Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Erum Zafar
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Wajiha Asif
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Umair Afzal
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Zoufishan Yousaf
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Amjad Zafar
- Department of Oncology, Mayo Hospital, Anarkali Bazar, Lahore, Pakistan
| | - Steve M Harakeh
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Samina Qamer
- Department of Zoology, Government College University, Faisalabad, Pakistan
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11
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Zhou Y, Zhao J, Fang J, Martin W, Li L, Nussinov R, Chan TA, Eng C, Cheng F. My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. Genome Biol 2021; 22:53. [PMID: 33514395 PMCID: PMC7845113 DOI: 10.1186/s13059-021-02269-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerating the development of precision cancer medicine protocols. MPM contains 490,245 mutations from over 10,800 tumor exomes across 33 cancer types in The Cancer Genome Atlas mapped to 94,563 structure-resolved/predicted protein-protein interaction interfaces ("edgetic") and 311,022 functional sites ("nodetic"), including ligand-protein binding sites and 8 types of protein posttranslational modifications. In total, 8884 survival results and 1,271,132 drug responses are obtained for these mapped interactions. MPM is available at https://mutanome.lerner.ccf.org .
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Junfei Zhao
- Department of Systems Biology, Herbert Irving Comprehensive Center, Columbia University, New York, NY, 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, 10032, USA
| | - Jiansong Fang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - William Martin
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH, 43210, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Timothy A Chan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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12
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Mehmood A, Kaushik AC, Wang Q, Li CD, Wei DQ. Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants. J Chem Inf Model 2021; 61:571-586. [PMID: 33513018 DOI: 10.1021/acs.jcim.0c00488] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Colorectal cancer is considered one of the leading causes of death that is linked with the Kirsten Rat Sarcoma (KRAS) harboring codons 13 and 61 mutations. The objective for this study is to search for clinically important codon 61 mutations and analyze how they affect the protein structural dynamics. Additionally, a deep-learning approach is used to carry out a similarity search for potential compounds that might have a comparatively better affinity. Public databases like The Cancer Genome Atlas and Genomic Data Commons were accessed for obtaining the data regarding mutations that are associated with colon cancer. Multiple analysis such as genomic alteration landscape, survival analysis, and systems biology-based kinetic simulations were carried out to predict dynamic changes for the selected mutations. Additionally, a molecular dynamics simulation of 100 ns for all the seven shortlisted codon 61 mutations have been conducted, which revealed noticeable deviations. Finally, the deep learning-based predicted compounds were docked with the KRAS 3D conformer, showing better affinity and good docking scores as compared to the already existing drugs. Taking together the outcomes of systems biology and molecular dynamics, it is observed that the reported mutations in the SII region are highly detrimental as they have an immense impact on the protein sensitive sites' native conformation and overall stability. The drugs reported in this study show increased performance and are encouraged to be used for further evaluation regarding the situation that ascends as a result of KRAS mutations.
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Affiliation(s)
- Aamir Mehmood
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, P. R. China
| | - Aman Chandra Kaushik
- Wuxi School of Medicine, Jiangnan University, Li Lake Avenue, Wuxi, Jiangsu 214122, China
| | - Qiankun Wang
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Cheng-Dong Li
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, P. R. China
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13
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Yang S, Xia J, Yang Z, Xu M, Li S. Lung cancer molecular mutations and abnormal glycosylation as biomarkers for early diagnosis. Cancer Treat Res Commun 2021; 27:100311. [PMID: 33465560 DOI: 10.1016/j.ctarc.2021.100311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Lung cancer is the leading cause of mortality and morbidity in tumor-related deaths in the world. Early detection of tumors can greatly improve the survival rate of patients. However, the lack of reliable blood biomarkers remains a major challenge for early diagnosis. The blood proteins secreted by the lung bronchi and bronchial arteries may have characteristic glycosylation patterns associated with tumors, which are different from normal physiological and pathological conditions. In this review, we outline the oncogenic drivers, signaling pathways related to KRAS, gene and protein mutations, and oncogenic regulation of protein glycosylation. Based on to the TCGA transcriptomics and antibody-based proteomics data, we discussed oncogene and glycoproteins detected in the blood as tumor biomarkers. We hypothesize that glycoproteins whose glycosylation can be reversed by targeted drugs may serve as potential tumor biomarkers.
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Affiliation(s)
- Shuang Yang
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, China
| | - Zeren Yang
- Applied Biomimetic, Gaithersburg, Maryland 20878, United States
| | - Mingming Xu
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shuwei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu 210033, China
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14
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Sheikhsofla F, Poopak B, Firuzyar S, Roudbari F, Ghadiany M. A Cross-Sectional Study for Evaluation of KRAS and BRAF Mutations by Reverse Dot Blot, PCR-RFLP, and Allele-Specific PCR Methods Among Patients with Colorectal Cancer. Avicenna J Med Biotechnol 2021; 13:183-191. [PMID: 34900144 PMCID: PMC8606106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/18/2021] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND KRAS and BRAF genes are the biomarkers in Colorectal Cancer (CRC) which play prognostic and predictive roles in CRC treatment. Nowadays, the selection of rapid and available methods for studying KRAS and BRAF mutations in anti-EGFR therapy of patients suffering from CRC plays a significant role. In this study, the mutations of these two oncogenes were evaluated by different methods. METHODS This study was performed on 50 Formalin-Fixed Paraffin-Embedded (FFPE) tissue blocks of patients diagnosed with colorectal cancer. After DNA extraction, KRAS and BRAF gene mutations were evaluated using reverse dot blot, and results were compared with PCR-RFLP and allele-specific PCR for KRAS and BRAF mutations, respectively. RESULTS KRAS gene mutations were detected in 42% of patients, of which 30% were in codon 12 region, and 12% in codon 13. The most frequent mutations of KRAS were related to G12D and 10% of patients had BRAF mutated genes. The type of KRAS gene mutations could be evaluated by reverse dot blot method. In general, the results of PCR-RFLP and allele-specific PCR were similar to the findings by reverse dot blot method. CONCLUSION These findings suggest that PCR-RFLP and allele-specific PCR methods are suitable for screening the presence of the mutations in KRAS and BRAF oncogenes. In fact, another method with more sensitivity is needed for a more accurate assessment to determine the type of mutations. Due to higher speed of detection, reduced Turnaround Time (TAT), and possible role of some KRAS point mutations in overall survival, reverse dot blot analysis seems to be an optimal method.
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Affiliation(s)
- Fatemeh Sheikhsofla
- Department of Cellular and Molecular Biology, University of Mazandaran, Mazandaran, Iran
| | - Behzad Poopak
- Department of Clinical Laboratory Sciences, Islamic Azad University, Tehran Medical Sciences Branch, Tehran, Iran,Corresponding author: Behzad Poopak, Ph.D., Department of Clinical Laboratory Sciences, Islamic Azad University, Tehran Medical Sciences Branch, Tehran, Iran, Tel: +98 21 22264144, Fax: +98 21 22264144, E-mail:
| | - Sajjad Firuzyar
- Razi Vaccine and Serum Research Institute of Karaj, Karaj, Iran
| | - Fatemeh Roudbari
- Department of Virology, University of Mazandaran, Mazandaran, Iran
| | - Mojtaba Ghadiany
- Department of Hematology and Oncology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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Pálfy G, Menyhárd DK, Perczel A. Dynamically encoded reactivity of Ras enzymes: opening new frontiers for drug discovery. Cancer Metastasis Rev 2020; 39:1075-1089. [PMID: 32815102 PMCID: PMC7680338 DOI: 10.1007/s10555-020-09917-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022]
Abstract
Decoding molecular flexibility in order to understand and predict biological processes-applying the principles of dynamic-structure-activity relationships (DSAR)-becomes a necessity when attempting to design selective and specific inhibitors of a protein that has overlapping interaction surfaces with its upstream and downstream partners along its signaling cascade. Ras proteins are molecular switches that meet this definition perfectly. The close-lying P-loop and the highly flexible switch I and switch II regions are the site of nucleotide-, assisting-, and effector-protein binding. Oncogenic mutations that also appear in this region do not cause easily characterized overall structural changes, due partly to the inherent conformational heterogeneity and pliability of these segments. In this review, we present an overview of the results obtained using approaches targeting Ras dynamics, such as nuclear magnetic resonance (NMR) measurements and experiment-based modeling calculations (mostly molecular dynamics (MD) simulations). These methodologies were successfully used to decipher the mutant- and isoform-specific nature of certain transient states, far-lying allosteric sites, and the internal interaction networks, as well as the interconnectivity of the catalytic and membrane-binding regions. This opens new therapeutic potential: the discovered interaction hotspots present hitherto not targeted, selective sites for drug design efforts in diverse locations of the protein matrix.
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Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
- Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, P.O.B. 32, Budapest, 1538, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary.
- Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, P.O.B. 32, Budapest, 1538, Hungary.
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary.
- Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, P.O.B. 32, Budapest, 1538, Hungary.
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16
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Kun EHS, Tsang YTM, Lin S, Pan S, Medapalli T, Malpica A, Richards JS, Gershenson DM, Wong KK. Differences in gynecologic tumor development in Amhr2-Cre mice with KRAS G12D or KRAS G12V mutations. Sci Rep 2020; 10:20678. [PMID: 33244099 PMCID: PMC7693266 DOI: 10.1038/s41598-020-77666-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/10/2020] [Indexed: 01/05/2023] Open
Abstract
How different KRAS variants impact tumor initiation and progression in vivo has not been thoroughly examined. We hypothesize that the ability of either KRASG12D or KRASG12V mutations to initiate tumor formation is context dependent. Amhr2-Cre mice express Cre recombinase in tissues that develop into the fallopian tubes, uterus, and ovaries. We used these mice to conditionally express either the KRASG12V/+or KRASG12D/+ mutation. Mice with the genotype Amhr2-Cre Pten(fl/fl) KrasG12D/+(G12D mice) had abnormal follicle structures and developed low-grade serous ovarian carcinomas with 100% penetrance within 18 weeks. In contrast, mice with the genotype Amhr2-Cre Pten(fl/fl) KrasG12V/+ (G12V mice) had normal follicle structures, and about 90% of them developed uterine tumors with diverse histological features resembling those of leiomyoma and leiomyosarcoma. Granulosa cell tumors also developed in G12V mice. Differences in cell-signaling pathways in the uterine tissues of G12D and G12V mice were identified using RNA sequencing and reverse-phase protein array analyses. We found that CTNNB1, IL1A, IL1B, TNF, TGFB1, APP, and IL6 had the higher activity in G12V mice than in G12D mice. These mouse models will be useful for studying the differences in signaling pathways driven by KrasG12V/+ or KrasG12D/+ mutations to aid development of targeted therapies for specific KRAS mutant variants. Our leiomyoma model driven by the KrasG12V/+ mutation will also be useful in deciphering the malignant progression from leiomyoma to leiomyosarcoma.
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Affiliation(s)
- Eucharist H S Kun
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Yvonne T M Tsang
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Sophia Lin
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Sophia Pan
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Tejas Medapalli
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Anais Malpica
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - JoAnne S Richards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - David M Gershenson
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Kwong-Kwok Wong
- Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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17
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Lastraioli E, Antonuzzo L, Fantechi B, Di Cerbo L, Di Costanzo A, Lavacchi D, Armenio M, Arcangeli A, Castiglione F, Messerini L, Di Costanzo F. KRAS and NRAS mutation detection in circulating DNA from patients with metastatic colorectal cancer using BEAMing assay: Concordance with standard biopsy and clinical evaluation. Oncol Lett 2020; 21:15. [PMID: 33240421 PMCID: PMC7681220 DOI: 10.3892/ol.2020.12276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
Patients with metastatic colorectal cancer (mCRC) are routinely screened for either K- and N-RAS to select the appropriate treatment. The present study aimed to evaluate the concordance between K- and NRAS status in the tissue (either primary tumor or metastasis) and the plasma of patients with mCRC and to identify the associations between K- and NRAS mutations in ctDNA and the clinicopathological parameters. Samples from a total of 31 patients with mCRC with measurable disease according to the Response Evaluation Criteria in Solid Tumors were analyzed. For all patients, K- and NRAS status was determined in the tissue by matrix-assisted laser desorption/ionization time of flight mass spectrometry. For the detection of RAS mutations in cell-free tumor DNA also defined as circulating tumor DNA (ctDNA), the OncoBEAM® RAS CRC kit (Sysmex Inostics) was used. A total of 6/31 tissue samples expressed wild-type KRAS, whereas 25/31 presented mutations. In addition, 7/31 plasma samples expressed wild-type KRAS, mutations were detected in 22/31 patients, and for 2/31 patients, the test did not provide a conclusive result. A total of 24/31 patients expressed wild-type NRAS, 6/31 had mutations and 1/21 was not informative. For the KRAS mutational status, a moderate concordance (agreement, 85.18%; Cohen's k, 0.513) between the tissue and plasma analysis was observed; for NRAS, a fair agreement (agreement, 83.33%; Cohen's k, 0.242) was obtained. In conclusion, both tissue and plasma analyses should be performed for the management of patients with mCRC. To better exploit the beads, emulsions, amplification, magnetics (BEAMing) technique in the clinical setting, studies aimed at determining the RAS status to monitor therapy and during follow-up are warranted.
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Affiliation(s)
- Elena Lastraioli
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Lorenzo Antonuzzo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Beatrice Fantechi
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Luisa Di Cerbo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Alessandro Di Costanzo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Daniele Lavacchi
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Miriam Armenio
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Annarosa Arcangeli
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Francesca Castiglione
- Section of Pathological Anatomy, Department of Health Sciences, University of Florence, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Luca Messerini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Francesco Di Costanzo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
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18
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Chen CC, Hsu CY, Lin HY, Zeng HQ, Cheng KH, Wu CW, Tsai EM, Hsieh TH. KRAS K104 modification affects the KRAS G12D-GEF interaction and mediates cell growth and motility. Sci Rep 2020; 10:17447. [PMID: 33060649 PMCID: PMC7567070 DOI: 10.1038/s41598-020-74463-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/24/2020] [Indexed: 11/09/2022] Open
Abstract
Mutant RAS genes play an important role in regulating tumors through lysine residue 104 to impair GEF-induced nucleotide exchange, but the regulatory role of KRAS K104 modification on the KRASG12D mutant remains unclear. Therefore, we simulated the acetylation site on the KRASG12D three-dimensional protein structure, including KRASG12D, KRASG12D/K104A and KRASG12D/K104Q, and determined their trajectories and binding free energy with GEF. KRASG12D/K104Q induced structural changes in the α2- and α3-helices, promoted KRAS instability and hampered GEF binding (ΔΔG = 6.14 kJ/mol). We found decreased binding to the Raf1 RBD by KRASG12D/K104Q and reduced cell growth, invasion and migration. Based on whole-genome cDNA microarray analysis, KRASG12D/K104Q decreased expression of NPIPA2, DUSP1 and IL6 in lung and ovarian cancer cells. This study reports computational and experimental analyses of Lys104 of KRASG12D and GEF, and the findings provide a target for exploration for future treatment.
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Affiliation(s)
- Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan.,Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Chia-Yi Hsu
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Hsiao-Yun Lin
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Hong-Qi Zeng
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Kuang-Hung Cheng
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Chia-Wei Wu
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung, 82445, Taiwan
| | - Eing-Mei Tsai
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan. .,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
| | - Tsung-Hua Hsieh
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung, 82445, Taiwan.
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19
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Making NSCLC Crystal Clear: How Kinase Structures Revolutionized Lung Cancer Treatment. CRYSTALS 2020. [DOI: 10.3390/cryst10090725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The parallel advances of different scientific fields provide a contemporary scenario where collaboration is not a differential, but actually a requirement. In this context, crystallography has had a major contribution on the medical sciences, providing a “face” for targets of diseases that previously were known solely by name or sequence. Worldwide, cancer still leads the number of annual deaths, with 9.6 million associated deaths, with a major contribution from lung cancer and its 1.7 million deaths. Since the relationship between cancer and kinases was unraveled, these proteins have been extensively explored and became associated with drugs that later attained blockbuster status. Crystallographic structures of kinases related to lung cancer and their developed and marketed drugs provided insight on their conformation in the absence or presence of small molecules. Notwithstanding, these structures were also of service once the initially highly successful drugs started to lose their effectiveness in the emergence of mutations. This review focuses on a subclassification of lung cancer, non-small cell lung cancer (NSCLC), and major oncogenic driver mutations in kinases, and how crystallographic structures can be used, not only to provide awareness of the function and inhibition of these mutations, but also how these structures can be used in further computational studies aiming at addressing these novel mutations in the field of personalized medicine.
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20
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Study of Ras Mutations' Prognostic Value in Metastatic Colorectal Cancer: STORIA Analysis. Cancers (Basel) 2020; 12:cancers12071919. [PMID: 32708575 PMCID: PMC7409181 DOI: 10.3390/cancers12071919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Colorectal cancer (CRC) is the second most common cause of cancer-specific death in both sexes in Western countries. KRAS mutations occur in about 50% of metastatic CRCs (mCRCs). The prognostic value of specific KRAS mutations still remains unexplored and unclear. Methods: Two hundred and forty KRAS wild-type and 206 KRAS/NRAS mutant consecutive unresectable mCRC patients with PS Eastern Cooperative Oncology Group (ECOG) 0 or 1, aged < 80 years, and with a life expectancy >3 months entered into this study. DNA was extracted from paraffin-embedded formalin-fixed tumour tissues, and it was sequenced with the Oncomine Solid Tumour DNA kit (Thermo Fisher Scientific, Waltham, MA, USA). Data were analysed using the Torrent Suite Software v5.0 (Thermo Fisher Scientific). The primary outcome was the analysis of the prognostic role of different KRAS mutations in terms of overall survival (OS). Results: There were no significant differences among the most prevalent mutations (p.G12D, p.G12V, p.G13D, p.G12A, p.G12C, and p.G12S) in terms of age (<65 vs. ≥65 years), gender (male vs. female), grading (G1/G2 vs. G3), side of primary tumour (left vs. right), pT, and pN. At the median follow-up of 25.6 months, there were 77 deaths in KRAS-mutated patients and 94 in wild-type patients. Three homogeneous prognostic groups were identified: wild-type patients (group A, median survival: 27.5 months), p.G13D/p.G12A/p.G12V/p.G12D mutants (group B, median survival: 17.3 months), and p.G12C/p.G12S mutants (group C, median survival: 5.0 months, p < 0.0001 according to Log Rank test). Upon multivariate analysis, metastatic involvement and p.G12C/p.G12S KRAS mutation group C (vs. other mutations) emerged as independent prognostic variables for survival. Conclusions: We show that mutant KRAS is a negative prognostic factor and that p.G12C/p.G12S variants present the worst clinical courses. This information suggests a clear difference among KRAS mutations, and it will be useful to test potentiated and/or innovative therapeutic strategies in p.G12C/p.G12S metastatic CRC patients.
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21
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Oncogenic G12D mutation alters local conformations and dynamics of K-Ras. Sci Rep 2019; 9:11730. [PMID: 31409810 PMCID: PMC6692342 DOI: 10.1038/s41598-019-48029-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 07/29/2019] [Indexed: 12/19/2022] Open
Abstract
K-Ras is the most frequently mutated oncoprotein in human cancers, and G12D is its most prevalent mutation. To understand how G12D mutation impacts K-Ras function, we need to understand how it alters the regulation of its dynamics. Here, we present local changes in K-Ras structure, conformation and dynamics upon G12D mutation, from long-timescale Molecular Dynamics simulations of active (GTP-bound) and inactive (GDP-bound) forms of wild-type and mutant K-Ras, with an integrated investigation of atomistic-level changes, local conformational shifts and correlated residue motions. Our results reveal that the local changes in K-Ras are specific to bound nucleotide (GTP or GDP), and we provide a structural basis for this. Specifically, we show that G12D mutation causes a shift in the population of local conformational states of K-Ras, especially in Switch-II (SII) and α3-helix regions, in favor of a conformation that is associated with a catalytically impaired state through structural changes; it also causes SII motions to anti-correlate with other regions. This detailed picture of G12D mutation effects on the local dynamic characteristics of both active and inactive protein helps enhance our understanding of local K-Ras dynamics, and can inform studies on the development of direct inhibitors towards the treatment of K-RasG12D-driven cancers.
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22
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Adeniji EA, Olotu FA, Soliman MES. Exploring the Lapse in Druggability: Sequence Analysis, Structural Dynamics and Binding Site Characterization of K-RasG12C Variant, a Feasible Oncotherapeutics Target. Anticancer Agents Med Chem 2019; 18:1540-1550. [PMID: 30019652 DOI: 10.2174/1871520618666180718110231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/28/2018] [Accepted: 07/04/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND The difficulty in druggability of K-Ras variant has presented a challenge in the treatment of cancer diseases associated with its dysfunctionality. Despite the identification of different binding sites, limited information exists in the literature about their characteristics. Therefore, identification, crossvalidation and characterization of its druggable sites would aid the design of chemical compounds that will arrest its dysfunctionality related oncogenesis. OBJECTIVE This study entails the identification, cross-validation and characterization of K-Ras G12C variant's binding sites for potential druggability, coupled with the elucidation of alterations in 3D conformations and dynamics. METHOD Molecular dynamics simulation was carried out on the inactive, the active and the hyperactive K-RasG12Cvariant using the amber software package. The SiteMap software was employed in identifying and characterizing the druggable binding sites while the validation of the binding sites was carried out with the SiteHound and MetaPocket servers. RESULTS Four druggable binding sites were identified, validated and characterized based on physicochemical attributes such as size, volume, degree of enclosure or exposure, degree of contact, hydrophobic/hydrophilic character, hydrophobic/hydrophilic balance and hydrogen-bonding features. Conformational studies also revealed that the K-Ras variant exhibited notable structural instability, increased flexibility and a strongly anticorrelated movement compared to the inactive and active wildtype forms. CONCLUSION The attributes of the characterized druggable sites will be useful in designing site-specific K-Ras inhibitors for the treatment of K-Ras variant associated cancer diseases.
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Affiliation(s)
- Emmanuel A Adeniji
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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Angeles AKJ, Yu RTD, Cutiongco-De La Paz EM, Garcia RL. Phenotypic characterization of the novel, non-hotspot oncogenic KRAS mutants E31D and E63K. Oncol Lett 2019; 18:420-432. [PMID: 31289513 PMCID: PMC6540134 DOI: 10.3892/ol.2019.10325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/02/2019] [Indexed: 12/13/2022] Open
Abstract
KRAS proto-oncogene, GTPase (KRAS) functions as a molecular switch at the apex of multiple signaling pathways controlling cell proliferation, differentiation, migration, and survival. Canonical KRAS mutants, such as those in codons 12 and 13, produce constitutively active oncoproteins that short-circuit epidermal growth factor receptor (EGFR)-initiated signaling, resulting in dysregulated downstream effectors associated with cellular transformation. Therefore, anti-EGFR therapy provides little to no clinical benefit to patients with activating KRAS mutations. Current genotyping procedures based on canonical mutation detection only account for ~40% of non-responders, highlighting the need to identify additional predictive biomarkers. In the present study, two novel non-hotspot KRAS mutations were functionally characterized in vitro: KRAS E31D was identified from a genetic screen of colorectal cancer specimens at the UP-National Institutes of Health. KRAS E63K is curated in the Catalogue of Somatic Mutations in Cancer database. Similar to the canonical mutants KRAS G12D and KRAS G13D, NIH3T3 cells overexpressing KRAS E31D and KRAS E63K showed altered morphology and were characteristically smaller, rounder, and highly refractile compared with their non-transformed counterparts. Filamentous actin staining also indicated cytoplasmic shrinkage, membrane ruffling, and formation of pseudopod protrusions. Further, they displayed higher proliferative rates and higher migratory rates in scratch wound assays compared with negative controls. These empirical findings suggest the activating impact of the novel KRAS mutations, which may contribute to resistance to anti-EGFR therapy. Complementary studies to elucidate the molecular mechanisms underlying the transforming effect of the rare mutants are required. In parallel, their oncogenic capacity in vivo should also be investigated.
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Affiliation(s)
- Arlou Kristina J Angeles
- Disease Molecular Biology and Epigenetics Laboratory, National Institute of Molecular Biology and Biotechnology, National Science Complex, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Ryan Timothy D Yu
- Disease Molecular Biology and Epigenetics Laboratory, National Institute of Molecular Biology and Biotechnology, National Science Complex, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Eva Maria Cutiongco-De La Paz
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, Manila 1000, Philippines.,Philippine Genome Center, University of the Philippines System, Quezon City 1101, Philippines
| | - Reynaldo L Garcia
- Disease Molecular Biology and Epigenetics Laboratory, National Institute of Molecular Biology and Biotechnology, National Science Complex, University of the Philippines Diliman, Quezon City 1101, Philippines.,Philippine Genome Center, University of the Philippines System, Quezon City 1101, Philippines
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24
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Anand R, Sanjeev B. Insights into the structural integrity and dynamics of siRNA–PAZ complex. J Biomol Struct Dyn 2017; 35:2987-2996. [DOI: 10.1080/07391102.2016.1227724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Richa Anand
- Department of Applied Sciences, Indian Institute of Information Technology-Allahabad, Allahabad , Uttar Pradesh 211012, India
| | - B.S. Sanjeev
- Department of Applied Sciences, Indian Institute of Information Technology-Allahabad, Allahabad , Uttar Pradesh 211012, India
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25
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Kwak MS, Cha JM, Yoon JY, Jeon JW, Shin HP, Chang HJ, Kim HK, Joo KR, Lee JI. Prognostic value of KRAS codon 13 gene mutation for overall survival in colorectal cancer: Direct and indirect comparison meta-analysis. Medicine (Baltimore) 2017; 96:e7882. [PMID: 28858102 PMCID: PMC5585496 DOI: 10.1097/md.0000000000007882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The clinical significance of KRAS codon 13 mutation in patients with colorectal cancer (CRC) remains controversial. A systematic review and meta-analysis is necessary for a more precise estimation of the predictive role of KRAS codon 13 mutations in CRC patients. METHODS We performed a systematic search using the MEDLINE, EMBASE, and Cochrane library databases from January 2000 to November 2016. The prognostic value of KRAS codon 13 mutation for overall survival (OS) was investigated by measuring the hazard ratio (HR) and 95% confidence interval (CI). Data were analyzed with Review Manager Version 5.3 and the Canadian Agency for Drugs and Technologies in Health software. RESULTS OS in CRC patients with KRAS codon 13 mutation was worse than that in CRC patients with KRAS wild-type (pooled HR = 1.37, 95% CI: 1.03-1.81, P = .03). Subgroup analysis of studies of enrolled CRC patients treated with antiepidermal growth factor receptor (EGFR) therapy showed no significant difference in OS associated with KRAS codon 13 mutation in comparison to KRAS wild-type (pooled HR = 1.57, 95% CI: 0.98-2.51, P = .06). In the indirect comparison, no statistically significant association was observed between codon 12 and 13 mutations for OS in CRC patients (pooled HR = 0.88, 95% CI: 0.65-1.20, P = .43). CONCLUSION The current meta-analysis suggests that Codon 13 mutation of KRAS gene seems to correlate with the OS of patients with CRC, but has similar OS to those with KRAS wild-type in patients receiving anti-EGFR therapy. No difference was detected in the OS of CRC patients with codon 13 mutation versus codon 12 mutation.
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Affiliation(s)
| | | | | | | | | | | | - Hyung Kyung Kim
- Department of Pathology, Kyung Hee University Hospital at Gang Dong, Kyung Hee University College of Medicine, Seoul, Korea
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26
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Marín-Ramos NI, Piñar C, Vázquez-Villa H, Martín-Fontecha M, González Á, Canales Á, Algar S, Mayo PP, Jiménez-Barbero J, Gajate C, Mollinedo F, Pardo L, Ortega-Gutiérrez S, Viso A, López-Rodríguez ML. Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling. Chemistry 2016; 23:1676-1685. [PMID: 27885731 DOI: 10.1002/chem.201604905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 12/11/2022]
Abstract
Despite more than three decades of intense effort, no anti-Ras therapies have reached clinical application. Contributing to this failure has been an underestimation of Ras complexity and a dearth of structural information. In this regard, recent studies have revealed the highly dynamic character of the Ras surface and the existence of transient pockets suitable for small-molecule binding, opening up new possibilities for the development of Ras modulators. Herein, a novel Ras inhibitor (compound 12) is described that selectively impairs mutated Ras activity in a reversible manner without significantly affecting wild-type Ras, reduces the Ras-guanosine triphosphate (GTP) levels, inhibits the activation of the mitogen-activated protein kinase (MAPK) pathway, and exhibits remarkable cytotoxic activity in Ras-driven cellular models. The use of molecular dynamics simulations and NMR spectroscopy experiments has enabled the molecular bases responsible for the interactions between compound 12 and Ras protein to be explored. The new Ras inhibitor binds partially to the GTP-binding region and extends into the adjacent hydrophobic pocket delimited by switch II. Hence, Ras inhibitor 12 could represent a new compound for the development of more efficacious drugs to target Ras-driven cancers; a currently unmet clinical need.
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Affiliation(s)
- Nagore I Marín-Ramos
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain.,CEI Campus Moncloa, UCM-UPM and CSIC, 28040, Madrid, Spain
| | - Carmen Piñar
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Ángel González
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Sergio Algar
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Paloma P Mayo
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Parque Tecnológico de Bizkaia, Edif. 801A, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48103, Bilbao, Spain
| | - Consuelo Gajate
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Faustino Mollinedo
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Leonardo Pardo
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Alma Viso
- Instituto de Química Orgánica General, IQOG-CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
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27
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Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions. Sci Rep 2016; 6:37012. [PMID: 27845397 PMCID: PMC5109477 DOI: 10.1038/srep37012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/21/2016] [Indexed: 12/11/2022] Open
Abstract
K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach –conditional time-delayed correlations (CTC) – using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations. Analyzing nucleotide-dependent intrinsic K-Ras motions with the new approach yields predictions that agree with the literature, showing that GTP-binding stabilizes K-Ras motions and leads to residue correlations with relatively long characteristic decay times. Furthermore, our study is the first to identify driver-follower relationships in correlated motions of K-Ras residue pairs, revealing the direction of information flow during allosteric modulation of its nucleotide-dependent intrinsic activity: active K-Ras Switch-II region motions drive Switch-I region motions, while α-helix-3L7 motions control both. Our results provide novel insights for strategies that directly target mutant K-Ras.
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28
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Abstract
RAS mutations are among the most common genetic alterations found in cancerous tumors but rational criteria or strategies for targeting RAS-dependent tumors are only recently emerging. Clinical and laboratory data suggest that patient selection based on specific RAS mutations will be an essential component of these strategies. A thorough understanding of the biochemical and structural properties of mutant RAS proteins form the theoretical basis for these approaches. Direct inhibition of KRAS G12C by covalent inhibitors is a notable recent example of the RAS mutation-tailored approach that establishes a paradigm for other RAS mutation-centered strategies.
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Affiliation(s)
- Steven K Montalvo
- School of Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lianbo Li
- Departments of Biochemistry & Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth D Westover
- Departments of Biochemistry & Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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29
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Cammarata MB, Schardon CL, Mehaffey MR, Rosenberg J, Singleton J, Fast W, Brodbelt JS. Impact of G12 Mutations on the Structure of K-Ras Probed by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2016; 138:13187-13196. [DOI: 10.1021/jacs.6b04474] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael B. Cammarata
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher L. Schardon
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jake Rosenberg
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jonathan Singleton
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Walter Fast
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
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30
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Li W, Qiu T, Ling Y, Guo L, Li L, Ying J. Molecular pathological epidemiology of colorectal cancer in Chinese patients with KRAS and BRAF mutations. Oncotarget 2016; 6:39607-13. [PMID: 26530529 PMCID: PMC4741849 DOI: 10.18632/oncotarget.5551] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/09/2015] [Indexed: 12/18/2022] Open
Abstract
An investigation of interactive effects of exogenous and endogenous factors and tumor molecular changes can lead to a better understanding of tumor molecular signatures in colorectal cancer. We here report a molecular pathological epidemiology study in a large cohort of 945 colorectal cancer patients. Mutations of KRAS (36.6%) and BRAF (3.46%) were nearly mutually exclusive. KRAS-mutated tumors were more common in female patients (odds ratio [OR] = 1.68; P = 0.0001) and never smokers (OR = 1.60; P = 0.001). Whereas BRAF-mutated tumors demonstrated no discrepancy in aspects of gender and smoking status compared with wild-type tumors. In addition, tumors with BRAF or KRAS mutations were in correlation with elevated serum level of carbohydrate antigen (CA19-9) and carcinoma embryonic antigen (CEA) and the combination of serum biomarkers and molecular mutation status may enhance the more precise risk stratification of CRC patients. Further studies are needed to define the mechanism brought about by the aforementioned epidemiologic and clinicopathologic characteristics that may help optimize cancer prevention and precision therapy.
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Affiliation(s)
- Wenbin Li
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Tian Qiu
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yun Ling
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lin Li
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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31
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Orue A, Rieber M. Optimized Multiplex Detection of 7 KRAS Mutations by Taqman Allele-Specific qPCR. PLoS One 2016; 11:e0163070. [PMID: 27632281 PMCID: PMC5025196 DOI: 10.1371/journal.pone.0163070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Establishing the KRAS mutational status of tumor samples is essential to manage patients with colorectal or lung cancer, since these mutations preclude treatment with monoclonal anti-epidermal growth factor receptor (EGFR) antibodies. We report an inexpensive, rapid multiplex allele-specific qPCR method detecting the 7 most clinically relevant KRAS somatic mutations with concomitant amplification of non-mutated KRAS in tumor cells and tissues from CRC patients. Positive samples evidenced in the multiplex assay were further subjected to individual allele-specific analysis, to define the specific mutation. Reference human cancer DNA harbouring either G12A, G12C, G12D, G12R, G12S, G12V and G13D confirmed assay specificity with ≤1% sensitivity of mutant alleles. KRAS multiplex mutation analysis usefulness was also demonstrated with formalin-fixed paraffin embedded (FFPE) from CRC biopsies. CONCLUSION Co-amplification of non-mutated DNA avoided false negatives from degraded samples. Moreover, this cost effective assay is compatible with mutation detection by DNA sequencing in FFPE tissues, but with a greater sensitivity when mutant DNA concentrations are limiting.
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Affiliation(s)
- Andrea Orue
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
| | - Manuel Rieber
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
- * E-mail:
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32
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Duffy MJ. Personalized treatment for patients with colorectal cancer: role of biomarkers. Biomark Med 2016; 9:337-47. [PMID: 25808438 DOI: 10.2217/bmm.15.3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The systemic treatment of patients with colorectal cancer (CRC) has traditionally been based on clinical and tumor histological criteria. Recently however, several prognostic and predictive biomarkers have been proposed for patients with newly diagnosed CRC, including the subgroup with stage II disease. Among the best validated prognostic biomarkers for CRC are CEA levels, MS instability status and certain gene signatures. Although no biomarker currently exists for identifying patients likely to benefit from chemotherapy, the mutational status of KRAS and NRAS is used to predict response to cetuximab and panitumumab. For upfront identification of patients at high risk of suffering from severe therapy-related toxicity, specific variants of dihydropyrimidine dehydrogenase may be measured for predicting toxicity from fluoropyrimidines and uridine diphosphate glucuronosyltransferase*28 (UGT1A1*28) for predicting toxicity from irinotecan.
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Waring P, Tie J, Maru D, Karapetis CS. RAS Mutations as Predictive Biomarkers in Clinical Management of Metastatic Colorectal Cancer. Clin Colorectal Cancer 2015; 15:95-103. [PMID: 26952655 DOI: 10.1016/j.clcc.2015.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/10/2015] [Accepted: 10/21/2015] [Indexed: 01/17/2023]
Abstract
The use of anti-epidermal growth factor receptor (EGFR) monoclonal antibody therapies in patients with metastatic colorectal cancer is guided by the presence of activating point mutations in codons 12, 13, 59, 61, 117, and 146 of the KRAS and NRAS genes in the primary tumor. Although these mutations have been incorporated into the prescribing information for both cetuximab and panitumumab, highlighted in the National Comprehensive Cancer Network Guidelines, and routinely tested, a number of controversial issues and unanswered questions related to these mutations and their clinical significance remain. In the present review, we explored the contradictory data related to the prognostic value of KRAS mutations, the reported frequent discordance of KRAS mutations, and the reported nonequivalence of some of these mutations. We also considered the issues related to incorporating additional mutations into the already accredited and approved assays and the challenges created by changing an assay's analytical and clinical limits of detection. We also discuss the lack of biologic data supporting the pathogenicity of newly described clinically actionable mutations and explore the uncertainty regarding the clinical significance of low-frequency mutations, highlighting the importance of correcting allele frequencies for tumor purity. We also considered the importance of distinguishing the significance of low-frequency RAS mutations in tumors previously not treated or treated with anti-EGFR therapies and explore new technologies capable of detecting emerging polyclonal RAS mutations that appear to confer drug resistance.
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Affiliation(s)
- Paul Waring
- Department of Pathology, University of Melbourne, Victoria, Australia
| | - Jeanne Tie
- Ludwig Colon Cancer Initiative Biomarker Laboratory, Ludwig Institute for Cancer Research, Melbourne, Victoria, Australia
| | - Dipen Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christos S Karapetis
- Flinders University, Flinders Centre for Innovation in Cancer, Flinders Medical Centre, Adelaide, South Australia, Australia.
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Endorsing good quality assurance practices in molecular pathology: risks and recommendations for diagnostic laboratories and external quality assessment providers. Virchows Arch 2015; 468:31-41. [PMID: 26306715 DOI: 10.1007/s00428-015-1839-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/06/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022]
Abstract
Quality assurance is an indispensable element in a molecular diagnostic laboratory. The ultimate goal is to warrant patient safety. Several risks that can compromise high quality procedures are at stake, from sample collection to the test performed by the laboratory, the reporting of test results to clinicians, and the organization of effective external quality assessment schemes. Quality assurance should therefore be safeguarded at each level and should imply a holistic multidisciplinary approach. This review aims to provide an overview of good quality assurance practices and discusses certain risks and recommendations to promote and improve quality assurance for both diagnostic laboratories and for external quality assessment providers. The number of molecular targets is continuously rising, and new technologies are evolving. As this poses challenges for clinical implementation and increases the demand for external quality assessment, the formation of an international association for improving quality assurance in molecular pathology is called for.
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35
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Predictive and prognostic markers in the treatment of metastatic colorectal cancer (mCRC): personalized medicine at work. Hematol Oncol Clin North Am 2015; 29:43-60. [PMID: 25475572 DOI: 10.1016/j.hoc.2014.09.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This article clarifies prognostic and predictive markers in the treatment of colorectal cancer. Multiple chemotherapeutic drugs are approved for metastatic colorectal cancer (mCRC), but available guidelines are often not helpful in directing drug selections. It would be desirable to define patient populations before chemotherapy by biomarkers that predict outcome and toxicities. RAS mutational evaluation remains the only established biomarker analysis in the treatment of mCRC. BRAF mutant tumors are associated with poor outcome. Chemotherapeutic combination therapies still remain the most active treatments in the armamentarium, and future trials should address the need to prospectively investigate and validate biomarkers.
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Docking studies of flavonoid compounds as inhibitors of β-ketoacyl acyl carrier protein synthase I (Kas I) of Escherichia coli. J Mol Graph Model 2015; 61:214-23. [PMID: 26292066 DOI: 10.1016/j.jmgm.2015.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 07/01/2015] [Accepted: 07/18/2015] [Indexed: 12/14/2022]
Abstract
Escherichia coli is one of the most frequent causes of many common bacterial infections, including cholecystitis, bacteremia, cholangitis, urinary tract infection (UTI), traveler's diarrhea and other clinical infections such as neonatal meningitis and pneumonia. The fatty acid biosynthesis is essential for the bacterial viability and growth. There are three types of β-ketoacyl acyl carrier protein synthase (KAS) which are important for overcoming the bacterial resistance problem. β-ketoacyl acyl carrier protein synthase I (KAS I) is member of the condensing enzyme family, which is a key catalyst in bacterial fatty acid biosynthesis, and thus an attractive target for novel antibioticsis related to the elongation of unsaturated fatty acids in bacterial fatty acid synthesis and can be a good therapeutic target of designing novel antibiotics. In this report, we performed docking study of E. coli (KAS I) and 50 flavonoids. Out of these 50 flavonoids, there are two compounds, genistein and isorhamnetin, that showed the superior binding energy while fully satisfying the conditions of drug likeliness. The predicted binding energy of genistein and isorhamnetin toward KAS I are -135.76kcal/mol and -132.42kcal/mol, respectively. These energies favorably compare to the biding energy of known drugs thiolactomicin and cerulenin that are -90.26kcal/mol and -99.64kcal/mol, respectively. The method used was docking with the selected E. coli (KAS I-PDB ID-1FJ4) using iGemdock. This was also found to obey the Lipinski's guidelines of five and to show the drug likeliness and bioavailability.
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Hunter JC, Manandhar A, Carrasco MA, Gurbani D, Gondi S, Westover KD. Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations. Mol Cancer Res 2015; 13:1325-35. [PMID: 26037647 DOI: 10.1158/1541-7786.mcr-15-0203] [Citation(s) in RCA: 469] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/20/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED KRAS mutations are the most common genetic abnormalities in cancer, but the distribution of specific mutations across cancers and the differential responses of patients with specific KRAS mutations in therapeutic clinical trials suggest that different KRAS mutations have unique biochemical behaviors. To further explain these high-level clinical differences and to explore potential therapeutic strategies for specific KRAS isoforms, we characterized the most common KRAS mutants biochemically for substrate binding kinetics, intrinsic and GTPase-activating protein (GAP)-stimulated GTPase activities, and interactions with the RAS effector, RAF kinase. Of note, KRAS G13D shows rapid nucleotide exchange kinetics compared with other mutants analyzed. This property can be explained by changes in the electrostatic charge distribution of the active site induced by the G13D mutation as shown by X-ray crystallography. High-resolution X-ray structures are also provided for the GDP-bound forms of KRAS G12V, G12R, and Q61L and reveal additional insight. Overall, the structural data and measurements, obtained herein, indicate that measurable biochemical properties provide clues for identifying KRAS-driven tumors that preferentially signal through RAF. IMPLICATIONS Biochemical profiling and subclassification of KRAS-driven cancers will enable the rational selection of therapies targeting specific KRAS isoforms or specific RAS effectors.
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Affiliation(s)
- John C Hunter
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Anuj Manandhar
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Martin A Carrasco
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
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Li W, Qiu T, Zhi W, Shi S, Zou S, Ling Y, Shan L, Ying J, Lu N. Colorectal carcinomas with KRAS codon 12 mutation are associated with more advanced tumor stages. BMC Cancer 2015; 15:340. [PMID: 25929517 PMCID: PMC4423107 DOI: 10.1186/s12885-015-1345-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/22/2015] [Indexed: 12/31/2022] Open
Abstract
Background KRAS mutation occurs in 35%-40% of colorectal cancer (CRC). The aim of our study was to evaluate the pathological and molecular features of specific KRAS mutated colorectal carcinomas. KRAS and BRAFV600E mutation tests were performed in 762 primary tumors from a consecutive cohort study of Chinese CRC patients. Methods DNA mismatch repair (MMR) status was determined by immunohistochemistry (IHC) staining. Assessment of KRAS and BRAF V600E mutational status was performed using a multiplex allele-specific PCR-based assay. Results Mutations of KRAS (34.8%) and BRAFV600E (3.1%) were nearly mutually exclusive. Both KRAS- and BRAF- mutated tumors were more likely to be located at proximal colon than wild-type (WT) carcinomas. KRAS-mutated carcinomas were more frequently observed in female patients (47.5% vs 37.1%, p = 0.005) and mucinous differentiation (34.7% vs 24.8%, p = 0.004), but have no difference between lymph node (LN) metastases and among pTNM stages. Whereas, BRAF-mutated carcinomas more frequently demonstrated histologic features such as proximal location (60.9% vs 20.9%, p = 0.001), low-grade histology (43.5% vs 18.0%, p = 0.005), mucinous differentiation (69.6% vs 25.9%, p = 0.001) and deficient MMR (dMMR) (21.7% vs 7.6%, p = 0.03). In particular, KRAS codon 12 mutated carcinomas had increased lymph node metastasis (odds ratio [OR] = 1.31; 95% confidence interval [CI] = 1.04 to 1.65; P = 0.02) and were more likely in higher disease stage (III-IV) than that of WT carcinomas (OR = 1.30; 95% CI = 1.03 to 1.64; P = 0.03). However, there were no significant differences in lymph node metastasis and disease stage between KRAS codon 13 mutated carcinoma and WT carcinoma patients. Conclusions In summary, KRAS codon 12 mutation, but not codon 13 mutation, is associated with lymph node metastasis and higher tumor stages.
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Affiliation(s)
- Wenbin Li
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Tian Qiu
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Wenxue Zhi
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Susheng Shi
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Shuangmei Zou
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Yun Ling
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Ling Shan
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Jianming Ying
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
| | - Ning Lu
- Department of Pathology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, National Cancer Center, Beijing, China.
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Zocche DM, Ramirez C, Fontao FM, Costa LD, Redal MA. Global impact of KRAS mutation patterns in FOLFOX treated metastatic colorectal cancer. Front Genet 2015; 6:116. [PMID: 25870609 PMCID: PMC4378307 DOI: 10.3389/fgene.2015.00116] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/06/2015] [Indexed: 12/14/2022] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most frequent events in oncology. Advances in molecular understanding of the processes of carcinogenesis have shed light on the fundamental mechanisms of tumorigenesis. Currently, knowledge of the molecular basis of its pathogenesis is being used to improve patient care and devise more rational therapeutics. Still, the role played by the mutation patterns of mutated genes in the clinical outcomes that patients on pharmacological treatment receive remains unclear. In this study, we propose to analyze the different clinical outcomes and disease prognosis of patients with stage IV CRC treated with FOLFOX chemotherapy (fluorouracil, leucovorin, oxaliplatin) based on different Kirsten ras (KRAS) mutation patterns. Methods: In this cohort study, 148 patients diagnosed with stage IV CRC and treated with FOLFOX were studied between 2008 and 2013. Mutational status of KRAS was determined. Progression-free survival (PFS) and overall survival (OS) were measured, and all deaths were verified. Survival analysis was performed using Kaplan–Meier analysis, comparison among groups was analyzed using the log-rank test, and multivariate analysis was conducted using Cox proportional-hazards regression. Results: Among a total of 148 patients, 48 (32%) had mutated KRAS, 77% at codon 12 and 23% at codon 13. The PFS was significantly worse in the mutant KRAS patients in comparison to wild type KRAS patients (p < 0.05). The OS did not show significant differences between the two groups. Multivariate analysis showed KRAS mutation as an independent negative prognostic factor for PFS. Among the various subtypes of KRAS mutation, G12D was significantly associated with a poor prognosis in PFS (p = 0.02). Conclusion: In our population, the KRAS mutation had an adverse impact on the prognosis for stage IV CRC patients treated with the FOLFOX regimen.
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Affiliation(s)
- David M Zocche
- Molecular and Cellular Biology Department, Instituto Universitario del Hospital Italiano de Buenos Aires - Hospital Italiano de Buenos Aires, Buenos Aires Argentina
| | - Carolina Ramirez
- Instituto de Ciencias Básicas y Medicina Experimental, Instituto Universitario del Hospital Italiano de Buenos Aires - Hospital Italiano de Buenos Aires, Buenos Aires Argentina
| | - Fernando M Fontao
- Molecular and Cellular Biology Department, Instituto Universitario del Hospital Italiano de Buenos Aires - Hospital Italiano de Buenos Aires, Buenos Aires Argentina
| | - Lucas D Costa
- Laboratory for Biological and Artificial Learning, Instituto de Ciencias Básicas y Medicina Experimental, Hospital Italiano de Buenos Aires, Buenos Aires Argentina
| | - María A Redal
- Molecular and Cellular Biology Department, Instituto Universitario del Hospital Italiano de Buenos Aires - Hospital Italiano de Buenos Aires, Buenos Aires Argentina ; Instituto de Ciencias Básicas y Medicina Experimental, Instituto Universitario del Hospital Italiano de Buenos Aires - Hospital Italiano de Buenos Aires, Buenos Aires Argentina
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Tack V, Ligtenberg MJL, Tembuyser L, Normanno N, Vander Borght S, Han van Krieken J, Dequeker EMC. External quality assessment unravels interlaboratory differences in quality of RAS testing for anti-EGFR therapy in colorectal cancer. Oncologist 2015; 20:257-62. [PMID: 25657200 PMCID: PMC4350801 DOI: 10.1634/theoncologist.2014-0382] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/02/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Regulations for the selection of patients with metastatic colorectal cancer for anti-EGFR treatment changed at the end of 2013. The set of mutations to be tested extended from KRAS codons 12 and 13 to KRAS and NRAS exons 2, 3, and 4. A European external quality assessment scheme monitored the performance of laboratories and evaluated the implementation of the new regulations. MATERIALS AND METHODS The 131 participating laboratories received 10 samples of formalin-fixed paraffin-embedded material, including RAS (exon 2, 3, 4) and BRAF mutations. Mock clinical data were provided for three cases. Using their routine methods, laboratories determined the genotypes and submitted three written reports. Assessors scored the results according to predefined evaluation criteria. RESULTS Half of the participants (49.3%) had completely implemented the new test requirements (codons 12, 13, 59, 61, 117, and 146 of KRAS and NRAS), and 96 laboratories (73.3%) made no genotype mistakes. Correct nomenclature, according to the Human Genome Variation Society, was used by 82 laboratories (62.6%). CONCLUSION Although regulations were effective for several months, many laboratories were not ready for full RAS testing in the context of anti-EGFR therapy. Nevertheless, in each participating country, there are laboratories that provide complete and correct testing. External quality assessments can be used to monitor implementation of new test regulations and to stimulate the laboratories to improve their testing procedures. Because the results of this program are available on the website of the European Society of Pathology, patients and clinicians can refer test samples to a reliable laboratory.
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Affiliation(s)
- Véronique Tack
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale" - IRCCS, Naples, Italy; Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Marjolijn J L Ligtenberg
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale" - IRCCS, Naples, Italy; Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Lien Tembuyser
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale" - IRCCS, Naples, Italy; Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Nicola Normanno
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale" - IRCCS, Naples, Italy; Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Sara Vander Borght
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale" - IRCCS, Naples, Italy; Department of Pathology, UZ Leuven, Leuven, Belgium
| | - J Han van Krieken
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale" - IRCCS, Naples, Italy; Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands; Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale" - IRCCS, Naples, Italy; Department of Pathology, UZ Leuven, Leuven, Belgium
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Kogita A, Yoshioka Y, Sakai K, Togashi Y, Sogabe S, Nakai T, Okuno K, Nishio K. Inter- and intra-tumor profiling of multi-regional colon cancer and metastasis. Biochem Biophys Res Commun 2015; 458:52-6. [PMID: 25623536 DOI: 10.1016/j.bbrc.2015.01.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 01/05/2023]
Abstract
Intra- and inter-tumor heterogeneity may hinder personalized molecular-target treatment that depends on the somatic mutation profiles. We performed mutation profiling of formalin-fixed paraffin embedded tumors of multi-regional colon cancer and characterized the consequences of intra- and inter-tumor heterogeneity and metastasis using targeted re-sequencing. We performed targeted re-sequencing on multiple spatially separated samples obtained from multi-regional primary colon carcinoma and associated metastatic sites in two patients using next-generation sequencing. In Patient 1 with four primary tumors (P1-1, P1-2, P1-3, and P1-4) and one liver metastasis (H1), mutually exclusive pattern of mutations was observed in four primary tumors. Mutations in primary tumors were identified in three regions; KARS (G13D) and APC (R876*) in P1-2, TP53 (A161S) in P1-3, and KRAS (G12D), PIK3CA (Q546R), and ERBB4 (T272A) in P1-4. Similar combinatorial mutations were observed between P1-4 and H1. The ERBB4 (T272A) mutation observed in P1-4, however, disappeared in H1. In Patient 2 with two primary tumors (P2-1 and P2-2) and one liver metastasis (H2), mutually exclusive pattern of mutations were observed in two primary tumors. We identified mutations; KRAS (G12V), SMAD4 (N129K, R445*, and G508D), TP53 (R175H), and FGFR3 (R805W) in P2-1, and NRAS (Q61K) and FBXW7 (R425C) in P2-2. Similar combinatorial mutations were observed between P2-1 and H2. The SMAD4 (N129K and G508D) mutations observed in P2-1, however, were nor detected in H2. These results suggested that different clones existed in primary tumors and metastatic tumor in Patient 1 and 2 likely originated from P1-4 and P2-1, respectively. In conclusion, we detected the muti-clonalities between intra- and inter-tumors based on mutational profiling in multi-regional colon cancer using next-generation sequencing. Primary region from which metastasis originated could be speculated by mutation profile. Characterization of inter- and inter-tumor heterogeneity can lead to underestimation of the tumor genomics landscape and treatment strategy of personal medicine.
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Affiliation(s)
- Akihiro Kogita
- Department of Surgery, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Yasumasa Yoshioka
- Department of Surgery, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Yosuke Togashi
- Department of Genome Biology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Shunsuke Sogabe
- Department of Surgery, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Takuya Nakai
- Department of Surgery, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kiyotaka Okuno
- Department of Surgery, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kinki University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
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Feng Q, Liang L, Ren L, Chen J, Wei Y, Chang W, Zhu D, Lin Q, Zheng P, Xu J. A specific KRAS codon 13 mutation is an independent predictor for colorectal cancer metachronous distant metastases. Am J Cancer Res 2015; 5:674-688. [PMID: 25973306 PMCID: PMC4396022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND In colorectal cancer, there are significant differences between synchronous and metachronous distant metastases. However in recent studies, synchronous and metachronous metastases were always lumped together, neglecting their clinical and molecular differences. The mechanism of the latency of metachronous metastases is still unclear. We conducted this study to reveal the relationship between EGFR pathways and metachronous metastases, and try to find efficient predictors. METHODS PCRs and pyrosequencing were used to detect KRAS, BRAF, PIK3CA and PTEN mutations in primary tumor tissues in a total of 281 patients from 2002 to 2008. Patients were identified into three groups: no-metastases group, synchronous-metastases group and metachronous-metastases group. Clinical and survival data were collected from a prospective database. RESULTS KRAS codon 13 mutation was an independent predictor only for metachronous distant metastases (OR = 11.857, P < 0.001), but not for synchronous metastases. Male gender (OR = 2.233, P = 0.024), primary tumor located at rectum (OR = 0.404, P = 0.041), and primary pN2 stage (OR = 3.361, P = 0.01) were also independent predictors for metachronous distant metastases. Different SNPs in KRAS worked significantly different in determining synchronous or metachronous metastases. BRAF mutation (Univariate, OR = 11.5, P = 0.039) and > 200 ng/ml preoperative CEA (Univariate, OR = 41, P = 0.011) potentially predicted metastases within 6 months after primary tumor resection. After metachronous metastases, radical resection (HR = 0.280, P = 0.002) was the most important protective factor for long-term survival. CONCLUSION There were significant clinical and molecular differences between synchronous and metachronous metastases. As an independent predictor, KRAS codon 13 mutation might be the key to explain the mechanism of colorectal cancer metachronous distant metastases. Together with clinical characteristics, it could aid in the early detection of metachronous metastases.
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Affiliation(s)
- Qingyang Feng
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Li Liang
- Department of Internal Medicine/Oncology, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Li Ren
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Jingwen Chen
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Ye Wei
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Wenju Chang
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Qi Lin
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Peng Zheng
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan UniversityShanghai, China
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BRAF V600E mutation and KRAS codon 13 mutations predict poor survival in Chinese colorectal cancer patients. BMC Cancer 2014; 14:802. [PMID: 25367198 PMCID: PMC4233032 DOI: 10.1186/1471-2407-14-802] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/17/2014] [Indexed: 11/25/2022] Open
Abstract
Background Mutations in KRAS, BRAF and PIK3CA are the most common somatic alterations found in the colorectal cancer (CRC) patients from Western countries; but their prevalence and prognostic value have not been adequately assessed in Asian patients. The aim of this study was to determine the mutation frequencies of these genes in Chinese CRC patients and to investigate their impact on prognosis. Methods The sequences of exon 2 of KRAS, exon 15 of BRAF and exons 9 and 20 of PIK3CA were evaluated by PCR and direct sequencing using DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues from primary CRC tumors of 214 patients (colon/rectum: 126/88). Results KRAS, BRAF and PIK3CA mutations were identified in 44.9% (96/214), 4.2% (9/214) and 12.3% (26/212) CRCs, respectively. The most frequent mutations in KRAS, BRAF and PIK3CA were G12D, V600E and H1047R, respectively. All BRAF and 80.8% PIK3CA mutations were from colon cancer patients. BRAF V600E was associated with advanced TNM (P < 0.001), more distant metastases (P = 0.025), and worse overall survival (OS, P < 0.001; multivariate HR = 4.2, P = 0.004) in colon cancer patients. Compared with KRAS wt/BRAF wt CRC patients (N = 109), those with KRAS codon 13 mutations (N = 25) had significantly worse OS (P = 0.016; multivariate HR = 2.7, P = 0.011), whereas KRAS codon 12-mutated cases were not significantly associated with survival. Among the three most common KRAS mutations, G13D (N = 23) showed significant association with poor OS (P = 0.024; multivariate HR = 2.6, P = 0.016) compared with KRAS wt/BRAF wt patients. Conclusion Our findings indicate that PI3K/RAS-RAF signaling pathway genes are frequently mutated in Chinese CRC patients, but have different characteristics than found in Western patients. BRAF V600E is an independent prognostic factor for Chinese patients. Our finding that KRAS codon 13 mutations (in particular G13D) are associated with inferior survival in BRAF wild-type CRCs in Chinese patients was not reported thus far. Our data emphasizes the importance of prospective evaluation of molecular features in CRC patients, because a single mutation type may represent a distinct biologic effect and clinical implication. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-802) contains supplementary material, which is available to authorized users.
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Bartley AN, Hamilton SR. Select biomarkers for tumors of the gastrointestinal tract: present and future. Arch Pathol Lab Med 2014; 139:457-68. [PMID: 25333834 DOI: 10.5858/arpa.2014-0189-ra] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Advances in molecular biomarkers of the gastrointestinal tract have contributed to a decline in the incidence of and mortality from diseases of the gastrointestinal tract. The discovery and clinical validation of new biomarkers are important to personalized cancer therapy, and numerous clinical trials are currently ongoing to help identify individualized therapy affecting these biomarkers and molecular mechanisms they represent. Distinct molecular pathways leading to cancers of the colorectum, esophagus, stomach, small bowel, and pancreas have been identified. Using biomarkers in these pathways to direct patient care, including selection of proper molecular testing for identification of actionable mutations and reporting the results of these biomarkers to guide clinicians and genetic counselors, is paramount. OBJECTIVE To examine and review select clinically actionable biomarkers of the colon, esophagus, stomach, small bowel, and pancreas, including present and future biomarkers with relevant clinical trials. DATA SOURCES Extensive literature review and practical and consultation experience of the authors. CONCLUSIONS Although numerous biomarkers have been identified and are currently guiding patient therapy, few have shown evidence of clinical utility in the management of patients with gastrointestinal cancers. Inconsistent results and discordant proposed algorithms for testing were identified throughout the literature; however, the potential for biomarkers to improve outcomes for patients with gastrointestinal cancer remains high. Continued advances through high-quality studies are needed.
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Affiliation(s)
- Angela N Bartley
- From Molecular Diagnostics, Department of Pathology, St. Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); and the Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas (Dr Hamilton)
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Bruera G, Cannita K, Tessitore A, Russo A, Alesse E, Ficorella C, Ricevuto E. The prevalent KRAS exon 2 c.35 G>A mutation in metastatic colorectal cancer patients: A biomarker of worse prognosis and potential benefit of bevacizumab-containing intensive regimens? Crit Rev Oncol Hematol 2014; 93:190-202. [PMID: 25459669 DOI: 10.1016/j.critrevonc.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 08/06/2014] [Accepted: 10/01/2014] [Indexed: 12/31/2022] Open
Abstract
Bevacizumab-containing chemotherapy differently predict increased efficacy in KRAS exon 2 mutant and wild-type metastatic colorectal cancer (MCRC) patients. Mutant compared to wild-type status did not significantly affect progression-free survival (PFS) and overall survival (OS) in patients fit for first line bevacizumab-containing FIr-B/FOx regimen, and after progression. In patients unfit for intensive regimens, mutant status significantly affected PFS, while not OS. Codon 12 KRAS mutations differentially affect GTPase function, and confer worse clinical behaviour. Prognostic relevance of the prevalent c.35 G>A KRAS mutation was retrospectively evaluated. Fit c.35 G>A mutant patients showed significantly worse OS compared to wild-type and to other mutant. After progression and in unfit patients, c.35 G>A mutation affected significantly worse PFS and OS. c.35 G>A mutant status does not significantly affect worse PFS in patients fit for first line FIr-B/FOx, and it may depend upon effectiveness of anti-VEGF-containing intensive regimen.
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Affiliation(s)
- Gemma Bruera
- Medical Oncology, S. Salvatore Hospital, University of L'Aquila, L'Aquila, Italy; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Katia Cannita
- Medical Oncology, S. Salvatore Hospital, University of L'Aquila, L'Aquila, Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Antonio Russo
- Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Corrado Ficorella
- Medical Oncology, S. Salvatore Hospital, University of L'Aquila, L'Aquila, Italy; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Enrico Ricevuto
- Medical Oncology, S. Salvatore Hospital, University of L'Aquila, L'Aquila, Italy; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
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Lochhead P, Chan AT, Giovannucci E, Fuchs CS, Wu K, Nishihara R, O'Brien M, Ogino S. Progress and opportunities in molecular pathological epidemiology of colorectal premalignant lesions. Am J Gastroenterol 2014; 109:1205-14. [PMID: 24935274 PMCID: PMC4125459 DOI: 10.1038/ajg.2014.153] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 04/18/2014] [Indexed: 02/06/2023]
Abstract
Molecular pathological epidemiology (MPE) is an integrative molecular and population health science that addresses the molecular pathogenesis and heterogeneity of disease processes. The MPE of colonic and rectal premalignant lesions (including hyperplastic polyps, tubular adenomas, tubulovillous adenomas, villous adenomas, traditional serrated adenomas, sessile serrated adenomas/sessile serrated polyps, and hamartomatous polyps) can provide unique opportunities for examining the influence of diet, lifestyle, and environmental exposures on specific pathways of carcinogenesis. Colorectal neoplasia can provide a practical model by which both malignant epithelial tumor (carcinoma) and its precursor are subjected to molecular pathological analyses. KRAS, BRAF, and PIK3CA oncogene mutations, microsatellite instability, CpG island methylator phenotype, and LINE-1 methylation are commonly examined tumor biomarkers. Future opportunities include interrogation of comprehensive genomic, epigenomic, or panomic datasets, and the adoption of in vivo pathology techniques. Considering the colorectal continuum hypothesis and emerging roles of gut microbiota and host immunity in tumorigenesis, detailed information on tumor location is important. There are unique strengths and caveats, especially with regard to case ascertainment by colonoscopy. The MPE of colorectal premalignant lesions can identify etiologic exposures associated with neoplastic initiation and progression, help us better understand colorectal carcinogenesis, and facilitate personalized prevention, screening, and therapy.
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Affiliation(s)
- Paul Lochhead
- 1] Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK [2] The first two authors contributed equally to this work
| | - Andrew T Chan
- 1] Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA [3] The first two authors contributed equally to this work
| | - Edward Giovannucci
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA [2] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA [3] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Charles S Fuchs
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Kana Wu
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Reiko Nishihara
- 1] Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael O'Brien
- Department of Pathology, Boston University Medical Center, Boston, Massachusetts, USA
| | - Shuji Ogino
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA [3] Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
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Ogino S, Lochhead P, Giovannucci E, Meyerhardt JA, Fuchs CS, Chan AT. Discovery of colorectal cancer PIK3CA mutation as potential predictive biomarker: power and promise of molecular pathological epidemiology. Oncogene 2014; 33:2949-55. [PMID: 23792451 PMCID: PMC3818472 DOI: 10.1038/onc.2013.244] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 12/18/2022]
Abstract
Regular use of aspirin reduces incidence and mortality of various cancers, including colorectal cancer. Anticancer effect of aspirin represents one of the 'Provocative Questions' in cancer research. Experimental and clinical studies support a carcinogenic role for PTGS2 (cyclooxygenase-2), which is an important enzymatic mediator of inflammation, and a target of aspirin. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use is associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation as a molecular biomarker that predicts response to aspirin therapy. The PI3K (phosphatidylinositol-4,5-bisphosphonate 3-kinase) enzyme has a pivotal role in the PI3K-AKT signaling pathway. Activating PIK3CA oncogene mutations are observed in various malignancies including breast cancer, ovarian cancer, brain tumor, hepatocellular carcinoma, lung cancer and colon cancer. The prevalence of PIK3CA mutations increases continuously from rectal to cecal cancers, supporting the 'colorectal continuum' paradigm, and an important interplay of gut microbiota and host immune/inflammatory reaction. MPE represents an interdisciplinary integrative science, conceptually defined as 'epidemiology of molecular heterogeneity of disease'. As exposome and interactome vary from person to person and influence disease process, each disease process is unique (the unique disease principle). Therefore, MPE concept and paradigm can extend to non-neoplastic diseases including diabetes mellitus, cardiovascular diseases, metabolic diseases, and so on. MPE research opportunities are currently limited by paucity of tumor molecular data in the existing large-scale population-based studies. However, genomic, epigenomic and molecular pathology testings (for example, analyses for microsatellite instability, MLH1 promoter CpG island methylation, and KRAS and BRAF mutations in colorectal tumors) are becoming routine clinical practices. In order for integrative molecular and population science to be routine practice, we must first reform education curricula by integrating both population and molecular biological sciences. As consequences, next-generation hybrid molecular biological and population scientists can advance science, moving closer to personalized precision medicine and health care.
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Affiliation(s)
- S Ogino
- 1] Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [3] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - P Lochhead
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - E Giovannucci
- 1] Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA [2] Department of Nutrition, Harvard School of Public Health, Boston, MA, USA [3] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - C S Fuchs
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A T Chan
- 1] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [2] Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
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Gil Ferreira C, Aran V, Zalcberg-Renault I, Victorino AP, Salem JH, Bonamino MH, Vieira FM, Zalis M. KRAS mutations: variable incidences in a Brazilian cohort of 8,234 metastatic colorectal cancer patients. BMC Gastroenterol 2014; 14:73. [PMID: 24720724 PMCID: PMC3997472 DOI: 10.1186/1471-230x-14-73] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 04/02/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND KRAS mutations are frequently found in colorectal cancer (CRC) indicating the importance of its genotyping in the study of the molecular mechanisms behind this disease. Although major advances have occurred over the past decade, there are still important gaps in our understanding of CRC carcinogenesis, particularly whether sex-linked factors play any role. METHODS The profile of KRAS mutations in the Brazilian population was analyzed by conducting direct sequencing of KRAS codons 12 and 13 belonging to 8,234 metastatic CRC patient samples. DNA was extracted from paraffin-embedded tissue, exon 1 was amplified by PCR and submitted to direct sequencing. The data obtained was analysed comparing different geographical regions, gender and age. RESULTS The median age was 59 years and the overall percentage of wild-type and mutated KRAS was 62.8% and 31.9%, respectively. Interestingly, different percentages of mutated KRAS patients were observed between male and female patients (32.5% versus 34.8%, respectively; p = 0.03). KRAS Gly12Asp mutation was the most prevalent for both genders and for most regions, with the exception of the North where Gly12Val was the most frequent mutation found. CONCLUSIONS To the best of our knowledge this is one of the largest cohorts of KRAS genotyping in CRC patients and the largest to indicate a higher incidence of KRAS mutation in females compared to males in Brazil. Nevertheless, further research is required to better address the impact of gender differences in colorectal cancer.
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Affiliation(s)
- Carlos Gil Ferreira
- Progenética Diagnósticos Moleculares, Av, Presidente Vargas, 962 3 Andar, Cep: 20071-002 Rio de Janeiro, RJ, Brazil.
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Yoon HH, Tougeron D, Shi Q, Alberts SR, Mahoney MR, Nelson GD, Nair SG, Thibodeau SN, Goldberg RM, Sargent DJ, Sinicrope FA. KRAS codon 12 and 13 mutations in relation to disease-free survival in BRAF-wild-type stage III colon cancers from an adjuvant chemotherapy trial (N0147 alliance). Clin Cancer Res 2014; 20:3033-43. [PMID: 24687927 DOI: 10.1158/1078-0432.ccr-13-3140] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE We examined the prognostic impact of specific KRAS mutations in patients with stage III colon adenocarcinoma receiving adjuvant FOLFOX alone or combined with cetuximab in a phase III trial (N0147). Analysis was restricted to BRAF-wild-type tumors, because BRAF mutation was associated with poor prognosis, and BRAF and KRAS mutations are mutually exclusive. EXPERIMENTAL DESIGN The seven most common KRAS mutations in codon 12 and codon 13 were examined in 2,478 BRAF-wild-type tumors. Because KRAS mutations in codon 12 (n = 779) or 13 (n = 220) were not predictive of adjuvant cetuximab benefit, study arms were pooled for analysis. Disease-free survival (DFS) was evaluated by HRs using Cox models. RESULTS KRAS mutations in codon 12 (multivariate HR, 1.52; 95% confidence interval, CI, 1.28-1.80; P < 0.0001) or codon 13 (multivariate HR, 1.36; 95% CI, 1.04-1.77; P = 0.0248) were significantly associated with shorter DFS compared with patients with wild-type KRAS/BRAF tumors, independent of covariates. KRAS codon 12 mutations were independently associated with proficient mismatch repair (P < 0.0001), proximal tumor site (P < 0.0001), low grade, age, and sex, whereas codon 13 mutations were associated with proximal site (P < 0.0001). CONCLUSION KRAS mutations in either codon 12 or 13 are associated with inferior survival in patients with resected stage III colon cancer. These data highlight the importance of accurate molecular characterization and the significant role of KRAS mutations in both codons in the progression of this malignancy in the adjuvant setting. Clin Cancer Res; 20(11); 3033-43. ©2014 AACR.
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Affiliation(s)
- Harry H Yoon
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - David Tougeron
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Qian Shi
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Steven R Alberts
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Michelle R Mahoney
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Garth D Nelson
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Suresh G Nair
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Stephen N Thibodeau
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Richard M Goldberg
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Daniel J Sargent
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
| | - Frank A Sinicrope
- Authors' Affiliations: Alliance Statistics and Data Center, Mayo Clinic, Rochester, Minnesota; Lehigh Valley Hospital, Allentown, Pennsylvania; and Ohio State University, Columbus, Ohio
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50
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KRAS mutations: analytical considerations. Clin Chim Acta 2014; 431:211-20. [PMID: 24534449 DOI: 10.1016/j.cca.2014.01.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/27/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second most common cause of cancer death globally. Significant improvements in survival have been made in patients with metastasis by new therapies. For example, Cetuximab and Panitumumab are monoclonal antibodies that inhibit the epidermal growth receptor (EGFR). KRAS mutations in codon 12 and 13 are the recognized biomarkers that are analyzed in clinics before the administration of anti-EGFR therapy. Genetic analyses have revealed that mutations in KRAS predict a lack of response to Panitumumab and Cetuximab in patients with metastatic CRC (mCRC). Notably, it is estimated that 35-45% of CRC patients harbor KRAS mutations. Therefore, KRAS mutation testing should be performed in all individuals with the advanced CRC in order to identify the patients who will not respond to the monoclonal EGFR antibody inhibitors. New techniques for KRAS testing have arisen rapidly, and each technique has advantages and disadvantages. Herein, we review the latest published literature specific to KRAS mutation testing techniques. Since reliability and feasibility are important issues in clinical analyses. Therefore, this review also summarizes the effectiveness and limitations of numerous KRAS mutation testing techniques.
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