The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors

AbstractCancer cells bearing distinct KRAS mutations exhibit variable sensitivity to SHP2 inhibitors (SHP2i). Here we show that cells harboring KRAS Q61H are uniquely resistant to SHP2i, and investigate the underlying mechanisms using biophysics, molecular dynamics, and cell-based approaches. Q61H mutation impairs intrinsic and GAP-mediated GTP hydrolysis, and impedes activation by SOS1, but does not alter tyrosyl phosphorylation. Wild-type and Q61H-mutant KRAS are both phosphorylated by Src on Tyr32 and Tyr64 and dephosphorylated by SHP2, however, SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. Phosphorylation of wild-type and Gly12-mutant KRAS, which are associated with sensitivity to SHP2i, confers resistance to regulation by GAP and GEF activities and impairs binding to RAF, whereas the near-complete GAP/GEF-resistance of KRAS Q61H remains unaltered, and high-affinity RAF interaction is retained. SHP2 can stimulate KRAS signaling by modulating GEF/GAP activities and dephosphorylating KRAS, processes that fail to regulate signaling of the Q61H mutant.

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2-Deoxyglucose Suppresses ERK Phosphorylation in LKB1 and Ras Wild-Type Non-Small Cell Lung Cancer Cells

PLoS ONE ◽

10.1371/journal.pone.0168793 ◽

2016 ◽

Vol 11 (12) ◽

pp. e0168793 ◽

Cited By ~ 14

Author(s):

Linlin Sun ◽

Xiuju Liu ◽

Haian Fu ◽

Wei Zhou ◽

Diansheng Zhong

Keyword(s):

Lung Cancer ◽

Small Cell Lung Cancer ◽

Cancer Cells ◽

Cell Lung Cancer ◽

Small Cell ◽

Lung Cancer Cells ◽

Wild Type ◽

Small Cell Lung ◽

Erk Phosphorylation

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Interplay Between KRAS and LZTR1 Protein Turnover, Controlled by CUL3/LZTR1 E3 Ubiquitin Ligase, is Disrupted by KRAS Mutations

10.1101/2021.11.23.469679 ◽

2021 ◽

Author(s):

Andreas Damianou ◽

Zhu Liang ◽

Benedikt M Kessler ◽

Frederik Lassen ◽

George Vere ◽

...

Keyword(s):

Quantitative Proteomics ◽

Feedback Loop ◽

Small Gtpase ◽

Wild Type ◽

Kras Mutations ◽

Gtp Hydrolysis ◽

Activating Mutations ◽

Ubiquitin E3 Ligase ◽

Regulatory Circuit ◽

Direct Feedback

KRAS is a proto-oncogene encoding a small GTPase. Mutations contribute up to 30% of human solid tumours including lung adenocarcinoma, pancreatic and colorectal carcinomas. Most KRAS activating mutations interfere with GTP hydrolysis, essential for its role as a molecular switch, leading to alterations in their molecular environment and oncogenic signalling. Here, APEX-2 proximity labelling was used to profile the molecular environment of wild type and G12D, G13D and Q61H activating mutants of KRAS under both, starvation and stimulation conditions. We demonstrate by quantitative proteomics the presence of known interactors of KRAS including a-RAF and LZTR1, which varied in abundance with wildtype and KRAS mutants. Notably, the KRAS mutations G12D, G13D and Q61H abrogate association with LZTR1. Wildtype KRAS and LZTR1, as part of the CUL3 ubiquitin E3 ligase complex, affect each other's protein stability, revealing a direct feedback loop mechanism. KRAS mutations disconnect this regulatory circuit, thereby contributing to oncogenesis.

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Engineered SIRPα Variants as Immunotherapeutic Adjuvants to Anticancer Antibodies

Science ◽

10.1126/science.1238856 ◽

2013 ◽

Vol 341 (6141) ◽

pp. 88-91 ◽

Cited By ~ 222

Author(s):

Kipp Weiskopf ◽

Aaron M. Ring ◽

Chia Chi M. Ho ◽

Jens-Peter Volkmer ◽

Aron M. Levin ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Immune Responses ◽

Cancer Cells ◽

Macrophage Activation ◽

Universal Method ◽

Wild Type ◽

High Affinity ◽

Macrophage Phagocytosis

CD47 is an antiphagocytic signal that cancer cells employ to inhibit macrophage-mediated destruction. Here, we modified the binding domain of human SIRPα, the receptor for CD47, for use as a CD47 antagonist. We engineered high-affinity SIRPα variants with about a 50,000-fold increased affinity for human CD47 relative to wild-type SIRPα. As high-affinity SIRPα monomers, they potently antagonized CD47 on cancer cells but did not induce macrophage phagocytosis on their own. Instead, they exhibited remarkable synergy with all tumor-specific monoclonal antibodies tested by increasing phagocytosis in vitro and enhancing antitumor responses in vivo. This “one-two punch” directs immune responses against tumor cells while lowering the threshold for macrophage activation, thereby providing a universal method for augmenting the efficacy of therapeutic anticancer antibodies.

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Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations

Briefings in Bioinformatics ◽

10.1093/bib/bbaa149 ◽

2020 ◽

Author(s):

Aman Chandra Kaushik ◽

Yan-Jing Wang ◽

Xiangeng Wang ◽

Dong-Qing Wei

Keyword(s):

Molecular Dynamics ◽

Pancreatic Cancer ◽

Cancer Patients ◽

Tp53 Mutation ◽

Cancer Cell Line ◽

Dynamics Analysis ◽

Wild Type ◽

Kras Mutations ◽

Novel Drugs ◽

Significant Difference

Abstract Background: The most frequently mutated gene pairs in pancreatic adenocarcinoma (PAAD) are KRAS and TP53, and our goal is to illustrate the multiomics and molecular dynamics landscapes of KRAS/TP53 mutation and also to obtain prospective novel drugs for KRAS- and TP53-mutated PAAD patients. Moreover, we also made an attempt to discover the probable link amid KRAS and TP53 on the basis of the abovementioned multiomics data. Method: We utilized TCGA & Cancer Cell Line Encyclopedia data for the analysis of KRAS/TP53 mutation in a multiomics manner. In addition to that, we performed molecular dynamics analysis of KRAS and TP53 to produce mechanistic descriptions of particular mutations and carcinogenesis. Result: We discover that there is a significant difference in the genomics, transcriptomics, methylomics, and molecular dynamics pattern of KRAS and TP53 mutation from the matching wild type in PAAD, and the prognosis of pancreatic cancer is directly linked with a particular mutation of KRAS and protein stability. Screened drugs are potentially effective in PAAD patients. Conclusions: KRAS and TP53 prognosis of PAAD is directly associated with a specific mutation of KRAS. Irinotecan and vandetanib are prospective drugs for PAAD patients with KRASG12Dmutation and TP53 mutation.

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5-epi-Sinuleptolide from Soft Corals of the Genus Sinularia Exerts Cytotoxic Effects on Pancreatic Cancer Cell Lines via the Inhibition of JAK2/STAT3, AKT, and ERK Activity

Molecules ◽

10.3390/molecules26226932 ◽

2021 ◽

Vol 26 (22) ◽

pp. 6932

Author(s):

Wan-Chi Tsai ◽

Wen-Hung Wang ◽

Bo-Cian Huang ◽

Chiung-Yao Huang ◽

Jyh-Horng Sheu

Keyword(s):

Pancreatic Cancer ◽

Cancer Cells ◽

Metastatic Potential ◽

Ductal Adenocarcinoma ◽

M Cell ◽

Cytotoxic Effects ◽

Pancreatic Cancer Cells ◽

Erk Phosphorylation ◽

Underlying Mechanisms ◽

Induced Apoptosis

Pancreatic ductal adenocarcinoma is one of the most lethal malignancies: more than half of patients are diagnosed with a metastatic disease, which is associated with a five-year survival rate of only 3%. 5-epi-Sinuleptolide, a norditerpene isolated from Sinularia sp., has been demonstrated to possess cytotoxic activity against cancer cells. However, the cytotoxicity against pancreatic cancer cells and the related mechanisms are unknown. The aim of this study was to evaluate the anti-pancreatic cancer potential of 5-epi-sinuleptolide and to elucidate the underlying mechanisms. The inhibitory effects of 5-epi-sinuleptolide treatment on the proliferation of pancreatic cancer cells were determined and the results showed that 5-epi-sinuleptolide treatment inhibited cell proliferation, induced apoptosis and G2/M cell cycle arrest, and suppressed the invasion of pancreatic cancer cells. The results of western blotting further revealed that 5-epi-sinuleptolide could inhibit JAK2/STAT3, AKT, and ERK phosphorylation, which may account for the diverse cytotoxic effects of 5-epi-sinuleptolide. Taken together, our present investigation unveils a new therapeutic and anti-metastatic potential of 5-epi-sinuleptolide for pancreatic cancer treatment.

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A Systems Mechanism for KRAS Mutant Allele Specific Responses to Targeted Therapy

10.1101/491621 ◽

2018 ◽

Author(s):

Thomas McFall ◽

Jolene K Diedrich ◽

Meron Mengistu ◽

Stacy L Littlechild ◽

Kendra V Paskvan ◽

...

Keyword(s):

Cancer Cells ◽

Genomic Medicine ◽

Interaction Strength ◽

Ras Signaling ◽

Wild Type ◽

Kras Mutations ◽

Ras Pathway ◽

Egfr Inhibition ◽

Ras Activation ◽

Allele Specific

A well-established genotype to phenotype relationship in genomic medicine is that activating KRAS mutations indicate resistance to anti-EGFR agents. We used a computational model of Ras signaling to investigate a confusing exception to this relationship whereby colorectal cancers with one specific, constitutively-active, mutant, KRAS G13D, respond to anti-EGFR agents. Our computational simulations of the biochemical processes that regulate Ras suggest EGFR inhibition reduces wild-type Ras activation in KRAS G13D mutant cancer cells more than in other KRAS mutant cancer cells. The model also reveals a non-intuitive, mutant-specific, dependency of wild-type Ras activation on EGFR. This dependency is determined by the interaction strength between a KRAS mutant and tumor suppressor neurofibromin. Our prospective experiments confirm this mechanism that arises from the systems-level regulation of Ras pathway signaling. Overall, our work demonstrates how systems approaches enable mechanism-based inference in genomic medicine.

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Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

10.26434/chemrxiv.11811660.v1 ◽

2020 ◽

Author(s):

Jin Soo Lim ◽

Jonathan Vandermause ◽

Matthijs A. van Spronsen ◽

Albert Musaelian ◽

Christopher R. O’Connor ◽

...

Keyword(s):

Machine Learning ◽

Molecular Dynamics ◽

Large Scale ◽

Materials Science ◽

Complete Characterization ◽

Layer By Layer ◽

Surface Restructuring ◽

Metastable Structures ◽

Mechanistic Investigation ◽

Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

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Exploration of the cofactor specificity of wild-type phosphite dehydrogenase and its mutant using molecular dynamics simulations

RSC Advances ◽

10.1039/d1ra00221j ◽

2021 ◽

Vol 11 (24) ◽

pp. 14527-14533

Author(s):

Kunlu Liu ◽

Min Wang ◽

Yubo Zhou ◽

Hongxiang Wang ◽

Yudong Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Wild Type ◽

Cofactor Specificity ◽

Phosphite Dehydrogenase ◽

Dynamics Simulations

Phosphite dehydrogenase (Pdh) catalyzes the NAD-dependent oxidation of phosphite to phosphate with the formation of NADH.

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Lif Deficiency Leads to Iron Transportation Dysfunction in Ameloblasts

Journal of Dental Research ◽

10.1177/00220345211011986 ◽

2021 ◽

pp. 002203452110119

Author(s):

L. Fan ◽

Y.J. Ou ◽

Y.X. Zhu ◽

Y.D. Liang ◽

Y. Zhou ◽

...

Keyword(s):

Tooth Development ◽

Iron Status ◽

Acid Resistance ◽

Blue Staining ◽

Maturation Stage ◽

Wild Type ◽

Stat3 Signaling ◽

Stat3 Signaling Pathway ◽

Stem Cell Pluripotency ◽

Underlying Mechanisms

Leukemia inhibitory factor (LIF), a member of the interleukin 6 family of cytokines, is involved in skeletal metabolism, blastocyst implantation, and stem cell pluripotency maintenance. However, the role of LIF in tooth development needs to be elucidated. The aim of the present study was to investigate the effect of Lif deficiency on tooth development and to elucidate the functions of Lif during tooth development and the underlying mechanisms. First, it was found that the incisors of Lif-knockout mice had a much whiter color than those of wild-type mice. Although there were no structural abnormalities or defective mineralization according to scanning electronic microscopy and computed tomography analysis, 3-dimensional images showed that the length of incisors was shorter in Lif−/− mice. Microhardness and acid resistance assays showed that the hardness and acid resistance of the enamel surface of Lif−/− mice were decreased compared to those of wild-type mice. In Lif−/− mice, whose general iron status was comparable to that of the control mice, the iron content of the incisors was significantly reduced, as confirmed by energy-dispersive X-ray spectroscopy (EDS) and Prussian blue staining. Histological staining showed that the cell length of maturation-stage ameloblasts was shorter in Lif−/− mice. Likewise, decreased expression of Tfrc and Slc40a1, both of which are crucial proteins for iron transportation, was observed in Lif−/− mice and Lif-knockdown ameloblast lineage cell lines, according to quantitative reverse transcription polymerase chain reaction, immunohistochemistry, and Western blot. Moreover, the upregulation of Tfrc and Slc40a1 induced by Lif stimulation was blocked by Stattic, a signal transducer and activator of transcription 3 (Stat3) signaling inhibitor. These results suggest that Lif deficiency inhibits iron transportation in the maturation-stage ameloblasts, and Lif modulates expression of Tfrc and Slc40a1 through the Stat3 signaling pathway during enamel development.

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Molecular Dynamics of Chloroplast Membranes Isolated from Wild-Type Barley and a Brassinosteroid-Deficient Mutant Acclimated to Low and High Temperatures

Biomolecules ◽

10.3390/biom11010027 ◽

2020 ◽

Vol 11 (1) ◽

pp. 27

Author(s):

Iwona Sadura ◽

Dariusz Latowski ◽

Jana Oklestkova ◽

Damian Gruszka ◽

Marek Chyc ◽

...

Keyword(s):

Molecular Dynamics ◽

Temperature Stress ◽

High Temperatures ◽

Biological Membrane ◽

Hydrophobic Core ◽

Wild Type ◽

Chloroplast Membranes ◽

Paramagnetic Resonance ◽

Photosynthetic Membranes

Plants have developed various acclimation strategies in order to counteract the negative effects of abiotic stresses (including temperature stress), and biological membranes are important elements in these strategies. Brassinosteroids (BR) are plant steroid hormones that regulate plant growth and development and modulate their reaction against many environmental stresses including temperature stress, but their role in modifying the properties of the biological membrane is poorly known. In this paper, we characterise the molecular dynamics of chloroplast membranes that had been isolated from wild-type and a BR-deficient barley mutant that had been acclimated to low and high temperatures in order to enrich the knowledge about the role of BR as regulators of the dynamics of the photosynthetic membranes. The molecular dynamics of the membranes was investigated using electron paramagnetic resonance (EPR) spectroscopy in both a hydrophilic and hydrophobic area of the membranes. The content of BR was determined, and other important membrane components that affect their molecular dynamics such as chlorophylls, carotenoids and fatty acids in these membranes were also determined. The chloroplast membranes of the BR-mutant had a higher degree of rigidification than the membranes of the wild type. In the hydrophilic area, the most visible differences were observed in plants that had been grown at 20 °C, whereas in the hydrophobic core, they were visible at both 20 and 5 °C. There were no differences in the molecular dynamics of the studied membranes in the chloroplast membranes that had been isolated from plants that had been grown at 27 °C. The role of BR in regulating the molecular dynamics of the photosynthetic membranes will be discussed against the background of an analysis of the photosynthetic pigments and fatty acid composition in the chloroplasts.

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