Search

With the insertion a segment of polarization-maintaining fiber (PMF) inside the cavity, abundant dynamics of group velocity locked vector solitons (GVLVSs) in Er-doped fiber laser have been investigated by using graphene oxide/polyvinyl alcohol (GO/PVA) film as a saturable absorber (SA). The generated Kelly sidebands in emission spectra reveal peak-valley or valley-peak alternation and slightly shift in two orthogonal components, which are the characteristics of GVLVSs. Through proper adjustment of polarization controllers (PCs) inside the EDFLs cavity, versatile vector soliton dynamics such as polarization locked GVLVSs (PL-GVLVSs), polarization rotation GVLVSs (PR-GVLVSs), dual wavelength GVLVSs, bound state GVLVSs, bunch GVLVSs and harmonic mode-locking GVLVSs (HML-GVLVSs) have been observed. The separation between two emission peaks from the dual wavelength GVLVSs was controlled by the Lyot filter and related to the insertion length of PMF inside the cavity. Unlike PL-GVLVSs, the period-doubling phenomenon has been found in two orthogonal components of the PR-GVLVSs. Besides, the bound state GVLVSs were generated showing strongly modulated interference fringes in emission spectrum. For the bunch and HML GVLVSs, the number of solitons inside the cavity increased with the pump power, and it showed the quintuple solitons and the 7th HML-GVLVSs at the highest pump power.

A new research perspective is proposed to optimize the topology of truss structure by force cone method, which involves force cone drawing rules and growth rules. Through the comparison with the mature variable density topology optimization method, the effectiveness of force cone method is verified. This kind of new method is simple and easy to understand (no need to master complex structural optimization design theory). Besides, it is time-saving in finite element calculations, and can obtain an optimized truss layout easily. By drawing the force cone, its application on a large radio telescope's back frame structure shows that, compared with the existing one in terms of structural stiffness, Root Mean Square (RMS) precision, and beam stress distribution, the optimized back frame using the force cone method has higher stiffness, better RMS, more uniform stress, and lighter weight.

Supplementary Figure 1. Somatic mutations detected in histiocytic neoplasms. Supplementary Figure 2. Frequencies of known activating kinase mutations in histiocytic neoplasms. Supplementary Figure 3. ARAF mutations and variants of unknown significance detected in BRAFV600E-wildtype, non-Langerhans Cell Histiocytic neoplasms. Supplementary Figure 4. Clinical and histological images of the non-Langerhans cell histiocytosis (non-LCH) lesions from index patients with kinase fusions identified by RNA-seq. Supplementary Figure 5. Gene expression analysis of histiocytic neoplasms by RNA-seq. Supplementary Table 1. Characteristics of patient samples with histiocytic neoplasms used in this study and genomic analysis utilized for each sample. Supplementary Table 2. Whole exome sequencing metrics. Supplementary Table 3. Somatic variants identified by whole exome and whole transcriptome sequencing and validated by droplet-digital PCR and/or custom-capture targeted next-generation sequencing with variant allele frequencies (VAFs). Supplementary Table 4. List of the top 1% of differentially expressed genes across histiocytic samples from mRNA sequencing. Supplementary Table 5. PCR primers with M13F2 and M13R2 tails (blue) for Sanger sequencing used in the targeted sequencing recurrence testing for MAP2K1 exons 2 and 3 and all coding regions of ARAF.

The effects of selective phosphoinositide 3-kinase (PI3K) and AKT inhibitors were compared in human tumor cell lines in which the pathway is dysregulated. Both caused inhibition of AKT, relief of feedback inhibition of receptor tyrosine kinases, and growth arrest. However, only the PI3K inhibitors caused rapid induction of cell death. In seeking a mechanism for this phenomenon, we found that PI3K inhibition, but not AKT inhibition, causes rapid inhibition of wild-type RAS and of RAF–MEK–ERK signaling. Inhibition of RAS–ERK signaling is transient, rebounding a few hours after drug addition, and is required for rapid induction of apoptosis. Combined MEK and AKT inhibition also promotes cell death, and in murine models of HER2+ cancer, either pulsatile PI3K inhibition or combined MEK and AKT inhibition causes tumor regression. We conclude that PI3K is upstream of RAS and AKT and that pulsatile inhibition of both pathways is sufficient for effective antitumor activity.Significance: We show that the RAS–ERK pathway is a key downstream effector pathway of oncogenic PI3K. Coordinate downregulation of AKT and ERK is necessary for induction of apoptosis and antitumor activity and can be accomplished with pulsatile dosing, which will likely decrease toxicity and allow administration of therapeutic doses. Cancer Discov; 4(3); 334–47. ©2014 AACR.This article is highlighted in the In This Issue feature, p. 259

Supplementary Figure S1: Representative H&E, phospho-ERK and FISH images of pre-dabrafenib (3) and post-dabrafenib (4) tumors. Supplementary Figure S2: WES analysis of copy number variation in pre- and postdabrafenib tumors. Supplementary Figure S3: Whole copy number profiles from WES of pre- and posttreatment tumors. Supplementary Figure S4: Homology alignment of BRAF p. L514 with residues in other tyrosine kinases. Supplementary Figure S5: Relative frequency of BRAF variant alleles in SK-BT-DR cells determined by individual clone sequencing. Supplementary Figure S6: BRAF V600E/L514V reduces dabrafenib sensitivity in NIH- 3T3 cells, related to Figure 2. Supplementary Figure S7: BRAF V600E/L514V confers biochemical resistance to dabrafenib over a time course, related to Figure 2G. Supplementary Figure S8: Comparison of IC50, IC75 and IC90 of dabrafenib against A375 cells expressing BRAF V600E and BRAF V600E/L514V, related to Figure 2H. Supplementary Figure S9: The BRAF V600E/L514V double mutant promotes homodimerization, related to Figure 3A and B. Supplementary Figure S10: BRAF L514V alone is hypoactive and associated with decreased ERK signaling that is not sensitive to dabrafenib. Supplementary Figure S11: BRAF V600E/L514V is inhibited by dabrafenib in a purified kinase assay, indicating that it is not a gatekeeper mutation. Supplementary Figure S12: Quantitation of p-MEK and p-ERK immunoblots, related to Figure 4B. Supplementary Figure S13: Comparison of IC50, IC75 and IC90 of trametinib against A375 expressing BRAF V600E and BRAF V600E/L514V, related to Figure 4C. Supplementary Figure S14: The BRAF V600E/L514V mutant mediates resistance to dabrafenib that cannot be completely overcome by trametinib or dabrafenib plus trametinib, related to Figure 4D. Supplementary Figure S15: V5, p-MEK, total MEK immunoblots, and quantitation of p-ERK immunoblots, related to Figure 5A. Supplementary Figure S16: Novel RAF dimer inhibitors, MEK inhibitor and ERK inhibitor equipotently inhibit cell growth in BRAF V600E and V600E/L514V expressing cells. Supplementary Figure S17: Novel RAF dimer inhibitor, MEK inhibitor and ERK inhibitor equipotently inhibit ERK signaling in BRAF V600E and V600E/L514V expressing cells. Supplementary Figure S18: BGB3245 binds mutant BRAF V600E monomer and second site of V600E/L514V dimer with similar affinity. Supplementary Table S1: Mutations identified by WES of pre-dabrafenib and postdabrafenib tumors. Supplementary Table S2: Secondary mutations associated with acquired resistance and occurring in residues homologous with L514 in BRAF. Supplementary Table S3: BRAF L514V allele frequency determined by ddPCR.

PDF file 93K, This file contains detailed description of experimental procedures as well as reagents utilized

PDF file 40K, Supplementary Figure S6. Induction of apoptosis by PI3K inhibition in HER2-amplified cells. Related to main Figure 6

Supplemental Data

Mutations at multiple sites in MEK1 occur in cancer, suggesting that their mechanisms of activation might be different. We analyzed 17 tumor-associated MEK1 mutants and found that they drove ERK signaling autonomously or in a RAS/RAF-dependent manner. The latter are sensitive to feedback inhibition of RAF, which limits their functional output, and often cooccur with RAS or RAF mutations. They act as amplifiers of RAF signaling. In contrast, another class of mutants deletes a hitherto unrecognized negative regulatory segment of MEK1, is RAF- and phosphorylation-independent, is unaffected by feedback inhibition of upstream signaling, and drives high ERK output and transformation in the absence of RAF activity. Moreover, these RAF-independent mutants are insensitive to allosteric MEK inhibitors, which preferentially bind to the inactivated form of MEK1. All the mutants are sensitive to an ATP-competitive MEK inhibitor. Thus, our study comprises a novel therapeutic strategy for tumors driven by RAF-independent MEK1 mutants.Significance: Mutants with which MEK1 mutants coexist and their sensitivity to inhibitors are determined by allele-specific properties. This study shows the importance of functional characterization of mutant alleles in single oncogenes and identifies a new class of MEK1 mutants, insensitive to current MEK1 inhibitors but treatable with a new ATP-competitive inhibitor. Cancer Discov; 8(5); 648–61. ©2018 AACR.See related commentary by Maust et al., p. 534.This article is highlighted in the In This Issue feature, p. 517

PDF file 67K, This file contains legends for supplementary figures S1-S7. It describes in detail what's included in each figure

Supplemental Table

supplementary tables, figures, and methods

We report the emergence of the novel MEK1V211D gatekeeper mutation in a patient with BRAFK601E colon cancer treated with the allosteric MEK inhibitor binimetinib and the anti-EGFR antibody panitumumab. The MEK1V211D mutation concurrently occurs in the same cell with BRAFK601E and leads to RAF-independent activity but remains regulated by RAF. The V211D mutation causes resistance to binimetinib by both increasing the catalytic activity of MEK1 and reducing its affinity for the drug. Moreover, the mutant exhibits reduced sensitivity to all the allosteric MEK inhibitors tested. Thus, this mutation serves as a general resistance mutation for current MEK inhibitors; however, it is sensitive to a newly reported ATP-competitive MEK inhibitor, which therefore could be used to overcome drug resistance.Significance:We report a resistance mechanism to allosteric MEK inhibitors in the clinic. A MEK1V211D mutation developed in a patient with BRAFK601E colon cancer on MEK and EGFR inhibitors. This mutant increases the catalytic activity of MEK1 and reduces its affinity for binimetinib, but remains sensitive to ATP-competitive MEK inhibitors.This article is highlighted in the In This Issue feature, p. 1143

Supplementary Materials include Supplementary Tables and Supplementary Figures and Legends.

This supplementary data file contains 5 figures pertaining to the tumor distribution of MEK1 hotspot mutations, functional characterization of further MEK1/2 mutants with and without MEK or ERK inhibitor treatment, and the sequence paralogy alignment of MEK1 and MEK2. This file also contains 4 tables detailing hotspot analysis q values for MEK1/2 mutants, tumor incidence of MEK1 in-frame deletions, and a summary of MEK1/2 paralogous residues and their concordant activation status.

BRAF V600E colorectal cancers are insensitive to RAF inhibitor monotherapy due to feedback reactivation of receptor tyrosine kinase signaling. Combined RAF and EGFR inhibition exerts a therapeutic effect, but resistance invariably develops through undefined mechanisms. In this study, we determined that colorectal cancer progression specimens invariably harbored lesions in elements of the RAS–RAF–MEK–ERK pathway. Genetic amplification of wild-type RAS was a recurrent mechanism of resistance in colorectal cancer patients that was not seen in similarly resistant melanomas. We show that wild-type RAS amplification increases receptor tyrosine kinase-dependent activation of RAS more potently in colorectal cancer than in melanoma and causes resistance only in the former. Currently approved RAF inhibitors inhibit RAF monomers but not dimers. All the drug-resistant lesions we identified activate BRAF V600E dimerization directly or by elevating RAS-GTP. Overall, our results show that mechanisms of resistance converge on formation of RAF dimers and that inhibiting EGFR and RAF dimers can effectively suppress ERK-driven growth of resistant colorectal cancer. Cancer Res; 77(23); 6513–23. ©2017 AACR.

Supplementary Figures 1-5: Supplementary Figure 1 - validation and characterization of acquired genomic alterations, Supplementary Figure 2 - RAS amplification leads to increased RAS-GTP and dimerization of RAF, Supplementary Figure 3 - Increase in NRAS expression is sufficient to cause resistance to RAF/EGFR inhibition in vitro in CRC, Supplementary Figure 4 - Increase in NRAS expression does not cause resistance to RAF inhibition in melanoma, Supplementary Figure 5 - Combined EGFR and RAF dimer inhibitors lead to better inhibition of signaling and tumor growth than RAF dimer inhibitor alone in BRAF V600E CRC.

Despite significant advances in cancer precision medicine, a significant hurdle to its broader adoption remains the multitude of variants of unknown significance identified by clinical tumor sequencing and the lack of biologically validated methods to distinguish between functional and benign variants. Here we used functional data on MAP2K1 and MAP2K2 mutations generated in real-time within a co-clinical trial framework to benchmark the predictive value of a three-part in silico methodology. Our computational approach to variant classification incorporated hotspot analysis, three-dimensional molecular dynamics simulation, and sequence paralogy. In silico prediction accurately distinguished functional from benign MAP2K1 and MAP2K2 mutants, yet drug sensitivity varied widely among activating mutant alleles. These results suggest that multifaceted in silico modeling can inform patient accrual to MEK/ERK inhibitor clinical trials, but computational methods need to be paired with laboratory- and clinic-based efforts designed to unravel variabilities in drug response.Significance:Leveraging prospective functional characterization of MEK1/2 mutants, it was found that hotspot analysis, molecular dynamics simulation, and sequence paralogy are complementary tools that can robustly prioritize variants for biologic, therapeutic, and clinical validation.See related commentary by Whitehead and Sebolt-Leopold, p. 4042

Loss of the RAS GTPase-activating protein (RAS-GAP) NF1 drives aberrant activation of RAS/MEK/ERK signaling and other effector pathways in the majority of malignant peripheral nerve sheath tumors (MPNST). These dysregulated pathways represent potential targets for therapeutic intervention. However, studies of novel single agents including MEK inhibitors (MEKi) have demonstrated limited efficacy both preclinically and clinically, with little advancement in overall patient survival. By interrogation of kinome activity through an unbiased screen and targeted evaluation of the signaling response to MEK inhibition, we have identified global activation of upstream receptor tyrosine kinases (RTK) that converges on activation of RAS as a mechanism to limit sensitivity to MEK inhibition. As no direct inhibitors of pan-RAS were available, an inhibitor of the protein tyrosine phosphatase SHP2, a critical mediator of RAS signal transduction downstream of multiple RTK, represented an alternate strategy. The combination of MEKi plus SHP099 was superior to MEKi alone in models of NF1-MPNST, including those with acquired resistance to MEKi. Our findings have immediate translational implications and may inform future clinical trials for patients with MPNST harboring alterations in NF1.Significance:Combined inhibition of MEK and SHP2 is effective in models of NF1-MPNST, both those naïve to and those resistant to MEKi, as well as in the MPNST precursor lesion plexiform neurofibroma.

Supplementary Table 1 shows raw data values corresponding to PamChip analysis.

Supplementary Figure Legends: Supplementary Figure 1 - validation and characterization of acquired genomic alterations, Supplementary Figure 2 - RAS amplification leads to increased RAS-GTP and dimerization of RAF, Supplementary Figure 3 - Increase in NRAS expression is sufficient to cause resistance to RAF/EGFR inhibition in vitro in CRC, Supplementary Figure 4 - Increase in NRAS expression does not cause resistance to RAF inhibition in melanoma, Supplementary Figure 5 - Combined EGFR and RAF dimer inhibitors lead to better inhibition of signaling and tumor growth than RAF dimer inhibitor alone in BRAF V600E CRC.

Supplementary Figures S1-S8. Levels of RAS-GTP in melanoma cell lines (S1); Changes in pERK and cyclin D1 levels as function of time in cells treated with the MEK inhibitor PD0325901 (S2); Sk-Mel-113 (NF1 null) melanoma cells are resistant to AKT inhibition (S3); Variability in induction of pMEK levels following exposure to four allosteric MEK inhibitors (S4); Exon-capture deep sequencing via IMPACT of the NF1 gene in M308 shows a nonsense Q1070* mutation (S5); Expression of activated RAS is sufficient to confer resistance to vemurafenib in Sk-Mel-239 (BRAF V600E) cells (S6); Sensitivity of A375 (BRAF V600E) cells to vemurafenib (S7); The MAPK pathway and the inhibitors used in the study of NF1-null cells (S8).