Functional differences drive the selection of NRAS mutants in melanoma

ABSTRACTDistinct NRAS mutants are enriched in various tumor types. Here, we generated a suite of fully congenic, conditional, Nras knock-in mouse models (LSL-Nras Q61R, -K, -L, -H, -P, -Q; G12D and G13D, -R) to test the hypothesis that melanocyte transformation requires functions specific to the NRAS mutants enriched in human melanoma (Q61R and Q61K). Consistent with the rarity of NRAS codon 12 and 13 mutants in human melanoma, spontaneous melanomas were rare or absent in mice expressing NRAS G12D, G13D or G13R. Mice expressing less common codon 61 alleles (Q61H, Q61P) also developed few or no tumors. NRAS Q61R, Q61K, or Q61L expression, by contrast, induced rapid melanoma onset with high penetrance. Cohorts of heterozygous mice containing one LSL-Nras Q61R and one LSL-Nras Q61K, -L, -H, -P, or -Q allele were generated to assess potential interactions between NRAS mutants. The ability of each Nras variant to substitute for an Nras Q61R allele was consistent with its own ability to drive spontaneous melanoma formation. However, LSL-Nras Q61Q/Q61R mice rarely developed tumors. In vitro experiments in mouse embryonic fibroblasts (MEFs) highlighted activation of the MAPK pathway as a defining difference between tumorigenic and non-tumorigenic NRAS mutants. Enhanced MAPK activation was associated with the promotion of BRAF-BRAF and BRAF-CRAF dimers. These results support the development of cancer preventative strategies specific to the properties of the commonly observed RAS mutants in each tumor type.

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Effect of bypass kinase pathways on acquired CDK4/6 inhibitor resistance.

Journal of Clinical Oncology ◽

10.1200/jco.2018.36.6_suppl.379 ◽

2018 ◽

Vol 36 (6_suppl) ◽

pp. 379-379

Author(s):

Renee De Leeuw ◽

Christopher McNair ◽

Matthew Joseph Schiewer ◽

Neermala Poudel Neupane ◽

Michael Augello ◽

...

Keyword(s):

Mapk Pathway ◽

Early Stage ◽

Mapk Signaling ◽

Cross Resistance ◽

Mek Inhibitors ◽

Mesenchymal Transition ◽

Inhibitor Resistance ◽

Tumor Types

379 Background: Cyclin Dependent Kinase-4/6 (CDK4/6) kinase inhibitors have shown clinical benefit in treatment of solid tumor types, including breast cancer. However, resistance is common, and the underpinning mechanisms of action are not well understood. Given the dependence of CDK4/6 inhibitors on retinoblastoma tumor suppressor (RB) function for activity, this class of agents may be particularly effective in tumor types for which RB loss is infrequent or occurs late in tumor progression. Methods: Here, models of acquired palbociclib resistance were generated in early stage, RB positive cancers, wherein it was shown acquired palbociclib resistance resulted in cross-resistance to other CDK4/6 inhibitors under clinical testing. Results: Cells showing acquired resistance exhibited aggressive in vitro and in vivo phenotypes without genetic loss of RB or RB pathway members, including enhanced proliferative capacity, migratory potential, and characteristics of epithelial to mesenchymal transition. Further analyses through integration of RNA sequencing and phospho-proteomics identified activation of the MAPK signaling pathway as a mediator of CDK4/6 inhibitor resistance, capable of bypassing CDK4/6 activity. However, this altered kinase dependence resulted in sensitization to MEK inhibitors, suggestive of new clinical opportunities in CDK4/6 resistant tumors. Conclusions: In sum, the studies herein not only identify activation of the MAPK pathway as capable of bypassing the CDK4/6 requirement and promoting aggressive tumor characteristics, but nominate MEK inhibitors as potential mechanisms to treat or prevent CDK4/6 inhibitor resistance.

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Cytostatic and Cytotoxic Effects of Recombinant Tumor Necrosis Factor-α on Sensitive Human Melanoma Cells In Vitro May Result in Selection of Cells with Enhanced Markers of Malignancy

Journal of Investigative Dermatology ◽

10.1111/1523-1747.ep12875823 ◽

1990 ◽

Vol 95 (6) ◽

pp. S223-S230 ◽

Cited By ~ 15

Author(s):

Christos C. Zouboulis ◽

Kathrin Schröder ◽

Claus Garbe ◽

Konstantin Krasagakis ◽

Sabine Krüger ◽

...

Keyword(s):

Tumor Necrosis Factor ◽

Tumor Necrosis ◽

Tumor Necrosis Factor Α ◽

Human Melanoma ◽

Cytotoxic Effects ◽

Factor Α ◽

Recombinant Tumor Necrosis Factor ◽

Necrosis Factor ◽

Selection Of

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The Circulating Cell-free Genome Atlas (CCGA) Study: Size selection of cell-free DNA (cfDNA) fragments.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.3103 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. 3103-3103 ◽

Cited By ~ 1

Author(s):

Darya Filippova ◽

Matthew H. Larson ◽

M. Cyrus Maher ◽

Robert Calef ◽

Monica Pimentel ◽

...

Keyword(s):

In Silico ◽

Potential Effect ◽

Classification Performance ◽

Size Selection ◽

Increased Sensitivity ◽

Cancer Types ◽

N 93 ◽

Tumor Types ◽

Selection Of

3103 Background: Detection of somatic copy number aberrations in individuals with cancer via cfDNA whole-genome sequencing (WGS) is challenging at low tumor fractions. Given that tumor-derived cfDNA fragments are shorter than those from healthy tissues, this exploratory analysis evaluated the potential effect of size selection on the ability to detect cancer. Methods: CCGA WGS libraries were in silico and in vitro size selected to estimate the change in tumor fraction by tumor types (breast, lung, and colorectal [CRC]) and stage (I-III vs IV). In silico analyses used clinically evaluable training set samples with WGS assay results (n = 1422: 560 non-cancer [NC], 862 cancer [C] stages I-IV); classification (cancer/non-cancer) performance was estimated using fragments within the 90-150 bp range. In vitro analyses used a subset of samples (n = 93: 28 NC, 65 C stages I-IV), including C cases sampled within a range of tumor fractions; tumor fraction was also measured at each progressive removal of maximum-length fragments (intervals of 10 bp: 150 bp down to 50 bp). Results: In silico and in vitro analyses, respectively, resulted in median 2.00±0.58-fold (at 6.91±2.64X depth) and 2.00±0.52-fold (at 23±4.45X depth) increases, in overall tumor fraction (compared to non-size-selected 36X depth). This was consistent across tumor types ( in silico: 1.78±0.73 breast, 2.00±0.58 CRC, 2.00±0.41 lung; in vitro: 2.00±0.82 breast, 2.51±0.52 CRC, 2.53±0.94 lung) and stages ( in silico: 2.00±0.74 I-III, 1.78±0.52 IV; in vitro: 2.00±0.55 I-III, 1.68±0.29 IV). Tumor fraction increased with initial fragment length titrations, but not following size selection to shorter lengths ( < 140 bp). Classifier trained on in silico size-selected data had increased sensitivity at 98% specificity compared to those trained on non-size-selected data (p < 1e-5). Conclusions: In silico and in vitro size selection consistently increased tumor fraction across cancer types and stages, and this increase was maximized by tuning the length range of size selection. Relative to full-depth data, classification performance improved significantly. These data suggest that size selection targeting cfDNA under 140 bp may enhance cfDNA-based cancer detection. Clinical trial information: NCT02889978.

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In vitro negative selection of viral superantigen-reactive TCR transgenic thymocytes by thymic dendritic cells

Immunology Letters ◽

10.1016/s0165-2478(97)87831-5 ◽

1997 ◽

Vol 56 (1-3) ◽

pp. 249

Author(s):

I Ferrero

Keyword(s):

Dendritic Cells ◽

Negative Selection ◽

Selection Of

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Clone selection of in vitro horseradish hairy root cultures

Planta Medica ◽

10.1055/s-0035-1565606 ◽

2015 ◽

Vol 81 (16) ◽

Author(s):

R Bertóti ◽

Á Alberti ◽

A Böszörményi ◽

R Könye ◽

T Horváth ◽

...

Keyword(s):

Hairy Root ◽

Hairy Root Cultures ◽

Root Cultures ◽

Clone Selection ◽

Selection Of

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Cluster Analysis of Antigenic Profiles of Tumors: Selection of Number of Clusters Using Akaike’s Information Criterion

Methods of Information in Medicine ◽

10.1055/s-0038-1634783 ◽

1990 ◽

Vol 29 (03) ◽

pp. 200-204 ◽

Cited By ~ 7

Author(s):

J. A. Koziol

Keyword(s):

Cluster Analysis ◽

Basic Problem ◽

Information Criterion ◽

Akaike's Information Criterion ◽

Cell Surface Antigens ◽

Number Of Clusters ◽

Akaike’S Information Criterion ◽

Multinomial Data ◽

Tumor Types ◽

Selection Of

AbstractA basic problem of cluster analysis is the determination or selection of the number of clusters evinced in any set of data. We address this issue with multinomial data using Akaike’s information criterion and demonstrate its utility in identifying an appropriate number of clusters of tumor types with similar profiles of cell surface antigens.

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Faculty Opinions recommendation of In vitro selection of a deoxyribozyme that can utilize multiple substrates.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1004319.49956 ◽

2002 ◽

Author(s):

Niles Lehman

Keyword(s):

In Vitro Selection ◽

Multiple Substrates ◽

Selection Of

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Faculty Opinions recommendation of CIS display: In vitro selection of peptides from libraries of protein-DNA complexes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1017658.206556 ◽

2004 ◽

Author(s):

Sachdev Sidhu

Keyword(s):

In Vitro Selection ◽

Dna Complexes ◽

Selection Of

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The Effects of Shock Vancomycin Concentrations on the Formation of Heteroresistance in Staphylococcus aureus

Antibiotics and Chemotherapy ◽

10.37489/0235-2990-2020-65-9-10-3-7 ◽

2020 ◽

Vol 65 (9-10) ◽

pp. 3-7

Author(s):

V. V. Gostev ◽

Yu. V. Sopova ◽

O. S. Kalinogorskaya ◽

M. E. Velizhanina ◽

I. V. Lazareva ◽

...

Keyword(s):

Staphylococcus Aureus ◽

In Vitro Selection ◽

Methicillin Resistant Staphylococcus Aureus ◽

High Concentration ◽

Short Term ◽

High Concentrations ◽

Selection Of ◽

Selection Of Resistance ◽

Test Cultures

Glycopeptides are the basis of the treatment of infections caused by MRSA (Methicillin-Resistant Staphylococcus aureus). Previously, it was demonstrated that antibiotic tolerant phenotypes are formed during selection of resistance under the influence of high concentrations of antibiotics. The present study uses a similar in vitro selection model with vancomycin. Clinical isolates of MRSA belonging to genetic lines ST8 and ST239, as well as the MSSA (ATCC29213) strain, were included in the experiment. Test isolates were incubated for five hours in a medium with a high concentration of vancomycin (50 μg/ml). Test cultures were grown on the medium without antibiotic for 18 hours after each exposure. A total of ten exposure cycles were performed. Vancomycin was characterized by bacteriostatic action; the proportion of surviving cells after exposure was 70–100%. After selection, there was a slight increase in the MIC to vancomycin (MIC 2 μg/ml), teicoplanin (MIC 1.5–3 μg/ml) and daptomycin (MIC 0.25–2 μg/ml). According to the results of PAP analysis, all strains showed an increase in the area under curve depending on the concentration of vancomycin after selection, while a heteroresistant phenotype (with PAP/AUC 0.9) was detected in three isolates. All isolates showed walK mutations (T188S, D235N, E261V, V380I, and G223D). Exposure to short-term shock concentrations of vancomycin promotes the formation of heteroresistance in both MRSA and MSSA. Formation of VISA phenotypes is possible during therapy with vancomycin.

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