Modeling DNA Dynamics under Steady Deforming Forces and Torques

AbstractCirculating tumor DNA (ctDNA) levels may predict response to anticancer drugs, including CDK4/6 inhibitors and endocrine therapy combinations (CDK4/6i+ET); however, critical questions remain unanswered such as which assay or statistical method to use. Here, we obtained paired plasma samples at baseline and week 4 in 45 consecutive patients with advanced breast cancer treated with CDK4/6i+ET. ctDNA was detected in 96% of cases using the 74-gene Guardant360 assay. A variant allele fraction ratio (VAFR) was calculated for each of the 79 detected mutations between both timepoints. Mean of all VAFRs (mVAFR) was computed for each patient. In our dataset, mVAFR was significantly associated with progression-free survival (PFS). Baseline VAF, on-treatment VAF or absolute changes in VAF were not associated with PFS, nor were CA-15.3 levels at baseline, week 4 or the CA-15.3 ratio. These findings demonstrate that ctDNA dynamics using a standardized multi-gene panel and a unique methodological approach predicts treatment outcome. Clinical trials in patients with an unfavorable ctDNA response are needed.

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Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures

Nature Communications ◽

10.1038/s41467-020-20258-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Shih-Chi Luo ◽

Hsin-Yi Yeh ◽

Wei-Hsuan Lan ◽

Yi-Min Wu ◽

Cheng-Han Yang ◽

...

Keyword(s):

Functional Analysis ◽

Structural Analysis ◽

Md Simulation ◽

Structural Basis ◽

High Fidelity ◽

Dna Dynamics ◽

Genomic Integrity ◽

Mismatched Dna ◽

Dna Backbone ◽

Loop 2

AbstractBoth high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases.

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Coumarin base-pair replacement as a fluorescent probe of ultrafast DNA dynamics

Tetrahedron ◽

10.1016/j.tet.2006.12.096 ◽

2007 ◽

Vol 63 (17) ◽

pp. 3450-3456 ◽

Cited By ~ 30

Author(s):

Robert S. Coleman ◽

Mark A. Berg ◽

Catherine J. Murphy

Keyword(s):

Fluorescent Probe ◽

Base Pair ◽

Dna Dynamics

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A Technique for Measuring Absolute Toe Pressures: Evaluation of Pressure-Sensitive Film Techniques

Foot & Ankle ◽

10.1177/107110079201300410 ◽

1992 ◽

Vol 13 (4) ◽

pp. 220-223 ◽

Cited By ~ 4

Author(s):

Alan S. Tuckman ◽

Frederick W. Werner ◽

Maria D. Fortino ◽

Joseph A. Spadaro

Keyword(s):

Soft Tissues ◽

Flat Surface ◽

Imaging System ◽

Accurate Method ◽

Total Force ◽

Confined Space ◽

Pressure Sensitive ◽

Sensitive Film ◽

Pressure Sensitive Film ◽

Deforming Forces

Although a number of pathologies of the forefoot in ballet dancers on pointe have been described, pressures and deforming forces have not been adequately measured. To evaluate the possible use of pressure-sensitive film (PSF) in measuring the pressures on the external soft tissues in such a confined space as the dancer's toe shoe, it was tested and calibrated with 20 cadaver toes. Each cadaver toe was internally stabilized and loaded longitudinally against PSF on a flat surface. The resultant films were analyzed with a video imaging system and the pressures and total forces were determined. Results showed that the linearity of the PSF to pressure had a regression value of 0.98. By using two sensitivity ranges of films, the total force measured by the PSF was found to be within 10% of the known applied force on each toe. The PSF, therefore, may very well be a useful and accurate method of measuring external soft tissue pressures on the forefoot.

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Early circulating tumor (ct) DNA dynamics and efficacy of lorlatinib: Analysis from the CROWN study.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.9011 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 9011-9011

Author(s):

Ross A. Soo ◽

Jean-Francois Martini ◽

Anthonie J. van der Wekken ◽

Shunsuke Teraoka ◽

Alice T. Shaw ◽

...

Keyword(s):

Clinical Outcomes ◽

Kinase Inhibitor ◽

Progression Free Survival ◽

Molecular Response ◽

Similar Response ◽

Dna Dynamics ◽

Paired Samples ◽

Biomarker Analysis ◽

Alk Positive ◽

Ctdna Analysis

9011 Background: Lorlatinib, a third-generation ALK tyrosine kinase inhibitor, significantly improved progression-free survival (PFS) and overall/intracranial responses vs crizotinib in patients (pts) with previously untreated ALK-positive advanced non-small cell lung cancer (NSCLC) in the ongoing randomized Phase 3 CROWN study (NCT03052608). To identify whether additional molecular biomarker analysis correlated with efficacy, we evaluated early ctDNA dynamics compared with clinical outcomes. Methods: Plasma samples were prospectively collected at screening (SC), week 4 (cycle 2, day 1 [C2D1]), week 24 (C7D1), and end of treatment for ctDNA analysis. ctDNA was analyzed using Guardant360CDx (Guardant Health, Inc., Redwood City, CA, USA). Mean variant allele fraction (VAF) of ALK alterations (fusions and/or mutations) and overall detected alterations at each time point and longitudinal mean change (dVAF) as (VAFC2D1) – (VAFSC) were calculated; dVAF <0 indicated decreased ctDNA at week 4. Objective tumor response and PFS were evaluated according to dVAF. These analyses were repeated vs ctDNA results at week 24. Additional correlation analyses between depth of molecular response and/or ctDNA clearance and clinical outcomes are ongoing. Results: Paired samples were available at SC and week 4 from 232 of 255 pts included in the ctDNA analysis: 118/130 (90.8%) in the lorlatinib arm and 114/125 (91.2%) in the crizotinib arm. ALK alterations were detected in 122/232 (52.6%) pts at SC (62/118 [52.5%] from the lorlatinib arm) but only 19/232 (8.2%) at week 4 (8/118 [6.8%] from the lorlatinib arm). Mean VAF of ALK alterations at week 4 was significantly decreased compared with SC in both treatment arms (lorlatinib -1.54, crizotinib -1.25; both P<0.0001; P=0.4239 between arms). In the lorlatinib arm, mean VAF at week 4 was significantly decreased compared with SC in pts with a complete or partial response (dVAF -1.53; n=47; P<0.0001), or stable disease (dVAF -1.37; n=12; P=0.0304). Similar results were observed in the crizotinib arm. In pts with dVAF <0 for ALK alterations, mean percent change from screening in tumor size was -40.8% with lorlatinib (n=59) and -38.7% with crizotinib (n=58). Only 2 pts had dVAF ≥0, both from the crizotinib arm. Median PFS for pts with dVAF <0 for ALK alterations was not reached in the lorlatinib arm (n=62), and was 7.4 months (95% CI, 7.2–9.3) in the crizotinib arm (n=58). Similar response and PFS data were observed in the analysis of dVAF for ALK alterations at week 24. Conclusions: Early ctDNA dynamics may predict lorlatinib efficacy in pts with previously untreated ALK-positive NSCLC. The magnitude of reduction in ctDNA at 4 weeks may be associated with better responses and potentially longer PFS. These findings further support the utility of dynamic ctDNA monitoring in ALK-positive NSCLC. Reference: Shaw AT, et al. N Engl J Med. 2020;383:2018-2029. Clinical trial information: NCT03052608.

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