Search

Supplementary Figure 1 from Temporal Dissection of Tumorigenesis in Primary Cancers

Supplementary Figure 2 from Temporal Dissection of Tumorigenesis in Primary Cancers

Supplementary Figure Legends 1-4, Methods from Temporal Dissection of Tumorigenesis in Primary Cancers

Supplementary Table 2 from Temporal Dissection of Tumorigenesis in Primary Cancers

Supplementary Figure 3 from Temporal Dissection of Tumorigenesis in Primary Cancers

Supplementary Figure 4 from Temporal Dissection of Tumorigenesis in Primary Cancers

Supplementary Table 1 from Temporal Dissection of Tumorigenesis in Primary Cancers

Desmoplastic melanoma is an uncommon variant of melanoma with sarcomatous histology, distinct clinical behavior and unknown pathogenesis. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes in a validation cohort of 42 cases. A high mutation burden (median of 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers. Mutation patterns strongly implicate ultraviolet radiation as the dominant mutagen, indicating a superficially located cell of origin. Newly identified alterations included recurrent promoter mutations of NFKBIE, encoding NF-κB inhibitor ɛ (IκBɛ), in 14.5% of samples. Common oncogenic mutations in melanomas, in particular in BRAF (encoding p.Val600Glu) and NRAS (encoding p.Gln61Lys or p.Gln61Arg), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS and PIK3CA, some of which are candidates for targeted therapies.

© 2015, National Academy of Sciences. All rights reserved. Melanoma is difficult to treat once it becomes metastatic. However, the precise ancestral relationship between primary tumors and their metastases is not well understood. We performed whole-exome sequencing of primary melanomas and multiple matched metastases from eight patients to elucidate their phylogenetic relationships. In six of eight patients, we found that genetically distinct cell populations in the primary tumor metastasized in parallel to different anatomic sites, rather than sequentially from one site to the next. In five of these six patients, the metastasizing cells had themselves arisen from a common parental subpopulation in the primary, indicating that the ability to establish metastases is a late-evolving trait. Interestingly, we discovered that individual metastases were sometimes founded by multiple cell populations of the primary that were genetically distinct. Such establishment of metastases by multiple tumor subpopulations could help explain why identical resistance variants are identified in different sites after initial response to systemic therapy. One primary tumor harbored two subclones with different oncogenic mutations in CTNNB1, which were both propagated to the same metastasis, raising the possibility that activation of wingless-type mouse mammary tumor virus integration site (WNT) signaling may be involved, as has been suggested by experimental models.

During the type-setting of the final version of the article [1] some of the additional files were swapped. The correct files are republished in this Erratum.

The coil−stretch transition in the extension of polymers in two-dimensional flows was investigated near a critical boundary defined by simple shear flow. Visualization of individual molecules revealed a sharp coil−stretch transition in the steady-state length of the polymer with increasing Weissenberg number (Wi) in flows where the magnitude of the elongational component (||E||) slightly exceeded the rotational component (||Ω||). However, unlike in pure elongational flow, large fluctuations in the length of the polymer were observed near the critical point of the transition. These fluctuations result in a “softening” of the phase transition between coiled and extended states of the polymer. In flows where ||Ω|| is slightly greater than ||E||, significant transient polymer deformation was observed. However, the average length of the polymer as a function of Wi increased much more slowly than in simple shear flow.

The efficiency and robustness of various numerical schemes have been evaluated by performing Brownian dynamics simulations of bead-rod and three popular nonlinear bead-spring chain models in uniaxial extension and simple shear flow. The bead-spring models include finitely extensible nonlinear elastic (FENE) springs, worm-like chain (WLC) springs, and Pade approximation to the inverse Langevin function (ILC) springs. For the bead-spring chains two new predictor–corrector algorithms are proposed, which are much superior to commonly used explicit and other fully implicit schemes. In the case of bead-rod chain models, the mid-point algorithm of Liu [J. Chem. Phys. 90 (1989) 5826] is found to be computationally more efficient than a fully implicit Newton’s method. Furthermore, the accuracy and computational efficiency of two different stress expressions for the bead-rod chains, namely the Kramers–Kirkwood and the modified Giesekus have been evaluated under both transient and steady conditions. It is demonstrated that the Kramers–Kirkwood with stochastic filtering is the preferred choice for transient flow while the Giesekus expression is better suited for steady state calculations. The issue of coarse graining from a bead-rod chain to a bead-spring chain has also been investigated. Though bead-spring chains are shown to capture only semi-quantitatively the response of the bead-rod chains in transient flows, a systematic coarse-graining procedure that provides the best description of bead-rod chains via bead-spring chains is presented.

We have investigated the dynamics of dilute (10−5C*) and semidilute (⩽6C*) DNA solutions both in steady and in the start-up of shear flow by combining fluorescence microscopy, bulk rheological measurements, and Brownian dynamics simulations. First, the microscopic states, i.e., the conformational dynamics of single DNA molecules in solution during the start-up of shear flow, were examined by fluorescence microscopy. To investigate the macroscopic response resulting from the changes in the microscopic state, the bulk shear viscosity of the same DNA solutions was also measured. While the transient dynamics of individual molecules is highly variable, an overshoot in the ensemble-averaged molecular extension is observed above a critical Wi following an overshoot in shear viscosity for both dilute and semidilute DNA solutions. These two overshoots are further analyzed and explained on a physical basis from our simulation findings. Based on the physical picture, we have derived a simple scaling to predict the s...

We present the results of Brownian dynamics simulations of a series of different polymer models which have been used to examine the recent experimental findings of Smith et al. (1999) who studied the dynamics of a single DNA molecule in steady shear flow. The steady average extension at various Weissenberg numbers (Wi) is shown to be well predicted by multimode nonlinear models. Quite surprisingly, the normalized average extension x/L asymptotes to less than 1/2 even for extremely large Wi and we discuss this result on a physical basis. The probability density function of molecular extension at various values of Wi using the Kramer’s chain and the finitely extensible nonlinear elastic dumbbell suggests that the number of internal modes is important in a model designed to capture the dynamics of a real DNA molecule. Three different frequency regimes in the power spectral density observed at finite Wi in the experiments are shown to arise from the coupling of the Brownian fluctuations in the gradient direct...

Squamous cell carcinomas (SCCs) are one of the most frequent forms of human malignancy, but, other than TP53 mutations, few causative somatic aberrations have been identified. We identified NOTCH1 or NOTCH2 mutations in ∼75% of cutaneous SCCs and in a lesser fraction of lung SCCs, defining a spectrum for the most prevalent tumor suppressor specific to these epithelial malignancies. Notch receptors normally transduce signals in response to ligands on neighboring cells, regulating metazoan lineage selection and developmental patterning. Our findings therefore illustrate a central role for disruption of microenvironmental communication in cancer progression. NOTCH aberrations include frameshift and nonsense mutations leading to receptor truncations as well as point substitutions in key functional domains that abrogate signaling in cell-based assays. Oncogenic gain-of-function mutations in NOTCH1 commonly occur in human T-cell lymphoblastic leukemia/lymphoma and B-cell chronic lymphocytic leukemia. The bifunctional role of Notch in human cancer thus emphasizes the context dependency of signaling outcomes and suggests that targeted inhibition of the Notch pathway may induce squamous epithelial malignancies.

Timely intervention for cancer requires knowledge of its earliest genetic aberrations. Sequencing of tumors and their metastases reveals numerous abnormalities occurring late in progression. A means to temporally order aberrations in a single cancer, rather than inferring them from serially acquired samples, would define changes preceding even clinically evident disease. We integrate DNA sequence and copy number information to reconstruct the order of abnormalities as individual tumors evolve for 2 separate cancer types. We detect vast, unreported expansion of simple mutations sharply demarcated by recombinative loss of the second copy of TP53 in cutaneous squamous cell carcinomas (cSCC) and serous ovarian adenocarcinomas, in the former surpassing 50 mutations per megabase. In cSCCs, we also report diverse secondary mutations in known and novel oncogenic pathways, illustrating how such expanded mutagenesis directly promotes malignant progression. These results reframe paradigms in which TP53 mutation is required later, to bypass senescence induced by driver oncogenes. Significance: Our approach reveals sequential ordering of oncogenic events in individual cancers, based on chromosomal rearrangements. Identifying the earliest abnormalities in cancer represents a critical step in timely diagnosis and deployment of targeted therapeutics. Cancer Discovery; 1(2); 137–43. © 2011 AACR. This article is highlighted in the In This Issue feature, p. 91

We examine the dynamics of DNA molecules in mixed flows where the ratio of vorticity to strain rate may be slightly above or below unity via Brownian dynamics simulation. We find that the chain dynamics in these flows are dramatically different than those found for simple shear flow. When the strain rate exceeds vorticity, the dynamics are found to be driven by the extra amount of straining. For vorticity-dominated flows, a periodicity in chain extension is observed with considerable chain deformation.

The microscopic and macroscopic response of a polymer solution in start-up shear flow was investigated using fluorescence microscopy of single molecules, bulk viscosity measurements, and Brownian dynamics simulations. An overshoot in viscosity was observed upon flow inception and understood via the observed molecular extension and by simulation findings. Increasing the polymer concentration up to six times the overlap concentration ( C(*)) has no effect on the character of the dynamics of individual molecules.

Background First-generation molecular profiles for human breast cancers have enabled the identification of features that can predict therapeutic response; however, little is known about how the various data types can best be combined to yield optimal predictors. Collections of breast cancer cell lines mirror many aspects of breast cancer molecular pathobiology, and measurements of their omic and biological therapeutic responses are well-suited for development of strategies to identify the most predictive molecular feature sets. Results We used least squares-support vector machines and random forest algorithms to identify molecular features associated with responses of a collection of 70 breast cancer cell lines to 90 experimental or approved therapeutic agents. The datasets analyzed included measurements of copy number aberrations, mutations, gene and isoform expression, promoter methylation and protein expression. Transcriptional subtype contributed strongly to response predictors for 25% of compounds, and adding other molecular data types improved prediction for 65%. No single molecular dataset consistently out-performed the others, suggesting that therapeutic response is mediated at multiple levels in the genome. Response predictors were developed and applied to TCGA data, and were found to be present in subsets of those patient samples. Conclusions These results suggest that matching patients to treatments based on transcriptional subtype will improve response rates, and inclusion of additional features from other profiling data types may provide additional benefit. Further, we suggest a systems biology strategy for guiding clinical trials so that patient cohorts most likely to respond to new therapies may be more efficiently identified.