Clonal evolution in breast cancer revealed by single nucleus genome sequencing.

Sequencing studies of breast tumour cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumours. Here we developed a whole-genome and exome single cell sequencing approach called nuc-seq that uses G2/M nuclei to achieve 91% mean coverage breadth. We applied this method to sequence single normal and tumour nuclei from an oestrogen-receptor-positive (ER(+)) breast cancer and a triple-negative ductal carcinoma. In parallel, we performed single nuclei copy number profiling. Our data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Using targeted single-molecule sequencing, many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumour mass. Using mathematical modelling we found that the triple-negative tumour cells had an increased mutation rate (13.3×), whereas the ER(+) tumour cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.

Impact of venous leg ulceration on health-related quality of life: A synthesis of data from randomized controlled trials compared to population norms.

Venous insufficiency is the most common cause of leg ulceration, but the impact of venous leg ulceration on health-related quality of life has not been adequately assessed. This study compared data from randomized controlled trials to population norms obtained from a large national population survey. We combined the baseline Short Form-36 (SF-36) version 1 data from two New Zealand randomized controlled trials that recruited participants with VLU and compared the pooled data to the population scores obtained from the New Zealand Health Survey using general linear regression to adjust for age, sex, and ethnicity differences between the cohorts. Baseline SF-36 scores obtained from 618 trial participants were compared to the SF-36 scores obtained from the 12,529 participants in the New Zealand Health Survey. Participants with VLU had significantly lower crude SF-36 scores across all eight SF-36 domains, but there was interaction between age and group. Adjusted mean differences for participants aged 65 years or younger were -25.8, -32.1, -21.2, -9.6, -7.6, -23.9, -21.5, and -9.3, respectively, for Physical Functioning, Role Physical, Bodily Pain, General Health, Vitality, Social Functioning, Role Emotional, and Mental Health whereas the adjusted mean differences for older participants were -15.7, -23.8, -13.8, -0.3 (nonsignificant), -4.6, -15.3, -21.2, and -6.6. This study is the first to compare a VLU population to norms from a general population survey and the first to show VLU interacts with age creating stronger impact in younger patients compared their age cohort. Younger patients may have need of more pastoral care as a consequence.

Low-dose aspirin as an adjuvant treatment for venous leg ulceration: study protocol for a randomized controlled trial (Aspirin4VLU).

AIM: The aim of this study was to determine the effect of low-dose aspirin on venous leg ulcer healing when used in addition to compression. BACKGROUND: The mainstay of treatment for venous leg ulcers is compression therapy and there are few adjuvant treatments to accelerate healing. DESIGN: Pragmatic, community-based, double-blind, randomized trial. METHODS: Participants with venous leg ulcers will receive either 150 mg aspirin or placebo daily for up to 24 weeks. Participants will receive background treatment with compression therapy (system of choice guided by participant and/or clinical preference) delivered through district nursing services. The primary outcome will be time-to-healing. Secondary outcomes will include proportion healed at 24 weeks, change in ulcer area, change in health-related quality of life, adherence, efficacy of blinding and adverse events. The trial was funded in June 2014. DISCUSSION: The trial commenced in March 2015 and is successfully recruiting. The trial is one of three trials that will contribute to an individual participant data meta-analysis to be undertaken at the York Trials Centre. TRIAL REGISTRATION: Registered 5 June 2014 ClinicalTrials.gov NCT02158806. Protocol version 1·1, 14 April 2015.

Pentoxifylline for treating venous leg ulcers.

BACKGROUND: Healing of venous leg ulcers is improved by the use of compression bandaging but some venous ulcers remain unhealed, and some people are unsuitable for compression therapy. Pentoxifylline, a drug which helps blood flow, has been used to treat venous leg ulcers. OBJECTIVES: To assess the effects of pentoxifylline (oxpentifylline or Trental 400) for treating venous leg ulcers, compared with a placebo or other therapies, in the presence or absence of compression therapy. SEARCH METHODS: For this fifth update we searched the Cochrane Wounds Group Specialised Register (searched 20 July 2012); The Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2012, Issue 7); Ovid MEDLINE (2010 to July Week 2 2012); Ovid MEDLINE (In-Process & Other Non-Indexed Citations, July 19, 2012); Ovid EMBASE (2010 to 2012 Week 28); and EBSCO CINAHL (2010 to July 13 2012). SELECTION CRITERIA: Randomised trials comparing pentoxifylline with placebo or other therapy in the presence or absence of compression, in people with venous leg ulcers. DATA COLLECTION AND ANALYSIS: One review author extracted and summarised details from eligible trials using a coding sheet. One other review author independently verified data extraction. MAIN RESULTS: No new trials were identified for this update. We included twelve trials involving 864 participants. The quality of trials was variable. Eleven trials compared pentoxifylline with placebo or no treatment. Pentoxifylline is more effective than placebo in terms of complete ulcer healing or significant improvement (RR 1.70, 95% CI 1.30 to 2.24). Pentoxifylline plus compression is more effective than placebo plus compression (RR 1.56, 95% CI 1.14 to 2.13). Pentoxifylline in the absence of compression appears to be more effective than placebo or no treatment (RR 2.25, 95% CI 1.49 to 3.39).More adverse effects were reported in people receiving pentoxifylline (RR 1.56, 95% CI 1.10 to 2.22). Nearly three-quarters (72%) of the reported adverse effects were gastrointestinal. AUTHORS' CONCLUSIONS: Pentoxifylline is an effective adjunct to compression bandaging for treating venous ulcers and may be effective in the absence of compression. The majority of adverse effects were gastrointestinal disturbances.

Prescribed exercise regimen versus usual care and hypochlorous acid wound solution versus placebo for treating venous leg ulcers: study protocol for a randomised controlled trial (Factorial4VLU).

INTRODUCTION: Compression is the mainstay of treatment for venous leg ulcers (VLUs) and there are few effective adjuvant treatments. There is only observational evidence supporting the use of hypochlorous acid (HOCl) as a topical wound solution on VLU and some limited randomised evidence for the effect of a prescribed regimen of exercise. METHODS AND ANALYSIS: The Factorial4VLU trial is a pragmatic, blinded, factorial randomised controlled trial, with 380 participants receiving either a prescribed exercise regimen compared with usual care and either active HOCl wound solution or placebo wound solution at each dressing change for up to 24 weeks. All participants will receive compression therapy. The primary outcome is the proportion of participants with healed VLU at 12 weeks after randomisation as adjudicated by blinded review of ulcer photographs. Secondary outcomes are proportion healed at 24 weeks, time to healing, estimated change in ulcer area, change in 2-Minute Walk Test, change in health-related quality of life, incidence of infection and incidence of all-cause adverse events. If either of the interventions shows a statistically significant positive difference on healing outcomes, cost-effectiveness will be modelled using a health service perspective. ETHICS AND DISSEMINATION: The Factorial4VLU trial received ethical approval from the Northern B Health and Disability Ethics Committee. We plan to publish the results within 1 year of trial completion and will include the results on the trial registration page. TRIAL REGISTRATION NUMBERS: Australia and New Zealand Clinical Trials Register (http://www.anzctr.org.au) (ACTRN12620000116921); Universal Trial Number (WHO) (U1111-1236-2997).

Wool-derived keratin dressings versus usual care dressings for treatment of slow healing venous leg ulceration: a randomised controlled trial (Keratin4VLU).

OBJECTIVE: To determine the effect of a keratin dressing for treating slow-to-heal venous leg ulcers (VLU) on VLU healing. DESIGN: Pragmatic parallel group randomised controlled trial. SETTING: Community-dwelling participants. PARTICIPANTS: People aged 18 or more years with VLU (either present for more than 26 weeks or ulcer area larger than 5 cm2 or both). INTERVENTION: Wool-derived keratin dressing or usual care formulary of non-medicated dressings, on a background treatment with compression. PRIMARY AND SECONDARY OUTCOME MEASURES: Healing at 24 weeks based on blinded assessment of ulcer photographs. Other outcomes included time to complete healing, change in ulcer area to 24 weeks, change in health-related quality of life and incidence of adverse events. RESULTS: We screened 1068 patients with VLU and randomised 143 participants (51.1% of target recruitment), 71 to the keratin dressing group and 72 to the usual care group.The mean age was 66.1 years (SD 15.9) and 53 participants (37.1%) were women. There were no significant differences between the groups on the primary outcome (risk difference -6.4%, 95% CI -22.5% to 9.7%), change in ulcer area (-1.9 cm2, 95% CI -16.5 to 12.8 cm2), time to complete healing (HR 0.80, 95% CI 0.52 to 1.23) or the incidence of adverse events (incidence rate ratio 1.19, 95% CI 0.89 to 1.59) in the intention-to-treat analyses. However, the direction of effect on the primary outcome was reversed in a per protocol analysis specified a priori (risk difference 6.2%, 95% CI -12.4% to 24.9%). CONCLUSION: The effect of adding a keratin dressing to the treatment regimen for prognostically slow-to-heal VLU remains unclear. TRIAL REGISTRATION NUMBER: NCT02896725.

Wool-derived keratin dressings versus usual care dressings for treatment of slow-healing venous leg ulceration: study protocol for a randomised controlled trial (Keratin4VLU).

INTRODUCTION: Keratins, filament-forming proteins found in vertebrate epithelium, are downregulated in slow-healing venous leg ulcers (VLU) compared with normal-healing VLU. Laboratory and animal model research has suggested exogenous keratins increase expression of endogenous keratins. A non-randomised controlled trial of an exogenous keratin dressing reported increased healing in slow-healing VLU. To date, no randomised controlled trial has been done to verify these promising findings. METHODS AND ANALYSIS: The Keratin4VLU trial is a single-blind, pragmatic, parallel group, randomised controlled trial of keratin dressings compared with usual care non-medicated dressings in patients with VLU where either (1) the ulcer area is greater than 5 cm2, (2) the ulcer has been present for more than 26 weeks or (3) both. All patients will receive compression therapy. The primary outcome is the proportion of patients with healed VLU at 24 weeks after randomisation as adjudicated by blinded review of an ulcer photograph. Secondary outcomes are time to healing, estimated change in ulcer area, change in health-related quality of life, agreement between blinded and unblinded assessors and adverse events. The analysis will be intention-to-treat on the primary and secondary outcomes (excepting health-related quality of life). ETHICS AND DISSEMINATION: The Keratin4VLU trial received ethical approval from the Northern A Health and Disability Ethics Committee. We plan to publish the results within 1 year of trial completion and will include the results on the trial registration page. TRIAL REGISTRATION NUMBER: NCT02896725; Pre-results.

Feasibility of monitoring advanced melanoma patients using cell-free DNA from plasma.

To determine the feasibility of liquid biopsy for monitoring of patients with advanced melanoma, cell-free DNA was extracted from plasma for 25 Stage III/IV patients, most (84.0%) having received previous therapy. DNA concentrations ranged from 0.6 to 390.0 ng/ml (median = 7.8 ng/ml) and were positively correlated with tumor burden as measured by imaging (Spearman rho = 0.5435, p = .0363). Using ultra-deep sequencing for a 61-gene panel, one or more mutations were detected in 12 of 25 samples (48.0%), and this proportion did not vary significantly for patients on or off therapy at the time of blood draw (52.9% and 37.5% respectively; p = .673). Sixteen mutations were detected in eight different genes, with the most frequent mutations detected in BRAF, NRAS, and KIT. Allele fractions ranged from 1.1% to 63.2% (median = 29.1%). Among patients with tissue next-generation sequencing, nine of 11 plasma mutations were also detected in matched tissue, for a concordance of 81.8%.

Low dose aspirin as adjuvant treatment for venous leg ulceration: pragmatic, randomised, double blind, placebo controlled trial (Aspirin4VLU).

Objective To determine the effect of low dose aspirin on ulcer healing in patients with venous leg ulcers.Design Pragmatic, community based, parallel group, double blind, randomised controlled trial.Setting Five community nursing centres in New Zealand.Participants 251 adults with venous leg ulcers who could safely be treated with aspirin or placebo: 125 were randomised to aspirin and 126 to placebo.Interventions 150 mg oral aspirin daily or matching placebo for up to 24 weeks treatment, with compression therapy as standard background treatment.Main outcome measures The primary outcome was time to complete healing of the reference ulcer (largest ulcer if more than one ulcer was present). Secondary outcomes included proportion of participants healed, change in ulcer area, change in health related quality of life, and adverse events. Analysis was by intention to treat.Results The median number of days to healing of the reference ulcer was 77 in the aspirin group and 69 in the placebo group (hazard ratio 0.85, 95% confidence interval 0.64 to 1.13, P=0.25). The number of participants healed at the endpoint was 88 (70%) in the aspirin group and 101 (80%) in the placebo group (risk difference -9.8%, 95% confidence interval -20.4% to 0.9%, P=0.07). Estimated change in ulcer area was 4.1 cm2 in the aspirin group and 4.8 cm2 in the placebo group (mean difference -0.7 cm2, 95% confidence interval -1.9 to 0.5 cm2, P=0.25). 40 adverse events occurred among 29 participants in the aspirin group and 37 adverse events among 27 participants in the placebo group (incidence rate ratio 1.1, 95% confidence interval 0.7 to 1.7, P=0.71).Conclusion Our findings do not support the use of low dose aspirin as adjuvant treatment for venous leg ulcers.Trial registration ClinicalTrials.gov NCT02158806.

Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer.

Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy.Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care.Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did (P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF (P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03).Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR.

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.

Aneuploidy is a hallmark of breast cancer; however, knowledge of how these complex genomic rearrangements evolve during tumorigenesis is limited. In this study, we developed a highly multiplexed single-nucleus sequencing method to investigate copy number evolution in patients with triple-negative breast cancer. We sequenced 1,000 single cells from tumors in 12 patients and identified 1-3 major clonal subpopulations in each tumor that shared a common evolutionary lineage. For each tumor, we also identified a minor subpopulation of non-clonal cells that were classified as metastable, pseudodiploid or chromazemic. Phylogenetic analysis and mathematical modeling suggest that these data are unlikely to be explained by the gradual accumulation of copy number events over time. In contrast, our data challenge the paradigm of gradual evolution, showing that the majority of copy number aberrations are acquired at the earliest stages of tumor evolution, in short punctuated bursts, followed by stable clonal expansions that form the tumor mass.

Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq.

A central challenge in oncology is how to kill tumors containing heterogeneous cell populations defined by different combinations of mutated genes. Identifying these mutated genes and understanding how they cooperate requires single-cell analysis, but current single-cell analytic methods, such as PCR-based strategies or whole-exome sequencing, are biased, lack sequencing depth or are cost prohibitive. Transposon-based mutagenesis allows the identification of early cancer drivers, but current sequencing methods have limitations that prevent single-cell analysis. We report a liquid-phase, capture-based sequencing and bioinformatics pipeline, Sleeping Beauty (SB) capture hybridization sequencing (SBCapSeq), that facilitates sequencing of transposon insertion sites from single tumor cells in a SB mouse model of myeloid leukemia (ML). SBCapSeq analysis of just 26 cells from one tumor revealed the tumor's major clonal subpopulations, enabled detection of clonal insertion events not detected by other sequencing methods and led to the identification of dominant subclones, each containing a unique pair of interacting gene drivers along with three to six cooperating cancer genes with SB-driven expression changes.

SNES: single nucleus exome sequencing.

Single-cell genome sequencing methods are challenged by poor physical coverage and high error rates, making it difficult to distinguish real biological variants from technical artifacts. To address this problem, we developed a method called SNES that combines flow-sorting of single G1/0 or G2/M nuclei, time-limited multiple-displacement-amplification, exome capture, and next-generation sequencing to generate high coverage (96%) data from single human cells. We validated our method in a fibroblast cell line, and show low allelic dropout and false-positive error rates, resulting in high detection efficiencies for single nucleotide variants (92%) and indels (85%) in single cells.

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations.

Human cancers are frequently polyploid, containing multiple aneuploid subpopulations that differ in total DNA content. In this study we exploit this property to reconstruct evolutionary histories, by assuming that mutational complexity increases with time. We developed an experimental method called Ploidy-Seq that uses flow-sorting to isolate and enrich subpopulations with different ploidy prior to next-generation genome sequencing. We applied Ploidy-Seq to a patient with a triple-negative (ER-/PR-/HER2-) ductal carcinoma and performed whole-genome sequencing to trace the evolution of point mutations, indels, copy number aberrations, and structural variants in three clonal subpopulations during tumor growth. Our data show that few mutations (8% to 22%) were shared between all three subpopulations, and that the most aggressive clones comprised a minority of the tumor mass. We expect that Ploidy-Seq will have broad applications for delineating clonal diversity and investigating genome evolution in many human cancers.

Pentoxifylline for treatment of venous leg ulcers: a systematic review.

INTRODUCTION: Venous ulcers are usually treated with compression therapy, but, because this treatment may not be effective for some people, adjuvant therapy could be beneficial. We did a systematic review of randomised controlled trials that compared pentoxifylline (with and without compression treatment) with placebo, or other treatments, in patients with venous leg ulcers. METHODS: We identified eight trials (547 adults), five of which compared pentoxifylline and compression with placebo and compression (n=445), and three of which compared pentoxifylline alone with placebo (102). Our main aim was to determine whether pentoxifylline, with or without compression, was effective in treatment of venous leg ulcers. Analysis was by intention to treat. FINDINGS: Pentoxifylline was more effective than placebo in complete healing or substantial improvement of venous leg ulcers (relative risk 1.49, 95% CI 1.11-2.01). Pentoxifylline with compression was also more effective than placebo and compression in complete healing (1.30, 1.10-1.54). Patients taking pentoxifylline had no more adverse events than those on placebo (1.25, 0.87-1.80). The most frequent adverse event was mild gastrointestinal disturbance (43%). INTERPRETATION: Our results suggest that pentoxifylline gives additional benefit to compression for venous leg ulcers, and is possibly effective for patients not receiving compression.