Abstract 4277: Measuring proliferation rates of distinct tumour clones using single-cell DNA sequencing

Background:

Tumour proliferation rate is a key phenotypic feature of cancer, with higher rates linked to poorer clinical outcomes. Thus far, proliferation rates have been measured using pathological or experimental techniques on bulk tumour samples. However, while tumours are heterogeneous compositions of distinct clones with varying levels of fitness, measuring the proliferation of individual clones has not been possible to date. We hypothesise that enabling the identification of the most proliferative clones would reveal genomic hallmarks of aggressive clones, or the prediction of their potential phenotype, e.g., metastatic potential.

Methods:

We have developed SPRINTER (Single-cell Proliferation Rate Inference in Neoplasms Through Evolutionary Routes), a novel computational method to measure proliferation rates in individual tumour clones using single-cell whole-genome DNA sequencing. To assess the accuracy and power of SPRINTER, we have also developed an experimental approach to DNA sequence >18,000 single cells, accurately separated in different DNA-replication phases. We have sequenced and applied SPRINTER to >10,000 non-small cell lung cancer cells from longitudinal and metastatic tumour samples within the TRACERx study and PEACE autopsy programme. We have further analysed published data from >10,000 breast cancer cells.

Results:

We demonstrate that SPRINTER can accurately identify subpopulations of cells with different proliferation rates using relatively small numbers of cells, in contrast to previous preliminary approaches. While our estimates are concordant with previous bulk experimental studies (5-40%), we importantly have identified clonal heterogeneity in proliferation rates. Using bulk analysis, we have identified patterns of dissemination of tumour clones in non-small cell lung cancer. Integrating this with single-cell data, our results indicate that more widely disseminating tumour clones have higher proliferation rates, suggesting a link between proliferation and dissemination potential. We additionally find that clones are more proliferative in the metastatic versus the primary setting. Furthermore, we have identified high proliferation clones that may have a selective advantage in a breast tumour, and have inferred that they likely arose recently in cancer evolution.

Conclusions:

We have developed a novel method that enables accurate identification of proliferation rates of individual tumour clones using single-cell DNA sequencing data, allowing the investigation of genomic hallmarks in highly proliferative clones that might lead to higher fitness.

Citation Format: Olivia Lucas, Sophie Ward, Rija Zaidi, Mark Hill, Emilia Lim, Haoran Zhai, Abigail Bunkum, Sonya Hessey, Michelle Dietzen, Andrew Rowan, Cristina Naceur-Lombardelli, Nnenna Kanu, Mariam Jamal-Hanjani, Charles Swanton, Simone Zaccaria. Measuring proliferation rates of distinct tumour clones using single-cell DNA sequencing. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4277.

Knee surgery and its evidence base

INTRODUCTION

Evidence driven orthopaedics is gaining prominence. It enables better management decisions and therefore better patient care. The aim of our study was to review a selection of the leading publications pertaining to knee surgery to assess changes in levels of evidence over a decade.

METHODS

Articles from the years 2000 and 2010 in The Knee, the Journal of Arthroplasty, Knee Surgery, Sports Traumatology, Arthroscopy, the Journal of Bone and Joint Surgery (American Volume) and the Bone and Joint Journal were analysed and ranked according to guidelines from the Centre for Evidence-Based Medicine. The intervening years (2003, 2005 and 2007) were also analysed to further define the trend.

RESULTS

The percentage of high level evidence (level I and II) studies increased albeit without reaching statistical significance. Following a significant downward trend, the latter part of the decade saw a major rise in levels of published evidence. The most frequent type of study was therapeutic.

CONCLUSIONS

Although the rise in levels of evidence across the decade was not statistically significant, there was a significant drop and then rise in these levels in the interim. It is therefore important that a further study is performed to assess longer-term trends. Recent developments have made clear that high quality evidence will be having an ever increasing influence on future orthopaedic practice. We suggest that journals implement compulsory declaration of a published study's level of evidence and that authors consider their study designs carefully to enhance the quality of available evidence.

The outcome of total ankle replacement

We performed a systematic review and meta-analysis of modern total ankle replacements (TARs) to determine the survivorship, outcome, complications, radiological findings and range of movement, in patients with end-stage osteoarthritis (OA) of the ankle who undergo this procedure. We used the methodology of the Cochrane Collaboration, which uses risk of bias profiling to assess the quality of papers in favour of a domain-based approach. Continuous outcome scores were pooled across studies using the generic inverse variance method and the random-effects model was used to incorporate clinical and methodological heterogeneity. We included 58 papers (7942 TARs) with an interobserver reliability (Kappa) for selection, performance, attrition, detection and reporting bias of between 0.83 and 0.98. The overall survivorship was 89% at ten years with an annual failure rate of 1.2% (95% confidence interval (CI) 0.7 to 1.6). The mean American Orthopaedic Foot and Ankle Society score changed from 40 (95% CI 36 to 43) pre-operatively to 80 (95% CI 76 to 84) at a mean follow-up of 8.2 years (7 to 10) (p < 0.01). Radiolucencies were identified in up to 23% of TARs after a mean of 4.4 years (2.3 to 9.6). The mean total range of movement improved from 23° (95% CI 19 to 26) to 34° (95% CI 26 to 41) (p = 0.01).

Our study demonstrates that TAR has a positive impact on patients’ lives, with benefits lasting ten years, as judged by improvement in pain and function, as well as improved gait and increased range of movement. However, the quality of evidence is weak and fraught with biases and high quality randomised controlled trials are required to compare TAR with other forms of treatment such as fusion.

Cite this article: Bone Joint J 2013;95-B:1500–7.

Interaction of gossypol with DNA

Gossypol, a polyphenolic binaphthyl dialdehyde found in cotton seeds, is a dietary mutagen and a potential male contraceptive. Its interaction with DNA was studied using a combination of S(1) nuclease hydrolysis and hydroxyapatite chromatography. Calf thymus DNA treated with increasing concentrations of gossypol showed a decreasing degree of S(1) nuclease hydrolysis. An increased thermal melting temperature of treated DNA was also observed. When native DNA, treated with gossypol, was chromatographed on hydroxyapatite, it eluted with a lower molarity of phosphate buffer, indicating a lower affinity of the DNA-drug complex for hydroxyapatite. When gossypol bound to DNA was removed by extraction with organic solvents, the resulting DNA samples showed increased S(1) nuclease hydrolysis and decreased thermal melting temperatures. These results indicated the formation of strand breaks in DNA. Gossypol was also shown to produce superoxide anion and singlet oxygen in aqueous solution. Strand breakage in DNA by gossypol may be caused by active oxygen species such as hydroxyl radical and singlet oxygen.

Abstract P2-10-05: Referral to Genetic Services (GS) and Mutation Yield in 1132 Individuals at Risk for Hereditary Breast Ovarian Cancer Syndromes (HBOC)

Background: Family history directs referral of unaffected individuals to GS and is the main strategy to identify hereditary breast ovarian cancer syndrome. In unaffected individuals with known familial mutations, potentially life saving information can be provided to a large number of these individuals at a very modest cost.

Objectives: 1) To determine the rate of deleterious mutations in high risk individuals, based on pedigree, and 2) to identify the origin of their referral. Methods:

Over a 5-year period (2004 -2009) we analyzed the source of referral for genetic testing and the mutations detected in 1132 consecutively tested individuals. Of 1132 patients tested for BRCA1 or BRCA2 mutations, 420 were unaffected by cancer and 712 had breast or ovarian cancer at the time consultation. We excluded those from families who were previously tested at our institution to limit the bias for mutation positivity.

Results:

Seven hundred and sixty five patients were tested via comprehensive BRCA analysis (63 patients also had BART analysis) and of those only 7% (55) had deleterious mutations. Only 3% (24) had mutations in BRCA1 gene, and 29 patients had deleterious mutations in BRCA2. Of the 63 patients who underwent BART only 3% (2) had large deletions in BRCA1 gene. Two hundred and seventy three patients were tested for the three known Ashkenazi mutations and 20% (57) had deleterious mutations 10% (28) in BRCA1 gene and 10% (29) in BRCA 2. Ninety four patients were tested for known family mutations with single site analysis and there were (57%) 54 had deleterious mutations 27% (26) in BRCA 1 gene and 29% (28) in BRCA 2. Referring source was: self 283 (25%), GYN 430 (38%), surgeon 283 (25%), PCP 136 (12%) cases. Conclusions:

Single site testing of a known mutation costs ∼ 400$ and in 94 patients (8%) gave rapid information about cancer risk. Of these 27% (26) unaffected individuals were identified as carrying deleterious mutations and 73% (68) individuals found out their cancer risk was average. The yield of testing by comprehensive BRCA analysis was 7%, M3 panel detected 20% deleterious mutation and single site analysis for known familial mutations had the lower cost and higher yield of 57%. Primary care physicians identified only 12% of patients with high risk for hereditary cancer syndromes.

Discussion:

Although family history is the cornerstone of high-risk patient referral to GS, primary care physicians referred only 12% of all patients at risk for HBOC. Attention to family history and increased public awareness of hereditary risk are effective means of identifying at risk populations for referral for GS. The yield of mutation detection is highest and cost effective in families with known mutations. Our yield of 57% detection in families with known mutations is likely an indication that not all family members at risk seek genetic counseling or are referred at the same center.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-10-05.

Strand scission in DNA induced by 5-hydroxytryptamine (serotonin) in the presence of copper ions

It has been proposed that considerable DNA damage may be caused by endogenous metabolites produced during the body's normal metabolic processes. Several metabolites including L-3,4-dihydroxyphenylalanine and dopamine have been previously shown to lead to oxidative DNA breakage in the presence of copper ions. 5-hydroxytryptamine or serotonin is an important neurotransmitter in brain and spinal cord and is involved in the control of sleep and consciousness, aggression and mood. In this paper we show that serotonin is also capable of causing strand cleavage in DNA in the presence of Cu(II) through an oxidative mechanism. Serotonin reduces Cu(II) to Cu(I) which is accompanied by the generation of hydroxyl radical. Spectroscopic data indicate that serotonin is able to bind to DNA and copper ions. Relative DNA cleavage efficiency and copper binding ability of serotonin and structurally related molecules tryptophan and melatonin indicates that the phenolic group in serotonin is required for strand cleavage activity.

Complexes involving gossypol, DNA and Cu(II)

Gossypol, a polyphenolic binaphthyl dialdehyde found in cotton seeds, is a dietary mutagen and a potential male contraceptive. We have earlier shown that in the presence of Cu(II) gossypol causes strand breakage in double stranded DNA and that active oxygen species are involved in this reaction. In this paper we present experiments to suggest that gossypol may be oxidised by Cu(II) to a gossypol radical that may directly react with DNA. Changes in absorption spectrum and fluorescence emission spectrum of gossypol indicated that it binds to both double stranded and single stranded DNA. Gossypol and Cu(II) were shown to form a charge transfer complex that decayed in an oxygen independent reaction. The rate of DNA degradation by gossypol-Cu(II) complex was found to be the same both in the presence and absence of molecular oxygen.

Strand scission in DNA by gossypol and Cu(II): role of Cu(I) and oxygen-free radicals

Gossypol, a polyphenolic binaphthyl dialdehyde found in cotton seeds, is a dietary mutagen and a potential male contraceptive. In the presence of Cu(II), gossypol caused breakage of supercoiled plasmid pBR322 DNA. The products were relaxed circles or a mixture of these and linear molecules. Other metal ions tested [Ni(II), Co(II), Mn(II), and Fe(II)] were ineffective or less effective in the DNA breakage reaction. In the case of gossypol-Cu(II) mediated cleavage, Cu(I) was shown to be an essential intermediate by using the Cu(I) sequestering reagent bathocuproine. By using job plots, it was established that in the absence of DNA, eight Cu(II) ions can be reduced by one gossypol molecule. The involvement of active oxygen species, such as singlet oxygen and H2O2, was established by the inhibition of DNA breakage by catalase and by sodium azide. It was further shown that gossypol is capable of directly producing H2O2.