Machine learning-based prediction of breast cancer growth rate in-vivo

BackgroundDetermining the rate of breast cancer (BC) growth in vivo, which can predict prognosis, has remained elusive despite its relevance for treatment, screening recommendations and medicolegal practice. We developed a model that predicts the rate of in vivo tumour growth using a unique study cohort of BC patients who had two serial mammograms wherein the tumour, visible in the diagnostic mammogram, was missed in the first screen.MethodsA serial mammography-derived in vivo growth rate (SM-INVIGOR) index was developed using tumour volumes from two serial mammograms and time interval between measurements. We then developed a machine learning-based surrogate model called Surr-INVIGOR using routinely assessed biomarkers to predict in vivo rate of tumour growth and extend the utility of this approach to a larger patient population. Surr-INVIGOR was validated using an independent cohort.ResultsSM-INVIGOR stratified discovery cohort patients into fast-growing versus slow-growing tumour subgroups, wherein patients with fast-growing tumours experienced poorer BC-specific survival. Our clinically relevant Surr-INVIGOR stratified tumours in the discovery cohort and was concordant with SM-INVIGOR. In the validation cohort, Surr-INVIGOR uncovered significant survival differences between patients with fast-growing and slow-growing tumours.ConclusionOur Surr-INVIGOR model predicts in vivo BC growth rate during the pre-diagnostic stage and offers several useful applications

Epigenetic mechanisms in virus-induced tumorigenesis

About 15–20% of human cancers worldwide have viral etiology. Emerging data clearly indicate that several human DNA and RNA viruses, such as human papillomavirus, Epstein–Barr virus, Kaposi’s sarcoma-associated herpesvirus, hepatitis B virus, hepatitis C virus, and human T-cell lymphotropic virus, contribute to cancer development. Human tumor-associated viruses have evolved multiple molecular mechanisms to disrupt specific cellular pathways to facilitate aberrant replication. Although oncogenic viruses belong to different families, their strategies in human cancer development show many similarities and involve viral-encoded oncoproteins targeting the key cellular proteins that regulate cell growth. Recent studies show that virus and host interactions also occur at the epigenetic level. In this review, we summarize the published information related to the interactions between viral proteins and epigenetic machinery which lead to alterations in the epigenetic landscape of the cell contributing to carcinogenesis

Exploring the views of being a proxy from the perspective of unpaid carers and paid carers: developing a proxy version of the Adult Social Care Outcomes Toolkit (ASCOT)

Background: Outcomes-based policy and administration of public services present a compelling argument for the value of outcomes data. However, there are a number of challenges inherent in collecting these data from people who are unable to complete a paper-based survey or interview due to cognitive or communication impairments. In this paper, we explore the views of being a proxy from the perspective of unpaid carers and paid carers who may be asked to act as a proxy on behalf of the person(s) they care for. We consider the key issues that need to be addressed when adapting an instrument designed to measure social care outcomes, the Adult Social Care Outcomes Tool (ASCOT), into a proxy-report tool. Methods: Participants took part in either a focus group (35 paid carers in eight focus groups), or a one-to-one interview (eight unpaid carers). All participants were recruited via carer organisations and care providers. Transcripts, field notes and audio data collected during focus groups and interviews were analysed using a thematic framework approach. Results: Participants agreed that any person acting as a proxy would need to be very familiar with the care recipient, as well as their needs and care provision. A number of provisions for proxy respondents were proposed to improve face validity and acceptability of completing a questionnaire by proxy, and to ensure that any potential bias is reduced in the design of the questionnaire. These included: providing two sets of response options for each proxy perspective (the proxy themselves and the proxy view of how they think the care recipient would respond); a comments box to help people explain why they have selected a given response option (especially where these indicate unmet need); and providing clear guidance for the proxy respondent on how they should complete the questionnaire. Conclusions: This study has shown some of the challenges involved in assessing outcomes by proxy and explored some potential ways these can be mitigated. The findings highlight the benefits of developing and testing proxy measures in a robust way to widen participation in social care research

The mechanism of DNA unwinding by the eukaryotic replicative helicase

Accurate DNA replication is tightly regulated in eukaryotes to ensure genome stability during cell division and is performed by the multi-protein replisome. At the core an AAA+ hetero-hexameric complex, Mcm2-7, together with GINS and Cdc45 form the active replicative helicase Cdc45/Mcm2-7/GINS (CMG). It is not clear how this replicative ring helicase translocates on, and unwinds, DNA. We measure real-time dynamics of purified recombinant Drosophila melanogaster CMG unwinding DNA with single-molecule magnetic tweezers. Our data demonstrates that CMG exhibits a biased random walk, not the expected unidirectional motion. Through building a kinetic model we find CMG may enter up to three paused states rather than unwinding, and should these be prevented, in vivo fork rates would be recovered in vitro. We propose a mechanism in which CMG couples ATP hydrolysis to unwinding by acting as a lazy Brownian ratchet, thus providing quantitative understanding of the central process in eukaryotic DNA replication