Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy.

Funder: Cancer Research UKSingle-cell RNA-seq reveals the role of pathogenic cell populations in development and progression of chronic diseases. In order to expand our knowledge on cellular heterogeneity, we have developed a single-nucleus RNA-seq2 method tailored for the comprehensive analysis of the nuclear transcriptome from frozen tissues, allowing the dissection of all cell types present in the liver, regardless of cell size or cellular fragility. We use this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy, and have discovered that ploidy states are associated with different metabolic potential, and gene expression in tetraploid mononucleated hepatocytes is conditioned by their position within the hepatic lobule. Our work reveals a remarkable crosstalk between gene dosage and spatial distribution of hepatocytes

Prostate cancer detection through unbiased capture of methylated cell-free DNA

Funding: Cancer Research UK, CRUK Career Development Fellowship, University of Cambridge W.D. Armstrong Trust Fund, John Black Prostate Cancer Foundation Young Investigator Award. This research was also supported by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014).Prostate cancer screening using prostate-specific antigen (PSA) has been shown to reduce mortality but with substantial overdiagnosis, leading to unnecessary biopsies. The identification of a highly specific biomarker using liquid biopsies, represents an unmet need in the diagnostic pathway for prostate cancer. In this study, we employed a method that enriches for methylated cell-free DNA fragments coupled with a machine learning algorithm which enabled the detection of metastatic and localized cancers with AUCs of 0.96 and 0.74, respectively. The model also detected 51.8% (14/27) of localized and 88.7% (79/89) of patients with metastatic cancer in an external dataset. Furthermore, we show that the differentially methylated regions reflect epigenetic and transcriptomic changes at the tissue level. Notably, these regions are significantly enriched for biologically relevant pathways associated with the regulation of cellular proliferation and TGF-beta signaling. This demonstrates the potential of circulating tumor DNA methylation for prostate cancer detection and prognostication.Peer reviewe

THE ELDERLY PROGNOSTIC INDEX (EPI) PREDICTS EARLY MORTALITY IN OLDER PATIENTS WITH DLBCL. A SUBSTUDY OF THE ELDERLY PROJECT BY THE FONDAZIONE ITALIANA LINFOMI (FIL)

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How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort.

During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic data set from Switzerland, comprising more than 143k sequences. We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage-dependent-something that is unknown at the time of sequencing-and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.IMPORTANCESwitzerland had one of the most comprehensive genomic surveillance systems during the COVID-19 pandemic. Such programs need to strike a balance between societal benefits and program costs. Our study aims to answer the question: How would surveillance outcomes have changed had we sequenced less? We find that some outcomes but also certain viral lineages are more affected than others by sequencing less. However, sequencing to around a third of the original effort still captured many important outcomes for the variants of concern such as their first detection but affected more strongly other measures like the detection of first transmission clusters for some lineages. Our work highlights the importance of setting predefined targets for a national genomic surveillance program based on which sequencing effort should be determined. Additionally, the use of a centralized surveillance platform facilitates aggregating data on a national level for rapid public health responses as well as post-analyses

A statistical framework for assessing pharmacological responses and biomarkers using uncertainty estimates

High-throughput testing of drugs across molecular-characterised cell lines can identify candidate treatments and discover biomarkers. However, the cells’ response to a drug is typically quantified by a summary statistic from a best-fit dose-response curve, whilst neglecting the uncertainty of the curve fit and the potential variability in the raw readouts. Here, we model the experimental variance using Gaussian Processes, and subsequently, leverage uncertainty estimates to identify associated biomarkers with a new Bayesian framework. Applied to in vitro screening data on 265 compounds across 1074 cancer cell lines, our models identified 24 clinically established drug-response biomarkers, and provided evidence for six novel biomarkers by accounting for association with low uncertainty. We validated our uncertainty estimates with an additional drug screen of 26 drugs, 10 cell lines with 8 to 9 replicates. Our method is applicable to any dose-response data without replicates, and improves biomarker discovery for precision medicine

Analyse de la prescription, de l'efficacité et de la tolérance des inhibiteurs de l'acétylcholinestérase dans la maladie d'Alzheimer

Résumé En suisse, trois inhibiteurs de l'acétylcholinestérase sont disponibles pour le traitement symptomatique de la maladie d'Alzheimer légère à modérée. Il s'agit du donépézil (Aricept®), de la galantamine (Reminyl®) et de la rivastigmine (Exelon®). Leur prescription est maintenant largement répandue, sur la base d'études ayant confirmé leur efficacité et leur tolérance. Le but de la présente étude a été d'évaluer si de tels résultats se retrouvent dans notre hôpital. Nous avons analysé les dossiers hospitaliers et interviewé les proches et les médecins traitants de 103 patients chez qui un tel traitement a été proposé ou initié dans notre centre de gériatrie, entre janvier 2001 et juillet 2003. Nos résultats montrent que le donépézil fut la molécule la plus fréquemment prescrite (50,6% des cas), suivie par la galantamine (44,2%). Après une année de traitement, seulement 54% des patients (n = 51) prenaient encore leur traitement. Une faible majorité des patients (52% selon les médecins traitants, 62% selon les proches) a favorablement répondu au traitement. Nos résultats confirment l'efficacité de ces molécules mais dans une proportion moindre que celle publiée dans la littérature et sans dégager de supériorité d'une molécule sur une autre. Sur le long terme (une année), le pourcentage d'abandon a été élevé et supérieur aux données de la littérature. Nous estimons que le grand âge des patients de notre collectif explique en partie cette discordance de résultats

Dreaming during COVID-19: The effects of a world trauma

On March 11, 2020, the World Health Organization (WHO) declared a state of health emergency affecting the entire world population. Given the serious practical and psychological difficulties and complications that have been experienced during this period, many scholars have created hypothesis, as a consequence, an increased possibility of developing post-traumatic stress disorder (PTSD) within the general population with significant implications for one's dream activity. Participants in the study were recruited via the instant messaging application 'WhatsApp' for a period of 14 days. The study consisted of three phases: the first phase provided information on the purpose of the research and how to carry it out; in the second phase, each participant, using the Bionian model of dream experience as a focus, was asked to write down dreams, emotions and free connections/associations related to the dream. At the end of the collection, the texts obtained were analysed by means of a qualitative analysis performed with the aid of the MAXQDA software. The study confirms the computational and exploratory analysis of the text carried out in the research of Pesonen et al. (2020), finding also in our sample the presence of the hypothesized clusters going to explain the manifestation of imagery related to COVID-19 also within the dream activity. To confirm this, the nightmare of participant number 6 of the study is reported. The following qualitative research has offered an insight into the traumatic nature of the COVID-19 pandemic, showing how many unmetabolized 'daytime elements' have been reproposed in the dream scenario, recalling the symptomatology of PTSD through the presence of distressing content that affect the quality of sleep and the daily life of the individual

Analyse de la prescription, de l'efficacité et de la tolérance des inhibiteurs de l'acétylcholinestérase dans la maladie d'Alzheimer

En Suisse, trois inhibiteurs de l'acétylcholinestérase sont disponibles pour le traitement symptomatique de la maladie d'Alzheimer légère à modérée. Il s'agit du donépézil (Aricept®), de la galantamine (Reminyl®) et de la rivastigmine (Exelon®). Leur prescription est maintenant largement répandue, sur la base d'études ayant confirmé leur efficacité et leur tolérance. Le but de la présente étude a été d'évaluer si de tels résultats se retrouvent dans notre hôpital. Nous avons analysé les dossiers hospitaliers et interviewé les proches et les médecins traitants de 103 patients chez qui un tel traitement a été proposé ou initié dans notre centre de gériatrie, entre janvier 2001 et juillet 2003. Nos résultats montrent que le donépézil fut la molécule la plus fréquemment prescrite (50,6% des cas), suivie par la galantamine (44,2%). Après une année de traitement, seulement 54% des patients (n = 51) prenaient encore leur traitement. Une faible majorité des patients (52% selon les médecins traitants, 62% selon les proches) a favorablement répondu au traitement. Nos résultats confirment l'efficacité de ces molécules mais dans une proportion moindre que celle publiée dans la littérature et sans dégager de supériorité d'une molécule sur une autre. Sur le long terme (une année), le pourcentage d'abandon a été élevé et supérieur aux données de la littérature. Nous estimons que le grand âge des patients de notre collectif explique en partie cette discordance de résultats