BSImp: imputing partially observed methylation patterns for evaluating methylation heterogeneity

DNA methylation is one of the most studied epigenetic modifications that has applications ranging from transcriptional regulation to aging, and can be assessed by bisulfite sequencing (BS-seq) at single base-pair resolution. The permutations of methylation statuses at bisulfite converted reads reflect the methylation patterns of individual cells. These patterns at specific genomic locations are sought to be indicative of cellular heterogeneity within a cellular population, which are predictive of developments and diseases; therefore, methylation heterogeneity has potentials in early detection of these changes. Computational methods have been developed to assess methylation heterogeneity using methylation patterns formed by four CpGs, but the nature of shotgun sequencing often give partially observed patterns, which makes very limited data available for downstream analysis. While many programs are developed to impute methylation levels genomewide, currently there is only one method developed for recovering partially observed methylation patterns; however, the program needs lots of data to train and cannot be used directly; therefore, we developed a probabilistic-based imputation method that uses information from neighbouring sites to recover partially observed methylation patterns speedily. It is demonstrated to allow for the evaluation of methylation heterogeneity at three times more regions genome-wide with high accuracy for data with moderate depth. To make it more user-friendly we also provide a computational pipeline for genome-screening, which can be used in both evaluating methylation levels and profiling methylation patterns genomewide for all cytosine contexts, which is the first of its kind. Our method allows for accurate estimation of methylation levels and makes evaluating methylation heterogeneity available for much more data with reasonable coverage, which has important implications in using methylation heterogeneity for monitoring changes within the cellular populations that were impossible to detect for the assessment of development and diseases.

Transcriptional Responses of Flavin-Containing Monooxygenase Genes in Scallops Exposed to PST-Producing Dinoflagellates Implying Their Involvements in Detoxification

Flavin-containing monooxygenase (FMO) is one of the most prominent xenobiotic metabolic enzymes. It can catalyze the conversion of heteroatom-containing chemicals to polar, readily excretable metabolites and is considered an efficient detoxification system for xenobiotics. Bivalves can accumulate paralytic shellfish toxins (PSTs) produced by dinoflagellates, especially during outbreaks of harmful algal blooms. Exploring FMO genes in bivalves may contribute to a better understanding of the adaptation of these species and the mechanisms of PSTs bioavailability. Therefore, through genome screening, we examined the expansion of FMO genes in two scallops (Patinopecten yessoensis and Chlamys farreri) and found a new subfamily (FMO_like). Our expression analyses revealed that, in both scallops, members of the FMO_N-oxide and FMO_like subfamilies were mainly expressed from the D-stage larvae to juveniles, whereas the FMO_GS-OX subfamily genes were mainly expressed at and prior to the trochophore stage. In adult organs, higher expressions of FMOs were observed in the kidney and hepatopancreas than in other organs. After exposure to PST-producing algae, expression changes in FMOs occurred in hepatopancreas and kidney of both scallops, with more members being up-regulated in hepatopancreas than in kidney for Alexandrium catenella exposure, while more up-regulated FMOs were found in kidney than in hepatopancreas of C. farreri exposed to A. minutum. Our findings suggest the adaptive functional diversity of scallop FMO genes in coping with the toxicity of PST-producing algae.

Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography–Ion Mobility Mass Spectrometry

Marine Thaumarchaeota (formerly known as the marine group I archaea) have received much research interest in recent years since these chemolithoautotrophic organisms are abundant in the subsurface ocean and oxidize ammonium to nitrite, which makes them a major contributor to the marine carbon and nitrogen cycles. However, few studies have investigated the chemical composition of their exometabolome and their contributions to the pool of dissolved organic matter (DOM) in seawater. This study exploits the recent advances in ion mobility mass spectrometry (IM-MS) and integrates this instrumental capability with bioinformatics to reassess the exometabolome of a model ammonia-oxidizing archaeon, Nitrosopumilus maritimus strain SCM1. Our method has several advantages over the conventional approach using an Orbitrap or ion cyclotron resonance mass analyzer and allows assignments or annotations of spectral features to known metabolites confidently and indiscriminately, as well as distinction of biological molecules from background organics. Consistent with the results of a previous report, the SPE-extracted exometabolome of N. maritimus is dominated by biologically active nitrogen-containing metabolites, in addition to peptides secreted extracellularly. Cobalamin and associated intermediates, including α-ribazole and α-ribazole 5′-phosphate, are major components of the SPE-extracted exometabolome of N. maritimus. This supports the proposition that Thaumarchaeota have the capacity of de novo biosynthesizing cobalamin. Other biologically significant metabolites, such as agmatidine and medicagenate, predicted by genome screening are also detected, which indicates that Thaumarchaeota have remarkable metabolic potentials, underlining their importance in driving elemental cycles critical to biological processes in the ocean.

Ethical issues of genome screening: review

Полногеномное и полноэкзомное секвенирование имеет общепризнанную клиническую значимость для диагностики орфанных заболеваний. Вследствие развития технологии секвенирования и последующего снижения затрат на тестирование, данные методы все чаще используются не только в клинических целях, но и в качестве инструмента скрининга здоровых индивидов. При проведении исследования по поводу подозрения на генетическое заболевание в семье и при тестировании здорового человека «по желанию» могут быть выявлены «случайные находки» с разной клинической значимостью. Однако в ряде профессиональных руководств появились рекомендации по систематическому поиску клинически значимых вторичных результатов - так называемому оппортунистическому скринингу. В соответствии с этим активно обсуждаются этические проблемы оппортунистического скрининга в контексте соразмерности пользы и рисков для тестируемого человека, информированного согласия и защиты его автономии и справедливости. Этические проблемы в связи с клиническим использованием анализа генома в Российской Федерации мало изучены. В данной обзорной статье описываются упомянутые проблемы и на основе международного опыта. Whole-genome and whole-exome sequencing have universally recognized clinical importance for the diagnosis of orphan diseases. Due to the development of sequencing technology and the subsequent reduction in diagnostic costs, these methods are increasingly used not only for clinical purposes, but also as a screening tool in healthy individuals. The study for suspected genetic disease in the family or testing a healthy person «optional» can be revealed «incidental findings» with different clinical significance. However, a number of professional guidelines recommend a systematic search for clinically significant secondary results - the so-called opportunistic screening. Accordingly, the ethical problems of opportunistic screening actively discussed, particularly in the context of the proportionality of the benefits and risks for the tested person, informed consent and the protection of autonomy and justice. Ethical problems of genetic counseling in modern economic and technical aspects in the Russian Federation have been little studied. This review article describes the problems mentioned, provides international experience and recommendations for solving the aforementioned problems.

Whole Genome Interpretation for a Family of Five

Although best practices have emerged on how to analyse and interpret personal genomes, the utility of whole genome screening remains underdeveloped. A large amount of information can be gathered from various types of analyses via whole genome sequencing including pathogenicity screening, genetic risk scoring, fitness, nutrition, and pharmacogenomic analysis. We recognize different levels of confidence when assessing the validity of genetic markers and apply rigorous standards for evaluation of phenotype associations. We illustrate the application of this approach on a family of five. By applying analyses of whole genomes from different methodological perspectives, we are able to build a more comprehensive picture to assist decision making in preventative healthcare and well-being management. Our interpretation and reporting outputs provide input for a clinician to develop a healthcare plan for the individual, based on genetic and other healthcare data.

SL-1 Activity on Nationwide Cancer Genome Screening Project for Advanced Solid Tumors; SCRUM-Japan GI-/MONSTAR-SCREEN

Advances in precision oncology have made genotyping mandatory for most advanced solid tumors to ensure proper therapy selection. However, the innovations remains limited by the realities of patient identification-actionable targets are present in only a small fraction of patients. We initiated a nationwide cancer genome screening project, SCRUM-Japan GI- (from 2015 to 19)/MONSTAR-SCREEN (since 2019) with the purpose of matching patients with interventional IND trials. We revealed requirement for tissue samples hampers recruitment, and genotyping using archival tumor samples provides information only at a single spatial and temporal point and fail to detect chronological tumor evolution and intratumoral heterogeneity, both of which are obstacles for proper therapy selection. We also demonstrated circulating tumor DNA (ctDNA) analysis using next-generation sequencing (NGS)-based methods have the potential of ctDNA analysis for genomic profiling as an alternative for tissue genotyping. Recently, gut microbiome has the promise in predictive value of therapy. Serial analyses with ctDNA and microbiome at pre- and post- cancer therapies are ongoing. Updated results will be presented.

Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen

A major bottleneck in nanocarrier and macromolecule development for therapeutic delivery is our limited understanding of the processes involved in their uptake into target cells. This includes their active interactions with membrane transporters that co-ordinate cellular uptake and processing. Current strategies to elucidate the mechanism of uptake, such as painstaking manipulation of individual effectors with pharmacological inhibitors or specific genetic knockdowns, are limited in scope and biased towards previously studied pathways or the intuition of the investigators. Furthermore, each of these approaches present significant off-target effects, clouding the outcomes. We set out to develop and examine an unbiased whole-genome screening approach using pooled CRISPR/Cas9 libraries for its ability to provide a robust and rapid approach to identify novel effectors of material uptake. Enabling this, we developed a methodology termed fast-library of inserts (FLI)-seq for library preparation and quantitative readout of pooled screens that shows improved technical reproducibility and is easier to perform than existing methods. In this proof-of-concept study we use FLI-seq to identify a solute carrier protein family member, SLC18B1, as a transporter for polymeric micellar nanoparticles, confirming the viability for this approach to yield novel insights into uptake mechanisms.