While much attention has gone towards ethical, legal, and social implications of direct-to-consumer genetic testing over the past decades, the rise of new forms of consumer omics has largely escaped scrutiny. In this paper, we analyze the product descriptions, promotional messages, terms of service, and privacy policies of five epigenetic and seven microbiomic testing companies. The advent of such tests online represents a significant shift in consumer omics, from a focus on inherited molecules with genetic tests, to broader (...) interest for information about the lives of individuals, such as chronological and biological age, exposures, and lifestyle. Building on previous literature about direct-to-consumer genetic testing, and taking this shift into account, we identify limitations, gaps and inconsistencies in current practices and policies of the new companies. Best practice standards and regulations applicable across different omic sample and data types is a necessary first step in the promotion of responsible consumer omics. (shrink)

Funding organizations around the world are adopting open science policies, resulting in a pressing need for open science programs. In response to the 2011 decadal survey, NASA sought to expand and accelerate omics research, releasing its GeneLab Strategic Plan in 2014. GeneLab is an open science data repository and analysis portal for spaceflight and space-relevant omics data. GeneLab’s output has been outstanding, but its full potential as a way to transform space biology has not yet been achieved. NASA (...) should pursue the development of GeneLab as an open science platorm in earnest. (shrink)

We review recent multi‐omics analyses of the coral heat stress response to explore the generality of the Oxidative Theory of Coral Bleaching (OTCB), which posits that algal symbiont release is the final act of defense by the coral host to survive alga‐derived oxidative stress. The OTCB is particularly relevant given that ocean warming, which is accelerating under climate change, has proven devastating for corals, leading to the bleaching phenotype and widespread reef loss. Multi‐omics results, in combination with other (...) data, such as genome‐wide association studies, support the idea that coral bleaching is a multifactorial response that reflects a wide array of causes and effects and is population‐specific under most conditions, with coral ploidy and genotype being critical to bleaching sensitivity. This perspective leverages the location, algal and prokaryotic microbiome, and host genotype‐specific aspects of coral resilience to promote a new “personal genomics” approach to coral conservation, analogous to that used in human health. (shrink)

The Diagnostic and Statistical Manual of Mental Disorders (DSM) is universally acknowledged as the prominent reference textbook for the diagnosis and assessment of psychiatric diseases. However, since the publication of its first version in 1952, controversies have been raised concerning its reliability and validity and the need for other novel clinical tools has emerged. Currently the DSM is in its fourth edition and a new fifth edition is expected for release in 2013, in an intense intellectual debate and in a (...) call for new proposals. (shrink)

Coral reef degradation has captured global attention from governments, conservationists, and researchers, who are making concerted efforts to develop sustainable solutions to support reef resilience in the face of environmental degradation. The goal is to empower local community efforts for effective marine resource management. However, one of the major barriers to coral conservation is the lack of timely and affordable population‐level health data, which can delay effective management responses. Although progress has been made in understanding the molecular basis of coral (...) health outcomes, more translational work is needed to develop cost‐effective, point‐of‐care (POC) diagnostic tools for real‐time monitoring. This review assesses the current state of translational omics‐based research for coral health monitoring, focusing on highlighting key gaps and actionable next steps to guide the implementation of effective, field‐ready tools for monitoring coral disease, reproduction, and thermal stress. These advancements can be used to advance urgent conservation needs and promote reef management by local communities. (shrink)

Whether due to simplicity or hypocrisy, the question of access to patient data for biomedical research is widely seen in the public discourse only from the angle of patient privacy. At the same time, the desire to live and to live without disability is of much higher value to the patients. This goal can only be achieved by extracting research insight from patient data in addition to working on model organisms, something that is well understood by many patients. Yet, most (...) biomedical researchers working outside of clinics and hospitals are denied access to patient records when, at the same time, clinicians who guard the patient data are not optimally prepared for the data’s analysis. Medical data collection is a time- and cost-intensive process that is most of all tedious, with few elements of intellectual and emotional satisfaction on its own. In this process, clinicians and bioinformaticians, each group with their own interests, have to join forces with the goal to generate medical data sets both from clinical trials and from routinely collected electronic health records that are, as much as possible, free from errors and obvious inconsistencies. The data cleansing effort as we have learned during curation of Singaporean clinical trial data is not a trivial task. The introduction of omics and sophisticated imaging modalities into clinical practice that are only partially interpreted in terms of diagnosis and therapy with today’s level of knowledge warrant the creation of clinical databases with full patient history. This opens up opportunities for re-analyses and cross-trial studies at future time points with more sophisticated analyses of the same data, the collection of which is very expensive. (shrink)

While the accumulation and increased circulation of genomic data have captured much attention over the past decade, privacy risks raised by the diversification and integration of omics have been la...

As part of a (bio)colonial project, the biological information of Indigenous Peoples has historically been under scientific scrutiny, with very limited benefits for communities and donors. Negative past experiences have contributed to further exclude Indigenous communities from novel developments in the field of omics research. Over the past decade, new guidelines, reflections, and projects of genetic research with Indigenous Peoples have flourished in Australia, providing opportunities to move the field into a place of respect and ethical relationships. This review (...) explores the ethical and cultural implications of the use of biological samples from Indigenous communities in biomedical research. A structured framework outlining emerging topics of interest for the development of respectful omics research partnerships with Indigenous Australians is presented. This paper highlights aspects related to Indigenous governance, community and individual consent, respectful handling of biological samples, data management, and communication in order to protect Indigenous interests and rights and to promote communities’ autonomy. (shrink)

The framework proposed by Dupras and Bunnik was developed in response to their recognition that standard regulations are increasingly inadequate to address the complex privacy issues created by the...

Many of milk's functional molecules could not be discovered until the right concordance of novel separation and analytical technologies were developed and applied. Many health-promoting components still await discovery due to technical challenges in their identification, isolation and testing. As new analytical technologies are assembled, new functional milk molecules will be discovered. Bovine milk is a source of a wide array of known bioactive compounds from a variety of molecular classes, including free glycans, lipids, glycolipids, peptides, proteins, glycoproteins, stem cells (...) and microRNA. Because milk is such a complex mixture, when analyzed without fractionation or purification, many components mask the analytical signal of others, so some components cannot be detected. Modern analytics allow for the discovery and characterization of hundreds of novel milk compounds with high-resolution and high-accuracy. Liquid chromatography paired with electrospray ionization allows the separation of peptides, glycans and glycolipids for improved mass spectrometric detection. Target proteins and glycoproteins can now be purified from intact milk or other dairy streams by chromatography in order to better characterize these proteins for new bioactivities. The combination of advanced analytics with the new engineering capabilities will allow for high molecular resolution and separation techniques that can be scaled-up to semi-industrial and industrial scale for translation of lab-based discoveries. Bioguided analysis and design of dairy processing side streams will result in the transformation of waste into isolated functional ingredients to add value to dietary products. (shrink)

Dupras and Bunnik’s strong statement against the normative approach of genetic exceptionalism, which can no longer be justified in the midst of multi-omic research, is of great importance fofor sound ethical reasoning about omic data. Furthermore, the authors’ explicit critique of a sole focus on genomics in normative considerations about data security and especially their nuanced depiction of sensitivity, (re)identification risks and discriminatory potential associated with epigenomic data in research and in private, commercial so-called “direct- to-consumer” epigenetic testing (as specified (...) in earlier works) might be a stepping stone for broadening the scope of normative discussions in other gene-ethics debates. Debates about therapeutic applications of tools such as CRISPR/Cas for example currently focus primarily on the genome and not on potential applications and ethical consequences of epigenome editing. Overcoming an exceptional focus on genomics and genetics by including the role of epigenomics into a primarily genome-centered normative debate is necessary to accommodate evolving biomedical fields of research. By means of conceptual clarification especially of the term “multi-omic contextualism” (Dupras and Bunnik 2021, 49) this commentary on Dupras, C., and E. M. Bunnik, "Toward a framework for assessing privacy risks in multi-omic research and databases" (The American Journal of Bioethics 2021 21 (12): 46–64. doi:10.1080/15265161.2020.1863516) argues that Dupras and Bunnik’s framework might currently be rather exceptional than contextual especially because extrinsic data properties are not primarily considered and that the framework is di-omic (genomic-epigenomic) rather than multi-omic because the meaning of multi-omics within the article appears to imply contextual factors. The highly relevant normative ideas on the problem of (re)identification risks and sensitivity of other than genomic, especially epigenomic, data presented by the authors are nevertheless, as Dupras and Bunnik assume (2021), likely to be relevant even beyond omics, for example, for imaging data, and it might thus be evaluated in future research whether multi-omic exceptionalism/contextualism could present a novel form of biological reductionism (Waggoner and Uller, "Epigenetic determinism in science and society," New Genetics and Society 2015 34 (2):177–95. doi: 10.1080/14636778.2015.10330522015), especially if primarily focused on the analysis of genomics and epigenomics. Dupras and Bunnik’s framework might then be made even stronger by making it broader. (shrink)

Background There is growing consensus in favor of returning individual specific research results that are clinically actionable, valid, and reliable. However, deciding what and how research results should be returned remains a challenge. Researchers are key stakeholders in return of results decision-making and implementation. Multi-omics data contains medically relevant findings that could be considered for return. We sought to understand researchers' views regarding the potential for return of results for multi-omics data from a large, national consortium generating multi- (...) class='Hi'>omics data. Methods Researchers from the Molecular Transducers of Physical Activity Consortium (MoTrPAC) were recruited for in-depth semi-structured interviews. To assess understanding of potential clinical utility for types of data collected and attitudes towards return of results in multi-omic clinical studies, we devised an interview guide focusing on types of results generated in the study for hypothetical return based on review of the literature and professional expertise of team members. The semi-structured interviews were recorded, transcribed verbatim and co-coded. Thematic trends were identified for reporting. Results We interviewed a total of 16 individuals representative of 11 sites and 6 research roles across MoTrPAC. Many respondents expressed positive attitudes regarding hypothetical multi-omics results return, citing participant rights to their data and perception of minimal harm. Ethical and logistical concerns around the return of multi-omics results were raised, and they often mirrored those in the published literature for genomic return of results including: uncertain clinical validity, a lack of expertise to communicate results, and an unclear obligation regarding whether to return multi-omics results. With the exception of privacy concerns, respondents were able to give examples within multi-omics of how each point was relevant. Further, researchers called for more guidance from funding agencies and increased researcher education regarding return of results. Conclusion Overall, researchers expressed positive attitudes toward multi-omic return of results in principle, particularly if medically actionable. However, competing ethical considerations, logistical constraints, and need for more external guidance were raised as key implementation concerns. Future studies should consider views and experiences of other relevant stakeholders, specifically clinical genomics professionals and study participants, regarding the clinical utility of multi-omics information and multi-omics results return. (shrink)

The aim of this article is to present how to build a community consisting of the sighted people and of the blind. Dom Bożego Narodzenia in Niepołomice in Poland is an example of such a community, as its members – the sighted people and the blind – form a community modelled on the family. The community was created out of the religious inspiration and its building is in accordance to the Christian values. In order to realise the aim of this (...) article, the author interviewed 10 community members (both the sighted and the blind). The received answers were subjected to quality research. The article presents the teaching of the Catholic Church which concerns the community life of people with disabilities and those fully able-bodied. The next step was to present the characteristics of the residents of the nursing home in Niepołomice. Building the community was presented in two dimensions: vertical and horizontal. The vertical dimension is connected with creating the community with God, and it is inspired by the Christian values in building the family relations. The horizontal dimension is connected with building the human community in its everyday life and in celebrating. Contribution: The research undertaken on the community well-being of people with visual disabilities has shown that such people are able to participate subjectively in building a home community similar to a family with sighted people. (shrink)

Genetic epidemiology is a rapidly advancing field due to the recent availability of large amounts of omics data. In recent years, it has become possible to obtain omics information at the single‐cell level, so genetic epidemiological models need to be updated to integrate with single‐cell expression data. In this perspective paper, we propose a cell population‐based framework for genetic epidemiology in the single‐cell era. In this framework, genetic diversity influences phenotypic diversity through the diversity of cell population profiles, (...) which are defined as high‐dimensional probability distributions of the state spaces of biomolecules of each omics layer. We discuss how biomolecular experimental measurement data can capture the different properties of this distribution. In particular, single‐cell data constitute a sample from this population distribution where only some coordinate values are observable. From a data analysis standpoint, we introduce methodology for feature extraction from cell population profiles. Finally, we discuss how this framework can be applied not only to genetic epidemiology but also to systems biology. (shrink)

In ‘Toward a Framework for Assessing Privacy Risks in Multi-Omic Research and Databases’ (Dupras and Bunnik 2021), we argued against the assessment of privacy risks and protection requirements base...

This paper argues that analyses of the ways in which Big Data has been enacted in other academic disciplines can provide us with concepts that will help understand the application of Big Data to social questions. We use examples drawn from our Science and Technology Studies analyses of -omic biology and high energy physics to demonstrate the utility of three theoretical concepts: primary and secondary inscriptions, crafted and found data, and the locus of legitimate interpretation. These help us to show (...) how the histories, organisational forms, and power dynamics of a field lead to different enactments of big data. The paper suggests that these concepts can be used to help us to understand the ways in which Big Data is being enacted in the domain of the social sciences, and to outline in general terms the ways in which this enactment might be different to that which we have observed in the ‘hard’ sciences. We contend that the locus of legitimate interpretation of Big Data biology and physics is tightly delineated, found within the disciplinary institutions and cultures of these disciplines. We suggest that when using Big Data to make knowledge claims about ‘the social’ the locus of legitimate interpretation is more diffuse, with knowledge claims that are treated as being credible made from other disciplines, or even by those outside academia entirely. (shrink)

Artificial intelligence (AI) strategies are revolutionizing genomics by extracting complex patterns that traditional statistical pipelines are likely to miss. This mini‐review aims to provide a concise overview of how AI is transforming major genomic technologies including variant calling, gene expression analysis, single‐cell transcriptomics, CRISPR‐Cas9 optimization, and multi‐omics integration. In genome sequencing, machine learning variant callers greatly improve the accuracy and the rate at which single nucleotide and structural variants are called. In bulk RNA‐Seq, AI augmented quantification, denoising, and differential (...) expression modules complement the highly established STAR‐featureCounts‐DESeq2 pipeline, revealing subtle signals in big data sets. In single cell transcriptomics, deep learning approaches enhance batch correction, automate cell type annotation, and track developmental trajectories, hence clarifying cellular heterogeneity. AI‐assisted guide RNA design, outcome prediction, and nuclease engineering enable more efficient CRISPR‐Cas9 editing, reducing experimental cycles, and off‐target effects. Finally, integrated platforms that combine genomic, transcriptomic, epigenomic, proteomic, and metabolomic layers provide an integrative view of cellular regulation and disease mechanisms. The review also covers current limitations, sparsity of data, model bias, privacy, and the need for standardized benchmarks and offers future directions in the form of interpretable models, collaborative learning, and open science practices. Together, these developments render AI an indispensable partner to unravel genomic complexity and accelerate precision medicine applications. (shrink)

Several metabolites serve as substrates for histone modifications and communicate changes in the metabolic environment to the epigenome. Technologies such as metabolomics and proteomics have allowed us to reconstruct the interactions between metabolic pathways and histones. These technologies have shed light on how nutrient availability can have a dramatic effect on various histone modifications. This metabolism–epigenome cross talk plays a fundamental role in development, immune function, and diseases like cancer. Yet, major challenges remain in understanding the interactions between cellular metabolism (...) and the epigenome. How the levels and fluxes of various metabolites impact epigenetic marks is still unclear. Discussed herein are recent applications and the potential of systems biology methods such as flux tracing and metabolic modeling to address these challenges and to uncover new metabolic–epigenetic interactions. These systems approaches can ultimately help elucidate how nutrients shape the epigenome of microbes and mammalian cells. (shrink)

The conference explored an extraordinary diversity of aging strategies in organisms ranging from short‐lived species to “immortal” animals and plants. Research on the biological processes of aging is at the brink of a revolution with respect to our understanding of its underlying mechanisms as well as our ability to prevent and cure a wide variety of age‐related pathologies.

[Without a theorising], a man might as well go into a gravel-pit and count the pebbles and describe the colours. How odd it is that anyone should not see that all observation must be for or against some view if it is to be of any service!Recent years have seen a steady shift of funding programs in biomedical research towards data collection, analysis, and management and its computational analysis. A sizable majority of new major funding opportunity announcements call for assembling (...) large sample banks and databases of molecular profiles of diseases or for computational tools for analysis, display, and distribution of the data. Large consortium projects, such as the Cancer Genome Atlas, the UK Biobank (Allen... (shrink)

The first 1000 days of life, from conception to 2 years, are a critical window for the influence of environmental exposures on the assembly of the oral microbiome, which is the precursor to dental caries (decay), one of the most prevalent microbially induced disorders worldwide. While it is known that the human microbiome is susceptible to environmental exposures, there is limited understanding of the impact of prenatal and early childhood exposures on the oral microbiome trajectory and oral health. A barrier (...) has been the lack of technology to directly measure the foetal "exposome", which includes nutritional and toxic exposures crossing the placenta. Another barrier has been the lack of statistical methods to account for the high dimensional data generated by‐omic assays. Through identifying which early life exposures influence the oral microbiome and modify oral health, these findings can be translated into interventions to reduce dental decay prevalence. (shrink)

The advent of omic technologies and, more specifically, the progress made with specific second- and third-generation sequencing technologies, gives us the possibility of knowing the particular sequence of individual genomes at a relatively affordable cost. In the not too distant future, these sequencing technologies combined with specific functional analysis will be used, at a genomic level and with a much finer degree of detail than the old molecular diagnostic tests, to identify the diseases associated with each person’s genetic map. New (...) dilemmas in different contexts have emerged with the advent of these technologies. From a bioethical perspective, the problem is not rooted in detailed research on the human genome per se, but in the purpose that can be given to information derived from this type of scientific research, which could become a useful tool for selecting, rejecting and discriminating against persons, because they have a hereditary disease or the potential to develop specific diseases in the future. This article analyzes the relationship between the eugenic mentality, the concept of quality of life, and genomic molecular diagnosis, when applied to human embryos for the purpose of preventing their implantation. Such action threatens the very life and dignity of a human being in its early stages of development. (shrink)

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called “omic” techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe the taxonomic structure (...) of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the ‘omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel ‘omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

In the last decades, Systems Biology (including cancer research) has been driven by technology, statistical modelling and bioinformatics. In this paper we try to bring biological and philosophical thinking back. We thus aim at making diferent traditions of thought compatible: (a) causality in epidemiology and in philosophical theorizing—notably, the “sufcient-component-cause framework” and the “mark transmission” approach; (b) new acquisitions about disease pathogenesis, e.g. the “branched model” in cancer, and the role of biomarkers in this process; (c) the burgeoning of (...) class='Hi'>omics research, with a large number of “signals” and of associations that need to be interpreted. In the paper we summarize frst the current views on carcinogenesis, and then explore the relevance of current philosophical interpretations of “cancer causes”. We try to ofer a unifying framework to incorporate biomarkers and omic data into causal models, referring to a position called “evidential pluralism”. According to this view, causal reasoning is based on both “evidence of diference-making” (e.g. associations) and on “evidence of underlying biological mechanisms”. We conceptualize the way scientists detect and trace signals in terms of information transmission, which is a generalization of the mark transmission theory developed by philosopher Wesley Salmon. Our approach is capable of helping us conceptualize how heterogeneous factors such as micro and macro-biological and psycho-social—are causally linked. This is important not only to understand cancer etiology, but also to design public health policies that target the right causal factors at the macro-level. (shrink)

Omics Big Data underpins genetic information and its expression for precision medicine, thereby accelerating the discovery of disease mechanisms, drug targets, and drug development. It has a wide range of applications, including clinical genomics and pharmacogenomics. This chapter offers a concise overview of various types of omics, current trends, and characteristics of the resulting omics big data. It also explores the applications of these data in the context of rare diseases, tumors, chronic diseases, and infectious diseases, along (...) with the challenges of data sharing. The discussion primarily focuses on analyzing the ethical issues and challenges in clinical genomics and proposing ethical guidelines for clinical genomic testing and interpretation. These guidelines were published as an expert consensus. (shrink)

Hans‐Jörg Rheinberger constructed his historical epistemology of epistemic things by analyzing experimental practices in molecular biology during the 1970s and 80s. With genetic sequencing and multi‐omics approaches, data has become a new resource in the life sciences, questioning the applicability of his concept of experimental system. By historicizing Rheinberger's epistemology, the paper focuses on its relatedness to Ludwik Fleck's notion of an aviso of resistance and points to a gradual shift in Rheinberger's emphasis, moving from an initial focus on (...) writing and its differentiality to work on materials, preparations, and representations. By anchoring visualization in these material practices, Rheinberger also sheds new light on the changing conditions of experimentation in the life sciences due to big data, where visualization emphasizes patterns and correlations rather than substrates. (shrink)

In recent years, exposome research has been put forward as the next frontier for the study of human health and disease. Exposome research entails the analysis of the totality of environmental exposures and their corresponding biological responses within the human body. Increasingly, this is operationalized by big-data approaches to map the effects of internal as well as external exposures using smart sensors and multiomics technologies. However, the ethical implications of exposome research are still only rarely discussed in the literature. Therefore, (...) we conducted a systematic review of the academic literature regarding both the exposome and underlying research fields and approaches, to map the ethical aspects that are relevant to exposome research. We identify five ethical themes that are prominent in ethics discussions: the goals of exposome research, its standards, its tools, how it relates to study participants, and the consequences of its products. Furthermore, we provide a number of general principles for how future ethics research can best make use of our comprehensive overview of the ethical aspects of exposome research. Lastly, we highlight three aspects of exposome research that are most in need of ethical reflection: the actionability of its findings, the epidemiological or clinical norms applicable to exposome research, and the meaning and action–implications of bias. (shrink)

Biobanks and biospecimen collections are becoming a primary means of delivering personalized diagnostics and tailoring individualized therapeutics. This shift towards precision medicine requires interactions among a variety of stakeholders, including the public, patients, healthcare providers, government, and donors. Very few studies have investigated the role of healthcare students in biobanking and biospecimen donations. The main aims of this study were to evaluate the knowledge of senior healthcare students about biobanks and to assess the students’ willingness to donate biospecimens and the (...) factors influencing their attitudes. A cross-sectional study was conducted among senior healthcare students at King Abdulaziz University, Saudi Arabia. The data were obtained using a self-administered questionnaire in English. In addition to the respondents’ biographical data section, the questionnaire assessed the respondents’ general knowledge about biobanking, the factors influencing their willingness to donate biospecimens to biobanks and their general attitudes towards biomedical research. A total of 597 senior healthcare students were included in the study. The general knowledge score was 3.2 out of 7. Only approximately 44% and 27% of students were aware of the terms “Human Genome Project” and “biobank,” respectively. The majority of the students were willing to donate biospecimens to biobanks. Multiple factors were significantly associated with their willingness to donate, including their perceived general health, past experience with both tissue testing and tissue donation, biobanking knowledge score and biomedical research attitude score. The main reasons for students’ willingness to donate were advancement of medical research and societal benefits, whereas misuse of biospecimens and confidentiality breaches were the main reasons for a reluctance to donate. Despite their strong willingness to donate biospecimens, students exhibited a notable lack of knowledge about biobanking and the HGP. To expedite the transition towards PM, it is highly recommended to enhance healthcare curricula by including more educational and awareness programmes to familiarize students with OMICs technologies in addition to the scope of research and clinical applications. (shrink)

This qualitative study of the opinions of legal guardians of minors with Systemic Inflammatory Response Syndrome (SIRS) in Turkey identifies and analyses the ethical challenges accompanying the management of paediatric SIRS patients and the collection of genetic data as part of a large multiomics dataset for the development of an AI-based tool for diagnostics and management of SIRS. Between January and June 2024, 14 problem-centred, semi-structured exploratory interviews with legal guardians of children with SIRS were conducted in Istanbul, Turkey. The (...) interview consisted of 19 open-ended questions. The interviews were digitally recorded, translated into English, and two independent researchers analysed the content of the information. Qualitative content and thematic analysis were performed to identify major ethical issues. The analysis identified five major topics: solidarity, autonomy, informed consent, protection of privacy, and AI-driven ethical issues. Solidarity was the most prominent topic and encompassed the aspects of motivation for participation, raising awareness, supporting communication, and loosening data protection. Parents expressed high respect for children’s autonomy. In the vein of the triadic relationship model, the necessity of children with SIRS participating in decision-making was supported by the interviewees as well as the reconfirmation of informed consent in case of future use of collected genetic data. Regarding the development of AI-tool for SIRS, five principles were identified: wide representation, confidentiality, trustworthiness, human control, and orientation. Our study contributes to the understanding of the ethical challenges accompanying the study of diagnostics using multi-omics data and derived treatment strategies of SIRS in children and adolescents. Different functions of solidarity linked it to the other major topics, thus composing a coherent picture of the ethical aspects of paediatric SIRS research. The identified principles of AI-development correspond to those in the Assessment List for Trustworthy Artificial Intelligence (ALTAI); thus, our research confirmed their real-life relevance and usefulness. (shrink)

Social scientists have shown that scientific characterizations of the egg and the sperm are shaped by gender stereotypes and cultural values. How have such characterizations been transformed by a recent embrace of -omics, when studies of reproduction increasingly go beyond genomics to incorporate proteomics, transcriptomics, exposomics, and other -omics perspectives? Scientists studying reproduction and analyzing eggs, sperm, and embryos are in some ways reimagining the roles, identities, and functions of gametes as fundamentally shaped by other molecular entities and (...) environments. Such relational understandings of substances and processes, however, continue to operate through a teleology that often conscripts more nuanced -omics reflection into familiar genomic visions of sex and reproduction. While ideas of the gene as an alienable object may be unraveling, -omics efforts to go beyond the egg and the sperm are frequently constricted by an understanding of reproduction that remains tied to individualized bodies and by a genomically infused interpretation of the gamete as life itself. (shrink)

Neuron–glioma interactions are critical drivers of glioma progression, with neuronal activity promoting tumor growth and invasion through paracrine signaling and direct synaptic input. Beyond well‐established glutamatergic synapses, recent discoveries revealed that GABAergic interactions also contribute to glioma proliferation. Here, we focus on how glioma cells decode neuronal cues via epigenetic mechanisms, including enhancer reprogramming, chromatin remodeling, and rewiring of 3D genome organization, with transcriptions factors such as SMAD3 and PITX1 orchestrating transcriptional programs that sustain neuron‐to‐glioma communication. Additionally, recent integration of (...) multi‐omics data highlights gene regulatory networks linked to GABAergic signaling as contributors to glioblastoma (GB) pathogenesis. We also underscore the distinct roles of GABAergic signaling across glioma subtypes, noting that, in GB, GABA‐related metabolic and paracrine mechanisms, rather than synaptic input, may drive tumor progression. Understanding how epigenetic reprogramming facilitates glioma integration into neural circuits opens new avenues to disrupt these malignant neuron–glioma interactions by targeting the epigenetic machinery. (shrink)

Neurons degenerate in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), causing progressive and inevitably fatal neurological decline. The best therapeutic strategies target underlying disease mediators, but after decades of intensive research, the causes of these neurodegenerative diseases remain elusive. Recently, coordinated activities of large consortia, increasing open access to large datasets, new methods such as cryo‐transmission electron microscopy, and advancements in high‐resolution omics technologies have offered new insights into the biology of disease that bring us closer to understanding (...) mechanisms of neurodegeneration. In particular, improved understanding of the roles of the key pathological protein TAR DNA binding protein 43 (TDP‐43) in disease has revealed intriguing new opportunities that provide hope for better diagnostic tools and effective treatments for ALS and FTD. (shrink)

Personalized Medicine (PM) is an evolving and often missinterpreted concept and no agreement of personalization exist. We examined the PM discourse towards foucauldian archeological and genealogical analysis to understand the meaning of “personalization” in medicine. In the archaeological analysis, the historical evolution is characterized by the coexistence of two epistemologies: the holistic vision and the omic sciences. The genealogical analysis shows how these epistemologies may affect the meaning of “person” and, consequently, the ontology of patients. Additionally, substitutions/confusions of the term (...) PM are related to continuously evolving medical knowledge and new technologies; different etymological roots of “personalization” and “person”; and cultural differences. In conclusion, if the definition of “personalization” in medicine is not clear, patients might get wrong expectations about what is achievable for their health. Therefore, epistemological trends should not be separated as they drive same goals: providing accurate diagnosis and treatments based on large data to predict disease progression. (shrink)

Dupras and Bunnik take on the particular privacy risks of multi-omics, in particular via a contrast and comparison of genomics and epigenomics, followed by a consideration of the issues in r...

In developing a framework for assessing privacy risks, Dupras and Bunnik’s “Toward a framework for assessing privacy risks in multi-omic research and databases” considers the question of whe...

Co-learning of multiple agents has been studied in co-learning settings, and how do they help, or many different disciplines under various guises. For hamper, learning and cooperation? example, the issue has been tackled by distributed • How do we characterize the process and the artificial intelligence, parallel and distributed com- dynamics of co-learning, conceptually, mathe- puting, cognitive psychology, social psychology, matically, or computationally? game theory (and other areas of mathematical econ- • how do social structures and relations interact omics), (...) sociology, anthropology, and many other with co-learning of multiple agents? related disciplines. (shrink)

Matrices that cannot be handled using conventional clustering, regression or classification methods are often found in every big data research area. In particular, datasets with thousands or millions of rows and less than a hundred columns regularly appear in biological so-called omic problems. The effectiveness of conventional data analysis approaches is hampered by this matrix structure, which necessitates some means of reduction. An evolutionary method called PreCLAS is presented in this article. Its main objective is to find a submatrix with (...) fewer rows that exhibits some group structure. Three stages of experiments were performed. First, a benchmark dataset was used to assess the correct functionality of the method for clustering purposes. Then, a microarray gene expression data matrix was used to analyze the method’s performance in a simple classification scenario, where differential expression was carried out. Finally, several classification methods were compared in terms of classification accuracy using an RNA-seq gene expression dataset. Experiments showed that the new evolutionary technique significantly reduces the number of rows in the matrix and intelligently performs unsupervised row selection, improving classification and clustering methods. (shrink)

Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage‐specific and stably expressed transcription factors, combined with input from environmental signals. Lineage‐specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome‐wide and multi‐omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional (...) dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre‐ and post‐commitment stage‐specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage‐specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity. (shrink)

Integration is now very successful in the field of life sciences: neuroscience, physiology, and a whole part of biology claim to be “integrative.” The term appears in the titles of scientific journals: Integrative Biology, Integrative and Comparative Biology, OMICS: A Journal of Integrative Biology, etc. However, this situation results from a complex genealogy. Initially mathematical like the notion of function, the concept penetrated into the field of life sciences in the second half of the nineteenth century. Its history meets (...) simultaneously Herbert Spencer’s evolutionism and Claude Bernard’s physiology. It will take a more specific meaning in John Hughlings Jackson’s, David Ferrier’s, and especially Charles Scott Sherrington’s neurologies. The following contesting of the Sherringtonian paradigm will not prevent the development of the notion in general physiology at John Barcroft’s instigation. We suggest here investigating the successive rectifications of the concept of integration, which every time express a different vision of the body and successively a strategy to be adopted to elucidate its physiology. (shrink)

Following the rediscovery of Mendelian genetics, food supply pressures and the rapid expansion of crop varieties with defined performance characteristics, international systems were set up throughout the 20 C to regulate the trade of seed, the protection of intellectual property and the sale of productive varieties of key agricultural crops. These systems are a highly connected but largely linear set of processes. System changes are slow to be adopted due to the cascade of effects that structural alteration would have globally. (...) Multi-omic technologies and the subsequent proliferation of data types used within modern breeding, offer the possibility to gain deeper insights into the performance characteristics of varieties. Current integration of data, standards and ownership structures limit their applications for wider purposes, both private and public. We explore how data within and between breeding programmes and the varietal approval and monitoring processes could be made FAIR. We examine what role expanded or aligned programmes of data collection and expanded trait evaluation at the point of varietal registration and evaluation, as well as on farm could have in ensuring the best linkage of public and private data to address some of the challenges society faces over the next 30 years with the required, rapid transition to sustainable agricultural systems. (shrink)

Epidemiological evidence supports a health‐promoting effect of the Mediterranean Diet (MedDiet), especially in the prevention of cardiovascular diseases. These cardiovascular benefits have been attributed to a number of components of the MedDiet such as monounsaturated fatty acids, antioxidant vitamins and phytochemicals. However, the underlying mechanisms remain unknown. Likewise, little is known about the genes that define inter‐individual variation in response to the MedDiet, although the TCF7L2 gene is emerging as an illustrative candidate for determining relative risk of cardiovascular events in (...) response to the MedDiet. Moreover, omics technologies are providing evidence supporting potential mechanisms, some of them implicating epigenetics (i.e. microRNAs, methylation), and certain data suggest that some traditional foods could contribute via microRNAs possibly acting as exogenous regulators of gene expression. Future research should aim at increasing and consolidating the nutrigenetic and nutrigenomic knowledge of the MedDiet in order to provide sound, personalized and optimized nutritional recommendations. (shrink)

Pre-natal exposure to acute maternal trauma or chronic maternal distress can confer increased risk for psychiatric disorders in later life. Acute maternal trauma is the result of unforeseen environmental or personal catastrophes, while chronic maternal distress is associated with anxiety or depression. Animal studies investigating the effects of pre-natal stress have largely used brief stress exposures during pregnancy to identify critical periods of fetal vulnerability, a paradigm which holds face validity to acute maternal trauma in humans. While understanding these effects (...) is undoubtably important, the literature suggests maternal stress in humans is typically chronic and persistent from pre-conception through gestation. In this review, we provide evidence to this effect and suggest a realignment of current animal models to recapitulate this chronicity. We also consider candidate mediators, moderators and mechanisms of maternal distress, and suggest a wider breadth of research is needed, along with the incorporation of advanced -omics technologies, in order to understand the neurodevelopmental etiology of psychiatric risk. (shrink)

A recent single cell mRNA sequencing study by Dueck et al. compares neuronal transcriptomes to the transcriptomes of adipocytes and cardiomyocytes. Single cell ‘omic approaches such as those used by the authors are at the leading edge of molecular and biophysical measurement. Many groups are currently employing single cell sequencing approaches to understand cellular heterogeneity in cancer and during normal development. These single cell approaches also are beginning to address long‐standing questions regarding nervous system diversity. Beyond an innate interest in (...) cataloging cell type diversity in the brain, single cell neuronal diversity has important implications for neurotypic neural circuit function and for neurological disease. Herein, we review the authors’ methods and findings, which most notably include evidence of unique expression profiles in some single neurons. (shrink)

Integration of knowledge concerning circadian rhythms, metabolic networks, and sleep‐wake cycles is imperative for unraveling the mysteries of biological cycles and their underlying mechanisms. During the last decade, enormous progress in circadian biology research has provided a plethora of new insights into the molecular architecture of circadian clocks. However, the recent identification of autonomous redox oscillations in cells has expanded our view of the clockwork beyond conventional transcription/translation feedback loop models, which have been dominant since the first circadian period mutants (...) were identified in fruit fly. Consequently, non‐transcriptional timekeeping mechanisms have been proposed, and the antioxidant peroxiredoxin proteins have been identified as conserved markers for 24‐hour rhythms. Here, we review recent advances in our understanding of interdependencies amongst circadian rhythms, sleep homeostasis, redox cycles, and other cellular metabolic networks. We speculate that systems‐level investigations implementing integrated multi‐omics approaches could provide novel mechanistic insights into the connectivity between daily cycles and metabolic systems. -/- . (shrink)

In this article I argue that the dominant discourse of our day is econ omic universalism. This has translated comfortably from modernity to postmodernity. Within this discourse real differences and inequalities are homogenized by narratives such as those of choice and diversity. I shall question this in two ways: first, by borrowing from French post- structuralism to rename the discourse a 'masculine economy', and thus to invoke a 'feminine economy' both as a philosophical structure of difference and as a deliberate (...) introduction of the body; second, by analysing economic narratives concerning women's work which tend to flatten out difference altogether or recast it as (well-advised) choice. Within this economic language game, I shall try to emphasize material differences and inequalities, in other words, I shall borrow from the language of opposition. I claim that only the asymmetrical oscillation between difference and opposition can attempt to prevent either one falling back into some kind of more or less comfortable universalism. (shrink)

Las Ciencias Ómicas se presentan con la potencialidad de realizar abordajes complejos del fenómeno que estudian como también de intervenir sobre la salud humana a partir del desarrollo de tecnologías de diagnóstico y tratamiento de enfermedades. Al respecto, mostramos un análisis epistemológico de las Ciencias Ómicas sobre la utilización y alcance de conceptualizaciones complejas de la acción génica en la relación genotipo-fenotipo. En particular, si suceden o no simplificaciones epistemológicas cuando se estudian enfermedades humanas. Nuestro análisis comparativo muestra que, en (...) general, en las Ciencias Ómicas hay conceptualizaciones tanto simples como complejas de la acción génica en la relación genotipo-fenotipo, mientras que en las investigaciones ómicas que abordan enfermedades humanas se encuentra una exacerbación de conceptualizaciones simplificantes. Se discute si dicha simplificación epistemológica se ve favorecida en un escenario de intervención en aspectos de salud como es la generación de conocimientos para tecnologías ómicas de diagnóstico y tratamiento de enfermedades. Así, tal como sucede en otros ámbitos de las Ciencias Naturales, para los estudios ómicos de enfermedades se genera un vínculo necesario entre simplificaciones epistemológicas y la promesa de intervención. (shrink)

Whether aging should be classified as a disease remains contentious. We propose a conceptual synthesis: aging is a meta-disease – a universal, upstream pathological condition that gives rise to the full spectrum of age-related disorders, as well as the structural and cosmetic changes historically dismissed as “normal aging.” This framework reflects a Hegelian dialectic, in which the traditional thesis (aging is a natural process) and the antithesis (aging is a disease) are integrated into a higher-order synthesis. This synthesis preserves the (...) valid insights of each while overcoming their limitations: aging is not a discrete disease, yet it is mechanistically central to disease emergence. It is thus the generative causal architecture from which age-related diseases arise—not itself a subset within pathology, but the ontological ground that gives rise to it. This reconceptualization rests on two core pillars. First, a set-theoretic nosology: aging defines the universal set A. Each age-related disease family constitutes a proper subset within A (e.g. cardiovascular disease V ⊂ A, neurodegeneration N ⊂ A). Cosmetic (K) and structural (T) changes comprise partially overlapping subsets (K ⊂ A, T ⊂ A, K ∩ T ≠ Ø). This formalism enables a precise explanation of comorbidity, multimorbidity, and the structural and cosmetic overlap of age-related conditions. Second, cellular senescence is the causal nexus: diverse molecular lesions converge on senescence, defined by irreversible proliferative arrest and activation of the senescence-associated secretory phenotype, and characterized by a distinctive multi-omic signature we term the senescome. Senescence functions as a pivotal biological switch—an “event horizon”—beyond which transient molecular insults are converted into chronic, system-wide dysfunction. Through these mechanisms, senescence is the causal generating set (S) inside A that initiates and propagates the various disease subsets. Cancer (C) is the exceptional set that reflects escape from senescence and lies largely outside S. This meta-disease framework situates geroscience within a causal ontology, defining aging as the generative source of pathology. As the antecedent ground of disease, aging thus emerges as the logical primary therapeutic target. Integrating these concepts clarifies terminology and provides formal coherence to International Classification of Diseases extension code XT9T (“Ageing-related”) and stem code MG2A (“Ageing-associated decline in intrinsic capacity”). It also provides practical levers for advancing biomarker portfolios, composite clinical trial endpoints, mechanism-based therapeutic development, regulatory frameworks, and reimbursement models for geroprotective interventions. We conclude by proposing a policy roadmap for translating the meta-disease paradigm into coordinated clinical, regulatory, and public health action, and by examining its implications for the purpose and future of medicine. (shrink)