Refusing epigenetics: indigeneity and the colonial politics of trauma.

Environmental epigenetics is increasingly employed to understand the health outcomes of communities who have experienced historical trauma and structural violence. Epigenetics provides a way to think about traumatic events and sustained deprivation as biological "exposures" that contribute to ill-health across generations. In Australia, some Indigenous researchers and clinicians are embracing epigenetic science as a framework for theorising the slow violence of colonialism as it plays out in intergenerational legacies of trauma and illness. However, there is dispute, contention, and caution as well as enthusiasm among these research communities.In this article, we trace strategies of "refusal" (Simpson, 2014) in response to epigenetics in Indigenous contexts. Drawing on ethnographic fieldwork conducted in Australia with researchers and clinicians in Indigenous health, we explore how some construct epigenetics as useless knowledge and a distraction from implementing anti-colonial change, rather than a tool with which to enact change. Secondly, we explore how epigenetics narrows definitions of colonial harm through the optic of molecular trauma, reproducing conditions in which Indigenous people are made intelligible through a lens of "damaged" bodies. Faced with these two concerns, many turn away from epigenetics altogether, refusing its novelty and supposed benefit for Indigenous health equity and resisting the pull of postgenomics.

Microbiome ownership for Indigenous peoples.

Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.

Community partnerships are fundamental to ethical ancient DNA research.

The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.

Investigating disparity in access to Australian clinical genetic health services for Aboriginal and Torres Strait Islander people.

Globally, there is a recognised need that all populations should be able to access the benefits of genomics and precision medicine. However, achieving this remains constrained by a paucity of data that quantifies access to clinical genomics, particularly amongst Indigenous populations. Using administrative data from clinical genetic health services across three Australian jurisdictions (states/territories), we investigate disparities in the scheduling and attendance of appointments among Aboriginal and/or Torres Strait Islander people, compared to non-Indigenous people. For 14,870 appointments scheduled between 2014-2018, adjusted Multivariate Poisson Regression models revealed that Aboriginal and/or Torres Strait Islander people were scheduled fewer appointments (IRR 0.73 [0.68-0.80], <0.001) and attended at lower rates (IRR 0.85 [0.78-0.93], <0.001). Within this population, adults, females, remote residents, and those presenting in relation to cancer or prenatal indications experienced the greatest disparity in access. These results provide important baseline data related to disparities in access to clinical genomics in Australia.

L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma.

L1CAM is a transmembrane protein expressed on neurons that was presumed to be found on neuron-derived extracellular vesicles (NDEVs) in human biofluids. We developed a panel of single-molecule array assays to evaluate the use of L1CAM for NDEV isolation. We demonstrate that L1CAM is not associated with extracellular vesicles in human plasma or cerebrospinal fluid and therefore recommend against its use as a marker in NDEV isolation protocols.

"This is my boy's health! Talk straight to me!" perspectives on accessible and culturally safe care among Aboriginal and Torres Strait Islander patients of clinical genetics services.

BACKGROUND: Aboriginal and Torres Strait Islander people do not enjoy equal access to specialist health services that adequately meet their needs. Clinical genetics services are at the vanguard of realising the health benefits of genomic medicine. As the field continues to expand in clinical utility and implementation, it is critical that Aboriginal and Torres Strait Islander people are able to participate and benefit equally to avoid further widening of the existing health gap. This is the first study to explore barriers to accessing clinical genetics services among Aboriginal and Torres Strait Islander people, which has been acknowledged as a key strategic priority in Australian genomic health policy. METHODS: A participatory design process engaged a majority-Aboriginal Project Reference Group and Aboriginal End-User Group. 63 semi-structured interviews were conducted with Aboriginal and/or Torres Strait Islander people who had accessed the government-funded clinical genetics service in Western Australia, Queensland or the Northern Territory between 2014 and 2018. The sample included patients, parents and carers. Participants were asked to recount their 'patient journey', from referral through to post-appointment and reflect on their perceptions of genetics and its implications for the health of themselves and their families. Analysis tracked chronological service engagement, followed by an inductive thematic approach. RESULTS: Barriers to access and engagement were present at each stage of the patient journey. These included challenges in obtaining a referral, long waiting periods, limited genetic literacy, absence of Aboriginal support services, communication challenges and lack of adequate psychosocial support and follow-up after attendance. Participants' overall experiences of attending a genetic health service were varied, with positive perceptions tied closely to a diagnosis being achieved. The experience of (and expectation for) recognition of cultural identity and provision of culturally safe care was low among participants. Unaddressed concerns continued to cause significant distress in some people years after their appointment took place. CONCLUSIONS: There is significant scope for improving the care provided to Aboriginal and Torres Strait Islander people at clinical genetics services. Immediate attention to minimising logistical barriers, developing relationships with Aboriginal Community Controlled Health Services and providing practical and specific cultural safety training for practitioners is required at the service-level. Our findings strongly support the development of guidelines or policies recognising the collective cultural needs of Aboriginal and Torres Strait Islander people in relation to genomic health care.

Biobank networking and globalisation: perspectives and practices of Australian biobanks.

Objective This study examined the practices and attitudes of Australian biobanks regarding access to samples and data, as well as local and global networking with other biobanks. Methods This was a mixed-methods study, including an online survey of Australian biobank administrators and qualitative interviews with survey participants. The survey examined the criteria applied when considering requests to share or network. The interviews explored attitudes and practices regarding sharing and networking. Results Most (90.9%; 30/33) biobanks offered access to their samples and data to others, principally for research (90.6%; 29/32). The most common criteria used to evaluate access requests included ethical oversight (84.8%; 28/33), scientific merit (84.8%; 28/33) and intended use (81.8%; 27/33). Just over two-thirds (69.7%; 23/33) of biobanks participated in Australian networks, and 39.1% (9/23) participated in global networks. Networking took the form of both sharing standardised operating procedures and policies (60.9%) and sharing samples and data (43.5%). Thirteen of the 16 interviewees participated in networks. Motivations for sharing included scientific necessity, sharing expertise and standardising operations and governance. Significant barriers to networking remain, including insufficient resources, inconsistent regulations and procedures, and cultural and political issues to do with the conduct of research. Conclusions Many Australian biobanks are already active participants in various types of global biobanking. If biobanks are to expand and make the most of their involvement in global networks, then important barriers need to be overcome. What is known about the topic? Biobanks that store human tissue and associated data are increasingly forming local, national and global networks. These networks create opportunities for enhancing the utility and sustainability of biobanks, but also raise considerable technical, legal and ethical challenges. What does this paper add? This paper reports findings from a mixed-methods study of Australian biobanks and reveals contemporary practices and perspectives concerning sample and data sharing, as well as local and global networking. It found most Australian biobanks currently take part in these activities. What are the implications for practitioners? Many Australian biobanks are networking in various ways across regional and national borders. A better understanding of current practices and views on significant and emerging issues is relevant to the diverse range of biobank stakeholders involved in any agenda to expand biobank networking, including patients, consumers, clinicians, scientists, policy makers and regulators.

A community-based co-designed genetic health service model for Aboriginal Australians.

BACKGROUND: Aboriginal and Torres Strait Islander people experience a greater burden of disease and die younger than non-Indigenous Australians, with Aboriginal people living in remote areas of the Northern Territory of Australia having the lowest life expectancy estimates. Despite a high burden of chronic disease among Aboriginal and Torres Strait Islander people, access to specialist health services remains low and models of care that increase engagement, may improve health outcomes. METHODS: We describe client and staff perspectives of a model of clinical genetics services provided by the MJD Foundation (MJDF) in geographically and culturally complex contexts within the Northern Territory of Australia. We seek to understand the MJDF model's success in supporting Aboriginal families with the familial, neurodegenerative condition Machado-Joseph disease and how it could be applied in the provision of other specialist services. Thematic analysis was undertaken on semi-structured interviews with primary health care staff (n = 2), Non-Aboriginal MJDF Staff (n = 7) and Aboriginal MJDF Clients / Community workers (n = 13). RESULTS: Four key themes regarding the MJDF model of service delivery were identified with the service being; 1) client led 2) accepting of various understandings of genetic disease causation 3) focused on relationships, continuity and trust between the service provider and the clients, and 4) committed to incorporating an inclusive whole-of-family practice. The MJDF model takes a community-based, person-and family-centred approach to successfully deliver effective specialist genetic health services in remote community settings. We propose that these approaches have broad application in the future design and delivery of specialist health services particularly in culturally complex settings.

Race in a genome: long read sequencing, ethnicity-specific reference genomes and the shifting horizon of race.

The sequencing of the human genome at the turn of the 21st century was hailed as revealing the overwhelming genetic similarity of human groups. Scholars of genomics have critiqued the subsequent persistence of race-based genetic science, but were reassured that the wide availability of gene sequencing would end the use of race as a proxy for genetic difference. Once an individual's whole gene sequence could be read, they hoped, their ethnoracial classification would become redundant. At the same time, genome science was recognising that the differences between human genomes went beyond the genome sequence to the structure of the genome itself. 'Structural variation' between genomes, including insertions, deletions, translocations, inversions, and copy number variations, mean that the 'universal' reference genome used for genome sequencing is not so universal. As conventional, 'short-read' sequencing wrongly assumes that all genomes have the same structure, significant genetic variation can be missed. This paper examines the twin phenomena that have been posed as a solution to the biases of short-read sequencing: 'long-read' sequencing and 'ethnicity-specific reference genomes'. Long-read sequencing is a method of generating a genome sequence that can be assembled de novo rather than relying on the reference genome. In recent years, a number of countries including China, Korea, and Denmark have used long-read sequencing and de novo assembly to develop 'national' reference genomes. Our analysis of one ethnicity-specific reference genome project, the Korean Reference Genome (KOREF), finds that it unduly emphasises the importance of population structural variation, framed in nationalist terms, and discounts the importance of individual structural variation. We argue that the intellectual labour required to make a Korean reference genome a coherent concept works to extend the horizon of race, prolonging the temporality of the 'meantime' in which race remains a seemingly valid concept in genomic science.

Indigenous Genetics and Rare Diseases: Harmony, Diversity and Equity.

Advances in our understanding of genetic and rare diseases are changing the face of healthcare. Crucially, the global community must implement these advances equitably to reduce health disparities, including between Indigenous and non-Indigenous peoples. We take an Australian perspective to illustrate some key areas that are fundamental to the equitable translation of new knowledge for the improved diagnosis of genetic and rare diseases for Indigenous people. Specifically, we focus on inequalities in access to clinical genetics services and the lack of genetic and phenomic reference data to inform diagnoses. We provide examples of ways in which these inequities are being addressed through Australian partnerships to support a harmonious and inclusive approach to ensure that benefits from traditional wisdom, community knowledge and shared experiences are interwoven to support and inform implementation of new knowledge from genomics and precision public health. This will serve to deliver benefits to all of our diverse citizens, including Indigenous populations.

Extracellular Vesicle Isolation and Analysis by Western Blotting.

Extracellular vesicles (EVs) are released by mammalian cells and are thought to be important mediators of intercellular communication. There are many methods for isolating EVs from cell culture media, but the most popular methods involve purification based on ultracentrifugation . Here, we provide a detailed protocol for isolating EVs by differential ultracentrifugation and analyzing EV proteins (such as the tetraspanins CD9 , CD63 and CD81 ) by western blotting.

Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy.

High-resolution fluorescence microscopy approaches enable the study of single objects or biological complexes. Single object studies have the general advantage of uncovering heterogeneity that may be hidden during the ensemble averaging which is common in any bulk conventional biochemical analysis. The implementation of single object analysis in the study of extracellular vesicles (EVs) may therefore be used to characterize specific properties of vesicle subsets which would be otherwise undetectable. We present a protocol for staining isolated EVs with a fluorescent lipid dye and attaching them onto a glass slide in preparation for imaging with total internal reflection fluorescence microscopy (TIRF-M) or other high-resolution microscopy techniques.

Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper.

The release of RNA-containing extracellular vesicles (EV) into the extracellular milieu has been demonstrated in a multitude of different in vitro cell systems and in a variety of body fluids. RNA-containing EV are in the limelight for their capacity to communicate genetically encoded messages to other cells, their suitability as candidate biomarkers for diseases, and their use as therapeutic agents. Although EV-RNA has attracted enormous interest from basic researchers, clinicians, and industry, we currently have limited knowledge on which mechanisms drive and regulate RNA incorporation into EV and on how RNA-encoded messages affect signalling processes in EV-targeted cells. Moreover, EV-RNA research faces various technical challenges, such as standardisation of EV isolation methods, optimisation of methodologies to isolate and characterise minute quantities of RNA found in EV, and development of approaches to demonstrate functional transfer of EV-RNA in vivo. These topics were discussed at the 2015 EV-RNA workshop of the International Society for Extracellular Vesicles. This position paper was written by the participants of the workshop not only to give an overview of the current state of knowledge in the field, but also to clarify that our incomplete knowledge - of the nature of EV(-RNA)s and of how to effectively and reliably study them - currently prohibits the implementation of gold standards in EV-RNA research. In addition, this paper creates awareness of possibilities and limitations of currently used strategies to investigate EV-RNA and calls for caution in interpretation of the obtained data.

Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia.

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.

Comparison of Cas9 activators in multiple species.

Several programmable transcription factors exist based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare Cas9 activator systems and examine their ability to induce robust gene expression in several human, mouse, and fly cell lines. We also explore the potential for improved activation through the combination of the most potent activator systems, and we assess the role of cooperativity in maximizing gene expression.

All in the Blood: A Review of Aboriginal Australians' Cultural Beliefs About Blood and Implications for Biospecimen Research.

Public participation in medical research and biobanking is considered key to advances in scientific discovery and translation to improved health care. Cultural concerns relating to blood have been found to affect the participation of indigenous peoples and minorities in research, but such concerns are rarely specified in the literature. This article presents a review of the role of blood in Australian Aboriginal cultures. We discuss the range of meanings and uses of blood in traditional culture, including their use in ceremonies, healing, and sorcery. We draw on more recent literature on Aboriginal Australians and biomedicine to consider how traditional beliefs may be changing over time. These findings provide an empirical basis for researchers and bioethicists to develop culturally grounded strategies to boost the participation of Aboriginal Australians in biomedical research. They also serve as a model for integrating anthropological literature with bioethical concerns that could be applied to other indigenous and minority groups.