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The Ecological Genome Project and the Promises of Ecogenomics for Society: Realising a Shared Vision as One Health.
No full textThis paper develops a vision for The Ecological Genome Project: an aspirational, global endeavour to connect human genomic sciences with the ethos of ecological sciences. The Project\u27s goal is to strengthen interdisciplinary networks that relate to diverse initiatives using genomic technologies, with respect to shared ethical frameworks and governance structures. To this end, this paper proposes a practical definition of ecogenomics to align various methodologies and values in a single environmental field using principles used to safeguard all forms of life in their habitats. We achieve this by using a One Health approach as a pretext for disparate disciplines to collaborate and also a lens to view the Ethical, Legal and Social Implications (ELSI) inherent in ecological systems
Retrograde mitochondrial signaling governs the identity and maturity of metabolic tissues.
No full textMitochondrial damage is a hallmark of metabolic diseases, including diabetes, yet the consequences of compromised mitochondria in metabolic tissues are often unclear. Here, we report that dysfunctional mitochondrial quality control engages a retrograde (mitonuclear) signaling program that impairs cellular identity and maturity in β-cells, hepatocytes, and brown adipocytes. Targeted deficiency throughout the mitochondrial quality control pathway, including genome integrity, dynamics, or turnover, impaired the oxidative phosphorylation machinery, activating the mitochondrial integrated stress response, eliciting chromatin remodeling, and promoting cellular immaturity rather than apoptosis to yield metabolic dysfunction. Indeed, pharmacologic blockade of the integrated stress response in vivo restored β-cell identity following loss of mitochondrial quality control. Targeting mitochondrial retrograde signaling may therefore be promising in the treatment or prevention of metabolic disorders
Activin E is a new guardian protecting against hepatic steatosis via inhibiting lipolysis in white adipose tissue.
Get PDFHepatic endoplasmic reticulum (ER) stress is implicated in the development of steatosis and its progression to nonalcoholic steatohepatitis (NASH). The ER in the liver can sustain metabolic function by activating defense mechanisms that delay or prevent the progression of nonalcoholic fatty liver disease (NAFLD). However, the precise mechanisms by which the ER stress response protects against NAFLD remain largely unknown. Recently, activin E has been linked to metabolic diseases such as insulin resistance and NAFLD. However, the physiological conditions and regulatory mechanisms driving hepatic Inhbe expression (which encodes activin E) as well as the metabolic role of activin E in NAFLD require further investigation. Here we found that hepatic Inhbe expression increased under prolonged fasting and ER stress conditions, which was mediated by ATF4, as determined by promoter analysis in a mouse model. Consistently, a positive correlation between INHBE and ATF4 expression levels in relation to NAFLD status was confirmed using public human NAFLD datasets. To investigate the role of activin E in hepatic steatosis, we assessed the fluxes of the lipid metabolism in an Inhbe-knockout mouse model. These mice displayed a lean phenotype but developed severe hepatic steatosis under a high-fat diet. The deficiency of Inhbe resulted in increased lipolysis in adipose tissue, leading to increased fatty acid influx into the liver. Conversely, hepatic overexpression of Inhbe ameliorated hepatic steatosis by suppressing lipolysis in adipose tissue through ALK7-Smad signaling. In conclusion, activin E serves as a regulatory hepatokine that prevents fatty acid influx into the liver, thereby protecting against NAFLD
The CD123 antibody-drug conjugate pivekimab sunirine exerts profound activity in preclinical models of pediatric acute lymphoblastic leukemia.
Get PDFAntibody–drug conjugates (ADCs) combining monoclonal antibodies with cytotoxic payloads are a rapidly emerging class of immune‐based therapeutics with the potential to improve the treatment of cancer, including children with relapse/refractory acute lymphoblastic leukemia (ALL). CD123, the α subunit of the interleukin‐3 receptor, is overexpressed in ALL and is a potential therapeutic target. Here, we show that pivekimab sunirine (PVEK), a recently developed ADC comprising the CD123‐targeting antibody, G4723A, and the cytotoxic payload, DGN549, was highly effective in vivo against a large panel of pediatric ALL patient‐derived xenograft (PDX) models (n = 39). PVEK administered once weekly for 3 weeks resulted in a median event‐free survival (EFS) of 57.2 days across all PDXs. CD123 mRNA and protein expression was significantly higher in B‐lineage (n = 65) compared with T‐lineage (n = 25) ALL PDXs (p \u3c 0.0001), and mice engrafted with B‐lineage PDXs achieved significantly longer EFS than those engrafted with T‐lineage PDXs (p \u3c 0.0001). PVEK treatment also resulted in significant clearance of human leukemia cells in hematolymphoid organs in mice engrafted with B‐ALL PDXs. Notably, our results showed no direct correlation between CD123 expression and mouse EFS, indicating that CD123 is necessary but not sufficient for in vivo PVEK activity. Importantly, a PDX with very high CD123 cell surface expression but resistant to in vivo PVEK treatment, failed to internalize the G4723A antibody while remaining sensitive to the PVEK payload, DGN549, suggesting a novel mechanism of resistance. In conclusion, PVEK was highly effective against a large panel of B‐ALL PDXs supporting its clinical translation for B‐lineage pediatric ALL
Chromosome 4 Duplication Associated with Strabismus Leads to Gene Expression Changes in iPSC-Derived Cortical Neurons.
Get PDFBACKGROUND/OBJECTIVES: Strabismus is the most common ocular disorder of childhood. Three rare, recurrent genetic duplications have been associated with both esotropia and exotropia, but the mechanisms by which they contribute to strabismus are unknown. This work aims to investigate the mechanisms of the smallest of the three, a 23 kb duplication on chromosome 4 (hg38|4:25,554,985-25,578,843).
METHODS: Using CRISPR and bridging oligos, we introduced the duplication into the Kolf2.1J iPSC line. We differentiated the parent line and the line with the duplication into cortical neurons using a three-dimensional differentiation protocol, and performed bulk RNASeq on neural progenitors (day 14) and differentiated neurons (day 63).
RESULTS: We successfully introduced the duplication into Kolf2.1J iPSCs by nucleofecting a bridging oligo for the newly formed junction along with cas9 ribonucleoparticles. We confirmed that the cells had a tandem duplication without inversion or deletion. The parent line and the line with the duplication both differentiated into neurons reliably. There were a total of 37 differentially expressed genes (DEGs) at day 63, 25 downregulated and 12 upregulated. There were 55 DEGs at day 14, 18 of which were also DEGs at day 63. The DEGs included a number of protocadherins, several genes involved in neuronal development, including
CONCLUSIONS: A copy number variant (CNV) that confers risk for strabismus affects gene expression of several genes involved in neural development, highlighting that strabismus most likely results from abnormal neural development, and identifying several new genes and pathways for further research into the pathophysiology of strabismus
Genetic context modulates aging and degeneration in the murine retina.
Get PDFBACKGROUND: Age is the principal risk factor for neurodegeneration in both the retina and brain. The retina and brain share many biological properties; thus, insights into retinal aging and degeneration may shed light onto similar processes in the brain. Genetic makeup strongly influences susceptibility to age-related retinal disease. However, studies investigating retinal aging have not sufficiently accounted for genetic diversity. Therefore, examining molecular aging in the retina across different genetic backgrounds will enhance our understanding of human-relevant aging and degeneration in both the retina and brain-potentially improving therapeutic approaches to these debilitating conditions.
METHODS: Transcriptomics and proteomics were employed to elucidate retinal aging signatures in nine genetically diverse mouse strains (C57BL/6J, 129S1/SvlmJ, NZO/HlLtJ, WSB/EiJ, CAST/EiJ, PWK/PhK, NOD/ShiLtJ, A/J, and BALB/cJ) across lifespan. These data predicted human disease-relevant changes in WSB and NZO strains. Accordingly, B6, WSB, and NZO mice were subjected to human-relevant in vivo examinations at 4, 8, 12, and/or 18M, including: slit lamp, fundus imaging, optical coherence tomography, fluorescein angiography, and pattern/full-field electroretinography. Retinal morphology, vascular structure, and cell counts were assessed ex vivo.
RESULTS: We identified common molecular aging signatures across the nine mouse strains, which included genes associated with photoreceptor function and immune activation. Genetic background strongly modulated these aging signatures. Analysis of cell type-specific marker genes predicted age-related loss of photoreceptors and retinal ganglion cells (RGCs) in WSB and NZO, respectively. Fundus exams revealed retinitis pigmentosa-relevant pigmentary abnormalities in WSB retinas and diabetic retinopathy (DR)-relevant cotton wool spots and exudates in NZO retinas. Profound photoreceptor dysfunction and loss were confirmed in WSB. Molecular analyses indicated changes in photoreceptor-specific proteins prior to loss, suggesting photoreceptor-intrinsic dysfunction in WSB. In addition, age-associated RGC dysfunction, loss, and concomitant microvascular dysfunction were observed in NZO mice. Proteomic analyses revealed an early reduction in protective antioxidant processes, which may underlie increased susceptibility to DR-relevant pathology in NZO.
CONCLUSIONS: Genetic context is a strong determinant of retinal aging, and our multi-omics resource can aid in understanding age-related diseases of the eye and brain. Our investigations identified and validated WSB and NZO mice as improved preclinical models relevant to common retinal neurodegenerative diseases
Species- and strain-specific microbial modulation of interferon, innate immunity, and epithelial barrier in 2D air-liquid interface respiratory epithelial cultures.
Get PDFBACKGROUND: The microbiome regulates the respiratory epithelium\u27s immunomodulatory functions. To explore how the microbiome\u27s biodiversity affects microbe-epithelial interactions, we screened 58 phylogenetically diverse microbes for their transcriptomic effect on human primary bronchial air-liquid interface (ALI) cell cultures.
RESULTS: We found distinct species- and strain-level differences in host innate immunity and epithelial barrier response. Strikingly, we found that host interferon, an antiviral response, was one of the most variable host processes. This variability was not driven by microbial phylogenetic diversity, bioburden, nor by the microbe\u27s ability to stimulate other innate immunity pathways.
CONCLUSIONS: Microbial colonization differentially stimulates host gene expression with variations observed across phylogenetically diverse microbes and across different strains of the same species. Our study provides a foundation for understanding how the respiratory microbiome\u27s biodiversity affects epithelial, and particularly antiviral, innate immunity
A Systematic Approach to Prioritise Diagnostically Useful Findings for Inclusion in Electronic Health Records as Discrete Data to Improve Clinical Artificial Intelligence Tools and Genomic Research.
Get PDFAIMS: The recent widespread use of electronic health records (EHRs) has opened the possibility for innumerable artificial intelligence (AI) tools to aid in genomics, phenomics, and other research, as well as disease prevention, diagnosis, and therapy. Unfortunately, much of the data contained in EHRs are not optimally structured for even the most sophisticated AI approaches. There are very few published efforts investigating methods for recording discrete data in EHRs that would not slow current clinical workflows or ways to prioritise patient characteristics worth recording. Here, we propose an approach to identify and prioritise findings (phenotypes) useful for differentiating diseases, with an initial focus on relatively common small B-cell lymphomas.
MATERIALS AND METHODS: A website enabling crowd-sourced recording of diseases and phenotypes was developed. An expert committee in the field of B-cell lymphomas standardised phenotype terminology for use in digital resources, and select terms were included in the Human Phenotype Ontology (HPO). A total of 100 patient lymph node biopsy samples were evaluated, and phenotypes were recorded as discrete data. Bayesian networks (BNs) were developed based on these data, and their diagnostic accuracy and ability to prioritise these phenotypes for inclusion in EHRs were assessed.
RESULTS: Out of 146 phenotypes identified from the website as potentially useful for differentiating four different lymphomas from each other and from benign lymph nodes, 70-75 were included in BNs. The diagnostic accuracy of different naïve BNs was 96.3% for non-marginal zone lymphoma cases and 50% for marginal zone lymphoma cases when all of the included phenotypes were used and 93.8% for non-marginal zone lymphoma cases and 27.5% for marginal zone lymphoma cases when only 15 phenotypes were included in the BNs.
CONCLUSION: This pilot provides a starting point for systematic improvement and a dataset for comparing related approaches
A year-long field study of buried plastics reveals underestimation of plastic pollution on Hawaiian beaches.
Get PDFGlobal models estimate that two-thirds of floating ocean plastic has accumulated in coastal areas since the 1950s, with Hawai\u27i\u27s windward shores particularly vulnerable due to their proximity to the North Pacific Garbage Patch. Our quarterly surveys revealed that 91 % of recovered plastic particles were buried below the surface (deeper than 2 cm), with most particles being small fragments (93 %) with an average mean max length of 6.7 ± 4.4 mm. This study offers new insights into subsurface plastic, exposing a previously hidden vertical distribution of plastic pollution. We observed significant variations in plastic abundance across depths, beaches, and sampling periods, along with a positive correlation between particle size and sand grain size. Additionally, through reconciliation science, we critically reflect on the cultural impacts of our research, emphasizing the importance of aligning plastic pollution studies with local community values and environmental stewardship
