scONE-seq: A one-tube single-cell multi-omics method enables simultaneous dissection of molecular phenotype and genotype heterogeneity from frozen tumors

Genomic and transcriptomic heterogeneity both play important roles in normal cellular function as well as in disease development. To be able to characterize these different forms of cellular heterogeneity in diverse sample types, we developed scONE-seq, which enables simultaneous transcriptome and genome profiling in a one-tube reaction. Previous single-cell-whole-genome-RNA-sequencing (scWGS-RNA-seq) methods require physical separation of DNA and RNA, often by physical separation of the nucleus from the cytoplasm. Most of these methods are labor-intensive and technically demanding, time-consuming, or require special devices, and they are not applicable to frozen samples that cannot generate intact single-cell suspensions. scONE-seq is a one-tube reaction which eliminates loss due to transfer steps, and thus is highly scalable and compatible with frozen biobanked tissue, generating data that is superior in quality compared to other applicable methods. We benchmarked scONE-seq against existing methods using cell lines and lymphocytes from a healthy donor, and we applied it to a 2-year-frozen astrocytoma sample profiling over 1,200 nuclei, subsequently identifying a unique transcriptionally normal-like tumor clone. scONE-seq makes it possible to perform large-scale single-cell multi-omics interrogation with ease on the vast quantities of biobanked tissue, which could transform the scale of future multi-omics single-cell cancer profiling studies.

scONE-seq: A one-tube single-cell multi-omics method enables simultaneous dissection of molecular phenotype and genotype heterogeneity from frozen tumors

Genomic and transcriptomic heterogeneity both play important roles in normal cellular function as well as in disease development. To be able to characterize these different forms of cellular heterogeneity in diverse sample types, we developed scONE-seq, which enables simultaneous transcriptome and genome profiling in a one-tube reaction. Previous single-cell-whole-genome-RNA-sequencing (scWGS-RNA-seq) methods require physical separation of DNA and RNA, often by physical separation of the nucleus from the cytoplasm. These methods are labor-intensive and technically demanding, time-consuming, or require special devices, and they are not applicable to frozen samples that cannot generate intact single-cell suspensions. scONE-seq is a one-tube reaction, thus is highly scalable and is the first scWGS-RNA-seq method compatible with frozen biobanked tissue. We benchmarked scONE-seq against existing methods using cell lines and lymphocytes from a healthy donor, and we applied it to a 2-year-frozen astrocytoma sample profiling over 1,200 nuclei, subsequently identifying a unique transcriptionally normal-like tumor clone. scONE-seq makes it possible to perform large-scale single-cell multi-omics interrogation with ease on the vast quantities of biobanked tissue, which could transform the scale of future multi-omics single-cell cancer profiling studies.

The Role of the Liver in Iron Homeostasis and What Goes Wrong?

Iron is an essential mineral that is vital for growth development, normal cellular function, synthesis of hormones and connective tissue, and most importantly, serves as a component of hemoglobin to carry oxygen to body tissues. The body finely regulates the amount of circulating and stored iron within the body to maintain concentration levels within range for optimal physiologic function. Without iron, the ability for cells to participate in electron transport and energy metabolism decreases. Furthermore, hemoglobin synthesis is altered, which leads to anemia and decreased oxygen delivery to tissue. Problems arise when there is too little or too much iron. This review explores the role of the liver in iron physiology, iron overload and discusses the most common causes of primary and secondary hepatic iron overload.

Significance of NPM1 Gene Mutations in AML

The aim of this literature review is to examine the significance of the nucleophosmin 1 (NPM1) gene in acute myeloid leukaemia (AML). This will include analysis of the structure and normal cellular function of NPM1, the type of mutations commonly witnessed in NPM1, and the mechanism by which this influences the development and progression of AML. The importance of NPM1 mutation on prognosis and the treatment options available to patients will also be reviewed along with current guidelines recommending the rapid return of NPM1 mutational screening results and the importance of employing a suitable laboratory assay to achieve this. Finally, future developments in the field including research into new therapies targeting NPM1 mutated AML are considered.

Neurons undergo pathogenic metabolic reprograming in models of familial ALS

SummaryNormal cellular function requires a rate of ATP production sufficient to meet demand. In most neurodegenerative diseases (including Amyotrophic Lateral Sclerosis, ALS), mitochondrial dysfunction is postulated raising the possibility of impaired ATP production and a need for compensatory maneuvers to sustain the ATP production/demand balance. We find in our rodent models of familial ALS (fALS), impairment in neuronal glycolytic flux with maintained or enhanced activity of the citric acid cycle. This rewiring of metabolism is associated with normal ATP levels and redox status, supporting the notion that mitochondrial function is not compromised in neurons expressing fALS genes. Genetic loss-of-function manipulation of individual steps in the glycolysis and the pentose phosphate pathway blunt the negative phenotypes seen in various fALS models. We propose that neurons adjust fuel utilization in the setting of neurodegenerative disease-associated mitochondrial dysfunction in a baleful manner and targeting this process can be healthful.

The Role of O-GlcNAcylation in Immune Cell Activation

O-GlcNAcylation is a dynamic post-translational modification where the sugar, O-linked β-N-acetylglucosamine (O-GlcNAc) is added to or removed from various cytoplasmic, nuclear, and mitochondrial proteins. This modification is regulated by only two enzymes: O-GlcNAc transferase (OGT), which adds O-GlcNAc, and O-GlcNAcase (OGA), which removes the sugar from proteins. O-GlcNAcylation is integral to maintaining normal cellular function, especially in processes such as nutrient sensing, metabolism, transcription, and growth and development of the cell. Aberrant O-GlcNAcylation has been associated with a number of pathological conditions, including, neurodegenerative diseases, cancer, diabetes, and obesity. However, the role of O-GlcNAcylation in immune cell growth/proliferation, or other immune responses, is currently incompletely understood. In this review, we highlight the effects of O-GlcNAcylation on certain cells of the immune system, especially those involved in pro-inflammatory responses associated with diabetes and obesity.

Structural and Functional Remodeling of Mitochondria in Cardiac Diseases

Mitochondria undergo structural and functional remodeling to meet the cell demand in response to the intracellular and extracellular stimulations, playing an essential role in maintaining normal cellular function. Merging evidence demonstrated that dysregulation of mitochondrial remodeling is a fundamental driving force of complex human diseases, highlighting its crucial pathophysiological roles and therapeutic potential. In this review, we outlined the progress of the molecular basis of mitochondrial structural and functional remodeling and their regulatory network. In particular, we summarized the latest evidence of the fundamental association of impaired mitochondrial remodeling in developing diverse cardiac diseases and the underlying mechanisms. We also explored the therapeutic potential related to mitochondrial remodeling and future research direction. This updated information would improve our knowledge of mitochondrial biology and cardiac diseases’ pathogenesis, which would inspire new potential strategies for treating these diseases by targeting mitochondria remodeling.

Chemical reporters to study mammalian O-glycosylation

Glycans play essential roles in a range of cellular processes and have been shown to contribute to various pathologies. The diversity and dynamic nature of glycan structures and the complexities of glycan biosynthetic pathways make it challenging to study the roles of specific glycans in normal cellular function and disease. Chemical reporters have emerged as powerful tools to characterise glycan structures and monitor dynamic changes in glycan levels in a native context. A variety of tags can be introduced onto specific monosaccharides via the chemical modification of endogenous glycan structures or by metabolic or enzymatic incorporation of unnatural monosaccharides into cellular glycans. These chemical reporter strategies offer unique opportunities to study and manipulate glycan functions in living cells or whole organisms. In this review, we discuss recent advances in metabolic oligosaccharide engineering and chemoenzymatic glycan labelling, focusing on their application to the study of mammalian O-linked glycans. We describe current barriers to achieving glycan labelling specificity and highlight innovations that have started to pave the way to overcome these challenges.

ninaD regulates cholesterol homeostasis from the midgut which protects against neurodegeneration

SUMMARYCholesterol is crucial to maintain normal cellular function. In human, it has also been involved in various neurodegeneration processes, as Niemann-Pick and Alzheimer diseases. Recently, we have identified a small nucleolar RNA (jouvence) required in the epithelial cells of the gut (enterocytes), and showed that its overexpression extends lifespan. A transcriptomic analysis has revealed a deregulation of several genes in jouvence mutants. Among them, ninaD encoding a mammalian homolog to class B Scavenger receptor is importantly upregulated. In Drosophila, ninaD is required for the uptake of the dietary carotenoid, used for the formation of rhodopsin. Here, we show that jouvence-deleted flies are deficient in cholesterol-ester, as well as old flies present neurodegenerative lesions. Restoring ninaD mRNA expression level in enterocytes restores the metabolic cholesterol-ester level, prevents neurodegeneration and extends lifespan, revealing a gut-brain axis. Our studies demonstrates that ninaD is a central regulator of cholesterol homeostasis and a longevity-promoting factor.

A 5′ UTR GGN repeat controls localisation and translation of a potassium leak channel mRNA through G-quadruplex formation

RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodelling attributed to normal cellular function. In this study, we characterise the G4 formation of a (GGN)13 repeat found within the 5′ UTR of the potassium 2-pore domain leak channel Task3 mRNA. Biophysical analyses show that this (GGN)13 repeat forms a parallel G4 in vitro exhibiting the stereotypical potassium specificity of G4s, remaining thermostable under physiological ionic conditions. Through mouse brain tissue G4-RNA immunoprecipitation, we further confirm that Task3 mRNA forms a G4 structure in vivo. The G4 is inhibitory to translation of Task3 in vitro and is overcome through activity of a G4-specific helicase DHX36, increasing K+ leak currents and membrane hyperpolarisation in HEK293 cells. Further, we observe that this G4 is fundamental to ensuring delivery of Task3 mRNA to distal primary cortical neurites. It has been shown that aberrant Task3 expression correlates with neuronal dysfunction, we therefore posit that this G4 is important in regulated local expression of Task3 leak channels that maintain K+ leak within neurons.