Single Nucleus Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Gliomas.

Gliomas, the predominant form of brain cancer, comprise diverse malignant subtypes with limited curative therapies available. The insufficient understanding of their molecular diversity and evolutionary processes hinders the advancement of new treatments. Technical complexities associated with formalin-fixed paraffin-embedded (FFPE) clinical samples hinder molecular-level analyses of gliomas. Current single-cell RNA sequencing (scRNA-seq) platforms are inadequate for large-scale clinical applications. In this study, automated snRandom-seq is developed, a high-throughput single-nucleus total RNA sequencing platform optimized for archival FFPE samples. This platform integrates automated single-nucleus isolation and droplet barcoding systems with the random primer-based scRNA-seq chemistry, accommodating a broad spectrum of sample types. The automated snRandom-seq is applied to analyze 116 492 single nuclei from 17 FFPE samples of various glioma subtypes, including rare clinical samples and matched primary-recurrent glioblastomas (GBMs). The study provides comprehensive insights into the molecular characteristics of gliomas at the single-cell level. Abundant non-coding RNAs (ncRNAs) with distinct expression profiles across different glioma clusters and uncovered promising recurrence-related targets and pathways in primary-recurrent GBMs are identified. These findings establish automated snRandom-seq as a robust tool for scRNA-seq of FFPE samples, enabling exploration of molecular diversities and tumor evolution. This platform holds significant implications for large-scale integrative and retrospective clinical research.

Lipidomics and single-cell RNA sequencing reveal lipid and cell dynamics of porcine glycerol-injured skeletal muscle regeneration model.

AIMS: Intramuscular fat (IMF) infiltration and extracellular matrix (ECM) deposition are characteristic features of muscle dysfunction, such as muscular dystrophy and severe muscle injuries. However, the underlying mechanisms of cellular origin, adipocyte formation and fibrosis in skeletal muscle are still unclear. MAIN METHODS: Pigs were injected with 50 % glycerol (GLY) to induce skeletal muscle injury and regeneration. The acyl chain composition was analyzed by lipidomics, and the cell atlas and molecular signatures were revealed via single-cell RNA sequencing (scRNA-seq). Adipogenesis analysis was performed on fibroblast/fibro-adipogenic progenitors (FAPs) isolated from pigs. KEY FINDINGS: The porcine GLY-injured skeletal muscle regeneration model was characterized by IMF infiltration and ECM deposition. Skeletal muscle stem cells (MuSCs) and FAP clusters were analyzed to explore the potential mechanisms of adipogenesis and fibrosis, and it was found that the TGF-ß signaling pathway might be a key switch that regulates differentiation. Consistently, activation of the TGF-ß signaling pathway increased SMAD2/3 phosphorylation and inhibited adipogenesis in FAPs, while inhibition of the TGF-ß signaling pathway increased the expression of PPARγ and promoted adipogenesis. SIGNIFICANCE: GLY-induced muscle injury and regeneration provides comprehensive insights for the development of therapies for human skeletal muscle dysfunction and fatty infiltration-related diseases in which the TGF-ß/SMAD signaling pathway might play a primary regulatory role.

High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome.

Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications in health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve comprehensive understanding of complex microbial communities together with their hosts is therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive responses states among species in Prevotella and Roseburia genus and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated the smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-word situations and promises new perspectives in the understanding of human microbiomes.

C-to-G editing generates double-strand breaks causing deletion, transversion and translocation.

Base editors (BEs) introduce base substitutions without double-strand DNA cleavage. Besides precise substitutions, BEs generate low-frequency 'stochastic' byproducts through unclear mechanisms. Here, we performed in-depth outcome profiling and genetic dissection, revealing that C-to-G BEs (CGBEs) generate substantial amounts of intermediate double-strand breaks (DSBs), which are at the centre of several byproducts. Imperfect DSB end-joining leads to small deletions via end-resection, templated insertions or aberrant transversions during end fill-in. Chromosomal translocations were detected between the editing target and off-targets of Cas9/deaminase origin. Genetic screenings of DNA repair factors disclosed a central role of abasic site processing in DSB formation. Shielding of abasic sites by the suicide enzyme HMCES reduced CGBE-initiated DSBs, providing an effective way to minimize DSB-triggered events without affecting substitutions. This work demonstrates that CGBEs can initiate deleterious intermediate DSBs and therefore require careful consideration for therapeutic applications, and that HMCES-aided CGBEs hold promise as safer tools.

Identifying the insomnia-related psychological issues associated with hyperarousal: A network perspective.

Hyperarousal, recognized as a fundamental characteristic of insomnia for decades, has yielded limited evidence concerning its direct psychological associations. This study aimed to explore the psychological factors linked to hyperarousal within the framework of interrelated variables. Two independent samples, comprising n = 917 and n = 652 young adults, were included in the study. Employing the first dataset as a discovery sample and the second dataset as a replication sample, network analyses were conducted using 26 variables derived from 17 scales. The objective was to estimate the direct and indirect associations between psychological issues, including hyperarousal and insomnia. Additionally, linear regression analysis was employed to assess the convergence of findings obtained from the network analysis. Network analyses in both samples converged to reveal direct associations between insomnia severity and several psychological factors, including negative sleep beliefs, physical fatigue, insomnia response to stress, hyperarousal, self-reported depression, and mental fatigue. Notably, the nodes with relative importance within the network include trait anxiety, depressive rumination, hyperarousal, perfectionism sub-dimension of concern over mistakes, and private self-consciousness. Hyperarousal is one of the key factors linking insomnia with a variety of psychological issues, including emotion-related factors (rumination, perveived stress), sleep-related factors (dysfunctional sleep beliefs and attitudes, insomnia response to stress, fatigue, chronotype), and self-related factors (self-consciousness, perfectionism). The results suggest that forthcoming strategies for enhancing the treatment efficacy of insomnia could consider supplementary interventions that specifically address hyperarousal, other factors directly linked to insomnia, or the hub nodes within the network.

The Impact of Sleep Deprivation on Brain Networks in Response to Social Evaluation Tasks.

Sleep loss may lead to negative bias during social interaction. In the current study, we conducted a revised social evaluation task experiment to investigate how sleep deprivation influences the self-referential and cognitive processes of social feedback. The experiment consisted of a first impression task and a social feedback task. Seventy-eight participants completed the first impression task and were divided into normal and poor sleep groups. The results of an independent samples t-test showed that participants who slept worse were less likely to socialize with others but did not evaluate others as less attractive. Afterward, 22 of the participants from the first impression task were recruited to complete the social feedback task during functional magnetic resonance imaging (fMRI) on the mornings following two different sleep conditions at night: one night of normal sleep and one night of sleep deprivation. The results of this within-subject design study showed that participants who experienced the latter condition showed increased activation within the default mode network (i.e. superior parietal lobule, precuneus, inferior parietal lobule, inferior temporal gyrus, and medial frontal gyrus) and anterior cingulate cortex (ACC) and stronger negative insula functional connectivity (FC) with the precuneus to negative feedback than positive feedback. The altered activation and behavioral pattern may indicate a negative bias for social cues. However, stronger negative coupling may indicate stronger cognitive control, which may protect against potential damage to self-concept. Our study suggested that sleep impairs most social functions, but may protect against impairment of important ones, such as self-concept.

Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq.

Bacteria colonize almost all parts of the human body and can differ significantly. However, the population level transcriptomics measurements can only describe the average bacteria population behaviors, ignoring the heterogeneity among bacteria. Here, we report a droplet-based high-throughput single-microbe RNA-seq assay (smRandom-seq), using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion for mRNA enrichment. smRandom-seq showed a high species specificity (99%), a minor doublet rate (1.6%), a reduced rRNA percentage (32%), and a sensitive gene detection (a median of ~1000 genes per single E. coli). Furthermore, smRandom-seq successfully captured transcriptome changes of thousands of individual E. coli and discovered a few antibiotic resistant subpopulations displaying distinct gene expression patterns of SOS response and metabolic pathways in E. coli population upon antibiotic stress. smRandom-seq provides a high-throughput single-microbe transcriptome profiling tool that will facilitate future discoveries in microbial resistance, persistence, microbe-host interaction, and microbiome research.

High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq.

Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank for clinical history and follow-up data. It is still challenging to achieve single cell/nucleus RNA (sc/snRNA) profile in FFPE tissues. Here, we develop a droplet-based snRNA sequencing technology (snRandom-seq) for FFPE tissues by capturing full-length total RNAs with random primers. snRandom-seq shows a minor doublet rate (0.3%), a much higher RNA coverage, and detects more non-coding RNAs and nascent RNAs, compared with state-of-art high-throughput scRNA-seq technologies. snRandom-seq detects a median of >3000 genes per nucleus and identifies 25 typical cell types. Moreover, we apply snRandom-seq on a clinical FFPE human liver cancer specimen and reveal an interesting subpopulation of nuclei with high proliferative activity. Our method provides a powerful snRNA-seq platform for clinical FFPE specimens and promises enormous applications in biomedical research.

Cold exposure alters lipid metabolism of skeletal muscle through HIF-1α-induced mitophagy.

BACKGROUND: In addition to its contractile properties and role in movement, skeletal muscle plays an important function in regulating whole-body glucose and lipid metabolism. A central component of such regulation is mitochondria, whose quality and function are essential in maintaining proper metabolic homeostasis, with defects in processes such as autophagy and mitophagy involved in mitochondria quality control impairing skeletal muscle mass and function, and potentially leading to a number of associated diseases. Cold exposure has been reported to markedly induce metabolic remodeling and enhance insulin sensitivity in the whole body by regulating mitochondrial biogenesis. However, changes in lipid metabolism and lipidomic profiles in skeletal muscle in response to cold exposure are unclear. Here, we generated lipidomic or transcriptome profiles of mouse skeletal muscle following cold induction, to dissect the molecular mechanisms regulating lipid metabolism upon acute cold treatment. RESULTS: Our results indicated that short-term cold exposure (3 days) can lead to a significant increase in intramuscular fat deposition. Lipidomic analyses revealed that a cold challenge altered the overall lipid composition by increasing the content of triglyceride (TG), lysophosphatidylcholine (LPC), and lysophosphatidylethanolamine (LPE), while decreasing sphingomyelin (SM), validating lipid remodeling during the cold environment. In addition, RNA-seq and qPCR analysis showed that cold exposure promoted the expression of genes related to lipolysis and fatty acid biosynthesis. These marked changes in metabolic effects were associated with mitophagy and muscle signaling pathways, which were accompanied by increased TG deposition and impaired fatty acid oxidation. Mechanistically, HIF-1α signaling was highly activated in response to the cold challenge, which may contribute to intramuscular fat deposition and enhanced mitophagy in a cold environment. CONCLUSIONS: Overall, our data revealed the adaptive changes of skeletal muscle associated with lipidomic and transcriptomic profiles upon cold exposure. We described the significant alterations in the composition of specific lipid species and expression of genes involved in glucose and fatty acid metabolism. Cold-mediated mitophagy may play a critical role in modulating lipid metabolism in skeletal muscle, which is precisely regulated by HIF-1α signaling.

Functional connectivity between dorsal attention and default mode networks mediates subjective sleep duration and depression in young females.

BACKGROUND: Depression prevails throughout the world. Young females are more likely to suffer from depression because of lack of sleep. METHODS: We recruited 405 young female participants to assess their subjective sleep duration and self-rating depression. The resting-state magnetic resonance imaging (rs-fMRI) data were collected to identify the brain regions related to sleep duration and depression, and a mediating model was established among sleep duration, depression and functional connectivity (FC) of rs-fMRI. RESULTS: Correlation analysis indicated that subjective sleep duration was negatively associated with self-rating depression in young females (r = -0.22, p < .001). The network connectivity between dorsal attention network (DAN) and default mode network (DMN) positively correlated with self-rating depression (r = 0.13, p < .05), and negatively correlated with subjective sleep duration (r = -0.14, p < .01). Furthermore, the mediation analysis revealed that the FC of DAN-DMN significantly mediated the effect of sleep duration on depression. LIMITATIONS: The study was a cross-section design and the sleep duration of the participants was subjectively reported. Future studies should consider to track the participants longitudinally and to measure the objective sleep duration by actigraph or polysomnography. CONCLUSIONS: The participants with less sleep duration are more prone to develop depression feelings. The FC of DAN-DMN mediated the effect of sleep duration on depression. Thus, the FC of DAN-DMN could be consider as a neural target to relieve depression by increasing sleep duration in young females.

Cellular and Transcriptional Dynamics during Brown Adipose Tissue Regeneration under Acute Injury.

Brown adipose tissue (BAT) is the major site of non-shivering thermogenesis and crucial for systemic metabolism. Under chronic cold exposures and high-fat diet challenges, BAT undergoes robust remodeling to adapt to physiological demands. However, whether and how BAT regenerates after acute injuries are poorly understood. Here, we established a novel BAT injury and regeneration model (BAT-IR) in mice and performed single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq to determine cellular and transcriptomic dynamics during BAT-IR. We further defined distinct fibro-adipogenic and myeloid progenitor populations contributing to BAT regeneration. Cell trajectory and gene expression analyses uncovered the involvement of MAPK, Wnt, and Hedgehog (Hh) signaling pathways in BAT regeneration. We confirmed the role of Hh signaling in BAT development through Myf5Cre-mediated conditional knockout (cKO) of the Sufu gene to activate Hh signaling in BAT and muscle progenitors. Our BAT-IR model therefore provides a paradigm to identify conserved cellular and molecular mechanisms underlying BAT development and remodeling.

Dual-Scale Textured Broadband Si-Based Light Absorber.

Various antireflective structures and methods are proposed to solve the optical loss of Si-based absorber devices. Dual-scale structures have received more concern from researchers in recent years. In this study, the finite difference time domain (FDTD) method is employed to investigate deeply the dependence of optical response on the geometric shape and size of structures. The micron cone shows lower reflectivity than other micron structures. Additionally, the lowest reflectivity region moves with the increasing height size of the cone structure. We proposed creatively a nanoripple-cone structure that maintains low reflectivity properties under varying incident angles whether in the visible region or the near-infrared region. Furthermore, the lower reflectivity is obtained with increasing micron cone and decreasing nanoripple. Finally, the dual-scale nanoripple-cone is fabricated directly and cost-effectively by a femtosecond laser instead of a two-step texture-on-texture way. The measured result shows that the high absorption above 98% extends to the mid-infrared region. This study provides directions for the fabrication of wideband Si-based absorber devices to reduce reflectivity, which exhibits a wide application potential and promotes the evolution of multi-laser processing.

Cold Exposure Induces Depot-Specific Alterations in Fatty Acid Composition and Transcriptional Profile in Adipose Tissues of Pigs.

Cold exposure promotes fat oxidation and modulates the energy metabolism in adipose tissue through multiple mechanisms. However, it is still unclear about heat-generating capacity and lipid mobilization of different fat depots without functional mitochondrial uncoupling protein 1 (UCP1). In this study, we kept finishing pigs (lack a functional UCP1 gene) under cold (5-7°C) or room temperature (22-25°C) and determined the effects of overnight cold exposure on fatty acid composition and transcriptional profiles of subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT). And the plasma metabolomes of porcine was also studied by LC-MS-based untargeted metabolomics. We found that the saturated fatty acids (SFAs) content was decreased in SAT upon cold exposure. While in VAT, the relative content of lauric acid (C12:0), myristic acid (C14:0) and lignoceric acid (C24:0) were decreased without affecting total SFA content. RNA-seq results showed SAT possess active organic acid metabolism and energy mobilization upon cold exposure. Compared with SAT, cold-induced transcriptional changes were far less broad in VAT, and the differentially expressed genes (DEGs) were mainly enriched in fat cell differentiation and cell proliferation. Moreover, we found that the contents of organic acids like creatine, acamprosate, DL-3-phenyllactic acid and taurine were increased in plasma upon overnight cold treatment, suggesting that cold exposure induced lipid and fatty acid metabolism in white adipose tissue (WAT) might be regulated by functions of organic acids. These results provide new insights into the effects of short-term cold exposure on lipid metabolism in adipose tissues without functional UCP1.

The regulatory role of dietary factors in skeletal muscle development, regeneration and function.

Skeletal muscle plays a crucial role in motor function, respiration, and whole-body energy homeostasis. How to regulate the development and function of skeletal muscle has become a hot research topic for improving lifestyle and extending life span. Numerous transcription factors and nutritional factors have been clarified are closely associated with the regulation of skeletal muscle development, regeneration and function. In this article, the roles of different dietary factors including green tea, quercetin, curcumin (CUR), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and resveratrol (RES) in regulating skeletal muscle development, muscle mass, muscle function, and muscle recovery have been summarized and discussed. We also reviewed the potential regulatory molecular mechanism of these factors. Based on the current findings, dietary factors may be used as a potential therapeutic agent to treat skeletal muscle dysfunction as well as its related diseases.

Dual Laser Beam Asynchronous Dicing of 4H-SiC Wafer.

SiC wafers, due to their hardness and brittleness, suffer from a low feed rate and a high failure rate during the dicing process. In this study, a novel dual laser beam asynchronous dicing method (DBAD) is proposed to improve the cutting quality of SiC wafers, where a pulsed laser is firstly used to introduce several layers of micro-cracks inside the wafer, along the designed dicing line, then a continuous wave (CW) laser is used to generate thermal stress around cracks, and, finally, the wafer is separated. A finite-element (FE) model was applied to analyze the behavior of CW laser heating and the evolution of the thermal stress field. Through experiments, SiC samples, with a thickness of 200 µm, were cut and analyzed, and the effect of the changing of continuous laser power on the DBAD system was also studied. According to the simulation and experiment results, the effectiveness of the DBAD method is certified. There is no more edge breakage because of the absence of the mechanical breaking process compared with traditional stealth dicing. The novel method can be adapted to the cutting of hard-brittle materials. Specifically for materials thinner than 200 µm, the breaking process in the traditional SiC dicing process can be omitted. It is indicated that the dual laser beam asynchronous dicing method has a great engineering potential for future SiC wafer dicing applications.

Cold Exposure Affects Lipid Metabolism, Fatty Acids Composition and Transcription in Pig Skeletal Muscle.

Cold exposure promotes glucose oxidation and modulates the lipid metabolism in adipose tissue, but it is still not fully clear whether cold exposure could affect meat quality and fatty acid metabolism in skeletal muscle of pig in vivo. Here, we kept finishing pigs under cold or room temperature overnight and determined the effects of cold exposure on meat quality, fatty acids composition and transcriptional changes in skeletal muscle of pigs. We found that cold exposure significantly reduced the meat colour24 h and pH24 h, without affecting carcass characteristics and other meat quality traits. Considerable changes were found in the proportions of individual fatty acids and the total content of saturated fatty acid, polyunsaturated fatty acids, monounsaturated fatty acid and n3-fatty acids. RNA-seq results showed upregulated fatty acid biosynthesis genes and downregulated mitochondrial beta-oxidation genes. The lipid metabolism in cold-treated longissimus dorsi muscle might be regulated by functions of the lipoprotein particle, the extracellular matrix, and the PPAR signaling pathways. Our study revealed the potential of cold exposure to regulate the lipid metabolism and fatty acid composition in skeletal muscle of farmed animals.

Association Between Weight Change and Leukocyte Telomere Length in U.S. Adults.

Objective: To investigate the association of dynamic weight change in adulthood with leukocyte telomere length among U.S. adults. Methods: This study included 3,886 subjects aged 36-75 years from the National Health and Nutrition Examination Survey (NHANES) 1999-2002 cycle. Survey-weighted multivariable linear regression with adjustments for potential confounders was utilized. Results: 3,386 individuals were finally included. People with stable obesity had a 0.130 kbp (95% CI: 0.061-0.198, P=1.97E-04) shorter leukocyte telomere length than those with stable normal weight (reference group) during the 10-year period, corresponding to approximately 8.7 years of aging. Weight gain from non-obesity to obesity shortened the leukocyte telomere length by 0.094 kbp (95% CI: 0.012-0.177, P=0.026), while normal weight to overweight or remaining overweight shortened the leukocyte telomere length by 0.074 kbp (95% CI: 0.014-0.134, P=0.016). The leukocyte telomere length has 0.003 kbp attrition on average for every 1 kg increase in weight from a mean age of 41 years to 51 years. Further stratified analysis showed that the associations generally varied across sex and race/ethnicity. Conclusions: This study found that weight changes during a 10-year period was associated with leukocyte telomere length and supports the theory that weight gain promotes aging across adulthood.

UCP1 Knockin Induces Lipid Dynamics and Transcriptional Programs in the Skeletal Muscles of Pigs.

Uncoupling protein 1 (UCP1), the hallmark protein responsible for nonshivering thermogenesis in adipose tissue (especially brown adipose tissue) has regained researchers' attention in the context of metabolic disorders following the realization that UCP1 can be activated in adult humans and reconstituted in pigs. Both skeletal muscle and adipose tissue are highly dynamic tissues that interact at the metabolic and hormonal level in response to internal and external stress, and they coordinate in maintaining whole-body metabolic homeostasis. Here, we utilized lipidomics and transcriptomics to identify the altered lipid profiles and regulatory pathways in skeletal muscles from adipocyte-specific UCP1 knock-in (KI) pigs. UCP1 KI changed the contents of glycerophospholipids and acyl carnitines of skeletal muscles. Several metabolic regulatory pathways were more enriched in the UCP1 KI skeletal muscle. Comparison of the transcriptomes of adipose and skeletal muscle suggested that nervous system or chemokine signaling might account for the crosstalk between these two tissues in UCP1 KI pigs. Comparison of the lipid biomarkers from UCP1 KI pigs and other mammals suggested associations between UCP1 KI-induced metabolic alternations and metabolic and muscle dysfunction. Our study reveals the lipid dynamics and transcriptional programs in the skeletal muscle of UCP1 KI pigs and suggests that a network regulates metabolic homeostasis between skeletal muscle and adipose tissue.

Single-cell RNA sequencing and lipidomics reveal cell and lipid dynamics of fat infiltration in skeletal muscle.

BACKGROUND: Ageing is accompanied by sarcopenia and intramuscular fat (IMAT) infiltration. In skeletal muscle, fat infiltration is a common feature in several myopathies and is associated with muscular dysfunction and insulin resistance. However, the cellular origin and lipidomic and transcriptomic changes during fat infiltration in skeletal muscle remain unclear. METHODS: In the current study, we generated a high IMAT-infiltrated skeletal muscle model by glycerol (GLY) injection. Single-cell RNA sequencing and lineage tracing were performed on GLY-injured skeletal muscle at 5 days post-injection (DPI) to identify the cell origins and dynamics. Lipidomics and RNA sequencing were performed on IMAT-infiltrated skeletal muscle at 14 DPI (or 17 DPI for the cold treatment) to analyse alterations of lipid compositions and gene expression levels. RESULTS: We identified nine distinct major clusters including myeloid-derived cells (52.13%), fibroblast/fibro/adipogenic progenitors (FAPs) (23.24%), and skeletal muscle stem cells (2.02%) in GLY-injured skeletal muscle. Clustering and pseudotemporal trajectories revealed six subpopulations in fibroblast/FAPs and 10 subclusters in myeloid-derived cells. A subpopulation of myeloid-derived cells expressing adipocyte-enriched genes and Pdgfra- /Cd68+ cells displayed lipid droplets upon adipogenic induction, indicating their adipogenic potential. Lipidomic analysis revealed the changes of overall lipid classes composition (e.g. triglycerides (TAGs) increased by 19.3 times, P = 0.0098; sulfoquinovosyl diacylglycerol decreased by 83%, P = 0.0056) and in the distribution of lipids [e.g. TAGs (18:2/18:2/22:6) increased by 181.6 times, P = 0.021] between GLY-group and saline control. RNA-seq revealed 1847 up-regulated genes and 321 down-regulated genes and significant changes in lipid metabolism-related pathways (e.g. glycerolipid pathway and glycerophospholipid pathway) in our model of GLY-injured skeletal muscle. Notably, short-term cold exposure altered fatty acid composition (e.g. saturated fatty acid decreased by 6.4%, P = 0.058) in fat-infiltrated muscles through directly affecting lipid metabolism pathways including PI3K-AKT and MAPK signalling pathway. CONCLUSIONS: Our results showed that a subpopulation of myeloid-derived cells may contribute to IMAT infiltration. GLY-induced IMAT infiltration changed the lipid composition and gene expression profiles. Short-term cold exposure might regulate lipid metabolism and its related signalling pathways in fat-infiltrated muscle. Our study provides a comprehensive resource describing the molecular signature of fat infiltration in skeletal muscle.

LKB1 Differently Regulates Adipogenesis in Intramuscular and Subcutaneous Adipocytes through Metabolic and Cytokine-Related Signaling Pathways.

Liver kinase B1 (LKB1) plays important and various roles in the differentiation and lipid metabolism of adipocytes. However, the current knowledge of the respective roles of LKB1 in subcutaneous fat (SCF) and intramuscular fat (IMF) adipocytes remains unclear. This study aimed to discover the different regulatory mechanisms of LKB1 in SCF and IMF adipocytes. We found that LKB1 overexpression inhibited adipogenesis in both SCF and IMF adipocytes, and SCF adipocytes were more sensitive to regulation by LKB1. Transcriptomics results showed that IMF adipocytes had many more differentially expressed genes (DEGs) than SCF adipocytes. Pathway analysis of the shared and distinct DEGs revealed that the main adipogenesis mechanism was similar between SCF and IMF adipocytes upon LKB1 overexpression, while regulatory and metabolic signaling pathways, such as MAPK, PPAR signaling pathways, were differently regulated by LKB1. Several cytokine-related pathways were only enriched in LKB1-overexpressing IMF adipocytes. Our study reveals different regulators and signaling pathways between SCF and IMF adipocytes under LKB1 overexpression, which may be potential targets to differentially control SCF and IMF deposition and improve our understanding of the regulatory mechanisms of IMF deposition.