SUMMARY Mechanical signals, such as those evoked by maximal-intensity contractions (MICs), can induce an increase in muscle mass. Rapamycin-sensitive signaling events are widely implicated in the regulation of this process; however, recent studies indicate that rapamycin-insensitive signaling events are also involved. Thus, to identify these events, we generate a map of the MIC-regulated and rapamycin-sensitive phosphoproteome. In total, we quantify more than 10,000 unique phosphorylation sites and find that more than 2,000 of these sites are significantly affected by MICs, but remarkably, only 38 of the MIC-regulated events are mediated through a rapamycin-sensitive mechanism. Further interrogation of the rapamycin-insensitive phosphorylation events identifies the S473 residue on Tripartite Motif-Containing 28 (TRIM28) as one of the most robust MIC-regulated phosphorylation sites, and extensive follow-up studies suggest that TRIM28 significantly contributes to the homeostatic regulation of muscle size and function as well as the hypertrophy that occurs in response to increased mechanical loading.

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Mechanical signals, such as those which are evoked during maximal intensity contractions (MIC), can induce an increase in skeletal muscle size. It has been widely concluded that this process is driven by the activation of rapamycin‐sensitive / mTORC1‐dependent signaling; however, recent studies have revealed that mTORC1‐independent signaling events might also be involved. Thus, in an effort to identify these events, we generated a comprehensive map of the MIC‐regulated, and rapamycin‐sensitive phosphoproteomes. In total, we identified over 2,400 unique MIC‐regulated phosphorylation events, of which, nearly 2,200 were unaffected by rapamycin. Interestingly, one of the most robust MIC‐regulated and rapamycin‐insensitive phosphorylation events was located on the S473 residue on a protein named TRIM28. This was intriguing because TRIM28 is a transcriptional intermediary factor that functions in a variety of biological processes and many of its regulatory effects are dependent on the phosphorylation of the S473 residue. Moreover, a recent study revealed that TRIM28 interacts with several skeletal muscle regulatory factors (e.g., MyoD and Mef2) and their transcriptional co‐repressors and co‐activators. Thus, to investigate the role of TRIM28 in the regulation of muscle size, we generated skeletal muscle specific and inducible TRIM28 knockout mice and then subjected these mice to various forms of mechanical stimuli. Collectively, our results indicated that: i) TRIM28 is not required for the mechanical activation of mTORC1 signaling, ii) TRIM28 plays a key role in the maintenance of normal muscle size, and iii) TRIM28 significantly contributes to the pathway via which mechanical stimuli induce hypertrophy. Taken together, these outcomes establish TRIM28 as a novel, mTORC1‐independent, component of the pathway via which mechanical signals regulate skeletal muscle size. Support or Funding Information NIHR01AR057347

Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are hepatic manifestations of metabolic syndrome and major indications for liver transplantation. Western diet contributes to disease pathogenesis, partially mediated through the gut microbiome, yet mechanisms remain elusive. Human epidemiological studies identified high dietary cholesterol intake as a NAFLD risk factor and it is essential to drive disease in murine models, yet little is known about its role in reshaping gut microbiota. Using the fast food (FF) diet murine model in germ‐free (GF) mice completely devoid of all microbes and their conventionally‐raised (control) counterparts harboring complex microbiomes, we hypothesized high dietary cholesterol‐induced gut microbiota impact NAFLD onset, progression, and severity. Male C57Bl/6 age‐matched GF and control mice were fed 1 of 4 semi‐purified diets: low‐fat (LF); high fat (HF); FF + 0.2% high cholesterol (FFHC); FF + 2% very high cholesterol (FFVHC) for 8 or 24 weeks. Fecal gut microbiota profiles were tracked over time via Illumina MiSeq 16S rRNA gene amplicon sequencing. Serum alanine transaminase (ALT) and lipopolysaccharide binding protein (LBP, an indicator of gut barrier function) were measured throughout the study. Livers were collected for histology and Illumina NovaSeq RNA‐sequencing. Despite equal caloric intake between GF and controls across diets, significant weight gain and increased liver weight to body weight ratios (P<0.05) were observed only in control mice fed FF diets. GF mice were largely protected from disease, with no elevation in plasma ALT, LBP, or histology‐based NAFLD activity score (NAS) regardless of treatment. Conversely, FFVHC control mice exhibited significantly elevated plasma ALT after 8 weeks on diet, which was exacerbated at 24 weeks relative to LF control and all GF groups. FF diets significantly increased (FFHC: P<0.05; FFVHC: P<0.01) plasma LBP after 24 weeks. Control mice fed FF diets exhibited severe steatosis, where FFVHC significantly increased NAS at 8 (P<0.05) and 24 (P<0.001) weeks relative to LF control and all GF groups. Microbiota profiling revealed no change in α‐diversity regardless of diet in control mice. β‐diversity analysis showed HF and FF diets, particularly FFVHC, rapidly shifted gut microbiota community membership after only 4 weeks, preceding disease onset and was further exacerbated over time. Liver RNA‐seq revealed FFVHC diet in control, but not GF, mice significantly enriched genes involved in the KEGG pathway, “antigen processing and presentation” (Bonferroni P<0.001) relative to HF‐fed counterparts at 24 weeks. Taken together, FF diet‐induced shifts in gut microbes are both a prerequisite for and precede NAFLD/NASH disease onset, which is exacerbated by increased dietary cholesterol, driving liver inflammation. These data provide unique insights into how Western diet components impact host‐microbe interactions in complex liver diseases, which may aid in identifying novel therapeutic interventions.

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Background Circadian rhythms are ubiquitous in nature, driving many bodily processes and behaviors, including sleep‐wake cycles and feeding patterns over 24 hours. We and others revealed gut microbes and their functional outputs also exhibit diurnal rhythms that are responsive to how much, what, and when food is consumed. These microbial cues are integrated into host circadian networks, serving as key regulators of metabolism. High fat (HF) diet disrupts diurnal microbial oscillations, impacting diet‐induced obesity (DIO). Apart from feeding, host factors that drive microbial oscillations, specifically in the small intestine, are complex and remain poorly understood. We hypothesized that HF diet disrupts coordination of diurnal rhythms between host‐derived antimicrobial peptides, particularly the host C‐type lectin Regenerating islet‐derived 3 gamma(Reg3γ), and gut microbial community membership, contributing to DIO and metabolic dysfunction. Results Distal ileal tissue and luminal contents were collected every 4 hours over a 12:12 LD cycle from regular chow (RC) vs. HF‐fed germ‐free (GF) and conventionally raised (CONV) C57Bl/6 age and sex‐matched mice. Ileal tissue gene expression analysis reveals diurnal Reg3γ expression is only observed in RC‐fed, but not HF‐fed, CONV mice. Illumina MiSeq 16S rRNA gene amplicon sequencing of ileal luminal contents indicates that HF diet significantly shifts microbial community membership with a corresponding reduction in oscillations relative to RC. Specific Lactobacillaceae bacteria selected by RC oscillate and exhibit positive correlation with Reg3γ expression, while HF promotes expansion of Clostridiales bacteria that negatively correlate with Reg3γ. Using both in vitro intestinal organoid and in vivomonoassociation of GF mice, we identified that exposure to bacterial strains representative of those selected by RC or HF diet elicit a bi‐directional interaction with Reg3γ; only RC‐driven Lactobacillus rhamnosus GG (LGG) induces diurnal Reg3γ expression, suggesting a bacteria‐specific effect. While dietary composition remains the primary driver of microbial oscillators, host factors such as Reg3γ provide secondary cues to drive abundance and oscillation of key gut microbes that are essential for host metabolic homeostasis. Conclusions Together, these results demonstrate transkingdom co‐evolved biological rhythms that are primarily influenced by diet, and reciprocal sensor‐effector signals between host and microbial components. The diurnal dynamics of host innate immune factors and specific diet‐induced ileal gut microbes are key for the maintenance of regional intestinal host‐microbe interactions and metabolic homeostasis.

Protein homeostasis plays a critical role in the regulation of skeletal muscle size, and the maintenance of skeletal muscle size contributes significantly to disease prevention and quality of life. Over the past few decades, it has become widely accepted that skeletal muscle size is controlled by the net balance between the rates of protein synthesis and protein degradation. Despite this assertion, the mechanisms that modulate this balance and lead to changes in muscle size remain incompletely defined. Nevertheless, advancements have been made. For instance, a recent study from our lab revealed that the myofiber‐specific loss of a transcriptional intermediary factor named TRIM28 led to a significant reduction in basal myofiber size and attenuated the increase in myofiber size that occurs in response to mechanical overload. Moreover, rigorous follow‐up studies indicate that the TRIM28 knockout‐induced deficits in myofiber size are not driven by a decrease in the rate of protein synthesis, but that this phenotype is instead associated with elevated levels of canonical markers of protein degradation. Together, these observations led to our central hypothesis that TRIM28 confers its effects on myofiber size via the regulation of protein degradation. Thus, in an effort to gain further insight into this possibility, we performed a deep RNA‐sequencing analysis, the results of which led to the identification of Mettl21c and Mettl21e as two genes whose expression were significantly downregulated by the loss of TRIM28. We were intrigued by this discovery because recent reports have implicated Mettl21c and Mettl21e in the regulation of protein degradation, and it has been shown that the loss of these proteins in muscle promotes aberrant protein degradation and reduces muscle size. Combined with our initial observations, it became apparent that Mettl21c and Mettl21e might be important parts of the pathway via which TRIM28 regulates protein degradation to control myofiber size. To test this theory, we generated expression plasmids encoding HA‐Mettl21c and HA‐Mettl21e, and then used electroporation to demonstrate that the expression of Mettl21c and Mettl21e in myofibers is sufficient to induce a robust hypertrophic response in control animals, and that the hypertrophic effect of Mettl21c, but not Mettl21e, is conserved in muscles lacking TRIM28. Collectively, these findings provide evidence that TRIM28 regulates myofiber size via the regulation of protein degradation, and that Mettl21c, but not Mettl21e, might play an important role in the pathway via which TRIM28 confers this effect.

Nonalcoholic fatty liver disease (NAFLD) is multifactorial in nature, affecting over a billion people worldwide. The gut microbiome has emerged as an associative factor in NAFLD, yet mechanistic contributions are unclear. Here, we show fast food (FF) diets containing high fat, added cholesterol, and fructose/glucose drinking water differentially impact short- vs. long-term NAFLD severity and progression in conventionally-raised, but not germ-free mice. Correlation and machine learning analyses independently demonstrate FF diets induce early and specific gut microbiota changes that are predictive of NAFLD indicators, with corresponding microbial community instability relative to control-fed mice. Shotgun metagenomics showed FF diets containing high cholesterol elevate fecal pro-inflammatory effectors over time, relating to a reshaping of host hepatic metabolic and inflammatory transcriptomes. FF diet-induced gut dysbiosis precedes onset and is highly predictive of NAFLD outcomes, providing potential insights into microbially-based pathogenesis and therapeutics.