Biology subjects

Banks, A. S.

Publications and source records attributed to Banks, A. S..

14 recordsLinked to original sources

bioRxiv2026

GDF3 is an endogenous antagonist of the ActE-ALK7/ACVR2 pathway in adipocytes

Metabolic dysfunction-associated steatotic liver disease (MASLD) and steatohepatitis (MASH) arise, in part, from excessive free fatty acid flux from adipose tissue to the liver. Activin E (ActE, encoded by INHBE) suppresses adipocyte lipolysis through the type I receptor ALK7 (ACVR1C). Loss-of-function variants in INHBE and ACVR1C reduce waist-to-hip ratio in humans, yet genetic knockouts in mice produce insulin resistance and hepatic steatosis, suggesting discrepancies between human and mouse biology. We identify GDF3, a TGF-{beta} superfamily ligand upregulated in obese adipose tissue, as the principal endogenous antagonist of ActE/ALK7 signaling. Human transcriptomic datasets reveal coordinated dysregulation: hepatic INHBE expression and circulating ActE protein are elevated in obesity, while adipose ACVR1C is downregulated and GDF3 is reciprocally upregulated. Using ALK7-selective reporter assays, we show GDF3 inhibits ActE-driven SMAD2/3 signaling as a competitive antagonist rather than the weak agonist previously proposed. ActE suppressed beta-adrenergic-stimulated lipolysis in mouse and human adipocytes and primary human adipose tissue; GDF3 overexpression abolished this effect. In diet-induced obese mice, inducible Gdf3 deletion reduced adipose lipolysis, resolved hepatic steatosis and fibrosis, and improved insulin sensitivity, benefits abolished by Inhbe knockdown, confirming dependence on ActE signaling. Predicted loss-of-function variants in INHBE show only nominal, WHR-dependent associations with type 2 diabetes risk, potentially confounded by hematological effects on HbA1c. Gdf3 deficiency synergized with the clinical-stage anti-activin receptor antibody Bimagrumab to amplify fat-mass loss and improve glucose homeostasis in multiple MASH models. These findings establish GDF3 as an endogenous antagonist of ActE-ALK7 signaling and nominate GDF3 inhibition as a therapeutic strategy for MASLD/MASH.

physiology↗

bioRxiv2026

A Preoptic Neurocircuit That Modulates Metabolic Flexibility

Precise, dynamic control of metabolic fuel usage in response to environmental challenges such as altered food availability or temperature change is essential for animal survival. In mammals, metabolic flexibility--the capacity to shift cellular metabolism between carbohydrate and fatty acid oxidation--is understood to be largely regulated by circulating hormones such as insulin and glucagon. However, the role of the central nervous system in coordinating fuel selection and tissue metabolic tuning remains underexplored. Here, we investigated the mechanisms that mediate metabolic reprogramming following the acute activation of torpor-associated glutamatergic Adcyap1+ torpor-regulating neurons in the anteroventral preoptic area (avPOAVglut2/PACAP). The activation of these neurons rapidly shifts whole-body fuel use from glucose to fatty acids, irrespective of fuel/food availability. This shift is associated with reduced glucose utilization stemming from the transient induction of selective insulin resistance in skeletal muscle. We find that this reduction in skeletal muscle glucose metabolism does not require direct muscle innervation but is rather mediated in part via corticosterone. In contrast to their activation, avPOAVglut2/PACAP neuronal silencing results in improved glucose tolerance, demonstrating powerful bidirectional control of tissue-specific glucose metabolism, whole-body glucose levels, and fuel usage. Together, our findings uncover a novel POA -skeletal muscle pathway that dynamically controls glucose utilization and metabolic flexibility.

neuroscience↗

bioRxiv2025

Microbial metabolism of mannitol as a tracer for the non-invasive measurement of oral-cecal transit

The timing of digestion after a meal reveals information essential for evaluating gastrointestinal function and overall digestive health. Alterations in transit time through the GI tract can reveal abnormalities such as delayed gastric emptying and provide critical insights into nutrient absorption dynamics. This information is particularly valuable for optimizing dietary interventions, managing metabolic conditions such as diabetes, and improving personalized nutrition strategies. Methods for measuring the oral to cecal transit time (OCTT) in murine models have significant limitations. We demonstrate a non-invasive approach in freely-moving non-anesthetized mice which quantifies the microbial digestion of the non-nutritive sweetener mannitol to CO2. We monitor cage air for the production of 13CO2 from 13C-enriched mannitol using Off-Axis Integrated Cavity Output Spectroscopy integrated with multiplexes indirect calorimetry. With this approach, we find mannitol oxidation is absent in mice following commensal depletion of the microbiota. In mice with conventional microbiota, the peak 13C-mannitol oxidation occurs proximal to the mouse cecum, allowing the quantitation of OCTT in mice. By tracking the output of 13CO2, this method provides highly granular, real-time data. We detect delayed OCTT with the use of pharmacological transit-altering compounds loperamide, a gut restricted opioid receptor agonist and also semaglutide, a GLP-1 receptor agonist. This approach may provide more physiologically relevant results in a range of genetic, environmental, and pharmacological research models.

physiology↗

bioRxiv2025

Comparative analysis of naked mole-rat thermogenesis and its potential to maintain euthermia in response to cold

The naked mole-rat (NMR) is a subterranean rodent known for its unique thermal biology, exceptional longevity and resistance to cancer and hypoxia. However, its thermal biology remains controversial, with various reports describing NMRs as poikilotherms, heterotherms, mesotherms or partial homeotherms. Here, we investigated whether the thermogenic potential of NMR brown adipose tissue and its UCP1 differ from those in mice and whether the lack of thermal insulation causes extreme changes in NMR body temperature upon cold exposure. Through longitudinal molecular, thermal, metabolic, and behavioral measurements, we found that NMRs initiated non-shivering thermogenesis and elevated body temperature but could not sustain it due to excessive heat loss and limits to substrate availability. Our results suggest that NMRs represent a unique thermoregulatory category that doesnt fit neatly into traditional classifications. In vitro and in vivo experiments showed that the NMR UCP1 is functional and can be activated and inhibited as expected for most other mammals. We further demonstrated that artificial insulation can partially restore thermoregulatory capabilities in NMRs. This study employs an advanced methodology to characterize the thermal biology of NMRs and helps resolve a long-standing controversy in the field. Significance StatementThis study provides critical insights into the thermal biology of naked mole-rats (NMRs), resolving long-standing controversies regarding their thermoregulatory strategies. We highlight the unique adaptations and limitations of NMR physiology by demonstrating that NMRs possess functional non-shivering thermogenesis and UCP1 but fail to maintain homeothermy due to excessive heat loss. Our findings suggest that artificial insulation can partially restore their thermoregulatory capabilities, offering a new perspective on the evolutionary and ecological significance of fur loss in NMRs. This research advances our understanding of mammalian thermal biology and presents an updated model for NMRs, bridging gaps between previous conflicting reports.

physiology↗

bioRxiv2023

Xiphoid nucleus of the midline thalamus controls cold-induced food seeking

Maintaining body temperature is calorically expensive for endothermic animals. Mammals eat more in the cold to compensate for energy expenditure, but the neural mechanism underlying this coupling is not well understood. Through behavioral and metabolic analyses, we found that mice dynamically switch between energy conservation and food-seeking states in the cold, the latter of which is primarily driven by energy expenditure rather than the sensation of cold. To identify the neural mechanisms underlying cold-induced food seeking, we use whole-brain cFos mapping and found that the xiphoid (Xi), a small nucleus in the midline thalamus, was selectively activated by prolonged cold associated with elevated energy expenditure but not with acute cold exposure. In vivo calcium imaging showed that Xi activity correlates with food-seeking episodes in cold conditions. Using activity-dependent viral strategies, we found that optogenetic and chemogenetic stimulation of cold-activated Xi neurons recapitulated cold-induced feeding, whereas their inhibition suppressed it. Mechanistically, Xi encodes a context-dependent valence switch promoting food-seeking behaviors in cold but not warm conditions. Furthermore, these behaviors are mediated by a Xi to nucleus accumbens projection. Our results establish Xi as a key region for controlling cold-induced feeding, an important mechanism for maintaining energy homeostasis in endothermic animals.

neuroscience↗

bioRxiv2022

GDF3 simultaneously antagonizes BMP signaling and activates TGFβ receptor signaling

Growth differentiation factor 3 (GDF3) is a relatively understudied member of the TGF{beta} superfamily that is highly expressed during development. However, the function of GDF3 in adult biology is contentious. We use in vivo approaches to show that GDF3 loss-of-function in adipose tissue of obese adult mice causes reduced body weight and improved whole-body insulin sensitivity. These effects are accompanied by altered regulation of genes targeted by the TGF{beta} superfamily in vivo. Using in vitro approaches, we show that GDF3 can influence both arms of the TGF{beta} superfamily: GDF3 simultaneously inhibits BMP signaling and activates activin-like SMAD 2/3 signaling. We identify the type II receptors mediating this activity. GDF3 binds to the type II receptors BMPR2, ACTRIIA and ACTRIIB and achieves dose-dependent inhibition of multiple BMP proteins including BMP2, BMP7, BMP9, BMP10, and BMP15 in vitro. We also find that GDF3 activates TGF{beta}/activin-like SMAD2/3 signaling. Unbiased expression profiling confirms that GDF3 both attenuates BMP2-regulated gene expression and drives TGF{beta}/activin-like gene expression. Together these results provide much needed clarity to both the molecular pathways involved in GDF3 signaling and the physiological effects of GDF3 loss of function.

cell biology↗

bioRxiv2022

Alternatively Spliced Landscape of PPARγ mRNA in Podocytes is Distinct from Adipose Tissue

Podocytes are highly differentiated epithelial cells, and their structural and functional integrity is compromised in a majority of glomerular and renal diseases, leading to proteinuria, chronic kidney disease, and kidney failure. Traditional agonists (e.g., pioglitazone) and selective modulators (e.g., GQ-16) of peroxisome-proliferator-activated-receptor-{gamma} (PPAR{gamma}) reduce proteinuria in animal models of glomerular disease and protect podocytes from injury via PPAR{gamma} activation. This indicates a pivotal role for PPAR{gamma} in maintaining glomerular function through preservation of podocytes distinct from its well-understood role in driving insulin sensitivity and adipogenesis. While its transcriptional role in activating adipokines and adipogenic genes is well-established in adipose tissue, liver and muscle, understanding of podocyte PPAR{gamma} signaling remains limited. We performed a comprehensive analysis of PPAR{gamma} mRNA variants due to alternative splicing, in human podocytes and compared with adipose tissue. We found that podocytes express the ubiquitous PPAR{gamma} Var 1 (encoding {gamma}1) and not Var2 (encoding {gamma}2), which is mostly restricted to adipose tissue and liver. Additionally, we detected expression at very low level of Var4, and barely detectable levels of other variants, Var3, Var11, VartORF4 and Var9, in podocytes. Furthermore, a distinct podocyte vs adipocyte PPAR-promoter-response-element containing gene expression, enrichment and pathway signature was observed, suggesting differential regulation by podocyte specific PPAR{gamma}1 variant, distinct from the adipocyte-specific {gamma}2 variant. In summary, podocytes and glomeruli express several PPAR{gamma} variants, including Var1 ({gamma}1) and excluding adipocyte-specific Var2 ({gamma}2), which may have implications in podocyte specific signaling and pathophysiology. This suggests that new selective PPAR{gamma} modulators can be potentially developed that will be able to distinguish between the two forms, {gamma}1 and {gamma}2, thus forming a basis of novel targeted therapeutic avenues.

molecular biology↗

bioRxiv2021

Absence of muricholic acid due to Cyp2c-deficiency protects against high fat diet-induced obesity in male mice but promotes liver damage

ObjectiveMurine-specific muricholic acids (MCAs) are reported to protect against obesity and associated metabolic disorders. However, the response of mice with genetic depletion of MCA to an obesogenic diet has not been evaluated. We used Cyp2c-deficient (Cyp2c-/-) mice, which lack MCAs and thus have a human-like bile acid (BA) profile, to directly investigate the potential role of MCAs in diet-induced obesity. MethodsMale and female Cyp2c-/- mice and wild-type controls were fed a standard chow diet or a high fat diet (HFD) for 18 weeks. We measured BA composition from a pool of liver, gallbladder, and intestine, as well as weekly body weight, food intake, lean and fat mass, systemic glucose homeostasis, energy expenditure, intestinal lipid absorption, fecal lipid, and energy content. ResultsCyp2c deficiency depleted MCAs and caused other changes in BA composition, namely a decrease in the ratio of 12-hydroxylated (12-OH) BAs to non-12-OH BAs, without altering the total BA levels. While wild-type male mice became obese after HFD-feeding, Cyp2c-/- male mice were protected from obesity and associated metabolic dysfunctions. Cyp2c-/- male mice also showed reduced intestinal lipid absorption and increased lipid excretion, which was reversed by oral gavage with the 12-OH BA, taurocholic acid. Cyp2c-/- mice also showed increased liver damage, which appeared stronger in females. ConclusionMCA does not protect against diet-induced obesity but may protect against liver injury. Reduced lipid absorption in Cyp2c-deficient male mice is potentially due to a reduced ratio of 12-OH/non-12-OH BAs.

physiology↗

bioRxiv2021

A gut-restricted lithocholic acid analog as an inhibitor of gut bacterial bile salt hydrolases

Bile acids play crucial roles in host physiology by acting as both detergents that aid in digestion and as signaling molecules that bind to host receptors. Gut bacterial bile salt hydrolase (BSH) enzymes perform the gateway reaction leading to the conversion of host-produced primary bile acids into bacterially modified secondary bile acids. Small molecule probes that target BSHs will help elucidate the causal roles of these metabolites in host physiology. We previously reported the development of a covalent BSH inhibitor with low gut permeability. Here, we build on our previous findings and describe the development of a second-generation gut-restricted BSH inhibitor with enhanced potency, reduced off-target effects, and durable in vivo efficacy. SAR studies focused on the bile acid core identified a compound, AAA-10, containing a C3-sulfonated lithocholic acid scaffold and an alpha-fluoromethyl ketone warhead as a potent pan-BSH inhibitor. This compound inhibits BSH activity in conventional mouse fecal slurries, bacterial cultures, and purified BSH proteins and displays reduced toxicity against mammalian cells compared to first generation compounds. Oral administration of AAA-10 to wild-type mice for 5 days resulted in a decrease in the abundance of the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA) in the mouse GI tract with low systemic exposure of AAA-10, demonstrating that AAA-10 is an effective tool for inhibiting BSH activity and modulating bile acid pool composition in vivo.

biochemistry↗

bioRxiv2021

Restored TDCA and Valine Levels Imitate the Effects of Bariatric Surgery

Obesity is widespread and linked to various co-morbidities. Bariatric surgery has been identified as the only effective treatment, promoting sustained weight loss and the remission of co-morbidities. We performed sleeve-gastrectomies (SGx) in a pre-clinical mouse model of diet-induced obesity (DIO), delineating the effects on long-term remission from obesity. SGx resulted in sustained weight loss and improved glucose tolerance. Mass-spectrometric metabolomic profiling revealed significantly reduced systemic levels of taurodeoxycholic acid (TDCA) and L-valine in DIO mice. Notably, TDCA and L-Valine levels were restored after SGx in both human and mice to levels comparable with lean controls. Strikingly, combined systemic treatment with TDCA and valine induced a profound weight loss in DIO mice analogous to effects observed after SGx. Utilizing indirect calorimetry, we confirmed reduced food intake as causal for TDCA/valine-mediated weight loss via a central inhibition of the melanin-concentrating hormone. In summary, we identified restored TDCA/valine levels as an underlying mechanism of SGx-derived effects on weight loss. Of translational relevance, TDCA and L-valine are presented as novel agents promoting weight loss while reversing obesity-associated metabolic disorders.

cell biology↗

bioRxiv2019

A big-data approach to understanding metabolic rate and response to obesity in laboratory mice

Maintaining a healthy body weight requires an exquisite balance between energy intake and energy expenditure. In humans and in laboratory mice these factors are experimentally measured by powerful and sensitive indirect calorimetry devices. To understand the genetic and environmental factors that contribute to the regulation of body weight, an important first step is to establish the normal range of metabolic values and primary sources contributing to variability in results. Here we examine indirect calorimetry results from two experimental mouse projects, the Mouse Metabolic Phenotyping Centers and International Mouse Phenotyping Consortium to develop insights into large-scale trends in mammalian metabolism. Analysis of nearly 10,000 wildtype mice revealed that the largest experimental variances are consequences of institutional site. This institutional effect on variation eclipsed those of housing temperature, body mass, locomotor activity, sex, or season. We do not find support for the claim that female mice have greater metabolic variation than male mice. An analysis of these factors shows a normal distribution for energy expenditure in the phenotypic analysis of 2,246 knockout strains and establishes a reference for the magnitude of metabolic changes. Using this framework, we examine knockout strains with known metabolic phenotypes. We compare these effects with common environmental challenges including age, and exercise. We further examine the distribution of metabolic phenotypes exhibited by knockout strains of genes corresponding to GWAS obesity susceptibility loci. Based on these findings, we provide suggestions for how best to design and conduct energy balance experiments in rodents, as well as how to analyze and report data from these studies. These recommendations will move us closer to the goal of a centralized physiological repository to foster transparency, rigor and reproducibility in metabolic physiology experimentation.

physiology↗

bioRxiv2019

Sleeve Gastrectomy enhances glucose utilization and remodels adipose tissue independent of weight loss

ObjectiveSleeve gastrectomy (SG) induces weight-loss independent improvements in glucose homeostasis by unknown mechanisms. We sought to identify the metabolic adaptations responsible for these improvements.\n\nMethodsNon-obese C57Bl6/J mice on standard chow underwent SG or sham surgery. Functional testing and indirect calorimetry were used to capture metabolic phenotypes. Tissue-specific glucose uptake was assessed by 18-FDG PET/CT and RNA sequencing was used for gene expression analysis.\n\nResultsIn this model, SG induced durable improvements in glucose tolerance despite not causing lasting changes in weight, fat/lean mass, or food intake. Indirect calorimetry revealed post-SG animals had respiratory exchange ratios (RER) nearing 1.0 on average and had daily RER excursions above 1.0, indicating preferential glucose utilization and increased energy demand, respectively. Sham operated mice demonstrate normal RER feeding/fasting excursions. PET/CT showed increased avidity within white adipose depots. Finally, SG led to an upregulation in the transcriptional pathways involved in energy metabolism, adipocyte maturation, and adaptive and innate immune cell chemotaxis and differentiation within the visceral adipose tissue.\n\nConclusionsSG induces a rapid, weight-loss independent shift towards glucose utilization and transcriptional remodeling of metabolic and immune pathways in visceral adipose tissue.

physiology↗

bioRxiv2019

Development of a Covalent Inhibitor of Gut Bacterial Bile Salt Hydrolases

Bile salt hydrolase (BSH) enzymes are widely expressed by human gut bacteria and catalyze the gateway reaction leading to secondary bile acid formation. Bile acids regulate key metabolic and immune processes by binding to host receptors. There is an unmet need for a potent tool to inhibit BSHs across all gut bacteria in order to study the effects of bile acids on host physiology. Here, we report the development of a covalent pan-inhibitor of gut bacterial BSH. From a rationally designed candidate library, we identified a lead compound bearing an alpha-fluoromethyl ketone warhead that modifies BSH at the catalytic cysteine residue. Strikingly, this inhibitor abolished BSH activity in conventional mouse feces. Mice gavaged with a single dose of this compound displayed decreased BSH activity and decreased deconjugated bile acid levels in feces. Our studies demonstrate the potential of a covalent BSH inhibitor to modulate bile acid composition in vivo.

microbiology↗

bioRxiv2017

CalR: A Web-based Analysis Tool for Indirect Calorimetry Experiments

We report a web-based tool for analysis of indirect calorimetry experiments which measure physiological energy balance. CalR easily imports raw data files, generates plots, and determines the most appropriate statistical tests for interpretation. Analysis with the general linear model (which includes ANOVA and ANCOVA) allows for flexibility to interpret experiments of obesity and thermogenesis. Users may also produce standardized output files of an experiment which can be shared and subsequently re-evaluated using CalR. This framework will provide the transparency necessary to enhance consistency and reproducibility in experiments of energy expenditure. CalR analysis software will greatly increase the speed and efficiency with which metabolic experiments can be organized, analyzed according to accepted norms, and reproduced--and will likely become a standard tool for the field. CalR is accessible at https://CalR.bwh.harvard.edu.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC=\"FIGDIR/small/213967_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (34K):\norg.highwire.dtl.DTLVardef@c27058org.highwire.dtl.DTLVardef@15dbe84org.highwire.dtl.DTLVardef@1870019org.highwire.dtl.DTLVardef@17a17c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗