Regulator of G-protein Signaling 14 Knockout (RGS14 KO) mice exhibit enhanced exercise capacity and health span, however the contribution of the gut microbiota to this phenotype remains unclear. This study integrated long-read rRNA operon amplicon sequencing and metabolomics to first determine how microbial composition and tissue metabolite profiles differ between RGS14 KO and their wild-type littermates. Next, we investigated how administration of antibiotics to perturb the gut microbiota may affect the RGS14 KO phenotype. Prior to antibiotic treatment (ABX), RGS14 KO mice outperformed WT littermates in maximal running distance and work performed, accompanied by elevated skeletal muscle citrate synthase, complex IV activity, and nitric oxide production. One week of ABX significantly reduced exercise capacity in both genotypes and markedly suppressed mitochondrial activity in RGS14 KO skeletal muscle. Gut microbiota profiling revealed similar phylum-level structure between genotypes but distinct species- and strain-level signatures. Metabolomics of brown adipose tissue (BAT) and quadriceps identified genotype-specific metabolic programs that were disrupted by ABX, including pathways related to amino acid metabolism, nucleotide turnover, and mitochondrial energetics. Collectively, these findings demonstrate that RGS14 KO mice harbor unique microbial and metabolic networks that support enhanced thermogenesis and exercise performance, and that microbiota depletion eliminates these advantages. This work establishes a mechanistic foundation connecting the gut microbiota to BAT and skeletal muscle metabolism, highlighting potential microbiome-targeted strategies to improve metabolic health and physical performance.

In mammals, hepatic urea cycle enzymes (UCEs) convert ammonia, the toxic nitrogenous waste, into urea for excretion. In hepatocellular carcinoma (HCC), UCE expression is often heterogeneously repressed, but its role in tumorigenesis is unclear. We show that, as in patients, UCE expression is markedly reduced in multiple HCC mouse models, including those driven by oncogenic c-MET/β-catenin, leading to impaired ammonia clearance, altered amino acid metabolism, and increased pyrimidine synthesis. In contrast, UCE expression is largely preserved in c-MET/sgAxin1 tumors, allowing assessment of the consequences of UCE loss. Silencing individual UCEs increases ammonia burden and accelerates HCC with reprogrammed amino acid and pyrimidine metabolism, supporting a causal role for defective ammonia detoxification in oncogenesis. Notably, dietary protein restriction lowers hepatic ammonia and slows tumor growth. These findings establish a mechanistic link between nitrogen overload and hepatocarcinogenesis and highlight protein restriction as a feasible therapeutic strategy for patients with impaired nitrogenous waste handling.

The gut microbiome influences immune and metabolic homeostasis. Our research using non-obese diabetic (NOD) mice revealed that early-life antibiotic exposure remodels the gut microbiome affecting metabolism and accelerating type 1 diabetes (T1D) incidence, with cecal material transplant (CMT) mitigating the damage. Now examining murine intestinal lipidomic profiles, we identified 747 compounds. Comparing the lipidomic profiles of cecal contents of conventional and germ-free mice and their diets, we identified 87 microbially-produced lipids reduced by antibiotic exposure but CMT-restored. Parallel analysis of human fecal lipid profiles after azithromycin-exposure showed significant alterations with substantial overlap with mice. In vitro co-culture with mouse macrophages or small intestinal epithelial cells and human colonic epithelial cells identified phospholipids that repress inflammation through the NFκB pathway. Oral administration of these phospholipids to antibiotic-treated NOD mice reduced expression of ileal genes involved in early stages of T1D pathogenesis. These findings indicate potential therapeutic anti-inflammatory roles of microbially-produced lipids.

Supplementary Fig. S2 shows the changes in metabolic profile after suberoylanilide hydroxamic acid (SAHA) treatment for 3 and 24 h.

Pathway analysis, originally developed for gene expression data, has been adapted for metabolomics. However, owing to the unique characteristics and constraints of metabolites compared with genes, pathway analysis in metabolomics often yields misleading or nonsensical results.

Supplementary Fig. S1 shows the top metabolites regulated by suberoylanilide hydroxamic acid (SAHA) treatment in lipopolysaccharide (LPS)-treated BEAS-2B cells.

Supplementary Table S4 shows the genes analyzed for significant differential expression in control vs. LPS and LPS vs. SAHA groups.

Dietary interventions show therapeutic potential in cancer, but systematic comparisons are lacking. We performed a dietary pan-amino acid dropout screen in an orthotopic model of NOTCH1-driven T-cell acute lymphoblastic leukemia and identified histidine depletion as uniquely antileukemic. Histidine-restricted diets extended survival of leukemic mice in a dose-dependent manner, while remaining well-tolerated. Mechanistically, multiomic profiling revealed that histidine deprivation-induced ribosome stalling activates GCN2 to suppress cholesterol biosynthesis pathways critical for leukemic proliferation. Dietary cholesterol supplementation partially reverted the antileukemic effects of histidine restriction in vivo. These findings couple histidine levels and translational control to cholesterol metabolism, which can be therapeutically exploited for cancer treatment. Our results suggest that defined dietary amino acid restrictions may expose broader therapeutic opportunities in diseases beyond cancer.

Tumors have diverse mutations and origins but a common requirement for increased proliferation is the need to elevate nutrient uptake and metabolism. mTOR complex 2 (mTORC2) signaling is often found upregulated in cancers but how it could promote tumorigenesis remains poorly understood. In mice with T-cell specific deficiency in PTEN, normal T cell differentiation occurs until the onset of lymphoma at around 10-20 weeks after birth. To address how lymphomagenesis is triggered, we monitored metabolism and mTOR signaling. We found that mTORC2 activation is progressively amplified during lymphomagenesis. This coincides with increasing levels of GFAT1, the rate-limiting enzyme of the de novo hexosamine biosynthetic pathway (HBP) while the amounts of UDP-GlcNAc, the product of the HBP, declined over time. Co-ablation of PTEN with either rictor (mTORC2 component) or GFAT1 prevents lymphomagenesis. Our findings suggest that during PTEN deficiency, limitation of UDP-GlcNAc during T cell differentiation could amplify mTORC2 signaling leading to lymphomagenesis. Supported by Initiative for Maximizing Student Development T32/PAR-24-031 Tumor Immunology: Checkpoints, Prevention, and Treatment (TIPT)

Mitochondrial fission is mediated by dynamin-related protein 1 (gene name DNM1L) and fusion by mitofusins (MFN1 and MFN2) and optic atrophy 1. The role of mitochondrial dynamics in liver disease and cancer remains poorly understood. We analyzed single, double, and triple liver-specific KO mice lacking mitochondrial fission and fusion proteins using systematic analyses of mitochondrial morphology, untargeted metabolomics, RNA-seq, hydrodynamic tail vein injection of oncogenes, and human hepatocellular carcinoma samples. Liver-specific Dnm1l-KO (L-Dnm1l-KO) mice showed increased alanine aminotransferase levels and hepatic fibrosis, with spontaneous liver tumors developing by 12 to 18 months of age. L-Mfn1- and L-Mfn2-KO mice showed no significant liver damage or tumor development, although a small percentage of L-Mfn1, Mfn2 double KO mice developed tumors. Dnm1l, Mfn1, and Mfn2 triple KO (TKO) mice experienced significantly reduced liver injury and fibrosis, along with decreased spontaneous and oncogene-induced tumorigenesis. L-Dnm1l-KO mice showed increased activation of the cGAS/STING/interferon pathway and pyrimidine metabolism, which were significantly normalized in TKO mice. Deletion of hepatic cGas reduced both basal and oncogene-induced liver injury and tumor development in L-Dnm1l-KO mice. These findings indicate that mitochondrial dynamics are crucial for maintaining hepatic pyrimidine metabolism and regulating the cGAS/STING-mediated immune response to prevent liver tumorigenesis.

Acute myeloid leukemia (AML) is the most prevalent and deadliest adult leukemia. Its frontline treatment uses the BH3 mimetic venetoclax to trigger mitochondria-dependent apoptosis. However, drug resistance nearly always develops, calling for therapies to circumvent it. Advanced microscopy and genome-wide CRISPRi screen analyses pinpointed mitochondrial adaptations primarily mediated by the master regulator of cristae shape optic atrophy 1 (OPA1) as critical for BH3 mimetics resistance. Resistant AML cells up-regulate OPA1 to modify their mitochondrial structure and evade apoptosis. MYLS22 and Opitor-0, two specific and nontoxic OPA1 inhibitors, promote apoptotic cristae remodeling and cytochrome c release, synergizing with venetoclax in AML cells and xenografts derived from AML patients ex vivo and in vivo. Mechanistically, OPA1 loss renders AML cells dependent on glutamine and sensitizes them to ferroptosis by activating ATF4-regulated integrated stress responses. Overall, our data clarify how OPA1 up-regulation allows AML cells' metabolic flexibility and survival and nominates specific OPA1 inhibitors as efficacious tools to overcome venetoclax resistance in leukemia.

Supplementary Table S1 shows the primer sequences of the genes used in the qPCR assay.

T-cell Acute Lymphoblastic Leukemia (T-ALL) is a hematological malignancy in need of novel therapeutic approaches. Here, we identify the ATP-citrate lyase ACLY as overexpressed in human T-ALL and as a promising therapeutic target for its treatment. To test the effects of ACLY in leukemia progression, we developed an isogenic model of NOTCH1-induced Acly conditional knockout leukemia. Importantly, we observed intrinsic antileukemic effects upon loss of ACLY, which further synergized with NOTCH1 inhibition in vivo. Metabolomic profiling upon ACLY loss revealed a metabolic crisis with reduced acetyl-CoA levels, as well as a decreased oxygen consumption rate. Gene expression profiling analyses showed that the transcriptional signature of ACLY loss very significantly correlates with the signature of MYC loss in vivo. Mechanistically, the decrease in acetyl-CoA led to reduced H3K27ac levels in Myc, resulting in transcriptional downregulation of Myc and drastically reduced MYC protein levels. Moreover, pharmacological inhibition of ACLY led to reduced MYC levels and antileukemic effects in human T-ALL cell lines and patient-derived xenografts (PDXs). Interestingly, our analyses also revealed a reciprocal relationship whereby ACLY itself is a direct transcriptional target of MYC, thus establishing a feedforward loop that is important for leukemia progression. Overall, our results identified a relevant ACLY-MYC axis and unveiled ACLY as a novel promising target for T-ALL treatment.

Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We develop a metabolomic-transcriptomic association analysis, and we find that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrate that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the peroxisome membrane to facilitate GABA production. Taken together, our results reveal a biochemical mechanism where SLC45A4 controls GABA production.

Indole-3-carbinol (I3C) is shown to possess multiple pharmacological activities such as anti-inflammatory, antimicrobial, antioxidant, antiviral, and anti-cancer activities. It is widely accepted as modulator of multiple signaling pathways particularly those related to cell cycle, cell growth and division, angiogenesis, apoptosis and immunity. We explored the metabolic reprogramming based on treatment with I3C in mice prostate tissue. In this study we utilized Pten knockout (KO)-induced prostate tumorigenesis mouse model to examine mechanism of action of I3C via metabolic rewiring. Phosphatase and tensin homolog deleted on chromosome 10 (Pten), a tumor suppressor gene is frequently found to be mutated or deleted in prostate cancer. Untargeted metabolomics was performed using liquid-chromatography mass-spectrometry (LC–MS) based platform to investigate Pten-dependent and Pten-independent metabolic targets of I3C. The most impacted pathways by I3C included pyrimidine metabolism, arginine and proline metabolism, porphyrin metabolism, citrate cycle and lipoic acid metabolism. These pathways taken together help in understanding the overall health beneficial effects of I3C.

Macroautophagy (autophagy hereafter) captures intracellular components and delivers them to lysosomes for degradation and recycling1. In adult mice, autophagy sustains metabolism to prevent wasting by cachexia and to survive fasting, and also suppresses inflammation, liver steatosis, neurodegeneration, and lethality2,3. Defects in autophagy contribute to metabolic, inflammatory and degenerative diseases, however, the specific mechanisms involved were unclear 4. Here we profiled metabolism and inflammation in adult mice with conditional, whole-body deficiency in an essential autophagy gene and found that autophagy deficiency altered fuel usage, and reduced ambulatory activity, energy expenditure, and food intake, and elevated circulating GDF15, CXCL10, and CCL2. While deletion of Gdf15 or Cxcl10 provided no or mild benefit, deletion of Ccl2 restored food intake, suppressed cachexia and rescued lethality of autophagy-deficient mice. To test if appetite suppression by CCL2 was responsible for lethal cachexia we performed single nucleus RNA sequencing of the hypothalamus, the center of appetite control in the brain. Notably, we found that autophagy deficiency was specifically toxic to PMCH and HCRT neurons that produce orexigenic neuropeptides that promote food intake, which was rescued by deficiency in CCL2. Finally, the restoration of food intake via leptin deficiency prevented lethal cachexia in autophagy-deficient mice. Our findings demonstrate a novel mechanism where autophagy prevents induction of a cachexia factor, CCL2, which damages neurons that maintain appetite, the destruction of which may be central to degenerative wasting conditions.

Aldehyde dehydrogenase 1a3 (ALDH1A3) activity is recognized as a pathogenic trait in cardiometabolic diseases and cancer, though the mechanisms by which ALDH1A3 promotes disease are unclear and effective therapeutic inhibitors of ALDH1A3 are lacking. Whereas the function of the ALDH1A enzymes in development is the conversion of retinaldehyde into all-trans retinoic acid (atRA) to activate retinoid nuclear receptor signaling, this pathway is paradoxically hypothesized as a cell-intrinsic tumor suppressor pathway. We resolve this paradox by showing that while ALDH1A3 is overexpressed across diverse cancers, ALDH1A3-expressing tumor cells lose sensitivity to retinoid signaling. Instead, atRA produced by ALDH1A3 acts in a paracrine fashion to activate retinoid nuclear receptor signaling in immune cells to suppress anti-tumor immunity. To inhibit ALDH1A3, we developed a hybrid in silico and high-throughput screening approach followed by medicinal optimization to identify first-in-class, oral and safe antagonists of ALDH1A3 with potent anti-tumor immunotherapeutic activity and an optimized drug development profile.