Small RNAs carry diverse terminal modifications that reflect their biogenesis and affect their stability and function. However, simultaneously discriminating these modifications remains challenging with existing methods. Here, we present Dual TERminal Modification analysis (Dual-TERM), a gel-based strategy that integrates enzymatic pretreatment with phenylboronic acid polyacrylamide gel electrophoresis (PBA-PAGE) to resolve 5' and 3' terminal modifications in small RNAs. Using synthetic RNAs, we demonstrated that Dual-TERM reliably distinguished four major 3' terminal ribose modifications (3'-OH, 3'-Nm, 3'-P, and 3'-cP) based on large band shifts and detected 5' phosphorylation status based on slight mobility changes. We validated the method with endogenous small RNAs-including miRNAs, piRNAs, and 5' tRNA halves-from mammals and plants, confirming species-specific modification patterns. With its simplicity and sensitivity, Dual-TERM provides a versatile tool for characterizing terminal modifications in small RNAs and has the potential to be adapted for high-throughput profiling when coupled with next-generation sequencing.

The translocation of bacteria from intestinal tracts into blood vessels and distal organs plays pivotal roles in the pathogenesis of numerous severe diseases. Intravital monitoring of bacterial translocation, however, is not yet feasible, which greatly hinders us from comprehending this spatially and temporally dynamic process. Here we report an in vivo fluorogenic labeling method, which enables in situ imaging of mouse gut microbiota and real-time tracking of the translocated bacteria. By mimicking the peptidoglycan stem peptide in bacteria, a tetrapeptide probe composed of alternating D- and L-amino acids and separately equipped with a fluorophore and a quencher on the N- and C-terminal amino acid, is designed. Because of its resistance to host proteases, it can be directly used in gavage and achieves fluorogenic labeling of the microbiota in the gut via the functioning of the L,D-transpeptidases of the labeled bacteria. Using intravital two-photon microscopy, we then successfully visualize the translocation of gut bacteria into the bloodstream and liver in obesity mouse models. This technique can help further exploration into the spatiotemporal activities of gut microbiota in vivo, and be valuable in investigating the less understood pathogenicity of bacterial translocation in many severe diseases.

The Mediator complex is an evolutionarily conserved transcriptional coactivator with well-characterized structure and function, though the roles of its dissociable subunits remain incompletely defined. Here, we demonstrate that Mediator subunit MED16 dissociates from the core complex to form a subcomplex with transcription factors UBP1 and TFCP2, and this interaction modulates transcriptional activation or repression in a context-dependent manner. Using protein purification coupled with mass spectrometry, we identified MED16 as a binding partner of UBP1-TFCP2. Gene expression analyses showed that UBP1 interacts with MED16 to activate a subset of silenced genes involved in lung homeostasis, angiogenesis, and cell proliferation. Conversely, the MED16-UBP1 interaction suppresses HIV-1 transcription, thereby reinforcing viral latency. Mechanistically, MED16 and UBP1 cooperatively bind the HIV-1 transcriptional start site (TSS) to inhibit preinitiation complex assembly. Genomic-scale analyses further demonstrated that transcription is activated when the UBP1-TFCP2 binding motif is proximal to the TSS, but repressed when the motif overlaps the TSS. Collectively, our findings identify a novel MED16-UBP1 interaction, define its dual role in transcriptional regulation, and highlight the therapeutic potential of targeting this axis in HIV-1 infection.

Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear. We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value < 0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value = 0.001, M2 = 0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC. Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression.

ETHNOPHARMACOLOGICAL RELEVANCE:Rhizome of Gastrodia elata Blume (RGE) is a valuable traditional Chinese Medicine (TCM) in the clinical practice. The Compendium of Materia Medica records that RGE has the effect of flatting liver wind out. It has sedative, analgesic, hypnotic, anticonvulsant, anti-hypertensive, anti-myocardial ischemia, anti-arrhythmic and anti-platelet aggregation effects. RGE is often used to relieve and treat vertigo, headache, hypertension, convulsions, and epilepsy in TCM clinic for thousands of years. Accumulated evidences have suggested that hypertension disease is related to the renin-angiotensin-aldosterone system (RAAS) disturbance. However, the potential pharmacodynamic components and anti-hypertensive mechanisms of RGE are unclear now. AIM OF THE STUDY:The active component and mechanism of RGE in treating hypertension were elucidated to strengthen the quality control and development of anti-hypertensive drugs. MATERIALS AND METHODS:The anti-hypertensive active components of RGE were analyzed by multi-dimensional qualitative analysis method including ethanol extract, in-vitro intestinal absorption, in-vivo plasma. The ultra high performance liquid chromatography-mass spectrometry (UPLC-Q-Exactive MS/MS) analysis technology was adopted to identify these components. Network pharmacology was applied to predicted anti-hypertensive active components, target proteins and pathways. Molecular docking was used to evaluate the potential molecular binding modes between 68 components and nine proteins. Spontaneously hypertensive rats (SHR) model was adopted to evaluate the activity of reducing systolic and diastolic blood pressure (SBP and DBP). Levels of renin, angiotcnsin II (Ang II) and aldosterone (ALD) in serum were determined by Elisa kit. Immunohistochemical were adopted to compare the changes of Ang II receptor 1 (AT1R) protein levels in SHR model and RGE groups. RESULTS:The multi-dimensional components qualitative analysis method of RGE was established. The results showed that 79, 70 and 30 components were identified in RGE ethanol extract, in-vitro intestinal absorption and in-vivo plasma, respectively. These components were mainly parishins, nucleosides, amino acids, phenolic acids, flavonoids, organic acids et al. Network pharmacology results showed that anti-hypertensive active components were nucleosides and organic acids. It was speculated that RGE could exert its anti-hypertensive effect by regulating aldosterone-regulated sodium reabsorption, renin-angiotensin system pathways and related target proteins. Molecular docking results showed that 21 components including parishins, nucleosides and phenolic acids were potential active components of anti-hypertensive. Taking together, parishin A, B, E, C, D, adenosine, N6-(4-hydroxybenzyl) adenosine, guanosine, ferulic acid were the main anti-hypertensive active components of RGE. Pharmacodynamic results showed that RGE (0.7 g·kg-1) at low dosage could reduce SBP and DBP of SHR in vivo. Meanwhile, RGE (1.4 g·kg-1) markedly reduced the contents of renin, angiotcnsin II and ALD (p < 0.05) of SHR. Immunohistochemical data demonstrated that RGE (0.7 g·kg-1) could downregulate the protein expression of AT1R. In general, RGE can significantly reduce blood pressure of SHR by regulating RAAS. CONCLUSION:The multi-dimensional components qualitative analysis combining network pharmacology and molecular docking technology provide a new perspective for discovering potential anti-hypertensive components of RGE. RGE possess anti-hypertensive activity by regulating multiple targets of RAAS. Thus, it has the potential to develop into the novel raw material of anti-hypertensive drugs.

Major depressive disorder (MDD) often begins during adolescence, a critical developmental period during which nearly 50% of lifetime cases emerge. Despite its high prevalence and impact, objective diagnostic biomarkers for adolescent MDD remain limited, particularly those related to gut microbiota. Our study examined potential co-diagnostic biomarkers from peripheral blood and fecal samples in adolescents with MDD. We enrolled drug-naïve adolescents with first-episode MDD (n = 46, aged ≤18 years, 71.74% female) and age-/sex-matched healthy controls (HCs, n = 44). The levels of tight junction proteins (Claudin-5, Zonulin, FABP) and inflammatory biomarkers (IL-6, IL-8, TNF-α, and CRP) were markedly elevated in the plasma of adolescents with MDD, indicating gut barrier dysfunction and systemic inflammation. The microbiome in MDD patients exhibited a lower Firmicutes-to-Bacteroidetes ratio. At the genus level, Intestinimonas and Barnesiella were significantly enriched, while Dialister and Collinsella were considerably reduced. Integrating Collinsella abundance with tight junction proteins and inflammatory markers significantly improved diagnostic performance, achieving an area under the curve (AUC) of 0.964. Moreover, Collinsella negatively correlated with sex, Claudin-5, and TNF-α. Claudin-5 was strongly associated with short-chain fatty acids (SCFAs)-related pathways, including alanine, aspartate, glutamate metabolism, D-glutamine and D-glutamate metabolism, and autophagy regulation. Treatment of Caco-2 cells with propionate and butyrate confirmed the regulatory effects of SCFAs on tight junction biomarkers. These findings suggest the interplay between gut dysbiosis, barrier dysfunction, and inflammation in adolescent MDD and support microbiota-host biomarkers as a promising strategy for improving MDD diagnostic precision.

Polycystic ovary syndrome (PCOS) affects 6%-10% of women of reproductive age and is known to be associated with disruptions in the gut bacteria. However, the role of the gut mycobiota in PCOS pathology remains unclear. Using culture-dependent and internal transcribed spacer 2 (ITS2)-sequencing methods, we discovered an enrichment of the gut-colonizable fungus Aspergillus tubingensis in 226 individuals, with or without PCOS, from 3 different geographical areas within China. Colonization of mice with A. tubingensis led to a PCOS-like phenotype due to inhibition of Aryl hydrocarbon receptor (AhR) signaling and reduced interleukin (IL)-22 secretion in intestinal group 3 innate lymphoid cells (ILC3s). By developing a strain-diversity-based- activity metabolite screening workflow, we identified secondary metabolite AT-C1 as an endogenous AhR antagonist and a key mediator of PCOS. Our findings demonstrate that an intestinal fungus and its secondary metabolite play a critical role in PCOS pathogenesis, offering a therapeutic strategy for improving the management of the disease.

Dampened antigen presentation underscores the resistance of pancreatic cancer to T cell-mediated anti-tumor immunity, rendering immunotherapy largely ineffective. By high-throughput CRISPR activation perturbation, we discovered that the transcriptional regulator MCRS1 significantly augmented the sensitivity of mouse pancreatic cancer cells to T cell immunity in vitro and in vivo. Mechanistically, MCRS1 interacted with the transcription factor and genome organizer YY1 to coordinately increase the chromatin accessibility and expression of MHC-I genes. Elevated MCRS1 subverted MHC-I suppression and activated anti-tumor T cells, which sensitized mouse pancreatic cancer to α-PD-1 therapy. Remarkably, high MCRS1 expression was associated with increased T cell infiltration and extended survival of patients with pancreatic cancer and was predictive of favorable responses to α-PD-1 therapy in patients with lung cancer. Together, our study uncovers that MCRS1 sensitizes cancer cells to T cell immunity by transcriptionally subverting MHC-I suppression, which enhances the effectiveness of α-PD-1 therapy in mice and humans, paving the way to further improve immunotherapy against solid tumors.

Here, we report a magnetogenetic system, based on a single anti-ferritin nanobody-TRPV1 receptor fusion protein, which regulated neuronal activity when exposed to magnetic fields. Adeno-associated virus (AAV)-mediated delivery of a floxed nanobody-TRPV1 into the striatum of adenosine-2a receptor-Cre drivers resulted in motor freezing when placed in a magnetic resonance imaging machine or adjacent to a transcranial magnetic stimulation device. Functional imaging and fiber photometry confirmed activation in response to magnetic fields. Expression of the same construct in the striatum of wild-type mice along with a second injection of an AAVretro expressing Cre into the globus pallidus led to similar circuit specificity and motor responses. Last, a mutation was generated to gate chloride and inhibit neuronal activity. Expression of this variant in the subthalamic nucleus in PitX2-Cre parkinsonian mice resulted in reduced c-fos expression and motor rotational behavior. These data demonstrate that magnetogenetic constructs can bidirectionally regulate activity of specific neuronal circuits noninvasively in vivo using clinically available devices.

Aspirin, also named acetylsalicylate, can directly acetylate the side-chain of lysine in protein, which leads to the possibility of unexplained drug effects. Here, the study used isotopic-labeling aspirin-d3 with mass spectrometry analysis to discover that aspirin directly acetylates 10 HDACs proteins, including SIRT1, the most studied NAD+-dependent deacetylase. SIRT1 is also acetylated by aspirin in vitro. It is also identified that aspirin directly acetylates lysine 408 of SIRT1, which abolishes SIRT1 deacetylation activity by impairing the substrates binding affinity. Interestingly, the lysine 408 of SIRT1 can be acetylated by CBP acetyltransferase in cells without aspirin supplement. Aspirin can inhibit SIRT1 to increase the levels of acetylated p53 and promote p53-dependent apoptosis. Moreover, the knock-in mice of the acetylation-mimic mutant of SIRT1 show the decreased production of pro-inflammatory cytokines and maintain intestinal immune homeostasis. The study indicates the importance of the acetylated internal functional site of SIRT1 in maintaining intestinal immune homeostasis.

Dysbiosis of the gut microbiota has been implicated in the pathogenesis of metabolic syndrome (MetS) and may impair host metabolism through harmful metabolites. Here, we show that Desulfovibrio, an intestinal symbiont enriched in patients with MetS, suppresses the production of the gut hormone glucagon-like peptide 1 (GLP-1) through the production of hydrogen sulfide (H2S) in male mice. Desulfovibrio-derived H2S is found to inhibit mitochondrial respiration and induce the unfolded protein response in intestinal L cells, thereby hindering GLP-1 secretion and gene expression. Remarkably, blocking Desulfovibrio and H2S with an over-the-counter drug, bismuth subsalicylate, improves GLP-1 production and ameliorates diet-induced metabolic disorder in male mice. Together, our study uncovers that Desulfovibrio-derived H2S compromises GLP-1 production, shedding light on the gut-relayed mechanisms by which harmful microbiota-derived metabolites impair host metabolism in MetS and suggesting new possibilities for treating MetS. The intestinal symbiont Desulfovibrio, which is enriched in individuals with metabolic syndrome, is found to suppress the production of GLP-1 in male mice. The over-the-counter drug bismuth subsalicylate inhibits the effect of Desulfovibrio and restores GLP-1 levels.

Infant formulas are often supplemented to foster the development of a healthy gut microbiota. In this issue of Cell Host & Microbe, Heppner et al. present an elaborate clinical trial examining the impact of formula supplementation on the development and circadian rhythmicity of the microbiota during the first year of life.

Readily available nutrient-rich foods exploit our inherent drive to overconsume, creating an environment of overnutrition. This transformative setting has led to persistent health issues, such as obesity and metabolic syndrome. The development of glucagon-like peptide-1 receptor (GLP-1R) agonists reveals our ability to pharmacologically manage weight and address metabolic conditions. Obesity is directly linked to chronic low-grade inflammation, connecting our metabolic environment to neurodegenerative diseases. GLP-1R agonism in curbing obesity, achieved by impacting appetite and addressing associated metabolic defects, is revealing additional benefits extending beyond weight loss. Whether GLP-1R agonism directly impacts brain health or does so indirectly through improved metabolic health remains to be elucidated. In exploring the intricate connection between obesity and neurological conditions, recent literature suggests that GLP-1R agonism may have the capacity to shape the neurovascular landscape. Thus, GLP-1R agonism emerges as a promising strategy for addressing the complex interplay between metabolic health and cognitive well-being.

Parkinson’s disease (PD), one of the most devastating neurodegenerative brain disorders, is characterized by the progressive loss of dopaminergic neurons in the substantia nigra (SN) and deposits of α-synuclein aggregates. Currently, pharmacological interventions for PD remain inadequate. The cell necroptosis executor protein MLKL (Mixed-lineage kinase domain-like) is involved in various diseases, including inflammatory bowel disease and neurodegenerative diseases; however, its precise role in PD remains unclear. Here, we investigated the neuroprotective role of MLKL inhibition or ablation against primary neuronal cells and human iPSC-derived midbrain organoids induced by toxic α-Synuclein preformed fibrils (PFFs). Using a mouse model (Tg-Mlkl−/−) generated by crossbreeding the SNCA A53T synuclein transgenic mice with MLKL knockout (KO)mice, we assessed the impact of MLKL deficiency on the progression of Parkinsonian traits. Our findings demonstrate that Tg-Mlkl−/− mice exhibited a significant improvement in motor symptoms and reduced phosphorylated α-synuclein expression compared to the classic A53T transgenic mice. Furthermore, MLKL deficiency alleviated tyrosine hydroxylase (TH)-positive neuron loss and attenuated neuroinflammation by inhibiting the activation of microglia and astrocytes. Single-cell RNA-seq (scRNA-seq) analysis of the SN of Tg-Mlkl−/− mice revealed a unique cell type-specific transcriptome profile, including downregulated prostaglandin D synthase (PTGDS) expression, indicating reduced microglial cells and dampened neuron death. Thus, MLKL represents a critical therapeutic target for reducing neuroinflammation and preventing motor deficits in PD.

We developed an analysis pipeline that can extract microbial sequences from spatial transcriptomic (ST) data and assign taxonomic labels, generating a spatial microbial abundance matrix in addition to the default host expression matrix, enabling simultaneous analysis of host expression and microbial distribution. We called the pipeline spatial metatranscriptome (SMT) and applied it on both human and murine intestinal sections and validated the spatial microbial abundance information with alternative assays. Biological insights were gained from these novel data that showed host-microbe interaction at various spatial scales. Finally, we tested experimental modification that can increase microbial capture while preserving host spatial expression quality and, by use of positive controls, quantitatively showed the capture efficiency and recall of our methods. This proof-of-concept work shows the feasibility of SMT analysis and paves the way for further experimental optimization and application.

Summary Psychological stress and its sequelae are a major public health problem. While the immune system has been implicated in the development of stress-related disorders, how the immune signals modulate neural responses to stress is poorly understood. Contrary to our expectations, we found that the immune cytokine Interleukin (IL)-22 is the key mediator of an immune-to-brain pathway that diminishes, rather than amplifies, stress-induced anxiety. We showed that stress induced T H 17 differentiation and IL-22 production in the intestine following barrier dysfunction and microbiota stimulation. IL-22 then directly signaled to septal neurons in the brain to mitigate anxiety-like behavior. Accordingly, mice treated with exogenous IL-22 showed resilience to chronic stress-induced anxiety disorders. Our study thus reveals a previously-unappreciated immune-to-brain axis that defends against psychological stress, suggesting a potential intervention strategy for stress-related mental diseases.

Allergic immunity is orchestrated by group 2 innate lymphoid cells (ILC2s) and type 2 helper T (Th2) cells prominently arrayed at epithelial- and microbial-rich barriers. However, ILC2s and Th2 cells are also present in fibroblast-rich niches within the adventitial layer of larger vessels and similar boundary structures in sterile deep tissues, and it remains unclear whether they undergo dynamic repositioning during immune perturbations. Here, we used thick-section quantitative imaging to show that allergic inflammation drives invasion of lung and liver non-adventitial parenchyma by ILC2s and Th2 cells. However, during concurrent type 1 and type 2 mixed inflammation, IFNγ from broadly distributed type 1 lymphocytes directly blocked both ILC2 parenchymal trafficking and subsequent cell survival. ILC2 and Th2 cell confinement to adventitia limited mortality by the type 1 pathogen Listeria monocytogenes. Our results suggest that the topography of tissue lymphocyte subsets is tightly regulated to promote appropriately timed and balanced immunity.

We developed an analysis pipeline that can extract microbial sequences from Spatial Transcriptomic data and assign taxonomic labels to them, generating a spatial microbial abundance matrix in addition to the default host expression one, enabling simultaneous analysis of host expression and microbial distribution. We applied it on both human and murine intestinal datasets and validated the spatial microbial abundance information with alternative assays. Finally, we present a few biological insights that can be gained from this novel data. In summary, this proof of concept work demonstrated the feasibility of Spatial Meta-transcriptomic analysis, and pave the way for future experimental optimization.