Xu, L.-L. | bioRxiv Science

bioRxiv2026

Metabolic specialization structures gut bacterial niches and drives colorectal cancer progression

Despite the established association between the gut microbiome and colorectal cancer (CRC), the functional distinction between microbial passengers and drivers of CRC progression remains unresolved. Here, we collected stool, blood, as well as paired tumor, and normal mucosa tissues from seventy-seven CRC patients to characterize the systemic and localized impact of the gut microbiome on early- and late-stage CRC. By deep shotgun metagenomic sequencing, we identified distinct bacterial species and functions residing in tumor versus normal mucosa, highlighting an enrichment of oral-associated bacteria in tumor tissues. Several of these species remained undetected in the stool microbiome analysis. We further combined bacterial culturing with untargeted metabolomics of bacteria enriched in tumor and normal mucosa tissues, revealing distinct clusters of metabolic potential. Functional testing of multiple members from one cluster comprising both tumor- and mucosa-enriched species revealed Leptotrichia wadei as a pro-tumorigenic bacterium in a murine CRC model. Single-nucleus RNA sequencing and in vitro experiments further demonstrated that L. wadei and its secretome induces M2 macrophage polarization to promote tumor growth. Overall, our study shows that metabolic specialization structures microbial colonization niches, while species-specific metabolic outputs identify functional drivers of CRC progression, and uncovers L. wadei as an oncogenic bacterium in CRC.

microbiology↗

bioRxiv2026

UBA1 Mitigates Myocardial Ischemia/Reperfusion Injury by Attenuating Endoplasmic Reticulum-Mitochondria Contacts via Pdzd8 ubiquitination

BACKGROUNDMyocardial ischemia/reperfusion injury (I/RI) represents a serious clinical complication in patients after acute myocardial infarction. Ubiquitin-activating enzyme 1 (UBA1) catalyzes the initial step of ubiquitination and plays a fundamental role in regulating protein homeostasis and related diseases. This study aims to elucidate the functional contribution of UBA1 to the pathogenesis of myocardial I/RI and to uncover its underlying mechanisms. METHODSSingle-cell RNA sequencing was employed to characterize UBA1 expression in human ischemic heart tissues. Myocardial I/R injury was examined in myocardial-specific UBA1 knockout (UBA1cko) mice, UBA1-overexpressing mice (rAAV9-UBA1), and corresponding controls. Neonatal rat cardiomyocytes underwent hypoxia/reoxygenation in vitro. Cardiac function and infarction were evaluated by echocardiography and pathological staining. Protein-protein interactions were analyzed via immunoprecipitation combined with mass spectrometry. The endoplasmic reticulum-mitochondrial contact sites (ERMCSs) and mitochondrial ultrastructure were evaluated through transmission electron microscopy and confocal imaging. RESULTSUBA1 expression was significantly downregulated in human and murine ischemic myocardium, especially in cardiomyocytes. UBA1cko mice exhibited aggravated I/RI with greater infarct size, impaired function, apoptosis, elevated intracellular Ca2+ levels, mitochondrial dysfunction, and ER stress, whereas UBA1 overexpression conferred cardioprotective effects. Mechanistically, UBA1 directly bound to and ubiquitinated Pdzd8, a key ERMCS-tethering protein, thereby promoting its degradation, which inhibited ERMCS formation and improved mitochondrial dysfunction and ER stress. Moreover, knockdown of Pdzd8 via rAAV9-siRNA effectively mitigated UBA1 knockout-induced myocardial damage. Additionally, administration of auranofin (AF), a U.S. Food and Drug Administration-approved drug for treating rheumatoid arthritis, markedly alleviated myocardial I/RI via activating UBA1 in vivo and in vitro. CONCLUSIONSUBA1 confers protection against myocardial I/RI by limiting ERMCS formation through Pdzd8 ubiquitination. Activating UBA1 or targeting Pdzd8 as a potential therapeutic strategy for the treatment of ischemic heart disease. GRAPHIC ABSTRACTA graphic abstract is available for this article. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIUBA1 expression is downregulated in human and murine ischemic myocardium, especially in cardiomyocytes. C_LIO_LICardiac deletion of UBA1 significantly exacerbates myocardial ischemia/reperfusion injury (I/RI), whereas cardiac UBA1 overexpression confers a marked protective effect. C_LIO_LIUBA1 interacts with Pdzd8 (PDZ domain containing 8) and facilitates its ubiquitination and subsequent degradation, which then reduces endoplasmic reticulum-mitochondria contact sites (ERMCSs) and ameliorates mitochondrial dysfunction and ER stress, protecting myocardial I/RI. C_LIO_LIPharmacological activation of UBA1 with the FDA-approved drug auranofin attenuates myocardial I/R injury and improves heart dysfunction. C_LI What Are the Clinical Implications?O_LIUBA1 represents a new therapeutic target for myocardial I/RI. C_LIO_LIActivating UBA1 or targeting Pdzd8 may offer a promising therapeutic strategy for mitigating myocardial I/RI and heart failure, underscoring its potential for clinical translation. C_LI

pathology↗

bioRxiv2025

A bioenergetic basis for multiorgan dysfunction in sepsis

Sepsis is a life-threatening multiorgan dysfunction that develops from a maladaptive host response to infection1. With an estimated 49 million cases per year and [~]11 million related deaths2, sepsis is a global WHO health priority3. Failure to overcome sepsis morbidity and lethality4,5 calls for alternative therapeutic approaches6-8. Here we report that adipocyte lipolysis is vital to prevent the pathogenesis of sepsis in mice. This protective response is evolutionary conserved, producing a plasma lipidomic profile9,10 that reflects on the severity of clinical sepsis. Mechanistically, adipocyte lipolysis fuels energy metabolism to sustain adaptive thermoregulation to infection, via insulin production and insulin receptor (INSR) signaling in adipocytes. This metabolic-based defense strategy does not impact on bacterial burden, establishing disease tolerance to infection11-14. In conclusion, adipocyte lipolysis induces insulin to rewire energy metabolism and support organ function in response to infection.

pathology↗