Cellular and Molecular Life Sciences最新文献

Background: Triple-negative breast cancer (TNBC) is a highly invasive and refractory subtype of breast cancer. Despite the promise of immune checkpoint blockade (ICB) therapy, response rates remain limited. The immune resistance driven by the tumor microenvironment has not yet been understood entirely, which hinders the personalized precision treatment of TNBC.

Methods: We integrated single-cell RNA data from 12 cohorts with TNBC and performed a multi-omics analysis combining spatial transcriptomics (ST), bulk RNA sequencing, and multiplex immunofluorescence (mIF) staining to identify immune-resistant subpopulations. Cell-to-cell communication was explored based on NicheNet and CellChat, and the function of CAF was verified by gene knockdown and overexpression in human mammary fibroblasts, followed by co-culture experiments with TNBC cell lines. ST and mIF data were used to analyze and verify cellular co-localization, while deconvolution was used to examine the relationship between two-cell characteristics and immunotherapy or antibody-drug conjugates (ADC) agent benefit.

Results: We identified CA9+cancer-associated fibroblasts (CA9+CAF) as a key subset enriched in non-responders to ICB that promotes immune resistance by establishing a hypoxic and immunosuppressive microenvironment via abnormal angiogenesis and glycolysis. ST and mIF analyses revealed a strong co-localization and interaction between CA9+CAF and SPP1+tumor-associated macrophages (SPP1+TAM), forming a stroma-myeloid axis that promotes immune escape through VEGFA/NRP2 axis in co-localization core region compared to the boundary. In vitro experiments demonstrated that the over-expression of CA9 in fibroblasts enhanced the proliferation, invasion, and migration of TNBC cells, while CA9 knockdown inhibited the tumorigenic effects. The high CA9+CAF/SPP1+TAM profile indicated a poor prognosis, reduced effector T cell infiltration, and attenuated response to immunotherapy, may benefit from TROP2, MUC1, and NECTIN4-based ADC agents. The result was validated in TNBC samples treated with neoadjuvant immunotherapy from our center.

Conclusion: This study unveils the critical immunosuppressive axis orchestrated by CA9+CAF and SPP1+TAM in TNBC, offering novel insights into the stromal regulatory mechanisms driving immune resistance. The cell-to-cell interaction signature holds promise as predictor of immunotherapy response and potential therapeutic target.

Background and objectives: The liver continuously adjusts its metabolic activity to synchronize the nutrient supply with the body's demands. This synchronization involves the complex coordination of acute metabolic needs, nutrient availability, and activity levels, which is orchestrated according to cyclic internal rhythms governed by the circadian clock. This study aimed to decipher the role of circadian rhythms in liver metabolic functions, including mitochondrial activities that are critical for energy production and metabolic adaptation.

Methods: We investigated rhythmic changes in liver metabolism via comprehensive multiomics and kinetic mathematical modeling. The liver proteome of male mice was analyzed and modeled, and complementary serum lipidomic and metabolomic analyses were performed. Mitochondrial proteins were examined to evaluate the role of mitochondria in the oscillating regulation of energy production.

Results: Most metabolic functions, particularly those related to carbohydrate and fatty acid metabolism, exhibit rhythmic patterns on a 12-hour rather than a 24-hour cycle. The importance of this rhythmicity is function-dependent and can account for 25% to 50% of the overall variability. Mitochondrial activities also exhibit temporal fluctuations that are closely linked to nutrient availability. The strong correlation between metabolic functions and serum metabolites highlights the precise alignment between physiological demand and metabolic performance.

Conclusions: Hepatic metabolic functions follow a 12-hour cycle rather than a 24-hour cycle, significantly contributing to the liver's ability to meet nutrient demands throughout the day. Mitochondrial dynamics, which are influenced by nutrient availability, play a central role in adapting energy production to the body's metabolic needs.

Hepatitis E virus (HEV), a leading cause of acute and chronic viral hepatitis, poses a persistent global health challenge. A deeper mechanistic understanding of virus-host interactions is critical for identifying therapeutic targets to mitigate HEV-associated disease. In this study, we employ a systems biology framework to comprehensively map metabolic and bioenergetic alterations induced by HEV genotypes 1 and 3 in HepG2/C3a-MAVS-KD cells, a robust model of HEV infection, enabling reliable assessment of virus- and host-driven cellular changes. Our analyses reveal extensive remodelling of host metabolism, including reprogramming of the tricarboxylic acid (TCA) cycle, mitochondrial oxidative phosphorylation (OXPHOS), fatty acid metabolism, and β-oxidation-pathways that collectively sustain the energetic and biosynthetic demands of viral infection. HEV infection also reshapes the cellular lipidome, increasing levels of long-chain neutral lipids and lipid droplet abundance, alongside elevated levels of pro-inflammatory oxylipins. Functional metabolic assays demonstrate a reliance on lipid-fuelled OXPHOS rather than glycolysis for efficient HEV infection. These findings uncover critical host metabolic dependencies exploited by HEV and offer a conceptual framework for targeting metabolic hubs as a therapeutic strategy against HEV infection. Author Summary: Viruses are obligate intracellular pathogens that reprogramme host cellular machinery to their advantage. Yet, the extent to which Hepatitis E virus (HEV) infection orchestrates metabolic reprogramming, and the implications of these changes for viral fitness, remain poorly defined. By integrating large-scale proteomics with lipid metabolic profiling, we delineate molecular strategies through which HEV subverts host lipid metabolism and mitochondrial function. Our findings provide mechanistic insight into how HEV infection modulates host metabolic pathways to its advantage, highlighting potential targets for therapeutic intervention.

Parkinson's disease (PD) is characterized by progressive neurodegeneration closely linked to neuroinflammation and oxidative stress-induced damage and is characterized by the loss of dopaminergic (DAergic) neurons and the inflammatory response associated with glial cells. RRx-001 (RRx, 2-bromo-1-(3,3-dinitroazetidin-1-yl)ethanone) is a small-molecule immunoregulator. Recent studies have shown that it strongly inhibits NLRP3 (NOD-like receptor family pyrin domain containing 3) inflammasome activation, which is crucial for influencing neuroinflammation. However, the mechanism underlying the effect of RRx on PD remains unclear. In this study, we explored the potential effects of RRX on 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mice, detected the transcriptome and metabolome of the substantia nigra, and performed 16 S microbial diversity sequencing and metabolomics of the intestinal tract. Our study revealed that RRx obviously relieves MPTP-induced DAergic neuronal loss and motor disorders. Mechanistically, RRx reversed the upregulated expression of lipocalin-2 (LCN2) and NLRP3 inflammasome activation in a PD model. Crucially, its protective effects on DAergic neurons involved improving LCN2-NLRP3 inflammasome activation-mediated astrocyte pyroptosis. RRx also reduced the levels of metabolites and signalling pathways associated with oxidative stress and PD in the substantia nigra. Furthermore, the 16 S rDNA analysis and metabolomic analysis of faecal pellets revealed that the intestinal tract of the RRx-treated PD mice presented a greater abundance of Deferribacterota at the phylum level than that of the PD model mice, and the gut microbiota metabolites and pathways were altered. Overall, the results of this study indicate that RRx has multiple effects on PD.

Naïve human pluripotent stem cells (hPSCs) represent an in vitro analog of the pre-implantation epiblast - the founder tissue of the embryo proper. A widely held assumption, based on prior studies in the mouse system, was that naïve hPSCs are restricted in their differentiation potential toward more mature stages of epiblast development, as a prelude to gastrulation. However, over the past 5 years, a growing body of literature has demonstrated that naïve hPSCs have an expanded lineage potential toward a broad range of embryonic and extraembryonic fates and can even be used as a starting point for generating 8-cell-like cells. The most emphatic demonstration of the broad lineage potential of naïve hPSCs is their remarkable capacity to self-organize into blastocyst-like structures ("blastoids") that model all three lineages of the pre-implantation embryo and can be cultured to post-implantation stages. Here, we discuss the broad spectrum of cell fates accessible from naïve hPSCs and the signaling pathways that guide the exit from the ground state of human pluripotency.

Super-enhancers (SEs) typically govern the expression of critical genes in the maintenance of cell identity. Recent advances suggest mitochondrial dysfunction contributes to pulmonary artery smooth muscle cell (PASMC) proliferation and inflammation in pulmonary hypertension (PH). However, the landscape of SEs in hypoxic PASMCs as well as hypoxia-induced target genes associated with SEs controlling the mitochondrial dysfunction remain to be fully characterized. In this study, we depicted the landscape of SE in hypoxic PASMCs by ChIP-seq, Hi-ChIP, and ChIP-qPCR assays and reveal a regulatory SE driven LncRNA, LINC01013. The effect of LINC01013 on proliferation and inflammation of PASMCs was evaluated through EdU incorporation, Western blotting and immunofluorescence. The molecular mechanism of LINC01013 was investigated by the study of RNA pull down and mass spectrometry. We profiled chromosome interactions in epigenetic regulation and identified SE-associated LINC01013 as a key mitochondrial dysfunction mediator in hypoxic PASMCs. The transcription factor CCAAT enhancer binding protein beta (CEBPB) was found to enrichment in LINC01013 SE and promoter, promoting LINC01013 transcription and overexpression in PASMCs under hypoxic conditions. Inhibition of LINC01013 reversed hypoxia-induced glycolysis and oxidative stress injury of PASMCs. Further investigation unveiled that LINC01013, which is partially located in mitochondria and interacted with heat shock protein family A member 9 (HSPA9) to mediate oligomerization of voltage dependent anion channel 1 (VDAC1), thereby leading to increased mitochondrial permeability and dysfunction. These findings demonstrate that SE-associated LINC01013 regulates the proliferation and inflammation of hypoxic PASMCs by orchestrating mitochondrial function, might be a potential therapeutic target for PH.

Non-obstructive azoospermia (NOA) is a critical subtype of male infertility associated with inflammation. However, the molecular mechanisms underlying this phenomenon remain poorly understood. This study investigated the role of the inflammation-activated long non-coding RNA SNHG1 in NOA pathogenesis. Using lipopolysaccharide (LPS)-induced orchitis mouse models and spermatogonium cell lines (GC-1 spg and TCAM-2), we observed that both SNHG1 and the transcription factor SP1 were significantly upregulated, correlating with spermatogonium proliferation and loss of stemness. Mechanistically, SP1 directly binds to and transcriptionally activates the SNHG1 promoter, whereas SNHG1 knockdown rescued LPS-induced spermatogonium dysfunction without affecting SP1 expression. RNA-seq revealed that SNHG1 overexpression activated the IL-17 A signaling pathway. Notably, IL-17 A receptor blockade (Brodalumab) reversed the SNHG1-mediated proliferation arrest and stemness. Our findings demonstrated that the SP1-SNHG1-IL-17 A axis drives inflammatory spermatogenic failure, suggesting IL-17 A inhibition as a potential therapeutic direction.

Background: Oral squamous cell carcinoma (OSCC) is the commonest invasive malignancy in the head and neck regions, with a worse prognosis. Recent studies revealed the role of nuclear receptor coactivator 7 (NCOA7) in promoting tumorigenesis. However, the molecular mechanism remains unclear.

Methods: Human OSCC tissues were collected and stained with H&E and NCOA7. The expression of NCOA7 in both normal and tumor tissues was compared, along with a correlation analysis with clinicopathological parameters. In vitro, NCOA7 was knocked down, and the proliferation, migration, invasion, and ferroptosis were evaluated using CCK-8, transwell and 3D spheroid migration and invasion assays, qRT-PCR, western blot, and immunocytochemistry. The effects of NCOA7 on intracellular reactive oxygen species (ROS) and ferroptosis in OSCC cells were investigated under the treatment of antioxidants N-Acetyl-L-cysteine (NAC), ferroptosis inhibitors deferoxamine mesylate (DFO) and ferrostatin-1 (Fer-1), and ferroptosis inducers erastin. The Institutional Ethics Committee approved all clinical protocols.

Results: Significantly high expression of NCOA7 was found in OSCC tissues and was linked to the advancement of OSCC. In vitro, NCOA7 knockdown statistically reduced the proliferation, migration, and invasion of OSCC cells, which could be rescued using NAC or Fer-1. Moreover, NCOA7 knockdown cells exhibited significantly high levels of ROS and ferroptosis, which could be reversed using NAC or DFO or Fer-1. Further investigations revealed that inhibiting ROS in OSCC cells reduced ferroptosis, while erastin could reverse its inhibitory effect.

Conclusions: NCOA7 promotes OSCC progression by inhibiting ferroptosis through ROS signaling. NCOA7 might be a new therapeutic target for OSCC.

Host-associated microbiomes can strongly influence viral infection outcomes, yet how minor variations in commensal bacterial composition modulate viral pathogenesis remain poorly understood. Here, we used Drosophila melanogaster to investigate how bacterial microbiome composition affects pathogenesis of enteric RNA viruses. Lactiplantibacillus plantarum supplementation increased bacterial microbiome diversity without altering total bacterial load, while Acetobacter pomorum supplementation had minimal impact on the bacterial microbiome. L. plantarum-enriched flies exhibited an additional ~ 15% reduction in lifespan from Drosophila A virus (DAV) infection despite showing reduced viral protein accumulation and similar viral RNA levels. The reduction in tolerance to viral infection required live bacteria and was observed only for DAV, as no change in mortality was observed with Nora virus or Drosophila C virus infections. Mechanistic investigations revealed that tolerance reduction occurs independently of transcriptional immune responses, as DAV-infected flies showed similar transcriptional profiles regardless of bacterial microbiome composition. Intestinal barrier function assays demonstrated that a large number of L. plantarum-supplemented flies died before developing signs of gut barrier disruption, suggesting that extra-intestinal mechanisms contribute to mortality; this interpretation is further supported by similar levels of intestinal damage markers observed in virus-infected flies under both microbiome conditions. Viral genomic sequencing ruled out microbiome-driven selection of more pathogenic viral variants, as no adaptive mutations were observed between microbiome conditions that could account for the differential pathogenesis. These findings describe how subtle shifts in microbiome composition modulate viral infection outcomes through pathways that operate independently of canonical immune responses, viral evolution, and intestinal damage.