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PubMed2025

Deciphering Pseudoendocrine Sarcoma: A Clinicopathological, Molecular, and Epigenetic Study Suggesting Biological Links With Solid Pseudopapillary Neoplasm of the Pancreas.

Pseudoendocrine sarcoma (PS) is a recently described neoplasm of uncertain differentiation, characterized by recurrent CTNNB1 mutations, frequent paravertebral location, and a neuroendocrine-like histomorphology. In this study, we report the clinicopathologic, immunohistochemical, transcriptomic, and epigenetic findings of 12 PS cases. The tumors affected 7 men and 5 women with a median age of 66 years and were located in the paraspinal/paravertebral region (n = 11) and the thigh (n = 1). Median tumor size was 82 mm (range, 32-170 mm). Histologically, the tumors comprised sheets and nests of epithelioid-to-ovoid cells with uniform nuclei and speckled chromatin, frequently associated with extracellular hyaline globules and fibrovascular cords/septa. Uncommon findings included microcalcifications, myxoid stroma, pseudopapillary, pseudoglandular, microcystic or corded architecture, and lumen and rosette-like structures. Necrosis was absent, and mitotic activity was low. On immunohistochemistry, the tumors showed aberrant nuclear staining for beta-catenin (8/8) and expression of CD56 (7/7), S100 (8/8), desmin (2/6), and androgen receptor (1/4). Pankeratin (AE1/AE3), progesterone receptor, synaptophysin, chromogranin, and INSM1 were negative. All tested cases harbored CTNNB1 mutations. Using a customized cohort, methylation profiling revealed that PS formed a common cluster with solid pseudopapillary neoplasm of the pancreas (SPNP), distinct from all methylation classes from the Heidelberg sarcoma classifier and a subset of paragangliomas. Transcriptomic analysis showed that PS formed an independent cluster from a control group of tumors (including SPNP). Differential gene expression analysis showed enrichment in genes of the Wnt signaling pathway (HALLMARK gene sets) and biological processes related to sensory perception, among others (gene ontology - biological process [GO-BP]). Additionally, upregulated genes were related to various fetal cell types from the cell type signature data set (MSigDB), particularly of neuronal and epithelial lineage. Immunohistochemical assessment of potential markers identified through gene expression analysis revealed focal-to-diffuse expression of GLUT1 (6/6) and focal/multifocal expression of Brachyury (4/9) and HuD (3/7). Follow-up information, available for 10 cases (median duration of 18 months; range, 7-69 months), showed local recurrences and metastatic spread in 2 patients each. Evidence of response to radiotherapy was documented in one tumor. Altogether, this study expands knowledge on PS and suggests biological links with SPNP, including a potential shared cell of origin.

Humans↗

PubMed2026

Multi-omics and experimental validation identify RAPGEF2 as a protective prognostic biomarker in clear cell renal cell carcinoma.

Kidney Renal Clear Cell Carcinoma (KIRC) is characterized by marked molecular heterogeneity and metabolic reprogramming, underscoring the need for reliable biomarkers for prognostic assessment and individualized treatment. RAPGEF2, a guanine nucleotide exchange factor has been implicated in cell adhesion and differentiation, but its role in KIRC remains unclear. In this study, we systematically evaluated the expression pattern, prognostic significance, genomic associations, biological function, and therapeutic relevance of RAPGEF2 in KIRC through integrated multi-omics analyses and experimental validation. Pan-cancer single-cell and Spatial transcriptomic analysis revealed heterogeneous RAPGEF2 expression across tumor types, with a relatively prominent signal in KIRC, where RAPGEF2 was mainly enriched in endothelial cells. Survival analyses in the TCGA-KIRC showed that high RAPGEF2 expression was significantly associated with favorable overall survival, disease-specific survival, and progression-free interval, and these findings were validated in independent ICGC_RECA-EU and E-MTAB-1980 cohorts. Multivariate Cox regression further confirmed RAPGEF2 as an independent protective prognostic factor. Immunohistochemistry in a tissue microarray cohort demonstrated that higher RAPGEF2 protein expression was associated with improved overall survival. Genomic analyses showed that low RAPGEF2 expression was related to higher mutational burden. Functional assays demonstrated that RAPGEF2 knockdown promoted KIRC progression. Enrichment analyses indicated that RAPGEF2 may be associated with metabolic pathway remodeling, while immunotherapy cohort analyses suggested its potential association with therapeutic benefit. Collectively, RAPGEF2 is identified as a protective prognostic biomarker and potential functional regulator in KIRC.

Biomarker↗

PubMed2026

Integrated RNA-seq and RNAi analyses reveal that ABCF2 is involved in defense against Vibrio parahaemolyticus in Penaeus vannamei.

The sustainable development of shrimp aquaculture is significantly compromised by Vibrio parahaemolyticus infections. Identifying host resistance genes and characterizing their immunological roles are essential for developing effective disease control strategies. In this study, we conducted a comparative transcriptomic analysis of intestinal tissues from Penaeus vannamei exhibiting varying degrees of pathological damage post-V. parahaemolyticus challenge to identify key resistance genes. KEGG enrichment analysis revealed that the ABC transporter pathway was markedly enriched among upregulated genes in both the 9 h vs 0 h and 48 h vs 0 h comparison groups. Based on the expression profiles and domain characteristics of genes within this pathway, the full transporter PvABCA3, half transporter PvABCC1, and soluble protein PvABCF2 were selected for RNAi assays. The result indicated that silencing PvABCF2, but not PvABCA3 and PvABCC1, significantly increased mortality, tissue damage, and Vibrio load in V. parahaemolyticus-challenged shrimp. Further investigation revealed that PvABCF2 silencing substantially suppressed the expression of antimicrobial peptides (AMPs), components of the proPO-activating system, and key genes involved in the JAK-STAT and NF-κB signaling pathways. These findings suggested that the increased susceptibility of shrimp to V. parahaemolyticus following PvABCF2 silencing may be associated with downregulation of these specific immune-related genes. Moreover, one SNP within PvABCF2 was found to be markedly associated with resistance to V. parahaemolyticus via SNP association analysis. Collectively, these results suggested that PvABCF2 was involved in defense response against V. parahaemolyticus and identified a potential molecular marker for disease-resistant breeding.

Animals↗

PubMedDate not supplied

Identification of differentially expressed genes in Dreissena polymorpha exposed to contaminants.

Development of transcriptome analysis methods such as differential display PCR and construction of subtractive libraries now makes it possible to profile gene expression in response to xenobiotic exposure. As an example of application of these methods, zebra mussels (Dreissena polymorpha) were treated with various contaminants such as Aroclor 1254, 3-methylcholanthrene, chrysene and atrazine. A total of 242 mRNAs were identified as differentially expressed. Analysis of these mRNAs should provide valuable information regarding detoxification mechanisms in this bivalve species. In addition, the use of cDNA array technology applied to these gene products may constitute a multi-marker approach to monitor the effect of contamination on this aquatic species.

Animals↗

PubMed2025

NEK9-mediated Wnt signalling repressor TLE3 rewires Docetaxel resistance in cancer cells by inducing pyroptosis.

BACKGROUND: Docetaxel is the most common chemotherapy regimen for several neoplasms, including advanced OSCC (Oral Squamous Cell Carcinoma). Unfortunately, chemoresistance leads to relapse and adverse disease outcomes. METHODS: We performed CRISPR-based kinome screening to identify potential players of Docetaxel resistance. Immunohistochemistry was performed to examine the expression profile of the target gene across tumour tissues. Global transcriptome analysis was performed to determine the molecular mechanism underlying Docetaxel resistance. NEK9 kinase assay was performed to identify a putative kinase inhibitor. RESULTS: Upon conducting CRISPR-based kinome screening, Never In Mitosis Gene-A Related Kinase-9 (NEK9) was identified as a major player of Docetaxel resistance in OSCC, prostate, and pancreatic cancer lines. NEK9 expression was found to be upregulated in chemotherapy non-responder OSCC patients as compared to responders. NEK9 ablation restores Docetaxel-induced cell death in chemoresistant cells. Mechanistically, we found that NEK9 deletion upregulates Transducin-like enhancer protein 3 (TLE3), which in turn represses Wnt signalling. Fostamatinib was identified as a potent NEK9 inhibitor that overcomes Docetaxel resistance. CONCLUSIONS: Our study demonstrated that NEK9 plays an important role in Docetaxel resistance. The novel combination of NEK9 inhibitor Fostamatinib and Docetaxel needs further clinical investigation in advanced OSCC.

Humans↗

PubMed2026

A pro-inflammatory metastasis-associated macrophage subset induces tumor-promoting mesothelial cell conversion in ovarian cancer via IL-1α secretion.

Tumor-associated macrophages (TAMs) are key regulators of the tumor microenvironment, yet the functional specialization of TAM subsets in metastatic progression remains incompletely defined. Here, we characterized distinct TAM populations contributing to tumor-promoting mesothelial cell conversion in high-grade ovarian carcinoma using single-cell RNA sequencing of patient-derived macrophages from ascites (ascTAMs) and omental metastases (omTAMs). TAMs from these anatomical sites were clearly distinguishable by polarization states, with omTAMs exhibiting a mixed M1⁺/M2⁺ phenotype, in contrast to the M1low/M2⁺ profile observed in ascTAMs. Transcriptomic analysis further revealed functional divergence of these subsets. Notably, omTAMs displayed gene signatures associated with mesothelial-to-mesenchymal transition (MMT), a critical process enabling tumor invasion across the peritoneal lining. Functionally, conditioned media from omTAMs, similar to that from classically activated M1 macrophages, induced MMT in primary mesothelial cells via TGFβ and ERK/p38 MAPK signaling pathways. This phenotypic transition enhanced transmesothelial tumor cell invasion. Proteomic analysis identified IL-1α as a key MMT-inducing factor secreted by pro-inflammatory macrophages. Mechanistically, IL-1α cooperates with TGFβ by activating an autocrine TGFβ/TGFBR1 feedback loop in mesothelial cells, thereby amplifying MMT. Consistent with these findings, IL1A expression was enriched in omTAM clusters across independent patient samples and was confirmed by immunohistochemical analysis of clinical samples. From a therapeutic perspective, our study identifies new avenues to counteract the mesothelial reprogramming driven by IL-1α⁺ TAMs, potentially impeding metastatic progression. Created in BioRender. Heidemann, S. (2026) https://BioRender.com/aeu6yd0 .

Female↗

PubMed2026

Immune profiling in a living human recipient of a gene-edited pig kidney.

Xenotransplantation of gene-edited pig kidneys offers a promising solution to the shortage of kidneys for organ transplantation. We recently performed a gene-edited pig kidney transplantation into a living human recipient with end-stage kidney disease. Here, using transcriptomics, proteomics, metabolomics and multiplexed imaging, we conducted high-dimensional immune profiling in this individual. Despite profound depletion of circulating T cells, early T cell-mediated rejection occurred within 1 week after transplantation, likely driven by subtherapeutic immunosuppression and the presence of residual CD8+ T cells in lymph nodes. This T cell-mediated rejection event was reversed by intensified immunosuppression. After treatment, adaptive immunity remained suppressed, whereas innate immune activation, characterized by sustained monocyte and macrophage activity along with elevated levels of interleukin-1 beta and granulocyte-macrophage colony-stimulating factor, persisted. Comparative transcriptomic analysis showed that xenograft rejection profiles resembled those typically observed in human allograft rejection, while also revealing unique innate immune signatures. We did not detect antibody-mediated rejection. The levels of circulating pig donor-derived cell-free DNA rose during the initial rejection episode and declined with treatment, supporting the potential of cell-free DNA measurements as a noninvasive biomarker of xenograft rejection. These findings define the distinct immune landscape of kidney xenotransplantation and highlight the need for regimens targeting both innate and adaptive immunity to improve outcomes.

Animals↗

PubMed2026

Cell wall-forming chitin synthases in a chytrid fungus.

Chitin is a critical structural component of fungal cell walls, yet our understanding of its synthesis across the kingdom Fungi remains limited. Here, we investigate chitin synthase diversity, transcription and localisation in the aquatic saprotrophic chytrid Rhizoclosmatium globosum, expanding insights into fungal cell wall biology beyond Dikaryan models. We identified 20 chitin synthase genes in the R. globosum genome, mostly canonical Division I and II types with conserved functional motifs. Transcriptomic analysis through zoospore, germling and immature thallus developmental stages revealed stage-specific expression patterns, with active gene diversity correlating with increasing morphological complexity. Using electroporation-based transformation and fluorescent fusion constructs, we indicate expression and localisation of two chitin synthases during cell development. Localisation patterns suggest dynamic redistribution from cytoplasmic dispersion in early encysted cells to concentrated signals at the sporangium wall. Expression in and around the apophysis indicates the importance of these structures in cell maintenance. Our findings highlight functional specialisation among chitin synthases and underscore the importance of cell wall integrity in chytrid development. This work establishes R. globosum as a genetically tractable model for studying chytrid cell biology and contributes to a broader understanding of fungal evolution and cell wall dynamics.

Biotechnology↗

PubMed2002

Differential gene expression in Entamoeba histolytica isolated from amoebic liver abscess.

The majority of human infections with the intestinal protozoan parasite Entamoeba histolytica remain asymptomatic. In a small proportion of infections, however, E. histolytica trophozoites penetrate the intestinal mucosa and disseminate to other organs, most commonly to the liver, where they induce abscess formation. It is believed that the ability of E. histolytica trophozoites to destroy host tissues and to survive within the liver is accomplished by a strong adaptive response, which requires the specific regulation of a number of amoeba proteins. Using differential display polymerase chain reaction (DD-PCR), we compared RNA expression between E. histolytica trophozoites isolated from liver abscesses of infected gerbils and those grown under normal culture conditions. A total of 3000 cDNA-derived amplicons were compared between the two groups of amoebae, which were calculated to represent about one-third of all E. histolytica mRNA species (transcriptome). Among these, 55 were found to be specifically present or absent in abscess-derived amoebae, of which 42 were successfully cloned and sequenced. Database searches and Northern blot analyses revealed that the 42 amplicons correspond to 29 independent E. histolytica genes, of which at least seven are specifically upregulated and five are downregulated in abscess-derived amoebae. Specific expression of most of these genes was not simply the result of a heat shock response, which might be expected during abscess formation, as only five of the genes revealed an expression profile similar to that found in amoebae cultured under elevated temperatures. The two genes specifically downregulated in abscess-derived amoebae encode members of a family of so far unknown proteins, which contain repetitive stretches of sequences that are rich in lysine and glutamic acid residues. In contrast, a diverse set of genes is specifically upregulated, encoding ribosomal proteins (S30, L37A), cyclophilin, ferredoxin 2 and GTP-binding protein RAB7D, supporting the notion that liver abscess formation requires the regulation and concerted action of a variety of amoeba proteins. These proteins are associated with stress response, signal transduction, regulation of transcription and vesicular trafficking. However, transcriptome analysis will not be sufficient to identify all proteins specifically upregulated during abscess formation, as at least an increase in the expression of actin was found to be regulated at the post-transcriptional level.

Actins↗

PubMed2003

Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis.

Unlike many pathogens that are overtly harmful to their hosts, Mycobacterium tuberculosis can persist for years within humans in a clinically latent state. Latency is often linked to hypoxic conditions within the host. Among M. tuberculosis genes induced by hypoxia is a putative transcription factor, Rv3133c/DosR. We performed targeted disruption of this locus followed by transcriptome analysis of wild-type and mutant bacilli. Nearly all the genes powerfully regulated by hypoxia require Rv3133c/DosR for their induction. Computer analysis identified a consensus motif, a variant of which is located upstream of nearly all M. tuberculosis genes rapidly induced by hypoxia. Further, Rv3133c/DosR binds to the two copies of this motif upstream of the hypoxic response gene alpha-crystallin. Mutations within the binding sites abolish both Rv3133c/DosR binding as well as hypoxic induction of a downstream reporter gene. Also, mutation experiments with Rv3133c/DosR confirmed sequence-based predictions that the C-terminus is responsible for DNA binding and that the aspartate at position 54 is essential for function. Together, these results demonstrate that Rv3133c/DosR is a transcription factor of the two-component response regulator class, and that it is the primary mediator of a hypoxic signal within M. tuberculosis.

Aspartic Acid↗

PubMed2026

Distal Recirculation of Enteral contents Augmented Mechanically (DREAM) Promotes Intestinal Adaptation and Restores Enterohepatic Signaling in Short Bowel Syndrome.

BACKGROUND & AIMS: Short bowel syndrome (SBS) leads to malabsorption and intestinal failure-associated liver disease. Intestinal adaptation (IA) driven by sustained enteral nutrition (EN) is essential, but EN delivery is limited after major resection. We developed DREAM (Distal Recirculation of Enteral contents Augmented Mechanically), which enables complete EN despite SBS, and enhances IA. We evaluated its efficacy in a translational large-animal model. METHODS: The study randomized 20 neonatal pigs to EN (control), SBS (75% resection), or DREAM. Growth, serum biochemistry, cytokines, intestinal morphology, barrier integrity, hepatic histology, and gene expression (quantitative polymerase chain reaction, RNA sequencing, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology enrichment) were analyzed. RESULTS: DREAM prevented hepatic and intestinal injury seen in SBS. Serum bilirubin (0.11 vs 5.14 mg/dL, P = .0008), γ-glutamyl transferase (23.2 vs 114.6 IU/L, P < .0001), and bile acids (9.7 vs 39 μmol/L, P = .0026) were significantly lower. Inflammatory cytokines (interferon-γ, P = .0296; interleukin 1β, P = .0349; and interleukin 6, P = .0189) and portal lipopolysaccharide (P = .0130) markedly improved. DREAM enhanced IA, increasing linear gut density (0.38 vs 0.209 g/cm, P < .0001), villus-to-crypt ratio (P = .0026), glucagon-like peptide 2 (P < .0001) and restored occludin and E-cadherin (P < .001). Hepatic bile salt export pump and cholesterol 7α-hydroxylase regulation were preserved (P = .0373 and P = .0034), and intestinal farnesoid X receptor, Takeda G-protein-coupled receptor 5, and epidermal growth factor signaling were reactivated (P < .01). Transcriptomic analysis confirmed improvements in metabolic, absorptive, and immune pathways. DREAM effluent demonstrated >80% macronutrient absorption within 6 hours (P < .0001). CONCLUSION: DREAM enables full EN in SBS, restoring absorption, mucosal integrity, and gut-liver homeostasis while preventing intestinal failure-associated liver disease. This approach represents a promising translational advance in SBS therapy.

Gut Atrophy↗

PubMed2002

Product dependence and bifunctionality compromise the ultrasensitivity of signal transduction cascades.

Covalent modification cycles are ubiquitous. Theoretical studies have suggested that they serve to increase sensitivity. However, this suggestion has not been corroborated experimentally in vivo. Here, we demonstrate that the assumptions of the theoretical studies, i.e., irreversibility and absence of product inhibition, were not trivial: when the conversion reactions are close to equilibrium or saturated by their product, "zero-order" ultrasensitivity disappears. For high sensitivities to arise, not only substrate saturation (zero-order) but also high equilibrium constants and low product saturation are required. Many covalent modification cycles are catalyzed by one bifunctional 'ambiguous' enzyme rather than by two independent proteins. This makes high substrate concentration and low product concentration for both reactions of the cycle inconsistent; such modification cycles cannot have high responses. Defining signal strength as ratios of modified (e.g., phosphorylated) over unmodified protein, signal-to-signal response sensitivity equals 1: signal strength should remain constant along a cascade of ambiguous modification cycles. We also show that the total concentration of a signalling effector protein cannot affect the signal emanating from a modification cycle catalyzed by an ambiguous enzyme if the ratio of the two forms of the effector protein is not altered. This finding may explain the experimental result that the pivotal signal transduction protein PII plus its paralogue GlnK do not control steady-state N-signal transduction in Escherichia coli. It also rationalizes the absence of strong phenotypes for many signal-transduction proteins. Emphasis on extent of modification of these proteins is perhaps more urgent than transcriptome analysis.

Enzymes↗

PubMed2024

Decorin suppresses tumor lymphangiogenesis: A mechanism to curtail cancer progression.

The complex interplay between malignant cells and the cellular and molecular components of the tumor stroma is a key aspect of cancer growth and development. These tumor-host interactions are often affected by soluble bioactive molecules such as proteoglycans. Decorin, an archetypical small leucine-rich proteoglycan primarily expressed by stromal cells, affects cancer growth in its soluble form by interacting with several receptor tyrosine kinases (RTK). Overall, decorin leads to a context-dependent and protracted cessation of oncogenic RTK activity by attenuating their ability to drive a prosurvival program and to sustain a proangiogenic network. Through an unbiased transcriptomic analysis using deep RNAseq, we identified that decorin down-regulated a cluster of tumor-associated genes involved in lymphatic vessel (LV) development when systemically delivered to mice harboring breast carcinoma allografts. We found that Lyve1 and Podoplanin, two established markers of LVs, were markedly suppressed at both the mRNA and protein levels, and this suppression correlated with a significant reduction in tumor LVs. We further identified that soluble decorin, but not its homologous proteoglycan biglycan, inhibited LV sprouting in an ex vivo 3D model of lymphangiogenesis. Mechanistically, we found that decorin interacted with vascular endothelial growth factor receptor 3 (VEGFR3), the main lymphatic RTK, and its activity was required for the decorin-mediated block of lymphangiogenesis. Finally, we identified that Lyve1 was in part degraded via decorin-evoked autophagy in a nutrient- and energy-independent manner. These findings implicate decorin as a biological factor with antilymphangiogenic activity and provide a potential therapeutic agent for curtailing breast cancer growth and metastasis.

Decorin↗

PubMed2002

Disrupted synaptic development in the hypoxic newborn brain.

Infants born prematurely risk significant life-long cognitive disability, representing a major pediatric health crisis. The neuropathology of this cohort is accurately modeled in mice subjected to sublethal postnatal hypoxia. Massively parallel transcriptome analysis using cDNA microchips (9,262 genes), combined with immunohistochemical and protein assays, reveals that sublethal hypoxia accentuates genes subserving presynaptic function, and it suppresses genes involved with synaptic maturation, postsynaptic function, and neurotransmission. Other significantly affected pathways include those involved with glial maturation, vasculogenesis, and components of the cortical and microtubular cytoskeleton. These patterns reveal a global dysynchrony in the maturation programs of the hypoxic developing brain, and offer insights into the vulnerabilities of processes that guide early postnatal cerebral maturation.

Animals↗

PubMed2001

Molecular cross-talk between the TRAIL and interferon signaling pathways.

TRAIL/APO-2L induces apoptosis in a variety of transformed cells and has potential as an anti-cancer therapeutic. The physiologic role of TRAIL is presumably more complex than merely activating caspase-mediated cell death. To shed light into TRAIL-mediated signaling, we used DNA microarrays to profile gene expression mediated by TRAIL in breast carcinoma cells. Primary response genes induced by TRAIL included a number of known NF-kappaB-dependent genes such as cIAP2, A20, and E-selectin. Remarkably, global transcriptome analysis revealed that TRAIL also induced a cohort of genes related to the interferon-signaling pathway. Assessing interferon-induced gene expression suggested various points of interaction with the TRAIL signaling pathway. Interestingly, while we observed interferon-mediated up-regulation of TRAIL, we also demonstrated a concomitant TRAIL-mediated induction of interferon-beta. Combining TRAIL and interferon in vitro, synergistically induced apoptosis and caspase activation in breast cancer cells. Together, these data indicate multiple levels of molecular cross-talk between the two diverse cytokines with anti-tumor properties.

Apoptosis↗

PubMed2026

Carrot Juice Intake Modulates Oncogenic and Inflammatory Pathways in Advanced Colorectal Adenomas: A Pilot Feasibility Study.

Carrots are a rich dietary source of carotenoids and polyacetylenes, bioactive compounds with demonstrated anti-inflammatory and anticancer properties in experimental models. Epidemiological evidence suggests that carrot consumption is associated with a reduced risk of colorectal cancer; however, clinical data linking carrot intake to molecular changes in premalignant colorectal tissue remain limited. In this pilot intervention study, 20 patients with advanced colorectal adenomas were enrolled. Fifteen participants consumed carrot juice daily for 21 days, while five served as untreated controls. Paired adenoma biopsies were collected before and after the intervention and were analyzed using gene expression microarrays to assess transcriptional responses. Carrot juice intake was well tolerated, with adherence exceeding 95% and no reported adverse events. Transcriptomic analysis revealed modulation of key pathways implicated in colorectal carcinogenesis, including downregulation of the WNT, PI3K-AKT, and MAPK signaling pathways, as well as cyclooxygenase-2-related inflammatory pathways and cytokine signaling. These changes were consistent with reduced oncogenic signaling and attenuation of inflammatory activity within adenoma tissue. In summary, short-term carrot juice consumption was associated with coordinated suppression of molecular pathways involved in colorectal adenoma progression. These findings provide preliminary clinical evidence that a whole-food dietary intervention may influence early carcinogenic processes and support the need for larger controlled studies evaluating clinical outcomes.

Journal Article↗

PubMed2025

ANXA3 hypomethylation as a prognostic biomarker in hepatitis B virus-related acute-on-chronic liver failure.

BACKGROUND: Hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) is associated with a poor prognosis. This research aimed to characterize the expression pattern and clinical value of Annexin A3 (ANXA3) in HBV-ACLF patients. METHODS: First of all, ACLF-related datasets were downloaded from the Gene Expression Omnibus (GEO) database to carry out bioinformatics analyses. RT-qPCR, ELISA, and Methylight were used to measure ANXA3 gene expression and promoter methylation levels. A validation cohort was leveraged to further validate the results. RESULTS: Transcriptome analysis showed that ANXA3 was among the most differentially expressed genes when comparing dead patients with HBV-ACLF to those with survivors. The mRNA and serum levels of ANXA3 were elevated, and methylation levels were decreased in HBV-ACLF patients. The PMR value of ANXA3 in patients with HBV-ACLF was negatively correlated with inflammation-related cytokines IL-6, TNF-α, and IL-1β, as well as quantitative clinical parameters AST, TBIL, PT, INR, NEUT%, and MELD score, and positively correlated with PTA (all p < 0.05). In HBV-ACLF patients, ANXA3 was considered to be an independent influence factor for the 90-day mortality. It was also found that ANXA3, especially hypomethylation, was associated with 28- and 90-day overall survival in patients with HBV-ACLF based on receiver operating characteristic (ROC) analysis, decision curve analysis (DCA), and Kaplan-Meier curves. CONCLUSIONS: ANXA3 hypomethylation has a prominent predictive value for short-term mortality in patients with HBV-ACLF and may serve as a promising biomarker of HBV-ACLF prognosis.

Humans↗

PubMed2026

Translation of scRNA-seq to a clinical blood test for infection diagnostics.

INTRODUCTION: Early and accurate triage of patients with febrile illness is crucial for appropriate treatment. While standard inflammatory biomarkers are often nonspecific, transcriptome analysis of peripheral blood has diagnostic potential. However, bulk gene expression data is often confounded by changes in cell count proportions, a more robust quantification of gene expression in specific single-cell types, such as monocytes, is required to serve as a reliable clinical biomarker. AREAS COVERED: Various methods to obtain single-cell-type gene expression results, including the gold standard of gene expression analysis after cell sorting and single-cell RNA sequencing, which are difficult to implement in the routine settings are discussed. Other method to interrogate gene expression of a single cell-type is needed. Finally, monocyte cell-type specific ratio-based biomarker (RBB, called Direct Leukocyte Single cell-type Transcript Abundance, or DIRECT LS-TA) which can estimate single cell-type (monocyte) specific gene expression without cell sorting is introduced. EXPERT OPINION: Traditional diagnostic test for differentiating infection has several limitations requiring breakthrough including turn-around time and cost. DIRECT LS-TA provides a reliable way to quantify monocyte-specific gene expression that strongly correlates with gold-standard methods. It is more affordable than single-cell RNA sequencing and can be readily implemented in clinical laboratories using widely available quantitative PCR or digital PCR machines.

Humans↗