Aberrant LYZ expression in tumor cells serves as the potential biomarker and target for HCC and promotes tumor progression via csGRP78

Transcriptome profiles of blastocysts originating from oocytes matured in follicular fluid from preovulatory follicles of greater or lesser maturity

BACKGROUND

Oocyte competence for early embryo development relies on intercellular communication between the maturing oocyte and preovulatory follicle. Preovulatory follicle maturity, as indicated by serum estradiol concentration or follicle diameter, has previously been linked to pregnancy, follicular fluid metabolites, cumulus-oocyte metabolism, and oocyte competency for embryo development. Such relationships indicate metabolic and developmental programming of the oocyte based on the preovulatory follicle's physiological status, but downstream impacts on the molecular signature of blastocysts have not been examined. We hypothesized that supplementing maturing oocytes with follicular fluid originating from preovulatory follicles of greater or lesser maturity would impact the transcriptome of resulting blastocysts and indicate metabolic programming of the embryo that originated from the oocyte's maturation environment. The objective was to investigate the effect of follicle maturity on the oocyte by examining the transcriptome of blastocysts originating from oocytes matured in the presence of follicular fluid from preovulatory follicles of greater or lesser maturity.

RESULTS

In vitro maturing oocytes were supplemented with follicular fluid collected from preovulatory follicles of greater or lesser maturity. Following identical embryo culture procedures, RNA-sequencing was performed on pools of 2 blastocysts (Greater, n = 12; Lesser, n = 15; all with stage code = 7 and quality code = 1). A total of 12,310 genes were identified in blastocysts after filtering to remove lowly abundant genes. There were 113 genes that differed in expression between blastocysts originating from oocytes matured in greater versus lesser maturity follicular fluid (eFDR < 0.01). Although no pathways were significantly enriched with differentially expressed genes, transcriptome profiles suggested improved Wnt/β-catenin signaling, metabolism, and protection from oxidative stress in blastocysts derived from oocytes matured in greater maturity follicular fluid, while potential unregulated cell growth presented in blastocysts resulting from the lesser follicle maturity treatment.

CONCLUSIONS

Follicular fluid from preovulatory follicles of greater physiological maturity may better prepare maturing oocytes for early embryo development. Furthermore, oocytes matured in follicular fluid from preovulatory follicles of lesser maturity may attempt to overcompensate for nutrient deficit during oocyte maturation, leading to uncontrolled cellular growth and increased oxidative stress.

Single-Cell Sequencing and Transcriptome Analysis Explored Changes in Midnolin-Related Immune Microenvironment and Constructed Combined Prognostic Model for Pancreatic Cancer

Background

Pancreatic cancer has one of the worst prognoses of any malignant tumor. The value of MIDN, midnolin-related genes and midnolin-related immune infiltrating cells (MICs) in the prognosis of pancreatic cancer remains unknown.

Methods

Single-cell analysis were used to identify midnolin-related genes. Immune cell infiltration was obtained using CIBERSORT. The prognostic midnolin-related genes were identified through the utilization of Cox regression and the least absolute selection operator (LASSO) approach. The combined prognostic model was created using multifactorial Cox regression analysis. Survival analyses, immune microenvironment assessments, drug sensitivity checks were performed to evaluate the combined model performance. Finally, cellular experiments were carried out to confirm MIDN significance in pancreatic cancer.

Results

The combined model was constructed based on MIDN expression, prognostic model of 10 midnolin-related genes and M1 cell infiltration. Most immune checkpoint-related genes were expressed at greater levels in the low-risk group, suggesting a greater chance of immunotherapy's benefits. The most significant model gene, MIDN, was shown to have a function by cellular tests. In pancreatic cancer, MIDN knockdown drastically decreased pancreatic cancer cell lines' activity, proliferation, and invasive potential.

Conclusion

The combined model helped assess the prognosis of pancreatic cancer and offered fresh perspectives on immunotherapy in particular.

S100P is a core gene for diagnosing and predicting the prognosis of sepsis

Sepsis, characterized as a severe systemic inflammatory response syndrome, typically originates from an exaggerated immune response to infection that gives rise to organ dysfunction. Serving as one of the predominant causes of death among critically ill patients, it's pressing to acquire an in-depth understanding of its intricate pathological mechanisms to strengthen diagnostic and therapeutic strategies. By integrating genomic, transcriptomic, proteomic, and metabolomic data across multiple biological levels, multi-omics research analysis has emerged as a crucial tool for unveiling the complex interactions within biological systems and unraveling disease mechanisms in recent years. Samples were collected from 23 cases of sepsis patients and 10 healthy volunteers from January 2019 to December 2020. The protein components in the samples were explored by independent data acquisition (DIA) analysis method, while Circular RNA (circRNA) categories were usually identified by RNA sequencing (RNA-seq) technology. Subsequent to the above steps, data quality monitoring was performed by employing software, and unqualified sequences were excluded, and conditions were set for differential expression network analysis (protein group and circRNA group were separately used log2 |FC|≥ 1 and log2 |FC|≥ 2, P < 0.050). Gene Ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) analysis were performed on common differentially expressed proteins, followed by protein-protein interaction between common differentially expressed genes and cytoscape software enrichment analysis, and subsequently its association with associated diseases (Disease Ontology (DO)) was investigated in an all-round manner. Afterwards, the distribution distinction of common differentially expressed genes in sepsis group and healthy volunteer group was displayed by heat map after Meta-analysis. Subsequent to the above procedures, pivotal targets with noticeable survival curve distinctions in two states were screened out after Meta-analysis. At last, their potential value was verified by in vitro cell experiment, which provided reference for further discussion of the diagnostic value and prognostic effect of target gene. A total of 174 DEPs and 308 DEcircRNAs were identified in the proteomics analysis, while a total of 12 common differentially expressed genes were identified after joint analysis. The protein-protein interaction (PPI) network suggested the degree of interaction between the dissimilar genes, and the heat map demonstrated their specific distribution in distinct groups. Through enrichment analysis, these proteins predominantly participated in a sequence of crucial processes such as intracellular material synthesis and secretion, changes in inflammatory receptors and immune inflammatory response. The meta-analysis identified that S100P is highly expressed in sepsis. As illustrated by the ROC curve, this gene has high clinical diagnostic value, and utimately confirmed its expression in sepsis through in vitro cell experiments. In these two groups of healthy people and septic patients, S100P demonstrated a more obvious trend of differential expression; Cell experiments also proved its value in diagnosis and prognosis judgment in sepsis; As a result, they may become diagnostic and prognostic markers for sepsis in clinical practice.

Photoactivated hydride therapy under hypoxia beyond ROS

As compared to oxidative phototherapy, studies on reactive reductive species-participating photodynamic therapy (PDT) are rare. Porphyrins are typical photosensitizers restricted by the oxygen level, but efficacy and selectivity are always incompatible in PDT. Herein, we report that phlorins are ideal hydride (H-) donors and explore a water-soluble triphenylphosphonium-modified zinc-coordinated porphyrin (mitoZnPor) for in situ photogeneration of zinc-cored phlorin (mitoZnPhl). Driven by 1,4-dihydronicotinamide adenine dinucleotide (NADH), the mitoZnPor/mitoZnPhl couple can reduce electron acceptors like iron heme and ubiquinone that play key roles in the mitochondrial electron transport chain (Mito-ETC). Under hypoxia, mitoZnPor showed excellent cancer-selectivity and a highly efficient in vitro PDT effect with IC50 at nanomolar levels and potent tumor growth inhibition in a 4T1 tumor-xenografted mouse model with good biosafety, which underlines the great potential of Mito-ETC targeted non-classical PDT via a H--transfer mechanism beyond reactive oxygen species (ROS) in precision cancer phototherapy using NADH as a biomarker and original electron donor.

The 2024 Report on the Human Proteome from the HUPO Human Proteome Project

The Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify at least one isoform of every protein-coding gene and (2) to make proteomics an integral part of multiomics studies of human health and disease. The past year has seen major transitions for the HPP. neXtProt was retired as the official HPP knowledge base, UniProtKB became the reference proteome knowledge base, and Ensembl-GENCODE provides the reference protein target list. A function evidence FE1-5 scoring system has been developed for functional annotation of proteins, parallel to the PE1-5 UniProtKB/neXtProt scheme for evidence of protein expression. This report includes updates from neXtProt (version 2023-09) and UniProtKB release 2024_04, with protein expression detected (PE1) for 18138 of the 19411 GENCODE protein-coding genes (93%). The number of non-PE1 proteins ("missing proteins") is now 1273. The transition to GENCODE is a net reduction of 367 proteins (19,411 PE1-5 instead of 19,778 PE1-4 last year in neXtProt). We include reports from the Biology and Disease-driven HPP, the Human Protein Atlas, and the HPP Grand Challenge Project. We expect the new Functional Evidence FE1-5 scheme to energize the Grand Challenge Project for functional annotation of human proteins throughout the global proteomics community, including π-HuB in China.

Pan-cancer analysis of CLDN18.2 shed new insights on the targeted therapy of upper gastrointestinal tract cancers

Background

CLDN18.2 is a widely researched drug target. However, previous research has primarily been based on immunohistochemistry results and focused on gastric cancer.

Methods

To analyze the potential cancer-targeting effect of CLDN18.2 from a multi-omics perspective, this study quantified CLDN18.2 expression in The Cancer Genome Atlas (TCGA) pan-cancer cohort. Thus, the relationships between CLDN18.2 expression and genomic alterations, immune infiltration, and prognosis were analyzed. Additionally, we performed analyses of the differentially expressed genes and enriched pathways between the high- and low-CLDN18.2 expression groups, as well as the corresponding drug sensitivity analyses.

Results

The results indicated that CLDN18.2 was highly expressed in pancreatic adenocarcinoma (PAAD), stomach adenocarcinoma (STAD), colorectal cancer (CRC), and esophageal carcinoma (ESCA). Moreover, the high- and low-CLDN18.2 expression groups presented significant differences in terms of genomic alterations and immune infiltration, such as the levels of methylation and CD4+ T cell infiltration. Furthermore, high CLDN18.2 expression was significantly associated with poor prognosis in bladder urothelial carcinoma (BLCA), ESCA, and PAAD. In upper gastrointestinal tract cancers (STAD, ESCA, and PAAD), downregulated gene-enriched pathways were associated with cell signaling, whereas upregulated gene-enriched pathways were associated with angiogenesis. Finally, we identified drugs associated with CLDN18.2 expression to which samples with different levels of expression were differentially sensitive.

Conclusion

CLDN18.2 was highly expressed in upper gastrointestinal tract cancers, and its expression had a significant effect on genomic alterations and the tumor microenvironment. Additionally, low CLDN18.2 expression was linked to favorable prognosis. Our study reveals the potential value of CLDN18.2 for tumor prognosis and targeted therapy in various cancers, especially upper gastrointestinal tract cancers.

IL-1β-induced epithelial cell and fibroblast transdifferentiation promotes neutrophil recruitment in chronic rhinosinusitis with nasal polyps

Neutrophilic inflammation contributes to multiple chronic inflammatory airway diseases, including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated with an unfavorable prognosis. Here, using single-cell RNA sequencing (scRNA-seq) to profile human nasal mucosa obtained from the inferior turbinates, middle turbinates, and nasal polyps of CRSwNP patients, we identify two IL-1 signaling-induced cell subsets-LY6D+ club cells and IDO1+ fibroblasts-that promote neutrophil recruitment by respectively releasing S100A8/A9 and CXCL1/2/3/5/6/8 into inflammatory regions. IL-1β, a pro-inflammatory cytokine involved in IL-1 signaling, induces the transdifferentiation of LY6D+ club cells and IDO1+ fibroblasts from primary epithelial cells and fibroblasts, respectively. In an LPS-induced neutrophilic CRSwNP mouse model, blocking IL-1β activity with a receptor antagonist significantly reduces the numbers of LY6D+ club cells and IDO1+ fibroblasts and mitigates nasal inflammation. This study implicates the function of two cell subsets in neutrophil recruitment and demonstrates an IL-1-based intervention for mitigating neutrophilic inflammation in CRSwNP.

D-Xylose Ameliorates Non-Alcoholic Fatty Liver Disease by Targeting Macrophage-expressed LYZ Gene

This study investigates the therapeutic effects of D-Xylose, a natural sugar, on non-alcoholic fatty liver disease (NAFLD), focusing on the expression of the lysozyme gene (LYZ) in macrophages. Using the single-cell dataset GSE136103 for NAFLD, researchers analyzed macrophage populations and other groups utilizing the Seurat package in R, while a differential analysis was performed on the NAFLD dataset GSE61260 using the limma package. Both in vitro and in vivo models, including cell culture, mouse models, RT-qPCR, Western blot, ELISA, and histopathological analyses, were employed to examine the effect of D-Xylose on lipid accumulation, LYZ expression, blood lipid levels, and inflammatory responses. The study found a significant upregulation of LYZ in free fatty acid (FFA)-treated cells and mouse liver tissues, with a subsequent reduction after D-Xylose intervention. Treatment with D-Xylose and Amlodipine led to a notable decrease in lipid accumulation, as evidenced by reduced triglyceride and cholesterol levels. D-Xylose demonstrated a greater improvement in lipid metabolism than Amlodipine. Additionally, D-Xylose significantly mitigated inflammatory responses, reducing levels of inflammatory markers such as IL1R, IL6, MYS8, TNF, NF-κB, and IL-1. Furthermore, D-Xylose administration significantly reduced liver weight and liver index, with a positive impact on serum liver function and blood lipid levels. The findings suggest that D-Xylose could be a therapeutic intervention for NAFLD by targeting LYZ expression in macrophages, thereby modulating lipid metabolism and inflammatory responses.

HCC spatial transcriptomic profiling reveals significant and potentially targetable cancer-endothelial interactions

BACKGROUND

HCC is a highly vascular tumor, and many effective drug regimens target the tumor blood vessels. Prior bulk HCC subtyping data used bulk transcriptomes, which contained a mixture of parenchymal and stromal contributions.

METHODS

We utilized computational deconvolution and cell-cell interaction analyses to cell type-specific (tumor-enriched and vessel-enriched) spatial transcriptomic data collected from 41 resected HCC tissue specimens.

RESULTS

We report that the prior Hoshida bulk transcriptional subtyping schema is driven largely by an endothelial fraction, show an alternative tumor-specific schema has potential prognostic value, and use spatially paired ligand-receptor analyses to identify known and novel (LGALS9 tumor-HAVCR2 vessel) signaling relationships that drive HCC biology in a subtype-specific and potentially targetable manner.

CONCLUSIONS

Our study leverages spatial gene expression profiling technologies to dissect HCC heterogeneity and identify heterogeneous signaling relationships between cancer cells and their endothelial cells. Future validation and expansion of these findings may validate novel cancer-endothelial cell interactions and related drug targets.

HGFK1 Enhances the Anti-Tumor Effects of Angiogenesis Inhibitors via Inhibition of CD90+ CSCs in Hepatocellular Carcinoma

The combination of anti-angiogenesis agents with immune-checkpoint inhibitors is a promising treatment for patients with advanced hepatocellular carcinoma (HCC); however, therapeutic resistance caused by cancer stem cells present in tumor microenvironments remains to be overcome. In this study, we report for the first time that the Kringle 1 domain of human hepatocyte growth-factor α chain (HGFK1), a previously described anti-angiogenesis peptide, repressed the sub-population of CD90+ cancer stem cells (CSCs) and promoted their differentiation and chemotherapy sensitivity mainly through downregulation of pre-Met protein expression and inhibition of Wnt/β-catenin and Notch pathways. Furthermore, we showed that the i.p. injection of PH1 (a tumor-targeted and biodegradable co-polymer), medicated plasmids encoding Endostatin (pEndo), HGFK1 genes (pEndo), and a combination of 50% pEndo + 50% pHGFK1 all significantly suppressed tumor growth and prolonged the survival of the HCC-bearing mice. Importantly, the combined treatment produced a potent synergistic effect, with 25% of the mice showing the complete clearance of the tumor via a reduction in the microvessel density (MVD) and the number of CD90+ CSCs in the tumor tissues. These results suggest for the first time that HGFK1 inhibits the CSCs of HCC. Furthermore, the combination of two broad-spectrum anti-angiogenic factors, Endo and HGFK1, is the optimal strategy for the development of effective anti-HCC drugs.

RRP8, associated with immune infiltration, is a prospective therapeutic target in hepatocellular carcinoma

BACKGROUND

Ribosomal RNA Processing 8 (RRP8) is a nucleolar Rossman fold-like methyltransferase that exhibits increased expression in many malignant tumours. However, the role of RRP8 in hepatocellular carcinoma (HCC) is still uncertain. We explored the relationships between RRP8 and prognosis and immune infiltration, as well as the putative pathological function and mechanism of RRP8 in HCC.

METHODS

Analysis of RRP8 expression across cancers was performed by using multiple databases. Associations between RRP8 expression and clinicopathological factors were further examined. Gene enrichment analysis was used to identify various putative biological activities and regulatory networks of RRP8 in HCC. The relationship between RRP8 expression and immune infiltration was confirmed by single-sample gene set enrichment analysis (ssGSEA). Univariate and multivariate Cox regression analyses were conducted to assess the impact of clinical variables on patient outcomes. Furthermore, a nomogram was constructed to estimate survival probability based on multivariate Cox regression analysis. Functional validation of RRP8 in HCC was performed with two different systems: doxycycline-inducible shRNA knockdown and CRISPR-Cas9 knockout.

RESULTS

RRP8 was markedly overexpressed in HCC clinical specimens compared to adjacent normal tissues. Further analysis demonstrated that RRP8 was directly connected to multiple clinical characteristics and strongly associated with various immune markers in HCC. Moreover, elevated RRP8 expression indicated an unfavourable prognosis. Our functional studies revealed that both knockdown and knockout of RRP8 dramatically attenuated liver cancer cells to proliferate and migrate. Knockout of RRP8 decreased the phosphorylation of MEK1/2 and β-catenin-(Y654) signalling pathway components; downregulated downstream signalling effectors, including Cyclin D1 and N-cadherin; and upregulated E-cadherin.

CONCLUSIONS

RRP8 is strongly implicated in immune infiltration and could be a potential therapeutic target in HCC.

RNF149 Promotes HCC Progression through Its E3 Ubiquitin Ligase Activity

Hepatocellular carcinoma (HCC) accounts for over 80% of cases among liver cancer, with high incidence and poor prognosis. Thus, it is of valuable clinical significance for discovery of potential biomarkers and drug targets for HCC. In this study, based on the proteomic profiling data of paired early-stage HCC samples, we found that RNF149 was strikingly upregulated in tumor tissues and correlated with poor prognosis in HCC patients, which was further validated by IHC staining experiments of an independent HCC cohort. Consistently, overexpression of RNF149 significantly promoted cell proliferation, migration, and invasion of HCC cells. We further proved that RNF149 stimulated HCC progression via its E3 ubiquitin ligase activity, and identified DNAJC25 as its new substrate. In addition, bioinformatics analysis showed that high expression of RNF149 was correlated with immunosuppressive tumor microenvironment (TME), indicating its potential role in immune regulation of HCC. These results suggest that RNF149 could exert protumor functions in HCC in dependence of its E3 ubiquitin ligase activity, and might be a potential prognostic marker and therapeutic target for HCC treatment.