HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC.

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma (HCC). Integrated 15 transcriptomic datasets of HCC clinical samples, the first version of HCC database (HCCDB v1.0) was released in 2018. Through the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets, it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and robustness. With four years having passed, the database now needs integration of recently published datasets. Furthermore, the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial architecture. Here, we present HCCDB v2.0, an updated version that combines bulk, single-cell, and spatial transcriptomic data of HCC clinical samples. It dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples, thereby enhancing the reliability of transcriptomic meta-analysis. A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections, respectively. A novel single-cell level and 2-dimension (sc-2D) metric is proposed as well to summarize cell type-specific and dysregulated gene expression patterns. Results are all graphically visualized in our online portal, allowing users to easily retrieve data through a user-friendly interface and navigate between different views. With extensive clinical phenotypes and transcriptomic data in the database, we show two applications for identifying prognosis-associated cells and tumor microenvironment. HCCDB v2.0 is available at http://lifeome.net/database/hccdb2.

AURKA knockdown inhibits esophageal squamous cell carcinoma progression through ferroptosis.

Aurora kinase A, as a pro-carcinogenic in gastric cancer and glioma kinase, is enhanced in several human tumors. However, it's regulatory mechanism in esophageal squamous cell carcinoma (ESCC) remains unclear. Thus, this study aimed to investigate the expression status, functional roles, and molecular mechanisms of AURKA in ESCC development. AURKA expression was analyzed by the screening of the GEO database and detected using an immunohistochemical method. The biological function of AURKA on ESCC was evaluated in vitro and in vivo. Western blot assay, malondialdehyde (MDA), iron, and glutathione (GSH) kits were utilized to assess changes in ferroptosis. Database analysis results showed that AURKA was a differential gene in ESCC and was highly expressed in human ESCC tissues. Functionally, AURKA knockdown decreased ESCC cell proliferation, invasion, and metastasis both in vitro and in vivo. Moreover, when AURKA was knockdown, cells were more correctly blocked in the G2/M phase, and the ferroptosis-related MDA and Fe increased, whereas the GSH reduced. Consistently, Glutathione peroxidase 4 (GPX4) and solute carrier family 7a member 11 (SLC7A11) expression were downregulated by AURKA knockdown. However, ferroptosis inhibitor partially restore ESCC cell proliferation, invasion, and metastasis caused by AURKA knockdown. AURKA knockdown enhances ferroptosis and acts against cancer progression in ESCC. AURKA acts as a tumor-promoting gene and may serve as potential target for ESCC treatment.

Decreased levels of hydrogen sulfide in the hypothalamic paraventricular nucleus contribute to sympathetic hyperactivity induced by cerebral infarction.

Paroxysmal sympathetic hyperactivity (PSH) is a common clinical feature secondary to ischemic stroke (IS), but its mechanism is poorly understood. We aimed to investigate the role of H2S in the pathogenesis of PSH. IS patients were divided into malignant (MCI) and non-malignant cerebral infarction (NMCI) group. IS in rats was induced by the right middle cerebral artery occlusion (MCAO). H2S donor (NaHS) or inhibitor (aminooxy-acetic acid, AOAA) were microinjected into the hypothalamic paraventricular nucleus (PVN). Compared with the NMCI group, patients in the MCI group showed PSH, including tachycardia, hypertension, and more plasma norepinephrine (NE) that was positively correlated with levels of creatine kinase, glutamate transaminase, and creatinine respectively. The 1-year survival rate of patients with high plasma NE levels was lower. The hypothalamus of rats with MCAO showed increased activity, especially in the PVN region. The levels of H2S in PVN of the rats with MCAO were reduced, while the blood pressure and renal sympathetic discharge were increased, which could be ameliorated by NaHS and exacerbated by AOAA. NaHS completely reduced the disulfide bond of NMDAR1 in PC12 cells. The inhibition of NMDAR by MK-801 microinjected in PVN of rats with MCAO also could lower blood pressure and renal sympathetic discharge. In conclusion, PSH may be associated with disease progression and survival in patients with IS. Decreased levels of H2S in PVN were involved in regulating sympathetic efferent activity after cerebral infarction. Our results might provide a new strategy and target for the prevention and treatment of PSH.

scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution.

SUMMARY: Single-cell RNA-seq (scRNA-seq) is a powerful technique for decoding the complex cellular compositions in the tumor microenvironment (TME). As previous studies have defined many meaningful cell subtypes in several tumor types, there is a great need to computationally transfer these labels to new datasets. Also, different studies used different approaches or criteria to define the cell subtypes for the same major cell lineages. The relationships between the cell subtypes defined in different studies should be carefully evaluated. In this updated package scCancer2, designed for integrative tumor scRNA-seq data analysis, we developed a supervised machine learning framework to annotate TME cells with annotated cell subtypes from 15 scRNA-seq datasets with 594 samples in total. Based on the trained classifiers, we quantitatively constructed the similarity maps between the cell subtypes defined in different references by testing on all the 15 datasets. Secondly, to improve the identification of malignant cells, we designed a classifier by integrating large-scale pan-cancer TCGA bulk gene expression datasets and scRNA-seq datasets (10 cancer types, 175 samples, 663 857 cells). This classifier shows robust performances when no internal confidential reference cells are available. Thirdly, scCancer2 integrated a module to process the spatial transcriptomic data and analyze the spatial features of TME. AVAILABILITY AND IMPLEMENTATION: The package and user documentation are available at http://lifeome.net/software/sccancer2/ and https://doi.org/10.5281/zenodo.10477296.

Hydrogen sulfide ameliorates endothelial dysfunction in aging arteries by regulating ferroptosis.

Aging causes vascular endothelial dysfunction. We aimed to investigate the causes of vascular endothelial dysfunction during aging using plasma and renal arteries from patients who underwent nephrectomy and animal models. The results showed that the endogenous H2S-producing enzyme cystathione-γ-lyase (CSE) protein expression was downregulated in renal artery tissue, plasma H2S levels were reduced. Moreover, elevated lipid peroxidation and iron accumulation levels led to ferroptosis and endothelial diastolic function in the renal arteries was impaired in the elderly group. H2S enhanced the endogenous CSE expression in the elderly group, promoted endogenous H2S production, decreased lipid peroxide expression, and inhibited ferroptosis, which in turn improved vascular endothelial function in the elderly group. In animal models, we also observed the same results. In addition, we applied NaHS, Ferrostatin-1 (ferroptosis inhibitor) and erastin (ferroptosis inducer) to incubate renal arteries of SD rats. The results showed that NaHS enhanced ferroptosis related proteins expression, inhibited ferroptosis and improved vascular endothelial function. We demonstrated that endothelial dysfunction associated with aging is closely related to reduced endogenous H2S levels and ferroptosis in vascular endothelial cells. Notably, H2S reduced lipid peroxidation levels in vascular endothelial cells, inhibited ferroptosis in vascular endothelial cells, and improved endothelial dysfunction.

A comparative study of [68Ga]Ga-FAPI-04 PET/MR and [18F]FDG PET/CT in the diagnostic accuracy and resectability prediction of ovarian cancer.

PURPOSE: To provide a theory for guiding clinical treatment by comparing the clinical application value of [18F]fluorodeoxyglucose ([18F]FDG) PET/CT and [68Ga]Ga-FAPI (fibroblast activating protein inhibitor) PET/MR in the diagnosis and evaluation of resectability of ovarian cancer. METHODS: Thirty patients with high clinical suspicion of ovarian malignancies were enrolled from July 2021 to October 2022 and underwent [18F]FDG PET/CT and [68Ga]Ga-FAPI-04 PET/MR within 5 days. Twenty patients underwent [18F]FDG PET/MR at once completing [18F]FDG PET/CT for consistency checking. Images were analysed for comparing SUVs and for judging incomplete resectability according to the peritoneal cancer index (PCI) and SUIDAN scoring system. The expression of FAP, HK2 and Ki67 was analysed by immunohistochemistry staining. RESULTS: There was no significant difference between PET/MR and PET/CT in SUVs-FDG at different locations (p > 0.05), and their diagnostic accuracies were similar. The diagnostic accuracy of [68Ga]Ga-FAPI-04 PET/MR had advantages for peritoneal metastasis since SUVsFAPI were higher (p < 0.01). The sensitivity of [68Ga]Ga-FAPI-04 PET/MR in the diagnosis of peridiaghragmatic metastases was higher because SUVmax in the liver was decreased (p < 0.001). [68Ga]Ga-FAPI-04 PET/MR might have advantages in diagnosing gastrointestinal invasion. In PCI score analysis, [68Ga]Ga-FAPI-04 PET/MR could partially correct missing or underestimated scores by [18F]FDG PET/CT, but the matching probability between left peri-intestinal metastasis scores was low and easy to overestimate. Interestingly, diaphragmatic metastasis detected by [68Ga]Ga-FAPI-04 PET/MR had the greatest correlation with the prediction of incomplete resectability (logistic regression p = 0.02). Through immunohistochemistry, the expression of FAP had a strong correlation with SUVmax-FAPI (p < 0.001), while the expression of HK2 was correlated with SUVmax-FDG (p < 0.01). In addition, SUVmax-FDG with Ki67 ≥ 20% was significantly higher than that with Ki67 < 20% (p < 0.05). CONCLUSIONS: [68Ga]Ga-FAPI-04 PET/MR had obvious advantages for metastases diagnosis and could more accurately assess tumour load and predict incomplete resectability. SUVmax-FDG was conducive to evaluating the degree of tumour malignancy.