Protein and metabolic profiles of tyrosine kinase inhibitors co-resistant liver cancer cells

Single-cell transcriptomic analysis of canine insulinoma reveals distinct sub-populations of insulin-expressing cancer cells

Canine malignant insulinoma is a rare, highly metastatic and life-threatening neuroendocrine tumour of pancreatic beta cells. To map the single-cell transcriptomic landscape of canine insulinoma for the first time, transcriptomic profiles of 5,532 cells were captured from two spontaneous insulinomas (Patient 1 and 2) and one associated metastasis (Patient 2) in two Boxer dogs. Distinct cancer, endocrine, and immune cell populations were identified. Notably, all three tumour samples contained two transcriptionally distinct insulin-expressing tumour cell populations (INS+ and INS+FOS low ), characterised here for the first time. These two cancer cell populations significantly differed by ~ 8,000 differentially expressed genes (DEGs), particularly tumour suppressor genes (e.g. TP53, EGR1) and cancer-related pathways (e.g., MAPK, p53). In contrast, COX7A2L was one of a few genes ubiquitously expressed and significantly upregulated (> 20-fold) in both insulin-expressing tumour populations compared to other captured populations. Both populations were also characterised by expression of chromogranin/secretogranin neuroendocrine tumour marker genes (e.g. CHGA, SCGN). There were far fewer gene expression differences observed between insulin-expressing tumour cells from the two patients (~ 600 DEGs) than between the two cancer cell populations within each patient. These DEGs included CLTRN, TMSB4X, CSRP2, LGALS2, and C15orf48. Unexpectedly for a tumour of endocrine origin, the metastasis in Patient 2 exhibited > 20-70 fold upregulation of exocrine pancreatic genes including CLPS, PRSS2, PRSS and CTRC. Immune cell analyses identified distinct infiltrating immune populations, including memory T cells and macrophages and revealed likely tumour-immune interactions, including the CD40-CD40L interaction. This study provides the first single-cell RNA sequencing (scRNA-seq) analysis of naturally occurring insulinoma in any species, revealing tumour cell heterogeneity, novel immune microenvironment features, and potential therapeutic targets. Despite its small scale, the findings highlight the utility of scRNA-seq in veterinary oncology and its translational potential for pancreatic neuroendocrine tumours across species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s44356-025-00026-3.

Uncovering proteome variations and concomitant quality changes of different drying methods Cordyceps sinensis by 4D-DIA structural proteomics

Introduction

Cordyceps sinensis is a fungus, serves dual purposes as both a medicinal herb and a food source. Due to its high water content, fresh Cordyceps sinensis is difficult to preserve, necessitating the drying necessary to process Cordyceps sinensis.

Methods

Using 4D-DIA proteomics, researchers analyzed the proteome profiles of fresh Cordyceps sinensis (CK) under three different drying conditions: vacuum freeze-drying (FD), oven-drying (OD), and air-drying (AD). In addition, it was found that the protein and free sulfhydryl content of Cordyceps sinensis decreased significantly and the disulfide bond content increased after different drying methods.

Results and discussion

A total of 3762 proteins were identified, showing variations between groups and high protein content. In the control groups consisting of fresh Cordyceps sinensis samples and the three drying methods, FD. vs CK exhibited the fewest differentially abundant proteins, with the majority being upregulated. On the other hand, CK vs OD displayed the greatest amount of distinct proteins, with a significant rise in both up-regulated and down-regulated proteins. Analysis of KEGG indicated that the distinct proteins were predominantly concentrated in pathways like the ribosome, synthesis of coenzymes, and metabolism of amino sugar and nucleotide sugar. Notably, there was a significant overlap between ribosome and ribosome biogenesis in eukaryotes pathways. The process of drying Cordyceps sinensis resulted in a significant upregulation of the expression of proteins linked to various metabolic pathways. This observation suggests that the drying treatment might activate or enhance certain biochemical processes within the organism, potentially influencing its overall metabolic activity. This finding highlights the importance of post-harvest dry methods on the biochemical properties of Cordyceps sinensis, which could have implications for its nutritional and medicinal value.This study provides a theoretical basis for the realization of Cordyceps sinensis resource utilization and storage methods, and provides theoretical support for guaranteeing the sustainable development of Cordyceps sinensis resources.

TMSB4X is a regulator of inflammation-associated ferroptosis, and promotes the proliferation, migration and invasion of hepatocellular carcinoma cells

BACKGROUND

Ferroptosis and inflammation are involved in cancer progression. The aim of this study was to identify inflammation-associated ferroptosis regulators in hepatocellular carcinoma (HCC).

METHODS

FerrDb database was searched for ferroptosis-related genes. RNA sequencing data and clinicopathologic information of HCC patients were downloaded from the Cancer Genome Atlas (TCGA) database. Weighted gene co-expression network analysis was applied to obtain the genes probably involved in inflammation-associated ferroptosis. Univariate Cox regression analysis was conducted to screen prognostic genes, and 10 machine learning algorithms were combined to find the optimal strategy to evaluate the prognosis of the patients based on the prognosis-related genes. The patients were divided into high risk group and low risk group, and the differentially expressed genes were obtained. Thymosin beta 4 X-linked (TMSB4X) was overexpressed or knocked down in HCC cell lines, and then qPCR, CCK-8, Transwell, flow cytometery assays were performed to detect the change of HCC cells' phenotypes, and Western blot was used to detect the change of ferroptosis markers.

RESULTS

157 genes related to inflammation and ferroptosis in HCC were obtained by WGCNA. rLasso algorithm, with the highest C-index, screened out 29 hub genes, and this model showed good efficacy to predict the prognosis of HCC patients. The patients in high risk group and low risk groups showed distinct molecular characteristics. TMSB4X was the most important gene which dominated the classification, and it was highly expressed in HCC samples. TMSB4X promoted the viability, migration and invasion, and repressed ferroptosis of HCC cells.

CONCLUSION

The risk model constructed based on the inflammation-associated ferroptosis regulators is effective to predict the clinical outcome of HCC patients. TMSB4X, involved in inflammation-associated ferroptosis, is a potential biomarker and therapeutic target for HCC.