Identification of potential core genes at single-cell level contributing to pathogenesis of pancreatic ductal adenocarcinoma through bioinformatics analysis

Single-cell transcriptome conservation in a multispecies comparative analysis of fresh and cryopreserved insulinoma cell lines

Background

Insulinoma is the most common pancreatic neuroendocrine tumour in dogs and humans. The understanding of driving factors and critical survival genes in insulinomas is limited and overall survival is poor for canine and human malignant insulinoma. This study aimed to use single-cell RNA-sequencing to conduct a multispecies analysis of insulinoma cell lines to understand their single-cell transcriptomic landscape. Secondly, the impact of freeze-thawing on the pancreatic beta single-cell transcriptome was investigated, to determine whether cryoarchiving of primary insulinoma samples may be feasible in future studies.

Methods

Single-cell transcriptomic analysis was performed using fresh and cryopreserved multispecies insulinoma cell lines (canINS, CM, INS-1 and MIN6). R and Seurat were used to perform cell clustering and specific cluster marker genes were identified by the FindMarkers function. Metascape was used to identify statistically enriched pathways for specific cell clusters. Differentially expressed genes between fresh and cryopreserved single-cell transcriptome profiles, were defined as genes with a log2 fold change > 0.25 and a Bonferroni-adjusted P < 0.05, based on the Wilcoxon rank sum test.

Results

Based on the specific cell line single-cell transcriptome profiles, five or six cell clusters were constructed per cell line. All cell lines expressed neuroendocrine markers and additionally INS-1 and MIN6 displayed a gene signature indicative of mature/functional pancreatic islet/beta-cells. DEPTOR, BICC1, GHR, CCNB2, CENPA, LMO4, VANGL1, and L1CAM were identified as cross-species conserved insulinoma cluster marker genes. Little effect was found of cryopreservation and thawing on overall gene expression at the single-cell level in insulinoma cell lines: only 6 and 29 genes had a log2 fold change > 1 in cryopreserved versus fresh canINS and CM, respectively.

Conclusions

canINS, CM, INS-1 and MIN6 are all principally relevant as insulinoma models and the demonstrated differences in their single-cell transcriptomic profiles could aid researchers in selecting the appropriate cell lines for specific study objectives. Cross-species conserved insulinoma cluster marker genes were identified that harbour oncogenes and their involvement in insulinoma tumourigenesis should be investigated in future studies. The good comparability between cryopreserved and fresh insulinoma cells allows for inclusion of cryopreserved insulinoma patient samples in future studies, which allows for reduced assay-based variability.

Supplementary Information

The online version contains supplementary material available at 10.1186/s44356-025-00025-4.

Intermediate conductance calcium-activated potassium channel (KCa3.1) in cancer: Emerging roles and therapeutic potentials

The KCa3.1 channel (also known as the KCNN4, IK1, or SK4 channel) is an intermediate-conductance calcium-activated potassium channel that regulates the membrane potential and maintains calcium homeostasis. Recently, KCa3.1 channels have attracted increasing attention because of their diverse roles in various types of cancers. In cancer cells, KCa3.1 channels regulate key processes, including cell proliferation, cell cycle, migration, invasion, tumor microenvironments, and therapy resistance. In addition, abnormal KCa3.1 expression in cancers is utilized to distinguish between tumor and normal tissues, classify cancer stages, and predict patient survival outcomes. This review comprehensively examines the current understanding of the contribution of KCa3.1 channels to tumor formation, metastasis, and its mechanisms. We evaluated the potential of KCa3.1 as a biomarker for cancer diagnosis and prognosis. Finally, we discuss the advances and challenges of applying KCa3.1 modulators in cancer treatment and propose approaches to overcome these obstacles. In summary, this review highlights the importance of this ion channel as a potent therapeutic target and prognostic biomarker of cancer.

Regulatory role of KCa3.1 in immune cell function and its emerging association with rheumatoid arthritis

Rheumatoid arthritis (RA) is a common autoimmune disease characterized by chronic inflammation. Immune dysfunction is an essential mechanism in the pathogenesis of RA and directly linked to synovial inflammation and cartilage/bone destruction. Intermediate conductance Ca²⁺-activated K⁺ channel (KCa3.1) is considered a significant regulator of proliferation, differentiation, and migration of immune cells by mediating Ca²⁺ signal transduction. Earlier studies have demonstrated abnormal activation of KCa3.1 in the peripheral blood and articular synovium of RA patients. Moreover, knockout of KCa3.1 reduced the severity of synovial inflammation and cartilage damage to a significant extent in a mouse collagen antibody-induced arthritis (CAIA) model. Accumulating evidence implicates KCa3.1 as a potential therapeutic target for RA. Here, we provide an overview of the KCa3.1 channel and its pharmacological properties, discuss the significance of KCa3.1 in immune cells and feasibility as a drug target for modulating the immune balance, and highlight its emerging role in pathological progression of RA.