Pyrimethamine upregulates BNIP3 to interfere SNARE-mediated autophagosome-lysosomal fusion in hepatocellular carcinoma

Establishment of a Lactylation-Related Gene Signature for Hepatocellular Carcinoma Applying Bulk and Single-Cell RNA Sequencing Analysis

Background: Lactylation is closely involved in cancer progression, but its role in hepatocellular carcinoma (HCC) is unclear. The present work set out to develop a lactylation-related gene (LRG) signature for HCC. Methods: The lactylation score of tumor and normal groups was calculated using the gene set variation analysis (GSVA) package. The single-cell RNA sequencing (scRNA-seq) analysis of HCC was performed in the "Seurat" package. Prognostic LRGs were selected by performing univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses to develop and validate a Riskscore model. Functional enrichment analysis was conducted by gene set enrichment analysis (GSEA) using the "clusterProfiler" package. Genomic characteristics between different risk groups were compared, and tumor mutational burden (TMB) was calculated by the "Maftools" package. Immune cell infiltration was assessed by algorithms of cell-type identification by estimating relative subsets of RNA transcript (CIBERSORT), microenvironment cell populations-counter (MCP-counter), estimating the proportions of immune and cancer cells (EPIC), tumor immune estimation resource (TIMER), and single-sample gene set enrichment analysis (ssGSEA). Immunotherapy response was predicted by the tumor immune dysfunction and exclusion (TIDE) algorithm. Drug sensitivity was analyzed using the "pRRophetic" package. A nomogram was established using the "rms" package. The expressions of the prognostic LRGs in HCC cells were verified by in vitro test, and cell counting kit-8 (CCK-8), wound healing, and transwell assays were carried out to measure the viability, migration, and invasion of HCC cells. Results: The lactylation score, which was higher in the tumor group than in the normal group, has been confirmed as an independent factor for the prognostic evaluation in HCC. Six prognostic LRGs, including two protective genes (FTCD and APCS) and four risk genes (LGALS3, C1orf43, TALDO1, and CCT5), were identified to develop a Riskscore model with a strong prognostic prediction performance in HCC. The scRNA-seq analysis revealed that LGALS3 was largely expressed in myeloid cells, while APCS, FTCD, TALDO1, CCT5, and C1orf43 were mainly expressed in hepatocytes. The high-risk group was primarily enriched in the pathways involved in tumor occurrence and development, with higher T cell infiltration. Moreover, the high-risk group was found to be less responsive to immunotherapy but was more sensitive to chemotherapeutic drugs. By integrating Riskscore and clinical features, a nomogram with a high predictive accuracy was developed. Additionally, C1orf43, CCT5, TALDO1, and LGALS3 were highly expressed in HCC cells. Silencing CCT5 inhibited the viability, migration, and invasion of HCC cells. Conclusion: The present work developed a novel LRG gene signature that could be considered a promising therapeutic target and biomarker for HCC.

Single-cell mitophagy patterns within the tumor microenvironment modulate intercellular communication, impacting the progression and prognosis of hepatocellular carcinoma

Background

Hepatocellular carcinoma (HCC) is a common malignant tumor of the digestive system with a high incidence that seriously threatens patients' lives and health. However, with the rise and application of new treatments, such as immunotherapy, there are still some restrictions in the treatment and diagnosis of HCC, and the therapeutic effects on patients are not ideal.

Methods

Two single-cell RNA sequencing (scRNA-seq) datasets from HCC patients, encompassing 25,189 cells, were analyzed in the study. We utilized non-negative matrix factorization (NMF) clustering to identify mitophagy patterns in HCC TME cells, including cancer-associated fibroblasts (CAFs), T cells, B cells, and tumor-associated macrophages (TAMs). Cell-to-cell communication was analyzed using the CellChat package, and pseudotime trajectory analysis was performed using the Monocle package. Gene regulatory networks were investigated with the SCENIC package, and survival analyses were conducted with mitophagy-related signatures.

Results

HCC samples analysis identified 22 clusters, including 7 principal cell types. Complex cell communications were observed among these cell types. Mitophagy-related CAFs, TAMs, CD8+ T cells, and B cells were identified. These subtypes had different biological states, cell-cell communications, and metabolic pathways. Mitophagy levels were elevated in tumor samples. Changes in mitophagy-related genes within specific cell subtypes were associated with different overall survival rates. However, mitophagy did not seem to affect the effectiveness of immunotherapy.

Conclusion

This study provides evidence that mitophagy within the HCC TME modulates intercellular communication, influencing tumor progression and patient prognosis. Targeting mitophagy may offer a promising approach to improve the long-term prognosis of HCC patients.

Parkin deficiency promotes liver cancer metastasis by TMEFF1 transcription activation via TGF-β/Smad2/3 pathway

Parkin (PARK2) deficiency is frequently observed in various cancers and potentially promotes tumor progression. Here, we showed that Parkin expression is downregulated in liver cancer tissues, which correlates with poor patient survival. Parkin deficiency in liver cancer cells promotes migration and metastasis as well as changes in EMT and metastasis markers. A negative correlation exists between TMEFF1 and Parkin expression in liver cancer cells and tumor tissues. Parkin deficiency leads to upregulation of TMEFF1 which promotes migration and metastasis. TMEFF1 transcription is activated by Parkin-induced endogenous TGF-β production and subsequent phosphorylation of Smad2/3 and its binding to TMEFF1 promotor. TGF-β inhibitor and TMEFF1 knockdown can reverse shParkin-induced cell migration and changes of EMT markers. Parkin interacts with and promotes the ubiquitin-dependent degradation of HIF-1α/HIF-1β and p53, which accounts for the suppression of TGF-β production. Our data have revealed that Parkin deficiency in cancer leads to the activation of the TGF-β/Smad2/3 pathway, resulting in the expression of TMEFF1 which promotes cell migration, EMT, and metastasis in liver cancer cells.

Pyrimethamine reduced tumour growth in pre-clinical cancer models: a systematic review to identify potential pre-clinical studies for subsequent human clinical trials

Pyrimethamine (PYR), a STAT3 inhibitor, has been shown to reduce tumour burden in mouse cancer models. It is unclear how much of a reduction occurred or whether the PYR dosages and route of administration used in mice were consistent with the FDA's recommendations for drug repurposing. Search engines such as ScienceDirect, PubMed/MEDLINE, and other databases, including Google Scholar, were thoroughly searched, as was the reference list. The systematic review includes fourteen (14) articles. The risk of bias (RoB) was assessed using SYRCLE's guidelines. Due to the heterogeneity of the data, no meta-analysis was performed. According to the RoB assessment, 13/14 studies fall into the moderate RoB category, with one study classified as high RoB. None adhered to the ARRIVE guideline for transparent research reporting. Oral (FDA-recommended) and non-oral routes of PYR administration were used in mice, with several studies reporting very high PYR dosages that could lead to myelosuppression, while oral PYR dosages of 30 mg/kg or less are considered safe. Direct human equivalent dose translation is probably not the best strategy for comparing whether the used PYR dosages in mice are in line with FDA-approved strength because pharmacokinetic profiles, particularly PYR's half-life (t1/2), between humans (t1/2 = 96 h) and mice (t1/2 = 6 h), must also be considered. Based on the presence of appropriate control and treatment groups, as well as the presence of appropriate clinically proven chemotherapy drug(s) for comparison purposes, only one study (1/14) involving liver cancer can be directed into a clinical trial. Furthermore, oesophageal cancer too can be directed into clinical trials, where the indirect effect of PYR on the NRF2 gene may suppress oesophageal cancer in patients, but this must be done with caution because PYR is an investigational drug for oesophageal cancer, and combining it with proven chemotherapy drug(s) is recommended.