Mitochondria-Related Transcriptome Characterization Associated with the Immune Microenvironment, Therapeutic Response and Survival Prediction in Pancreatic Cancer

(1) Background: Pancreatic cancer (PC) is one of the most lethal tumors. Mitochondrial dysfunction has been reported to be involved in cancer development; however, its role in PC has remained unclear. (2) Methods: The differentially expressed NMGs were selected between PC and normal pancreatic tissue. The NMG-related prognostic signature was established by LASSO regression. A nomogram was developed based on the 12-gene signature combined with other significant pathological features. An extensive analysis of the 12 critical NMGs was performed in multiple dimensions. The expression of some key genes was verified in our external cohort. (3) Results: Mitochondria-related transcriptome features was obviously altered in PC compared with normal pancreas tissue. The 12-NMG signature showed good performance in predicting prognosis in various cohorts. The high- and low-risk groups exhibited notable diversity in gene mutation characteristics, biological characteristics, chemotherapy response, and the tumor immune microenvironment. Critical gene expression was demonstrated in our cohort at the mRNA and protein levels and in organelle localization. (4) Conclusions: Our study analyzed the mitochondrial molecular characterization of PC, proving the crucial role of NMGs in PC development. The established NMG signature helps classify patient subtypes in terms of prognosis prediction, treatment response, immunological features, and biological function, providing a potential therapeutic strategy targeting mitochondrial transcriptome characterization

Mitochondria-Related Transcriptome Characterization Associated with the Immune Microenvironment, Therapeutic Response and Survival Prediction in Pancreatic Cancer

(1) Background: Pancreatic cancer (PC) is one of the most lethal tumors. Mitochondrial dysfunction has been reported to be involved in cancer development; however, its role in PC has remained unclear. (2) Methods: The differentially expressed NMGs were selected between PC and normal pancreatic tissue. The NMG-related prognostic signature was established by LASSO regression. A nomogram was developed based on the 12-gene signature combined with other significant pathological features. An extensive analysis of the 12 critical NMGs was performed in multiple dimensions. The expression of some key genes was verified in our external cohort. (3) Results: Mitochondria-related transcriptome features was obviously altered in PC compared with normal pancreas tissue. The 12-NMG signature showed good performance in predicting prognosis in various cohorts. The high- and low-risk groups exhibited notable diversity in gene mutation characteristics, biological characteristics, chemotherapy response, and the tumor immune microenvironment. Critical gene expression was demonstrated in our cohort at the mRNA and protein levels and in organelle localization. (4) Conclusions: Our study analyzed the mitochondrial molecular characterization of PC, proving the crucial role of NMGs in PC development. The established NMG signature helps classify patient subtypes in terms of prognosis prediction, treatment response, immunological features, and biological function, providing a potential therapeutic strategy targeting mitochondrial transcriptome characterization

Comprehensive analysis of the prognosis and immune infiltration landscape of RNA methylation-related subtypes in pancreatic cancer

Abstract Background RNA methylation refers to a form of methyl modification in RNA that modulates various epigenetic alterations. Mounting studies have focused on its potential mechanisms in cancer initiation and progression. However, the prognostic value and potential role of RNA methylation in the immune microenvironment of pancreatic cancer remain unclear. Methods Comprehensive bioinformatics analysis was performed to illuminate the expression profiles of RNA methylation modulators. In addition, the ConsensusClusterPlus algorithm was utilized to identify two remarkably different subtypes, and a feasible risk stratification method was established to accurately estimate prognosis. In addition, we validated our signature at the cytology and histology levels and conducted functional experiments to explore the biological functions of our key genes. Results Two subtypes with remarkable survival differences were identified by the consensus clustering algorithm. Cluster 2 tended to have higher expression levels of RNA methylation regulators and to be the high RNA methylation group. In addition, cluster 1 exhibited a significantly higher abundance of almost all immune cells and increased immune checkpoint expression compared to cluster 2. Chemotherapeutic sensitivity analysis indicated that there were significant differences in the sensitivity of four of the six drugs between different subgroups. Mutation investigation revealed a higher mutation burden and a higher number of mutations in cluster 2. An accurate and feasible risk stratification method was established based on the expression of key genes of each subtype. Patients with low risk scores exhibited longer survival times in one training (TCGA) and two validation cohorts (ICGC, GSE57495), with p values of 0.001, 0.0081, and 0.0042, respectively. In addition, our signature was further validated in a cohort from Fudan University Shanghai Cancer Center. The low-risk group exhibited higher immune cell abundance and immune checkpoint levels than the high-risk group. The characteristics of the low-risk group were consistent with those of cluster 1: higher stromal score, estimate score, and immune score and lower tumor purity. Additionally, cell function investigations suggested that knockdown of CDKN3 remarkably inhibited the proliferation and migration of pancreatic cancer cells. Conclusions RNA methylation has a close correlation with prognosis, immune infiltration and therapy in pancreatic cancer. Our subtypes and risk stratification method can accurately predict prognosis and the efficacy of immune therapy and chemotherapy

Turning towards nonimmunoreactive tumors: Evaluation of cancer-associated fibroblasts enables prediction of the immune microenvironment and treatment sensitivity in pancreatic cancer

Increasing evidence has confirmed that cancer-associated fibroblasts (CAFs) recruit and induce regulatory T cells (Tregs) and macrophages but inhibit cytotoxic T lymphocyte infiltration to a certain extent, indicating that CAFs have a significant influence on the immunosuppressive microenvironment. However, the effect of CAFs on the immune microenvironment and immunotherapy response in pancreatic cancer remains unclear. Our research identified remarkable variation in CAF-associated molecules in multiple cancer types at the genetic and transcriptome levels. Two phenotypes were identified for 476 pancreatic cancer samples, and the different phenotypes exhibited significant variation in immune and inflammatory characteristics. Phenotype 1 exhibited higher levels of immune infiltration and lower expression of tumor-associated gene signatures than phenotype 2. We used a multipart approach to assess the prognostic value of CAF-associated molecules and constructed a CAF score model that could accurately predict patient prognosis. The CAF score accurately predicted infiltrating immune cell abundance, chemosensitivity, and the response to immunotherapy. Additionally, we found that the CAF-associated molecule FGFR4 may promote the proliferation and migration and inhibit the apoptosis of pancreatic cancer cells and is correlated with immune infiltration, suggesting its potential role as an oncogene. CAFs may promote the malignant biological behavior of pancreatic cancer through FGFR4. In summary, our research highlights potential relationships of the dysregulation of CAF-associated molecules with genome alterations and carcinogenesis in multiple malignancies. Our CAF-associated phenotypes and scoring system may enhance the understanding of pancreatic cancer chemotherapy sensitivity and immunotherapy response, providing new insights for personalized chemotherapy and immunotherapy

Radical antegrade modular pancreatosplenectomy (RAMPS) versus standard retrograde pancreatosplenectomy (SRPS) for resectable body and tail pancreatic adenocarcinoma: protocol of a multicenter, prospective, randomized phase III control trial (CSPAC-3)

Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy. Radical surgical resection offers the only potential cure. There is increasing agreement that radical antegrade modular pancreatosplenectomy (RAMPS) may benefit patients with tumors in the body and tail of the pancreas. To address this, the Chinese Study Group for Pancreatic Cancer (CSPAC)-3 trial is proposed to compare the effect of RAMPS and standard retrograde pancreatosplenectomy (SRPS) on patient survival and preoperative safety Methods The randomized controlled trial will be multicenter and two-armed with blinded outcomes and intention-to-treat analysis. Three hundred patients with resectable body and tail pancreatic adenocarcinoma will be enrolled and randomly assigned to RAMPS or SRPS. Adjuvant chemotherapy based on an initial regimen will be recommended 4–6 weeks after surgery if no serious complication occurs. The hypothesis that RAMPS improves survival outcomes compared with SRPS will be tested using a superiority trial. The primary outcome will be overall survival (OS). Secondary outcomes will include recurrence-free survival (RFS), R0 resection rate, the number of harvested lymph nodes, postoperative complications, and quality of life scores. Discussion The use of RAMPS has increased over the past decade. It is reported that RAMPS is superior to SRPS in improving both the rate of R0 resection and lymph node yield. Despite these advantages, however, there is little high-level documentation of the superiority of RAMPS in terms of survival and this needs to be investigated. To address this issue, CSPAC has instigated the first prospective, randomized phase III control trials, aiming to explore the optimal surgical strategy for improving the prognosis and OS of patients with left-sided pancreatic cancer Trial registration Chinese Clinical Trial Registry ChiCTR2100053844; pre-results. Registered on December 1, 2021

Generation of An Endogenous FGFR2–BICC1 Gene Fusion/58 Megabase Inversion Using Single-Plasmid CRISPR/Cas9 Editing in Biliary Cells

Fibroblast growth factor receptor 2 (FGFR2) gene fusions are bona fide oncogenic drivers in 10–15% of intrahepatic cholangiocarcinoma (CCA), yet currently there are no cell lines publically available to study endogenous FGFR2 gene fusions. The ability of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 to generate large yet precise chromosomal rearrangements has presented the possibility of engineering endogenous gene fusions for downstream studies. In this technical report, we describe the generation of an endogenous FGFR2–Bicaudal family RNA binding protein 1 (BICC1) fusion in multiple independent cholangiocarcinoma and immortalized liver cell lines using CRISPR. BICC1 is the most common FGFR2 fusion partner in CCA, and the fusion arises as a consequence of a 58-megabase-sized inversion on chromosome 10. We replicated this inversion to generate a fusion product that is identical to that seen in many human CCA. Our results demonstrate the feasibility of generating large megabase-scale inversions that faithfully reproduce human cancer aberrations