PLCG2 as a potential indicator of tumor microenvironment remodeling in soft tissue sarcoma

Functional Profiling of Soft Tissue Sarcoma Using Mechanistic Models

Soft tissue sarcoma is an umbrella term for a group of rare cancers that are difficult to treat. In addition to surgery, neoadjuvant chemotherapy has shown the potential to downstage tumors and prevent micrometastases. However, finding effective therapeutic targets remains a research challenge. Here, a previously developed computational approach called mechanistic models of signaling pathways has been employed to unravel the impact of observed changes at the gene expression level on the ultimate functional behavior of cells. In the context of such a mechanistic model, RNA-Seq counts sourced from the Recount3 resource, from The Cancer Genome Atlas (TCGA) Sarcoma project, and non-diseased sarcomagenic tissues from the Genotype-Tissue Expression (GTEx) project were utilized to investigate signal transduction activity through signaling pathways. This approach provides a precise view of the relationship between sarcoma patient survival and the signaling landscape in tumors and their environment. Despite the distinct regulatory alterations observed in each sarcoma subtype, this study identified 13 signaling circuits, or elementary sub-pathways triggering specific cell functions, present across all subtypes, belonging to eight signaling pathways, which served as predictors for patient survival. Additionally, nine signaling circuits from five signaling pathways that highlighted the modifications tumor samples underwent in comparison to normal tissues were found. These results describe the protective role of the immune system, suggesting an anti-tumorigenic effect in the tumor microenvironment, in the process of tumor cell detachment and migration, or the dysregulation of ion homeostasis. Also, the analysis of signaling circuit intermediary proteins suggests multiple strategies for therapy.

Landscape of Genetic Mutations in Appendiceal Cancers

In appendiceal cancers, the most frequently mutated genes are (i) KRAS, which, when reactivated, restores signal transduction via the RAS-RAF-MEK-ERK signaling pathway and stimulates cell proliferation in the early stages of tumor transformation, and then angiogenesis; (ii) TP53, whose inactivation leads to the inhibition of programmed cell death; (iii) GNAS, which, when reactivated, links the cAMP pathway to the RAS-RAF-MEK-ERK signaling pathway, stimulating cell proliferation and angiogenesis; (iv) SMAD4, exhibiting typical tumor-suppressive activity, blocking the transmission of oncogenic TGFB signals via the SMAD2/SMAD3 heterodimer; and (v) BRAF, which is part of the RAS-RAF-MEK-ERK signaling pathway. Diverse mutations are reported in other genes, which are part of secondary or less critical signaling pathways for tumor progression, but which amplify the phenotypic diversity of appendiceal cancers. In this review, we will present the main genetic mutations involved in appendix tumors and their roles in cell proliferation and survival, and in tumor invasiveness, angiogenesis, and acquired resistance to anti-growth signals.

Identification of immune cell infiltration and effective biomarkers of polycystic ovary syndrome by bioinformatics analysis

BACKGROUND

Patients with polycystic ovary syndrome (PCOS) exhibit a chronic inflammatory state, which is often accompanied by immune, endocrine, and metabolic disorders. Clarification of the pathogenesis of PCOS and exploration of specific biomarkers from the perspective of immunology by evaluating the local infiltration of immune cells in the follicular microenvironment may provide critical insights into disease pathogenesis.

METHODS

In this study, we evaluated immune cell subsets and gene expression in patients with PCOS using data from the Gene Expression Omnibus database and single-sample gene set enrichment analysis.

RESULTS

In total, 325 differentially expressed genes were identified, among which TMEM54 and PLCG2 (area under the curve = 0.922) were identified as PCOS biomarkers. Immune cell infiltration analysis showed that central memory CD4⁺ T cells, central memory CD8⁺ T cells, effector memory CD4⁺ T cells, γδ T cells, and type 17 T helper cells may affect the occurrence of PCOS. In addition, PLCG2 was highly correlated with γδ T cells and central memory CD4⁺ T cells.

CONCLUSIONS

Overall, TMEM54 and PLCG2 were identified as potential PCOS biomarkers by bioinformatics analysis. These findings established a basis for further exploration of the immunological mechanisms of PCOS and the identification of therapeutic targets.

Aggressive progression to EGFR tyrosine kinase inhibitors in advanced NSCLC patients: concomitant mutations, prognostic indicator and subsequent management

BACKGROUND

EGFR tyrosine kinase (TKIs) are recommend as the first-line treatment for non-small cell lung cancer (NSCLC) patients with EGFR mutation. However, some patients experience aggressive progression with a progression-free survival (PFS) less than 6 months on the first-line EGFR TKI therapy. Therefore, our study is to analyze the potential influencing factors including clinical features, biomarkers, concomitant mutations et al. METHODS: A total of 1073 NSCLC patients with EGFR mutation in a multi-center study from January 2019 to December 2021. The datum pathological and molecular characteristics were collected. The area under the receiver operating characteristic (ROC) curve was used to evaluate the predictive effect of Ki-67 on the first-line TKI. The curve of PFS was conducted by Kaplan-Meier method and tested by bilateral log-rank. Cox regression model was used to predict and evaluate PFS of different variables. Chi-square or Fisher analysis was used for correlation between groups.

RESULTS

55 patients who show aggressive progression (PFS ≤ 6 months) on the first-line TKI therapy were analyzed in this study, while 71 with slow progression (PFS > 6 months). Concomitant mutations including AXIN2, P2CG and RAD51C mutations occurred only in the aggressively progressive group (P = 0.029). Correlation between Ki-67 index and the aggressive progression of the first-line TKI therapy was significant statistically different (P < 0.05). In the second-line therapy, the PFS of chemotherapy in combination with other treatments was better than single TKIs in the first ten months.

CONCLUSION

NSCLC harbored EGFR and concomitant mutations (such as AXIN2, PLCG2 and RAD51C), and/or Ki-67 high expression may indicate the aggressive progression to the first-line EGFR-TKI.

PLCG2 can exist in eccDNA and contribute to the metastasis of non-small cell lung cancer by regulating mitochondrial respiration

Extrachromosomal circular DNAs (eccDNAs) participate in tumorigenesis and tumor progression. However, the role and mechanism of eccDNAs have yet to be elucidated in non-small cell lung cancer (NSCLC). In our research, three surgically matched NSCLC tissue samples, NSCLC cell lines (H1299, A549, and H460), and a normal lung cell line (MRC-5) were used as study objects. High-throughput eccDNA sequencing and bioinformatics analysis were performed to study the distribution pattern and level of eccDNA expression. The upregulated candidate eccDNA-encoding PLCG2 was validated by routine PCR. Plasmid transfection, RNA interference, qRT‒PCR and western blotting experiments were used to verify the expression level of PLCG2. Our results showed that the chromosome distribution, length distribution, and genomic annotation of the eccDNAs were comparable between the NSCLC and normal groups. Nevertheless, there were no significant differences in eccDNAs between NSCLC tissues and matched normal lung tissues. The eccDNA derived from PLCG2 was upregulated in NSCLC cells. TCGA analysis and immunohistochemistry showed that PLCG2 was highly expressed in lung cancer tissues and tended to be associated with poor outcome. We also demonstrated that PLCG2 can promote metastasis through the regulation of mitochondrial respiration. These results suggested that PLCG2 identified by eccDNA sequencing acts as an oncogene and might be a new biomarker for NSCLC diagnosis and prognosis evaluation.

Identification of genes related to immune enhancement caused by heterologous ChAdOx1-BNT162b2 vaccines in lymphocytes at single-cell resolution with machine learning methods

The widely used ChAdOx1 nCoV-19 (ChAd) vector and BNT162b2 (BNT) mRNA vaccines have been shown to induce robust immune responses. Recent studies demonstrated that the immune responses of people who received one dose of ChAdOx1 and one dose of BNT were better than those of people who received vaccines with two homologous ChAdOx1 or two BNT doses. However, how heterologous vaccines function has not been extensively investigated. In this study, single-cell RNA sequencing data from three classes of samples: volunteers vaccinated with heterologous ChAdOx1-BNT and volunteers vaccinated with homologous ChAd-ChAd and BNT-BNT vaccinations after 7 days were divided into three types of immune cells (3654 B, 8212 CD4+ T, and 5608 CD8+ T cells). To identify differences in gene expression in various cell types induced by vaccines administered through different vaccination strategies, multiple advanced feature selection methods (max-relevance and min-redundancy, Monte Carlo feature selection, least absolute shrinkage and selection operator, light gradient boosting machine, and permutation feature importance) and classification algorithms (decision tree and random forest) were integrated into a computational framework. Feature selection methods were in charge of analyzing the importance of gene features, yielding multiple gene lists. These lists were fed into incremental feature selection, incorporating decision tree and random forest, to extract essential genes, classification rules and build efficient classifiers. Highly ranked genes include PLCG2, whose differential expression is important to the B cell immune pathway and is positively correlated with immune cells, such as CD8+ T cells, and B2M, which is associated with thymic T cell differentiation. This study gave an important contribution to the mechanistic explanation of results showing the stronger immune response of a heterologous ChAdOx1-BNT vaccination schedule than two doses of either BNT or ChAdOx1, offering a theoretical foundation for vaccine modification.

Identification of N6-methylandenosine related lncRNA signatures for predicting the prognosis and therapy response in colorectal cancer patients

Despite recent advances in surgical and multimodal therapies, the overall survival (OS) of advanced colorectal cancer (CRC) patients remains low. Thus, discerning sensitive prognostic biomarkers to give the optimistic treatment for CRC patients is extremely critical. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play an important role in CRC progression. Nonetheless, few studies have focused on the impact of m6A-related lncRNAs on the prognosis, tumor microenvironment (TME) and treatment of CRC. In this study, 1707 m6A-related lncRNAs were identified through Pearson correlation analysis and Weighted co-expression network analysis (WGCNA) using The Cancer Genome Atlas (TCGA) cohort. Then, 28 m6A-related prognostic lncRNAs were screened by univariate Cox regression analysis, followed by identifying two clusters by consensus clustering analysis. A prognostic model consisted of 8 lncRNA signatures was constructed by the least absolute shrinkage and selection operator (LASSO). Kaplan–Meier curve analysis and a nomogram were performed to investigate the prognostic ability of this model. The risk score of prognostic model act as an independent risk factor for OS rate. Functional enrichment analysis indicated that lncRNA signatures related tumor immunity. The low-risk group characterized by increased microsatellite instability-high (MSI-H), mutation burden, and immunity activation, indicated favorable odds of OS. Moreover, the lncRNA signatures were significantly associated with the cancer stem cell (CSC) index and drug sensitivity. In addition, 3 common immune genes shared by the lncRNA signatures were screened out. We found that these immune genes were widely distributed in 2 cell types of TME. Finally, a ceRNA network was constructed to identify ZEB1-AS1 regulatory axis in CRC. We found that ZEB1-AS1 was significantly overexpressed in tumor tissues, and was related to the metastasis of EMT and the chemoresistance of 5-Fu in CRC. Therefore, our study demonstrated the important role of m6A-related lncRNAs in TME remodeling. Moreover, these results illustrated the levels of ZEB1-AS1 might be valuable for predicting the progression and prognosis of CRC, and further provided a new target for the diagnosis and treatment of CRC patients.

Emerging Biomarkers and the Changing Landscape of Small Cell Lung Cancer

Simple Summary

Small cell lung cancer (SCLC) is an aggressive cancer representing 15% of all lung cancers. Unlike other types of lung cancer, treatments for SCLC have changed very little in the past 20 years and therefore, the survival rate remains low. This is due, in part, to the lack of understanding of the biological basis of this disease and the previous idea that all SCLCs are the same. Multiple recent studies have identified that SCLCs have varying biological activity and can be divided into four different groups. The advantage of this is that each of these four groups responds differently to new treatments, which hopefully will dramatically improve survival. Additionally, the aim of these new treatments is to specifically target these biological differences in SCLC so normal/non cancer cells are unaffected, leading to decreased side effects and a better quality of life. There is still a lot unknown about SCLC, but these new findings offer a glimmer of hope for patients in the future.

Abstract

Small cell lung cancer (SCLC) is a high-grade neuroendocrine malignancy with an aggressive behavior and dismal prognosis. 5-year overall survival remains a disappointing 7%. Genomically, SCLCs are homogeneous compared to non-small cell lung cancers and are characterized almost always by functional inactivation of RB1 and TP53 with no actionable mutations. Additionally, SCLCs histologically appear uniform. Thus, SCLCs are currently managed as a single disease with platinum-based chemotherapy remaining the cornerstone of treatment. Recent studies have identified expression of dominant transcriptional signatures which may permit classification of SCLCs into four biologically distinct subtypes, namely, SCLC-A, SCLC-N, SCLC-P, and SCLC-I. These groups are readily detectable by immunohistochemistry and also have potential predictive utility for emerging therapies, including PARPi, immune checkpoint inhibitors, and DLL3 targeted therapies. In contrast with their histology, studies have identified that SCLCs display both inter- and intra-tumoral heterogeneity. Identification of subpopulations of cells with high expression of PLCG2 has been linked with risk of metastasis. SCLCs also display subtype switching under therapy pressure which may contribute furthermore to metastatic ability and chemoresistance. In this review, we summarize the recent developments in the understanding of the biology of SCLCs, and discuss the potential diagnostic, prognostic, and treatment opportunities the four proposed subtypes may present for the future. We also discuss the emerging evidence of tumor heterogeneity and plasticity in SCLCs which have been implicated in metastasis and acquired therapeutic resistance seen in these aggressive tumors.

Endothelial Phospholipase Cγ2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy

Therapeutic vascular endothelial growth factor (VEGF) replenishment has met with limited success for the management of critical limb-threatening ischemia. To improve outcomes of VEGF therapy, we applied single-cell RNA sequencing (scRNA-seq) technology to study the endothelial cells of the human diabetic skin. Single-cell suspensions were generated from the human skin followed by cDNA preparation using the Chromium Next GEM Single-cell 3' Kit v3.1. Using appropriate quality control measures, 36,487 cells were chosen for downstream analysis. scRNA-seq studies identified that although VEGF signaling was not significantly altered in diabetic versus nondiabetic skin, phospholipase Cγ2 (PLCγ2) was downregulated. The significance of PLCγ2 in VEGF-mediated increase in endothelial cell metabolism and function was assessed in cultured human microvascular endothelial cells. In these cells, VEGF enhanced mitochondrial function, as indicated by elevation in oxygen consumption rate and extracellular acidification rate. The VEGF-dependent increase in cell metabolism was blunted in response to PLCγ2 inhibition. Follow-up rescue studies therefore focused on understanding the significance of VEGF therapy in presence or absence of endothelial PLCγ2 in type 1 (streptozotocin-injected) and type 2 (db/db) diabetic ischemic tissue. Nonviral topical tissue nanotransfection technology (TNT) delivery of CDH5 promoter-driven PLCγ2 open reading frame promoted the rescue of hindlimb ischemia in diabetic mice. Improvement of blood flow was also associated with higher abundance of VWF+/CD31+ and VWF+/SMA+ immunohistochemical staining. TNT-based gene delivery was not associated with tissue edema, a commonly noted complication associated with proangiogenic gene therapies. Taken together, our study demonstrates that TNT-mediated delivery of endothelial PLCγ2, as part of combination gene therapy, is effective in diabetic ischemic limb rescue.