Systematic investigation of metabolic reprogramming in different cancers based on tissue-specific metabolic models

The identification of essential cellular genes is critical for validating drug targets

Accurately identifying biological targets is crucial for advancing treatment options. Essential genes, vital for cell or organism survival, hold promise as potential drug targets in disease treatment. Although many studies have sought to identify essential genes as therapeutic targets in medicine and bioinformatics, systematic reviews on their relationship with drug targets are relatively rare. This work presents a comprehensive analysis to aid in identifying essential genes as potential targets for drug discovery, encompassing their relevance, identification methods, successful case studies, and challenges. This work will facilitate the identification of essential genes as therapeutic targets, thereby boosting new drug development.

Glucose metabolism involved in PD-L1-mediated immune escape in the malignant kidney tumour microenvironment

Programmed death receptor-ligand 1 (PD-L1) plays a crucial role in immune evasion by tumour cells. Most tumour cells exhibit energy dependency and acquire energy from glycolysis. However, the relationship between glucose metabolism and PD-L1 expression remains unclear. In this study, changes in PD-L1 expression in renal carcinoma cells were evaluated during glucose deficiency and recovery, and PD-L1 could inversely regulate glycolysis. In addition, the possible signalling pathways activated by a low level of glucose to regulate PD-L1 were tested experimentally. The results showed that glucose deficiency could upregulate PD-L1 expression in two renal cancer cell lines, 786-O and OS-RC-2. Although the native levels of PD-L1 differed in the two cell lines, the upregulated PD-L1 expression was repristinated after glucose recovery. Moreover, epidermal growth factor receptor (EGFR) expression was upregulated in both cell lines with glucose deficiency. The use of an EGFR inhibitor reversed the upregulation of PD-L1 expression induced by glucose deficiency and inhibited the phosphorylation of extracellular regulated protein kinases 1 and 2 (ERK1/2). EGFR activated by epidermal growth factor (EGF) induced PD-L1 expression and ERK1/2 phosphorylation. Furthermore, an ERK1/2 inhibitor inhibited the phosphorylation of c-Jun and decreased the elevated PD-L1 expression induced by glucose deficiency. In addition, this study also showed that 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFK-2/FBPase 3 or PFKFB3) mediated upregulation of the level of glycolysis to improve the adverse environment through PD-L1 induction. Therefore, glucose metabolism can regulate the expression of PD-L1 through the EGFR/ERK/c-Jun pathway in renal cancer, and elevated PD-L1 can also regulate glycolysis by improving the expression of PFKFB3. The findings of this study could provide a new multiple target treatment for renal cell carcinoma (RCC) therapy.

Multi-Approach Bioinformatics Analysis of Curated Omics Data Provides a Gene Expression Panorama for Multiple Cancer Types

Studies describing the expression patterns and biomarkers for the tumoral process increase in number every year. The availability of new datasets, although essential, also creates a confusing landscape where common or critical mechanisms are obscured amidst the divergent and heterogeneous nature of such results. In this work, we manually curated the Gene Expression Omnibus using rigorous filtering criteria to select the most homogeneous and highest quality microarray and RNA-seq datasets from multiple types of cancer. By applying systems biology approaches, combined with machine learning analysis, we investigated possible frequently deregulated molecular mechanisms underlying the tumoral process. Our multi-approach analysis of 99 curated datasets, composed of 5,406 samples, revealed 47 differentially expressed genes in all analyzed cancer types, which were all in agreement with the validation using TCGA data. Results suggest that the tumoral process is more related to the overexpression of core deregulated machinery than the underexpression of a given gene set. Additionally, we identified gene expression similarities between different cancer types not described before and performed an overall survival analysis using 20 cancer types. Finally, we were able to suggest a core regulatory mechanism that could be frequently deregulated.

Role of mitochondria in rescuing glycolytically inhibited subpopulation of triple negative but not hormone-responsive breast cancer cells

Triple-negative breast cancer (TNBC) subtype is among the most aggressive cancers with the worst prognosis and least therapeutic targetability while being more likely to spread and recur. Cancer transformations profoundly alter cellular metabolism by increasing glucose consumption via glycolysis to support tumorigenesis. Here we confirm that relative to ER-positive cells (MCF7), TNBC cells (MBA-MD-231) rely more on glycolysis thus providing a rationale to target these cells with glycolytic inhibitors. Indeed, iodoacetate (IA), an effective GAPDH inhibitor, caused about 70% drop in MDA-MB-231 cell viability at 20 μM while 40 μM IA was needed to decrease MCF7 cell viability only by 30% within 4 hours of treatment. However, the triple negative cells showed strong ability to recover after 24 h whereas MCF7 cells were completely eliminated at concentrations <10 μM. To understand the mechanism of MDA-MB-231 cell survival, we studied metabolic modulations associated with acute and extended treatment with IA. The resilient TNBC cell population showed a significantly greater count of cells with active mitochondria, lower apoptotic markers, normal cell cycle regulations, moderately lowered ROS, but increased mRNA levels of p27 and PARP1; all compatible with enhanced cell survival. Our results highlight an interplay between PARP and mitochondrial oxidative phosphorylation in TNBC that comes into play in response to glycolytic disruption. In the light of these findings, we suggest that combined treatment with PARP and mitochondrial inhibitors may provide novel therapeutic strategy against TNBC.