GFOD1 and peejar are promising markers for clear-cell renal cell carcinoma disease progression

Molecular insight into the potential functional role of pseudoenzyme GFOD1 via interaction with NKIRAS2

The glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family includes a variety of oxidoreductases with a wide range of substrates that utilize NAD or NADP as redox cofactor. Human contains two members of this family, namely glucose-fructose oxidoreductase domain-containing protein 1 and 2 (GFOD1 and GFOD2). While GFOD1 exhibits low tissue specificity, it is notably expressed in the brain, potentially linked to psychiatric disorders and severe diseases. Nevertheless, the specific function, cofactor preference, and enzymatic activity of GFOD1 remain largely unknown. In this work, we find that GFOD1 does not bind to either NAD or NADP. Crystal structure analysis unveils that GFOD1 exists as a typical homodimer resembling other family members, but lacks essential residues required for cofactor binding, suggesting that it may function as a pseudoenzyme. Exploration of GFOD1-interacting partners in proteomic database identifies NK-κB inhibitor-interacting Ras-like 2 (NKIRAS2) as one potential candidate. Co-immunoprecipitation (co-IP) analysis indicates that GFOD1 interacts with both GTP- and GDP-bound forms of NKIRAS2. The predicted structural model of the GFOD1-NKIRAS2 complex is validated in cells using point mutants and shows that GFOD1 selectively recognizes the interswitch region of NKIRAS2. These findings reveal the distinct structural properties of GFOD1 and shed light on its potential functional role in cellular processes.

Distribution of transcripts of the GFOD gene family members gfod1 and gfod2 in the zebrafish central nervous system

The glucose-fructose oxidoreductase domain containing gene family (GFOD) is small and contains only two members in human (GFOD1 and GFOD2). Information about its function is scarce. As the name implies the proteins contain an enzyme-defining domain, however, if this is functional and has enzymatic activity remains to be shown. A single nucleotide polymorphism situated in an intron of GFOD1 was found to be associated with inattentive symptomology in patients with attention-deficit/hyperactivity disorder. Further, in a large schizophrenia genome-wide association study the GFOD2 locus was found to be associated with the psychiatric condition. Until now, however, it is unclear what specific functions are associated with the two GFOD-family members, if they might be involved in neurodevelopment and how this may relate to the development of psychiatric disorders. In order to gain first insights into the hypothesis that GFOD-family members are involved in brain development and/or function we performed RNA in situ hybridization on zebrafish (Danio rerio) tissues at different developmental stages. We found that both family members are expressed in the central nervous system at embryonic, larvae and adult stages. We were able to define subtle differences of expression of the two gfod genes and we showed that a subset of GABAergic neurons express gfod1. Taken together, we conclude that both gfod gene family members are expressed in overlapping as well as in distinct regions in the zebrafish central nervous system. Our data suggest that gfod1 and gfod2 are relevant both for the developing and adult zebrafish brain. This study paves the way for further functional analyses of this yet unexplored gene family.

Long non-coding RNA GAS5 sensitizes renal cell carcinoma to sorafenib via miR-21/SOX5 pathway

Although the use of sorafenib appears to increase the survival rate of renal cell carcinoma (RCC) patients, there is also a proportion of patients who exhibit a poor primary response to sorafenib treatment. Therefore, it is critical to elucidate the mechanisms underlying sorafenib resistance and find representative biomarkers for sorafenib treatment in RCC patients. Herein, we identified that a long noncoding RNA GAS5 was downregulated in sorafenib nonresponsive RCCs. GAS5 overexpression conferred sorafenib sensitive to nonresponsive RCC cells, whereas knockdown of GAS5 promoted responsive RCC cells resistant to sorafenib treatment in vitro and in vivo. Mechanistically, GAS5 functioned as competing endogenous RNA to repress miR-21, which controlled its down-stream target SOX5. We proposed that GAS5 was responsible for sorafenib resistance in RCC cells and GAS5 exerted its function through the miR-21/ SOX5 axis. Our findings suggested that GAS5 downregulation may be a new marker of poor response to sorafenib and GAS5 could be a potential therapeutic target for sorafenib treatment in RCC.

Identifying Cancer Specific Driver Modules Using a Network-Based Method

Detecting driver modules is a key challenge for understanding the mechanisms of carcinogenesis at the pathway level. Identifying cancer specific driver modules is helpful for interpreting the different principles of different cancer types. However, most methods are proposed to identify driver modules in one cancer, but few methods are introduced to detect cancer specific driver modules. We propose a network-based method to detect cancer specific driver modules (CSDM) in a certain cancer type to other cancer types. We construct the specific network of a cancer by combining specific coverage and mutual exclusivity in all cancer types, to catch the specificity of the cancer at the pathway level. To illustrate the performance of the method, we apply CSDM on 12 TCGA cancer types. When we compare CSDM with SpeMDP and HotNet2 with regard to specific coverage and the enrichment of GO terms and KEGG pathways, CSDM is more accurate. We find that the specific driver modules of two different cancers have little overlap, which indicates that the driver modules detected by CSDM are specific. Finally, we also analyze three specific driver modules of BRCA, BLCA, and LAML intersecting with well-known pathways. The source code of CSDM is freely accessible at https://github.com/fengli28/CSDM.git.