Global Characterization of Metabolic Genes Regulating Survival and Immune Infiltration in Osteosarcoma

Background: The alterations in metabolic profile of tumors have been identified as one of the prognostic hallmarks of cancers, including osteosarcoma. These alterations are majorly controlled by groups of metabolically active genes. However, the regulation of metabolic gene signatures in tumor microenvironment of osteosarcoma has not been well explained.Objectives: Thus, we investigated the sets of previously published metabolic genes in osteosarcoma patients and normal samples.Methods: We applied computational techniques to identify metabolic genes involved in the immune function of tumor microenvironment (TME) and survival and prognosis of the osteosarcoma patients. Potential candidate gene PAICS (phosphoribosyl aminoimidazole carboxylase, phosphoribosyl aminoimidazole succino carboxamide synthetase) was chosen for further studies in osteosarcoma cell lines for its role in cell proliferation, migration and apoptosis.Results: Our analyses identified a list of metabolic genes differentially expressed in osteosarcoma tissues. Next, we scrutinized the list of genes correlated with survival and immune cells, followed by clustering osteosarcoma patients into three categories: C1, C2, and C3. These analyses led us to choose PAICS as potential candidate gene as its expression showed association with poor survival and negative correlation with the immune cells. Furthermore, we established that loss of PAICS induced apoptosis and inhibited proliferation, migration, and wound healing in HOS and MG-63 cell lines. Finally, the results were supported by constructing and validating a prediction model for prognosis of the osteosarcoma patients.Conclusion: Here, we conclude that metabolic genes specifically PAICS play an integral role in the immune cell infiltration in osteosarcoma TME, as well as cancer development and metastasis.

Association of CCR5Δ32 Deletion and Human Cytomegalovirus Infection With Colorectal Cancer in Tunisia

Background and objectives: Human cytomegalovirus (HCMV) and genetic polymorphisms of the chemokine receptor 5 have been suggested as factors associated with the progression of colorectal cancer (CRC). The aim of the study was to evaluate the associations of both CCR5Δ32 genetic deletion and/or HCMV virus infection with CRC in Tunisia. Materials and methods: The association between HCMV and CRC was validated by Nested PCR technology performed for HCMV and HCMV-specific serum IgG and IgM antibodies were investigated by enzyme-linked immunosorbent assay. Experiments were carried out on 40 tumor and 35 peri-tumor tissues, 100 blood from CRC patients and on 140 blood samples from healthy subjects and finaly serum samples of 80 patients with CRC and 100 healthy individuals. A conventional PCR has been optimized for the detection of CCR5Δ32 in100 CRC patients and 100 healthy subjects. Results: Our results show that HCMV is significantly active in 93% of patients compared to 60% in controls (p < 0.0001, OR = 8.85, 95% CI: 3.82 -20.50). Compared to the healthy controls, the titers of IgG and IgM antiCMV antibodies in CRC patients were significantly higher than in healthy subjects (p value < 0,0001 for IgG and IgM). Statistical analysis revealed a lack of association between CCR5Δ32 mutation and colorectal cancer (p = 0.788, OR = 1.265, 95% CI: 0.228-7.011). Conclusion: our data confirmed that the HCMV infection was related to the development of CRC and that CRC cells may be infected more favorably by HCMV. Given the importance of the CCR5 in inflammation and therefore CRC progression, further studies still needed to evaluate CCR5 role as a potential candidate gene for CRC susceptibility under other polymorphisms.

Identification and Cloning of a CC-NBS-NBS-LRR Gene as a Candidate of Pm40 by Integrated Analysis of Both the Available Transcriptional Data and Published Linkage Mapping

Wheat powdery mildew, caused by the obligate parasite Blumeria graminis f. sp. tritici, severely reduces wheat yields. Identifying durable and effective genes against wheat powdery mildew and further transferring them into wheat cultivars is important for finally controlling this disease in wheat production. Pm40 has been widely used in wheat breeding programs in Southwest China due to the spectrum and potentially durable resistance to powdery mildew. In the present study, a resistance test demonstrated that Pm40 is still effective against the Bgt race E20. We identified and cloned the TraesCS7B01G164000 with a total length of 4883 bp, including three exons and two introns, and encoded a protein carrying the CC-NBS-NBS-LRR domain in the Pm40-linked region flanked by two EST markers, BF478514 and BF291338, by integrating analysis of gene annotation in wheat reference genome and both sequence and expression difference in available transcriptome data. Two missense mutations were detected at positions 68 and 83 in the CC domain. The results of both cosegregation linkage analysis and qRT-PCR also suggested that TraesCS7B01G164000 was a potential candidate gene of Pm40. This study allowed us to move toward the final successfully clone and apply Pm40 in wheat resistance improvement by gene engineering.

Sobp modulates the transcriptional activation of Six1 target genes and is required during craniofacial development

ABSTRACT Branchio-oto-renal syndrome (BOR) is a disorder characterized by hearing loss, and craniofacial and/or renal defects. Variants in the transcription factor Six1 and its co-factor Eya1, both of which are required for otic development, are linked to BOR. We previously identified Sobp as a potential Six1 co-factor, and SOBP variants in mouse and humans cause otic phenotypes; therefore, we asked whether Sobp interacts with Six1 and thereby may contribute to BOR. Co-immunoprecipitation and immunofluorescence experiments demonstrate that Sobp binds to and colocalizes with Six1 in the cell nucleus. Luciferase assays show that Sobp interferes with the transcriptional activation of Six1+Eya1 target genes. Experiments in Xenopus embryos that either knock down or increase expression of Sobp show that it is required for formation of ectodermal domains at neural plate stages. In addition, altering Sobp levels disrupts otic vesicle development and causes craniofacial cartilage defects. Expression of Xenopus Sobp containing the human variant disrupts the pre-placodal ectoderm similar to full-length Sobp, but other changes are distinct. These results indicate that Sobp modifies Six1 function and is required for vertebrate craniofacial development, and identify Sobp as a potential candidate gene for BOR.

GLIS1, a potential candidate gene affect fat deposition in sheep tail

Fat deposition in sheep tails is as a result of a complicated mechanism. Mongolian sheep (MG) and Small Tail Han sheep (STH) are two fat-tailed Chinese indigenous sheep breeds while DairyMeade and East Friesian (DS) are two thin-tailed dairy sheep breeds recently introduced to China. In this study, population genomics analysis was applied to identify candidate genes associated with sheep tails based on an in-depth whole-genome sequencing of MG, STH and DS. The selective signature analysis demonstrated that GLIS1, LOC101117953, PDGFD and T were in the significant divergent regions between DS and STH–MG. A nonsynonymous point mutation (g.27807636G>T) was found within GLIS1 in STH–MG and resulted in a Pro to Thr substitution. As a pro-adipogenic factor, GLIS1 may play critical roles in the mesodermal cell differentiation during fetal development affecting fat deposition in sheep tails. This study gives a new insight into the genetic basis of species-specific traits of sheep tails.

Association of a non-synonymous SNP of IL17RA gene with litter size traits in Large White and Landrace pigs

Interleukin-17 receptor A (IL17RA) is one of the cytokine receptors of the pro-inflammatory interleukin-17 (IL17) cytokine family. The IL17 and IL17RA genes are involved in inflammatory and immune responses as well as reproductive process of mammals. The purposes of this study were to examine polymorphisms in the porcine IL17RA gene and to assess its effects on litter size traits in Large White and Landrace pigs. Three non-synonymous single nucleotide polymorphisms (SNPs) in the porcine IL17RA gene were verified. The porcine IL17RA c.785C>T (p.Ala262Val) was found to be segregating in the Large White and Landrace pigs. No polymorphisms in the coding region of the porcine IL17RA gene at the two non-synonymous SNPs loci of c.997G>A (p.Val333Ile) and c.1962T>G (p.Asp654Glu) were found. The porcine IL17RA c.785C>T polymorphism was significantly associated with the total number born (TNB) and the number born alive (NBA) in Large White pigs (P<0.05). Moreover, the porcine IL17RA c.785C>T was significantly associated with the TNB, NBA, total birth weight (TBW), and total weaning weight of piglets at 21 days (TWW) in Landrace pigs (P<0.05). These results supported the importance of the porcine IL17RA gene in the litter size traits of pigs. Thus, the porcine IL17RA could be used as a potential candidate gene for improving litter size traits in pig breeding.

Sobp modulates Six1 transcriptional activation and is required during craniofacial development

ABSTRACTBranchio-oto-renal syndrome (BOR) is a disorder characterized by hearing loss, craniofacial and/or renal defects. Mutations in the transcription factor Six1 and its cofactor Eya1, both required for otic development, are linked to BOR. We previously identified Sobp as a potential Six1 cofactor and SOBP mutations in mouse and humans cause otic phenotypes; therefore, we asked whether Sobp interacts with Six1 and thereby may contribute to BOR. Co-IP and immunofluorescence experiments demonstrate that Sobp binds to and co-localizes with Six1 in the cell nucleus. Luciferase assays show that Sobp represses Six1+Eya1 transcriptional activation. Experiments in Xenopus embryos that either knockdown or increase expression show that Sobp is required for formation of ectodermal domains at neural plate stages. In addition, altering Sobp levels disrupts otic vesicle development and causes craniofacial cartilage defects. Expression of Xenopus Sobp containing the human mutation disrupts the pre-placodal ectoderm similar to full-length Sobp, but other changes are distinct. These results indicate that Sobp modifies Six1 function, is required for vertebrate craniofacial development, and identifies Sobp as a potential candidate gene for BOR and other deafness syndromes.Summary statementSobp interacts with Six1 in the cell nucleus and represses the Six1+Eya1 transcriptional activation. In Xenopus embryos, Sobp functions during early stages of inner ear development.

Usp41, a Potential Candidate Gene in Development of Breast Cancer

Background: Breast cancer is the most common cancer diagnosed among women and is the second leading cause of cancer death. It is of great significance to explore potential candidate targets. Methods: Cell function assays, siRNA, western blot, mass spectrum, flow cytometry, and other molecular biology techniques were conducted to verify the function of USP41 to breast cancer cell line. Results: The results indicate that USP41 (ubiquitin-specific proteases 41) expression is positively related to breast cancer progression. USP41 overexpression greatly enhanced breast cancer colony-forming ability, proliferation and migration. In contrast, USP41 knockdown significantly inhibited breast cancer colony-forming ability, proliferation and migration. Moreover, association of USP41 with RACK1 (Receptor for activated C kinase 1) was proved by mass spectrum, indicating its potential role in TGF-β signaling. Conclusions: USP41 can be a potential therapeutic target against breast cancer via RACK1.

Pharmacokinetics and Pharmacogenetics of Dabigatran

Dabigatran etexilate is a prodrug of dabigatran, a oral direct inhibitor of thrombin. Pharmacokinetics of dabigatran etexilate doesn’t have the disadvantages of vitamin K antagonists. However, pharmacokinetics and pharmacogenetics of dabigatran are variable. This can affect both effectiveness and safety of anticoagulant therapy. It is considered that CES1 enzyme and P-glycoprotein (CES1 and ABCB1 genes accordingly) play important role in pharmacokinetics of dabigatran etexilate. UDP-glucuronosyltransferase enzymes UGT2B15, UGT1A9, UGT2B7 (UGT2B15, UGT1A9, UGT2B7 genes accordingly) take part in the metabolism of active dabigatran. Presence of these gene’s single-nucleotide variants (SNV) can affect effectiveness and safety of dabigatran etexilate usage. The goal of this review is analysis of associated researches of SNV genes CES1 and ABCB1 and search for new candidate genes that reveal effectiveness and safety of dabigatran etexilate usage.Materials and methods. The search for full-text publications in Russian and English languages containing key words “dabigatran etexilate”, “dabigatran”, “pharmacokinetics”, “effectiveness”, “safety” was carried out amongst literature of the past twenty years with the use of eLibrary, PubMed, Web of Science, OMIM data bases. Pharmacokinetics and pharmacogenetics of dabigatran etexilate are considered in this review. The hypothesis about UDP-glucuronosyltransferase enzymes influence on dabigatran metabolism was examined. Nowadays more than 2000 SNV CES1 and ABCB1 genes are identified, but their potential influence on pharmacokinetics of dabigatran etexilate and its active metabolite (dabigatran) in clinical practice needs to be further researched. Role of SNV UDP-glucuronosyltransferase genes (UGT2B15, UGT1A9, UGT2B7) in dabigatran’s effectiveness and safety is not explored enough. However, UGT2B15 gene can be a potential candidate gene for research on safety of this drug.

GLIS1, a Potential Candidate Gene Affect Fat Deposition in Sheep Tail

Fat deposition in sheep tails has complicated mechanisms. In this study, the population genomics analysis has been applied to identify candidate genes associated with fat tails based on high depth whole-genome sequencing of Mongolia sheep (MG, fat-tailed), Small Tail Han sheep (STH, fat-tailed) and two dairy sheep breeds DairyMeade and East Friesian (DS, thin-tailed). The selective signature analysis demonstrated that GLIS1, LOC101117953, PDGFD and T were in the significant divergent regions between DS and STH-MG. A nonsynonymous point mutation (g. 27807636G>T) was found within GLIS1 in STH-MG and resulting in a Pro to Thr substitution. As a pro-adipogenic factor, GLIS1 may play critical roles in the mesodermal cell differentiation during sheep fetal development and affect the fat deposition in sheep tails. This study provides a new insight into the genetic basis of species-specific traits of fat tails.