Investigation of new candidate genes in retinoblastoma using the TruSight One “clinical exome” gene panel

Akdeniz, Demet; Tunçer, Şeref Buğra; Kebudi, Rejin; Çelik, Betül; Kuru, Gozde; Kilic, Seda; Erdoğan, Özge; Avsar, Mukaddes; Bay, Sema Büyükkapu; Tuncer, Samuray; Yazıcı, Hülya

doi:10.1002/mgg3.785

Cited by 11 publications

(9 citation statements)

References 49 publications

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“…The gene clec7a that encodes a glycoprotein with a distinct role in innate immunity regulation was up-regulated after CAP treatment 39 . While clec7a over-expression conferred a prior drug resistance in leukemic cells 40 , 41 and was prognostic of poor prostate cancer relapse-free survival 42 , it constituted as one member of the immune-related prognostic panel associated with favorable melanoma survival 43 whose mutation has been associated with immunodeficiency and the pathogenesis of retinoblastoma 44 .…”

Section: Discussionmentioning

confidence: 99%

Hsa_circRNA_0040462: a sensor of cells' response to CAP treatment with double-edged roles on breast cancer malignancy

Tian¹,

Zhang²,

Zhang³

et al. 2022

Int. J. Med. Sci.

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Cold atmospheric plasma (CAP) represents a novel onco-therapeutic approach that has demonstrated its efficacy in many types of tumors. The efficacy of CAP is dose-dependent that determines the panel of tumors feasible for receiving CAP treatment under a certain parameter configuration. Identifying markers for easy and fast prognosis of tumors' sensitivity in response to CAP exposure is of critical value towards optimized therapeutic outcome, the lack of which has largely limited the translation of CAP into clinics. Circular RNAs represent a novel type of biomarkers for disease diagnosis that is featured by easy detection and stability. Through whole transcriptome sequencing, followed by in vitro validations, computational predictions and preliminary functional studies, we identified hsa_circRNA_0040462 as a sensor of breast cancer cells' response to CAP treatment. Yet we warrant the use of hsa_circRNA_0040462 as an onco-therapeutic target given its double-edged roles on breast cancer progression, i.e., suppressive on the growth and promotive on the migrative ability of triple negative breast cancer cells. Our study for the first time focused on markers prognostic of CAP's efficacy and tumors' sensitivity to CAP treatment under a certain parameter configuration, and reported hsa_circRNA_0040462 as a sensor of cells' response to CAP treatment. Also, the uncovered dual roles of hsa_circRNA_0040462 further advanced our knowledge on the complex yet critical regulatory functionalities of circular RNAs in cancer progression.

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Section: Discussionmentioning

confidence: 99%

Hsa_circRNA_0040462: a sensor of cells' response to CAP treatment with double-edged roles on breast cancer malignancy

Tian¹,

Zhang²,

Zhang³

et al. 2022

Int. J. Med. Sci.

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“…The germline inactivation of RB1 gene has been found in 25-35% of retinoblastoma (54). Expression of DNMT1, which is responsible for global genome methylation in cells, is elevated by the loss of RB1 (12,15).…”

Section: Discussionmentioning

confidence: 99%

High levels of global genome methylation in patients with retinoblastoma

Yazıcı

Tigli

et al. 2020

Oncol Lett

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Retinoblastoma is a tumor of the embryonic neural retina in young children. The DNA methyltransferase 1 (DNMT1) gene has been demonstrated to be transcriptionally activated in cells lacking retinoblastoma 1 (RB1). Thus, there is a direct interaction between DNMT1 and RB1 in vivo. The present study hypothesized that uncontrolled DNMT1, DNMT2 and DNMT3 expression may lead to a high level of global genome methylation causing a second hit or where both alleles are altered, in RB1 and/or inactivation of other genes in retinal cells. To test this, the global genome methylation levels were analyzed in 69 patients with retinoblastoma, as well as 26 healthy siblings and 18 healthy unrelated children as the control groups. Peripheral blood and tumor tissue samples were obtained from 32 patients. The expression levels of DNMT genes were also determined in cell lines. Based on the median levels of global genome methylation in patients, higher genome-wide methylation levels in peripheral blood were associated with a 3.33-fold increased risk for retinoblastoma in patients compared with all healthy controls (95% confidence interval, 0.98-11.35; P<0.0001). The level of global genome methylation and the expression of DNMT genes were increased in the WERI-RB-1 cell line, which has a mutated RB1 gene, compared with a wild-type RB1-expressing cell line. These results supported the hypothesis that epigenetic alterations, as well as mutations in RB1, may be associated with the oncogenesis and inheritance of retinoblastoma. The repression of genes that interact with RB1, such as the DNMT gene family, may be important in patients with retinoblastoma with alterations in RB1, and may serve a role in the treatment and regression of retinoblastoma.

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“…64 The c.G1162A:p. G388R variant in the FGFR4 gene which is also known for its oncogenic transformation activity was reported as a candidate gene for predicting the clinical development and assessing the stage of the disease in patients with advanced-stage retinoblastoma. 60,65 The evaluation in the light of this information shows that the detection of FGFR4 (NM_001354984), Exon9, HET, c.1162G>A, p.(Gly388Arg) variant only in the spouses of the siblings (KY107, and KY103), and in their children (KY108, and KY101) but not in the family members with high cancer burden suggest that additional studies are required for its pathogenic effect.…”

Section: Fgfr4mentioning

confidence: 99%

Identification of candidate genes in a family with cancer overload by whole-exome sequencing

Ödemiş¹,

Kebudi²,

Hassani³

et al. 2022

Turk J Pediatr

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Background. Approximately 120 out of every 1 million children in the world develop cancer each year. In Turkey, 2500-3000 children are diagnosed with new cancer each year. The causes of childhood cancer have been studied for many years. It is known that many cancers in children, as in adults, cause uncontrolled cell growth, and develop as a result of mutations in genes that cause cancer. Methods. The investigation of family history within this context in the study, a total of 13 individuals consisting of all children and adults in the family were examined using the whole-exome sequencing (WES) with the individuals who were diagnosed with cancer in the family, who were detected to have different cancer profiles, and defined as high risk and to determine the gene or genes through which the disease has developed. Results. At the end of the study, a total of 30 variants with a pathogenic record in the family were identified. A total of 10 pathogenic variants belonging to 8 different genes from these variants have been associated with various cancer risks. Conclusions. A significant scientific contribution has been made to the mechanism of disease formation by studying a family with a high cancer burden and by finding the genes associated with the disease. In addition, by the results obtained, family members with cancer predisposition were selected after a risk analysis conducted in this family, and the necessary examinations and scans were recommended to provide an early diagnostic advantage.

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Investigation of new candidate genes in retinoblastoma using the TruSight One “clinical exome” gene panel

Cited by 11 publications

References 49 publications

Hsa_circRNA_0040462: a sensor of cells' response to CAP treatment with double-edged roles on breast cancer malignancy

Hsa_circRNA_0040462: a sensor of cells' response to CAP treatment with double-edged roles on breast cancer malignancy

High levels of global genome methylation in patients with retinoblastoma

Identification of candidate genes in a family with cancer overload by whole-exome sequencing

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