Identification of candidate cancer genes involved in human retinoblastoma by data mining

Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes

Analysis of RNA-sequencing (RNA-seq) data is an effective means to analyze the gene expression levels under specific conditions and discover new biological knowledge. More than 74,000 experimental series with RNA-seq have been stored in public databases as of 20 October 2021. Since this huge amount of expression data accumulated from past studies is a promising source of new biological insights, we focused on a meta-analysis of 1783 runs of RNA-seq data under the conditions of two types of stressors: oxidative stress (OS) and hypoxia. The collected RNA-seq data of OS were organized as the OS dataset to retrieve and analyze differentially expressed genes (DEGs). The OS-induced DEGs were compared with the hypoxia-induced DEGs retrieved from a previous study. The results from the meta-analysis of OS transcriptomes revealed two genes, CRIP1 and CRIP3, which were particularly downregulated, suggesting a relationship between OS and zinc homeostasis. The comparison between meta-analysis of OS and hypoxia showed that several genes were differentially expressed under both stress conditions, and it was inferred that the downregulation of cell cycle-related genes is a mutual biological process in both OS and hypoxia.

Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms

Background

The Cancer Genome Anatomy Project (CGAP) xProfiler and cDNA Digital Gene Expression Displayer (DGED) have been made available to the scientific community over a decade ago and since then were used widely to find genes which are differentially expressed between cancer and normal tissues. The tissue types are usually chosen according to the ontology hierarchy developed by NCBI. The xProfiler uses an internally available flat file database to determine the presence or absence of genes in the chosen libraries, while cDNA DGED uses the publicly available UniGene Expression and Gene relational databases to count the sequences found for each gene in the presented libraries.

Results

We discovered that the CGAP approach often includes libraries from dependent or irrelevant tissues (one third of libraries were incorrect on average, with some tissue searches no correct libraries being selected at all). We also discovered that the CGAP approach reported genes from outside the selected libraries and may omit genes found within the libraries. Other errors include the incorrect estimation of the significance values and inaccurate settings for the library size cut-off values. We advocated a revised approach to finding libraries associated with tissues. In doing so, libraries from dependent or irrelevant tissues do not get included in the final library pool. We also revised the method for determining the presence or absence of a gene by searching the UniGene relational database, revised calculation of statistical significance and sorted the library cut-off filter.

Conclusion

Our results justify re-evaluation of all previously reported results where NCBI CGAP expression data and tools were used.

Correlation of overexpression of HMGA1 and HMGA2 with poor tumor differentiation, invasion, and proliferation associated with let-7 down-regulation in retinoblastomas

In addition to RB1, the causative genes involved in the tumorigenesis and progression of retinoblastomas remain to be elucidated. High-mobility group A1 and high-mobility group A2 proteins are expressed at high levels in various benign and malignant tumors and are associated with expressions of malignant phenotypes and poor prognoses. Reduction in let-7 expression levels was detected in cancers; it may be related to high-mobility group A1 and high-mobility group A2 overexpressions. Little is known about the correlations among high-mobility group A1, high-mobility group A2, and let-7 expression and clinicopathologic features of retinoblastoma. In our study, the expressions of high-mobility group A1 and high-mobility group A2 were studied in 44 retinoblastomas by immunohistochemical analysis. Semiquantitative reverse transcription-polymerase chain reaction was used to assay the let-7 expression levels in 28 nontumor retina and 44 tumor samples. Nuclear immunostaining of high-mobility group A1 and high-mobility group A2 was frequently observed in retinoblastomas (68% and 75%, respectively). Expression levels of both high-mobility group A1 and high-mobility group A2 were significantly higher in poorly differentiated retinoblastomas than in well-differentiated retinoblastomas (P < .05 and P < .0001, respectively). In addition, overexpressions of high-mobility group A1 and high-mobility group A2 were more frequently detected in poorly differentiated tumors than in well-differentiated tumors (P < .01 and P = .0001, respectively). High-mobility group A2 expression levels were significantly higher in invasive tumors than in noninvasive tumors (P < .05). In addition, the MIB-1 labeling index was higher in poorly differentiated tumors than in well-differentiated tumors (P < .0001). Our study revealed that high-mobility group A1 and high-mobility group A2 expressions correlated with the MIB-1 labeling index (R = 0.327, P = .029; R = 0.602, P < .0001; respectively). The let-7 was expressed in high levels in all 28 nontumor retina samples. However, reduced expression levels of let-7 were observed in 17 (39%) tumors. A potentially inverse correlation exists between the expression levels of let-7 and high-mobility group A1 (r = -0.247, P = .105). In addition, a significantly inverse association was detected between let-7 and high-mobility group A2 and MIB-1 labeling index (r = -0.31, P = .04; r = -0.392, P = .007, respectively). Our findings imply that the overexpressions of high-mobility group A1, high-mobility group A2, and down-regulation of let-7 may be associated with tumorigenesis and progression of retinoblastomas.

Discovery of novel serum biomarkers for prenatal Down syndrome screening by integrative data mining

Background

To facilitate the experimental search for novel maternal serum biomarkers in prenatal Down Syndrome screening, we aimed to create a set of candidate biomarkers using a data mining approach.

Methodology/Principal Findings

Because current screening markers are derived from either fetal liver or placental trophoblasts, we reasoned that new biomarkers can primarily be found to be derived from these two tissues. By applying a three-stage filtering strategy on publicly available data from different sources, we identified 49 potential blood-detectable protein biomarkers. Our set contains three biomarkers that are currently widely used in either first- or second-trimester screening (AFP, PAPP-A and fβ-hCG), as well as ten other proteins that are or have been examined as prenatal serum markers. This supports the effectiveness of our strategy and indicates the set contains other markers potentially applicable for screening.

Conclusions/Significance

We anticipate the set will help support further experimental studies for the identification of new Down Syndrome screening markers in maternal blood.

Retinoblastoma: what is new in 2007-2008

PURPOSE OF REVIEW

This review highlights many of the most important articles published from June 2007 to May 2008 on retinoblastoma. Significant advances in molecular biology, translational research, and clinical reports are detailed.

RECENT FINDINGS

The most significant recent findings in the molecular biology of retinoblastoma include the evidence for aneuploidy and genomic instability as cancer causes rather than the long-held Knudson's 'two-hit' hypothesis; the evidence that retinoma may represent a precursor lesion for retinoblastoma prior to the acquisition of genomic instability; and the evidence that a horizontal interneuron may be the cell of origin in murine knockout retinoblastoma and may be capable of clonal expansion after differentiation. Translational studies also demonstrate promise for the use of topotecan and 2-deoxy-D-glucose in children. Finally, the introduction of intraarterial chemotherapy for human intraocular retinoblastoma appears to be safe and effective and may eliminate the need for enucleation in many patients.

SUMMARY

Exciting new advances in both the basic science and clinical applications of new therapies continue to emerge for this rare disease. We expect that local control rates even for advanced intraocular retinoblastoma will soon reach 100% in the developed world as a result of new findings in the clinic and in the laboratory.