Parallel barcoding of antibodies for DNA‐assisted proteomics

DNA‐assisted proteomics technologies enable ultra‐sensitive measurements in multiplex format using DNA‐barcoded affinity reagents. Although numerous antibodies are available, nowadays targeting nearly the complete human proteome, the majority is not accessible at the quantity, concentration, or purity recommended for most bio‐conjugation protocols. Here, we introduce a magnetic bead‐assisted DNA‐barcoding approach, applicable for several antibodies in parallel, as well as reducing required reagents quantities up to a thousand‐fold. The success of DNA‐barcoding and retained functionality of antibodies were demonstrated in sandwich immunoassays and standard quantitative Immuno‐PCR assays. Specific DNA‐barcoding of antibodies for multiplex applications was presented on suspension bead arrays with read‐out on a massively parallel sequencing platform in a procedure denoted Immuno‐Sequencing. Conclusively, human plasma samples were analyzed to indicate the functionality of barcoded antibodies in intended proteomics applications.     

Lessons from Yeast on Emerging Roles of the ATAD2 Protein Family in Gene Regulation and Genome Organization

ATAD2, a remarkably conserved, yet poorly characterized factor is found upregulated and associated with poor prognosis in a variety of independent cancers in human. Studies conducted on the yeast Saccharomyces cerevisiae ATAD2 homologue, Yta7, are now indicating that the members of this family may primarily be regulators of chromatin dynamics and that their action on gene expression could only be one facet of their general activity. In this review, we present an overview of the literature on Yta7 and discuss the possibility of translating these findings into other organisms to further define the involvement of ATAD2 and other members of its family in regulating chromatin structure and function both in normal and pathological situations.     

In silico evidence of high frequency of miRNA-related SNPs in Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is the dominant histological type of esophageal cancer significantly reported in developing nations. There is an increasing evidence suggesting that single nucleotide polymorphisms (SNPs) in the untranslated regions of genes (3′-UTRs) targeted by microRNAs (miRNAs) can change the target gene's expression and thereby affect the individual's cancer risk. Thus, in support of the role of SNPs occurring in miRNA target sites (miR-TS-SNPs) in the cancer, we analyzed the next generation sequencing data of 10 ESCC patients. In each patient, about 3,000 SNPs in 3′-UTRs were obtained in their whole-exome sequencing profiles. We applied two separate methods, manual and computational in silico approaches, to predict the miR-TS-SNPs with more effects on the miRNA–target interactions. dbSNP, 1000G, ExAC, Iranome, miRandb, miRCancer, TargetScan, Human, miRNASNP2 and miRBase databases were used for positive selection of miR-TS-SNPs and DIANA-miRPath v3.0 for pathway analysis. We identified six rare germline miR-TS-SNPs and two other ones with unknown miR-TS-SNPs. We interestingly observed all of these variants in only one patient, which can be evidence of the relationship between miR-TS-SNPs and cancer incidence. The study of cancer genetics including miR-TS-SNPs reveals miRNAs and their related pathways, which will be greatly useful in cancer research from noninvasive biomarkers to new treatments.     

Sertoli cell tumor causing prepubertal gynecomastia in a boy with peutz-jeghers syndrome: the outcome of 1-year treatment with the aromatase inhibitor testolactone

Peutz-Jeghers syndrome (PJS) is a rare disorder characterized by benign intestinal hamartomatous polyps and mucocutaneous pigmentation, and with an increased risk for intestinal and extra-intestinal neoplasms. Sertoli cell tumors in boys with PJS have been increasingly recognized as a cause of prepubertal gynecomastia. However, an association between nephrocalcinosis and PJS has not been reported before. We report on a 7.25-year-old boy with PJS, bilateral gynecomastia, Sertoli cell tumor and nephrocalcinosis, and present the outcome of 1-year treatment with the aromatase inhibitor testolactone. The patient presented with bilateral breast and testis enlargement, and mucocutaneous pigmentation. Testicular ultrasound revealed parenchymal multiple microcalcifications. Histopathological examination was consistent with Sertoli cell tumors. Nephrocalcinosis due to idiopathic renal hypercalciuria was also detected. The aromatase inhibitor testolactone was begun in an attempt to prevent acceleration in skeletal maturation. One-year treatment with testolactone reduced the breast base diameter from 7 to 3 cm, and bone age advanced 1.2 years during this period. Our case demonstrates that waiting for the effect of aromatase inhibitors on gynecomastia before making a decision for mastectomy may be a reasonable option. We also consider that the association between PJS and nephrocalcinosis may be a coincidence.