Unrecognized hepatitis B in pre-screened children with hematologic and oncologic conditions.

BACKGROUND: This study evaluates the effectiveness and interpretation of hepatitis B (HBV) screening in an at-risk cohort of children with cancer or blood disorders. PROCEDURE: We conducted a retrospective epidemiologic analysis of children who screened positive for HBV (HBsAg, HbcAb) from 1999 to 2009 at a quaternary children's hospital, focusing on patients with hematologic and oncologic conditions. Descriptive statistics were generated for demographics and serologies. Follow-up of positive serologies and clinical outcomes were analyzed. RESULTS: A total of 12,754 children were screened for HBV. Of 391 that screened positive, 118 had a hematologic or oncologic diagnosis. Leukemia, anemia, and thrombocytopenia comprised 84% of diagnoses. The majority (98%) tested HBcAb positive but only 20% received confirmatory HBV DNA testing. Three patients (13% of those HBV DNA tested) were identified to have chronic disease. HBV was not a known pre-existing condition, and chemotherapy preceded HBV diagnosis in all cases. CONCLUSIONS: The majority of children with cancer or blood disorders who screened HBV positive did not receive follow-up DNA testing, exposing them to reactivation risk and delaying definitive therapy. HBcAb may be the only indicator of chronic HBV infection and DNA confirmation should be routine. Our findings suggest a significant number of additional patients eligible for HBV treatment may have been identified with reflexive DNA testing.

Discovery of novel microRNAs in female reproductive tract using next generation sequencing.

MicroRNAs (miRNAs) are small non-coding RNAs that mediate post-transcriptional gene silencing. Over 700 human miRNAs have currently been identified, many of which are mutated or de-regulated in diseases. Here we report the identification of novel miRNAs through deep sequencing the small RNAome (<30 nt) of over 100 tissues or cell lines derived from human female reproductive organs in both normal and disease states. These specimens include ovarian epithelium and ovarian cancer, endometrium and endometriomas, and uterine myometrium and uterine smooth muscle tumors. Sequence reads not aligning with known miRNAs were each mapped to the genome to extract flanking sequences. These extended sequence regions were folded in silico to identify RNA hairpins. Sequences demonstrating the ability to form a stem loop structure with low minimum free energy (<-25 kcal) and predicted Drosha and Dicer cut sites yielding a mature miRNA sequence matching the actual sequence were considered putative novel miRNAs. Additional confidence was achieved when putative novel hairpins assembled a collection of sequences highly similar to the putative mature miRNA but with heterogeneous 3'-ends. A confirmed novel miRNA fulfilled these criteria and had its "star" sequence in our collection. We found 7 distinct confirmed novel miRNAs, and 51 additional novel miRNAs that represented highly confident predictions but without detectable star sequences. Our novel miRNAs were detectable in multiple samples, but expressed at low levels and not specific to any one tissue or cell type. To date, this study represents the largest set of samples analyzed together to identify novel miRNAs.

Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells.

BACKGROUND: MicroRNAS (miRNAS: a class of short non-coding RNAs) are emerging as important agents of post transcriptional gene regulation and integral components of gene networks. MiRNAs have been strongly linked to stem cells, which have a remarkable dual role in development. They can either continuously replenish themselves (self-renewal), or differentiate into cells that execute a limited number of specific actions (pluripotence). METHODOLOGY/PRINCIPAL FINDINGS: In order to identify novel miRNAs from narrow windows of development we carried out an in silico search for micro-conserved elements (MCE) in adult tissue progenitor transcript sequences. A plethora of previously unknown miRNA candidates were revealed including 545 small RNAs that are enriched in embryonic stem (ES) cells over adult cells. Approximately 20% of these novel candidates are down-regulated in ES (Dicer(-/-)) ES cells that are impaired in miRNA maturation. The ES-enriched miRNA candidates exhibit distinct and opposite expression trends from mmu-mirs (an abundant class in adult tissues) during retinoic acid (RA)-induced ES cell differentiation. Significant perturbation of trends is found in both miRNAs and novel candidates in ES (GCNF(-/-)) cells, which display loss of repression of pluripotence genes upon differentiation. CONCLUSION/SIGNIFICANCE: Combining expression profile information with miRNA target prediction, we identified miRNA-mRNA pairs that correlate with ES cell pluripotence and differentiation. Perturbation of these pairs in the ES (GCNF(-/-)) mutant suggests a role for miRNAs in the core regulatory networks underlying ES cell self-renewal, pluripotence and differentiation.