Identification and function of long non-coding RNA

Long non-coding (lnc) RNAs are defined as non-protein coding RNAs distinct from housekeeping RNAs such as tRNAs, rRNAs, and snRNAs, and independent from small RNAs with specific molecular processing machinery such as micro- or piwi-RNAs. Recent studies of lncRNAs across different species have revealed a diverse population of RNA molecules of differing size and function. RNA sequencing studies suggest transcription throughout the genome, so there is a need to understand how sequence relates to functional and structural relationships amongst RNA molecules. Our synthesis of recent studies suggests that neither size, presence of a poly-A tail, splicing, direction of transcription, nor strand specificity are of importance to lncRNA function. Rather, relative genomic position in relation to a target is fundamentally important. In this review, we describe issues of key importance in functional assessment of lncRNA and how this might apply to lncRNAs important in neurodevelopment

Chromosome structural variants: Epidemiology, identification and contribution to human diseases

Editorial on the Research Topic: Chromosome structural variants: Epidemiology, identification and contribution to human diseases.Human chromosome structural variants (SVs) are balanced/unbalanced genomic abnormalities that include translocation, inversion, insertion, and deletion/duplication (also known as copy-number variants, CNVs) events with a size of >50 bp. Currently, the capability of genome sequencing in the research and clinical fields has increased our capacity to detect cryptic SVs and further delineate the complexity of karyotypically/microarray detectable SVs. This has increased our knowledge of pathogenicity mechanisms by considering dysregulation of gene expression through position effects and complex interactions between gene dosage and mutational burden. However, much of the contribution of SVs to human disease is left to explore, as the incidence of SVs is still underestimated owing to limitations of current sequencing technologies and analytical pipelines, and few studies have comprehensively integrated SV information with single nucleotide variants in congenital diseases. Rigorous investigation of SV pathogenicity is warranted for clinical applications. The Research Topic in this issue is divided into three main sections: three articles demonstrate methodologies in SV identification and pathogenicity annotation; five papers discuss the spectrum of SVs in individuals with different indications; and two reports characterize sequence complexity of SVs [...].CCM acknowledges NIH P01 GM061354 and support by the NIHR Manchester Biomedical Research Centreinfo:eu-repo/semantics/publishedVersio

The κ-Deleting Element: Germline and Rearranged, Duplicated and Dispersed Forms

Human light chain genes are used in a κ before λ order. Accompanying this hierarchy is the rearrangement of a κ-deleting element (Kde) which eliminates the kappa locus before λ gene rearrangement. In approximately 60% of rearrangements the Kde recombines at a conserved heptamer within the Jκ-Cκ intron. We demonstrated that aberrant V/J rearrangements possessing apparent N nucleotides existed 5\u27 to the Jκ-Kde rearrangements. This suggests that the Kde may selectively eliminate nonfunctional V/J alleles. A κ-producing cell that displayed the unusual finding of λ gene rearrangement demonstrated a rearranged Kde. This rearrangement was a Vκ/Kde recombination and the heptamer-11 bp spacer-nonamer flanking the Vκ is the target site of the Kde 40% of the time. The mouse possesses a counterpart to the Kde (recombining sequence [RS]) and the highly conserved regions surround the heptamer-spacer-nonamer signals. No complete protein product was predicted from the germline Kde near its break-point and no consistent fusion product was predicted from either the V/Kde or V/J-Kde rearrangements. A distal portion of the Kde is duplicated and is present at 2q11 as well as 2p11. The evolutionary conservation of the kappa-elimination event, the duplication and maintenance of the Kde indicates that it has a function. A portion of the Kde may still prove to encode a trans-acting factor that directly affects λ rearrangement. A certain role for the Kde is its site-specific rearrangement, which destroys ineffective κ genes and sets the stage for λ gene utilization

Complex cytogenetic rearrangements at the DURS1 locus in syndromic Duane retraction syndrome

Key Clinical Message A patient with syndromic Duane retraction syndrome harbors a chromosome 811.1q13.2 inversion and 8p11.1-q12.3 marker chromosome containing subregions with differing mosaicism and allele frequencies. This case highlights the potential requirement for multiple genetic methods to gain insight into genotype–phenotype correlation, and ultimately into molecular mechanisms that underlie human disease

Spectrum of genes involved in a unique case of Potocki Schaffer syndrome with a large chromosome 11 deletion

Letter to the Editor

Hereditary leiomyomatosis and renal cell cancer: Cutaneous lesions & atypical fibroids

Objective: To report a diagnosis of hereditary leiomyomatosis and renal cell cancer (HLRCC) syndrome following initial presentation with multiple cutaneous lesions. Design: Case report. Design classification N/A. Setting: Academic tertiary care center. Patient(s) 27-year-old nulligravid woman who presented with multiple red-brown lesions on her skin found to have cutaneous and uterine leiomyoma. Intervention(s) Biopsy of cutaneous lesions and fertility sparing robot-assisted laparoscopic myomectomy (RALM). Main outcome measures(s) Histological assessment of uterine leiomyoma. Results(s) Pathologic examination of uterine leiomyoma revealed diffuse atypia and fumarate hydratase loss phenotype concerning for genetic syndrome. Follow-up DNA sequencing via Sanger sequencing confirmed a pathogenetic R2333H mutation consistent with HLRCC. Conclusion(s) Consideration of HLRCC on differential diagnosis when patients present with cutaneous nodules and atypical or early onset uterine leiomyoma provides opportunity for early surveillance, family member testing, and more thoughtful surgical planning. Precis 27-year-old woman with multiple cutaneous lesions is found to have uterine leiomyomas and undergoes robotic myomectomy. Genetic testing of uterine leiomyomas reveals mutation in fumarate hydratase, etiologic in hereditary leiomyomatosis and renal cell cancer (HLRCC)

Patient Preferences for Follow-up After Recent Excision of a Localized Melanoma

Importance The standard model of follow-up posttreatment of localized melanoma relies on clinician detection of recurrent or new melanoma, through routinely scheduled clinics (clinician-led surveillance). An alternative model is to increase reliance on patient detection of melanoma, with fewer scheduled visits and increased support for patients’ skin self-examination (SSE) (eg, using smartphone apps to instruct, prompt and record SSE, and facilitate teledermatology; patient-led surveillance). Objective To determine the proportion of adults treated for localized melanoma who prefer the standard scheduled visit frequency (as per Australian guideline recommendations) or fewer scheduled visits (adapted from the Melanoma Follow-up [MELFO] study of reduced follow-up). Design, Setting, and Participants This survey study used a telephone interview for surveillance following excision of localized melanoma at an Australian specialist center. We invited a random sample of 400 patients who had completed treatment for localized melanoma in 2014 to participate. They were asked about their preferences for scheduled follow-up, and experience of follow-up in the past 12 months. Those with a recurrent or new primary melanoma diagnosed by the time of interview (0.8-1.7 years since first diagnosis) were asked about how it was first detected and treated. SSE practices were also assessed. Main Outcomes and Measures Proportion preferring standard vs fewer scheduled clinic visits, median delay between detection and treatment of recurrent or new primary melanoma, and SSE practices. Results Of the 262 people who agreed to be interviewed, the mean (SD) age was 64.3 (14.3) years, and 93 (36%) were women. Among the 230 people who did not have a recurrent or new primary melanoma, 149 vs 81 preferred the standard vs fewer scheduled clinic visits option (70% vs 30% after adjusting for sampling frame). Factors independently associated with preferring fewer visits were a higher disease stage, melanoma on a limb, living with others, not having private health insurance, and seeing a specialist for another chronic condition. The median delay between first detection and treatment of recurrent or new primary melanoma was 7 and 3 weeks, respectively. Only 8% missed a scheduled visit, while 40% did not perform SSE or did so at greater than 3-month intervals. Conclusions and Relevance Some patients with melanoma may prefer fewer scheduled visits, if they are supported to do SSE and there is rapid clinical review of anything causing concern (patient-led surveillance)

Intravenous Leiomyomatosis: An Unusual Intermediate between Benign and Malignant Uterine Smooth Muscle Tumors

Intravenous leiomyomatosis is an unusual smooth muscle neoplasm with quasi-malignant intravascular growth but a histologically banal appearance. Herein, we report expression and molecular cytogenetic analyses of a series of 12 intravenous leiomyomatosis cases to understand better the pathogenesis of intravenous leiomyomatosis. All cases were analyzed for expression of HMGA2, MDM2 and CDK4 proteins by immunohistochemistry based on our previous finding of der(14)t(12;14)(q14.3;q24) in intravenous leiomyomatosis. Seven of 12 (58%) intravenous leiomyomatosis cases expressed HMGA2, and none expressed MDM2 or CDK4. Co-localization of hybridization signals for probes from the HMGA2 locus (12q14.3) and from 14q24 by interphase fluorescence in situ hybridization (FISH) was detected in a mean of 89.2% of nuclei in HMGA2-positive cases by immunohistochemistry, but in only 12.4% of nuclei in negative cases, indicating an association of HMGA2 expression and this chromosomal rearrangement (p=8.24×10−10). Four HMGA2-positive cases had greater than two HMGA2 hybridization signals per cell. No cases showed loss of a hybridization signal by interphase FISH for the frequently deleted region of 7q22 in uterine leiomyomata. One intravenous leiomyomatosis case analyzed by array comparative genomic hybridization revealed complex copy number variations. Finally, expression profiling was performed on three intravenous leiomyomatosis cases. Interestingly, hierarchical cluster analysis of the expression profiles revealed segregation of the intravenous leiomyomatosis cases with leiomyosarcoma rather than with myometrium, uterine leiomyoma of the usual histological type, or plexiform leiomyoma. These findings suggest that intravenous leiomyomatosis cases share some molecular cytogenetic characteristics with uterine leiomyoma, and expression profiles similar to that of leiomyosarcoma cases, further supporting their intermediate, quasi-malignant behavior