A homozygous balanced reciprocal translocation suggests LINC00237 as a candidate gene for MOMO (macrosomia, obesity, macrocephaly, and ocular abnormalities) syndrome

Successful birth after preimplantation genetic testing for a couple with two different reciprocal translocations and review of the literature

BACKGROUND

Preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) is widely applied in couples with single reciprocal translocation to increase the chance for a healthy live birth. However, limited knowledge is known on the data of PGT-SR when both parents have a reciprocal translocation. Here, we for the first time present a rare instance of PGT-SR for a non-consanguineous couple in which both parents carried an independent balanced reciprocal translocation and show how relevant genetic counseling data can be generated.

METHODS

The precise translocation breakpoints were identified by whole genome low-coverage sequencing (WGLCS) and Sanger sequencing. Next-generation sequencing (NGS) combining with breakpoint-specific polymerase chain reaction (PCR) was used to define 24-chromosome and the carrier status of the euploid embryos.

RESULTS

Surprisingly, 2 out of 3 day-5 blastocysts were found to be balanced for maternal reciprocal translocation while being normal for paternal translocation and thus transferable. The transferable embryo rate was significantly higher than that which would be expected theoretically. Transfer of one balanced embryo resulted in the birth of a healthy boy.

CONCLUSION(S)

Our data of PGT-SR together with a systematic review of the literature should help in providing couples carrying two different reciprocal translocations undergoing PGT-SR with more appropriate genetic counseling.

Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci

The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.

Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications

Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.

Long Noncoding RNAs in Atherosclerosis: JACC Review Topic of the Week

Atherosclerosis is a complex and chronic disease characterized by lipid deposition in the vessel wall that leads to an inflammatory and proliferative cascade involving smooth muscle, endothelial, and immune cells. Despite substantial improvements in our understanding of mechanisms contributing to atherosclerosis and overall reduction in cardiovascular mortality, the absolute disease burden remains substantially high. The recent discovery of a new group of mediators known as long noncoding ribonucleic acids (lncRNAs) offers a unique opportunity for the development of novel diagnostic and therapeutic tools in atherothrombotic disease. A number of studies suggest that lncRNAs are important mediators in health and disease, and rapidly accumulating evidence implicates lncRNAs in regulatory circuits controlling atherosclerosis. In this review, the authors outline important contributions of lncRNAs to atherosclerosis and its associated risk factors, including hypercholesterolemia, diabetes, hypertension, and obesity.

Psychological and cognitive evaluation of autism in a patient with MOMO syndrome: a case report and literature review

MOMO is an acronym for macrosomia, obesity, macrocephaly and ocular abnormalities. The syndrome was first described in 1993, with a total of nine patients published thus far. All the cases presented intellectual disability and in one case autism was described. We present a new case of a patient with MOMO syndrome, who consulted for hallucinatory phenomena. He completed a neuropsychological, clinical and cognitive evaluation, showing a borderline intelligence quotient and fulfilled the criteria for autism spectrum disorder. This is the first neurocognitive evaluation of a patient with MOMO, supporting the use of standardized scales in order to assess the autism and other psychiatric comorbidities in patients with genetics syndromes.

Established and emerging strategies to crack the genetic code of obesity

Tremendous progress has been made in the genetic elucidation of obesity over the past two decades, driven largely by technological, methodological and organizational innovations. Current strategies for identifying obesity-predisposing loci/genes, including cytogenetics, linkage analysis, homozygosity mapping, admixture mapping, candidate gene studies, genome-wide association studies, custom genotyping arrays, whole-exome sequencing and targeted exome sequencing, have achieved differing levels of success, and the identified loci in aggregate explain only a modest fraction of the estimated heritability of obesity. This review outlines the successes and limitations of these approaches and proposes novel strategies, including the use of exceptionally large sample sizes, the study of diverse ethnic groups and deep phenotypes and the application of innovative methods and study designs, to identify the remaining obesity-predisposing genes. The use of both established and emerging strategies has the potential to crack the genetic code of obesity in the not-too-distant future. The resulting knowledge is likely to yield improvements in obesity prediction, prevention and care.

Loss of renal SNX5 results in impaired IDE activity and insulin resistance in mice

AIMS/HYPOTHESIS

We hypothesised that renal sorting nexin 5 (SNX5) regulates the insulin-degrading enzyme (IDE) and, thus, circulating insulin levels. We therefore studied the dynamic interaction between SNX5 and IDE in human renal proximal tubule cells (hRPTCs), as well as in rat and mouse kidneys.

METHODS

The regulation of IDE by SNX5 expressed in the kidney was studied in vitro and in vivo. Snx5 or mock siRNA was added to immortalised hRPTCs (passage <20) in culture or selectively infused, via osmotic mini-pump, into the remnant kidney of uninephrectomised mice and rats.

RESULTS

SNX5 co-localised with IDE at the plasma membrane and perinuclear area of hRPTCs and in the brush border membrane of proximal tubules of human, rat, and mouse kidneys. Insulin increased the co-localisation and co-immunoprecipitation of SNX5 and IDE in hRPTCs. Silencing SNX5 in hRPTCs decreased IDE expression and activity. Renal-selective silencing of Snx5 (SNX5 protein: 100 ± 25 vs 29 ± 10, p < 0.05 [% of control]) in C57Bl/6J mice decreased IDE protein (100 ± 13 vs 57 ± 6, p < 0.05 [% of control]) and urinary insulin excretion, impaired the responses to insulin and glucose, and increased blood insulin and glucose levels. Spontaneously hypertensive rats (SHRs) had increased blood insulin and glucose levels and decreased renal SNX5 (100 ± 27 vs 29 ± 6, p < 0.05 [% of control]) and IDE (100 ± 5 vs 75 ± 4, p < 0.05 [% of control]) proteins, compared with normotensive Wistar-Kyoto (WKY) rats. Kidney Snx5-depleted WKY rats also had increased blood insulin and glucose levels. The expression of SNX5 and IDE was decreased in RPTCs from SHRs and hypertensive humans compared with cells from normotensive volunteers, indicating a common cause for hyperinsulinaemia and hypertension.

CONCLUSIONS/INTERPRETATION

Renal SNX5 positively regulates IDE expression and function. This study is the first to demonstrate the novel and crucial role of renal SNX5 in insulin and glucose metabolism.

A Clinical Review of Generalized Overgrowth Syndromes in the Era of Massively Parallel Sequencing

The overgrowth syndromes are important to diagnose, not just for accurate genetic counseling, but also for knowledge surrounding cancer surveillance and prognosis. There has been a recent expansion in the number of genes associated with a mendelian overgrowth phenotype, so this review updates previous classifications of overgrowth syndromes. We also describe a clinical and molecular approach to the investigation of individuals presenting with overgrowth. This review aims to assist the clinical diagnosis of generalized overgrowth syndromes by outlining the salient features of well-known overgrowth syndromes alongside the many syndromes that have been discovered and classified more recently. We provide key clinical "handles" to aid clinical diagnosis and a list of genes to aid with panel design when using next generation sequencing, which we believe is frequently needed due to the overlapping phenotypic features seen between overgrowth syndromes.

Long Noncoding RNAs in Mammalian Development and Diseases

Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively. These transcripts regulate epigenetic processes and constitute an important layer of regulatory information essential for organismal development and play a causative role in diseases. The noncoding RNA-directed regulatory circuit controls complex characteristics. Sequence variations in noncoding RNAs influence evolution, quantitative traits, and disease susceptibility. This chapter presents an account on a class of such noncoding transcripts that are longer than 200 nucleotides (long noncoding RNA-lncRNA) in mammalian development and diseases.

LncRNA ZNF503-AS1 promotes RPE differentiation by downregulating ZNF503 expression

Long noncoding RNAs (lncRNAs) have important roles in various biological processes. Our previous work has revealed that dedifferentiation of retinal pigment epithelium (RPE) cells contributes to the pathology of age-related macular degeneration (AMD). Herein, we show roles of lncRNAs in RPE differentiation. We used microarray to identify lncRNA expression profiles in human induced pluripotent stem cells (hiPSCs) and hiPSC-derived RPE cells. A total of 217 differentially expressed lncRNAs along with the differentiation were initially identified, among which 13 lncRNAs showed a consistent fold change of over 2. LncRNA ZNF503-AS1, located in the cytoplasm of RPE cells, was found consistently upregulated along with RPE differentiation, and downregulated in the RPE-choroid of AMD patients. In vitro study further suggested that ZNF503-AS1 insufficiency could inhibit RPE differentiation, and promote its proliferation and migration. As ZNF503-AS1 is transcribed from the antisense strand of the ZNF503 gene locus, we further revealed its regulatory role in ZNF503 expression. ZNF503-AS1 was reversely correlated with ZNF503 expression. Our results also suggested that ZNF503 could inhibit RPE differentiation, and promote its proliferation and migration. Thus, ZNF503-AS1 potentially promotes RPE differentiation through downregulation of ZNF503 expression. In addition, nuclear factor-κB was recognized as a potential upstream transcript factor for ZNF503-AS1, which might participate in promoting RPE differentiation by regulating the expression of ZNF503-AS1. Taken together, our study identifies a group of RPE differentiation relevant lncRNAs, and the potential role of ZNF503-AS1 in the pathology of atrophic AMD, which might help with the intervention of AMD patients.

Precise long non-coding RNA modulation in visual maintenance and impairment

Long non-coding RNAs (lncRNAs) are remarkably powerful, flexible and pervasive cellular regulators. With the help of cheaper RNA-seq, high-throughput screening of lncRNAs has become widely applied and has identified large numbers of specific lncRNAs in various physiological or pathological processes. Vision is known to be a complex and vital perception that comprises 80% of the sensory information we receive. A consensus has been reached that normal visual maintenance and impairment are primarily driven by gene regulation. Recently, it has become understood that lncRNAs are key regulators in most biological processes, including cell proliferation, apoptosis, differentiation, immune responses, oxidative stress and inflammation. Our review is intended to provide insight towards a comprehensive view of the precise modulation of lncRNAs in visual maintenance and impairment. We also highlight the challenges and future directions in conducting lncRNA studies, particularly in patients whose lncRNAs may hold expanded promise for diagnostic, prognostic and therapeutic applications.

A systematic review of genetic syndromes with obesity

Syndromic monogenic obesity typically follows Mendelian patterns of inheritance and involves the co-presentation of other characteristics, such as mental retardation, dysmorphic features and organ-specific abnormalities. Previous reviews on obesity have reported 20 to 30 syndromes but no systematic review has yet been conducted on syndromic obesity. We searched seven databases using terms such as 'obesity', 'syndrome' and 'gene' to conduct a systematic review of literature on syndromic obesity. Our literature search identified 13,719 references. After abstract and full-text review, 119 relevant papers were eligible, and 42 papers were identified through additional searches. Our analysis of these 161 papers found that 79 obesity syndromes have been reported in literature. Of the 79 syndromes, 19 have been fully genetically elucidated, 11 have been partially elucidated, 27 have been mapped to a chromosomal region and for the remaining 22, neither the gene(s) nor the chromosomal location(s) have yet been identified. Interestingly, 54.4% of the syndromes have not been assigned a name, whereas 13.9% have more than one name. We report on organizational inconsistencies (e.g. naming discrepancies and syndrome classification) and provide suggestions for improvements. Overall, this review illustrates the need for increased clinical and genetic research on syndromes with obesity.

Longitudinal SNP-set association analysis of quantitative phenotypes

Many genetic epidemiological studies collect repeated measurements over time. This design not only provides a more accurate assessment of disease condition, but allows us to explore the genetic influence on disease development and progression. Thus, it is of great interest to study the longitudinal contribution of genes to disease susceptibility. Most association testing methods for longitudinal phenotypes are developed for single variant, and may have limited power to detect association, especially for variants with low minor allele frequency. We propose Longitudinal SNP-set/sequence kernel association test (LSKAT), a robust, mixed-effects method for association testing of rare and common variants with longitudinal quantitative phenotypes. LSKAT uses several random effects to account for the within-subject correlation in longitudinal data, and allows for adjustment for both static and time-varying covariates. We also present a longitudinal trait burden test (LBT), where we test association between the trait and the burden score in linear mixed models. In simulation studies, we demonstrate that LBT achieves high power when variants are almost all deleterious or all protective, while LSKAT performs well in a wide range of genetic models. By making full use of trait values from repeated measures, LSKAT is more powerful than several tests applied to a single measurement or average over all time points. Moreover, LSKAT is robust to misspecification of the covariance structure. We apply the LSKAT and LBT methods to detect association with longitudinally measured body mass index in the Framingham Heart Study, where we are able to replicate association with a circadian gene NR1D2.

Novel Insights into the Role of Long Noncoding RNA in Ocular Diseases

Recent advances have suggested that long noncoding RNAs (lncRNAs) are differentially expressed in ocular tissues and play a critical role in the pathogenesis of different types of eye diseases. Here, we summarize the functions and mechanisms of known aberrantly-expressed lncRNAs and present a brief overview of relevant reports about lncRNAs in such ocular diseases as glaucoma, proliferative vitreoretinopathy (PVR), diabeticretinopathy (DR), and ocular tumors. We intend to highlight comprehensive studies that provide detailed data about the mechanisms of lncRNAs, their applications as diagnostic or prognostic biomarkers, and their potential therapeutic targets. Although our understanding of lncRNAs is still in its infancy, these examples may provide helpful insights into the methods by which lncRNAs interfere with ocular diseases.