Molecular analysis using targeted next generation DNA sequencing and clinical spectrum of Mexican patients with isovaleric acidemia.

Isovaleric acidemia (IVA) is an inborn error of metabolism caused by deficiency of isovaleryl-CoA dehydrogenase. IVA clinical picture includes gastroenterological and progressive neurological symptoms which can lead to permanent disability and death. Early detection by newborn screening (NBS) and treatment promotes normal development. In this study, clinical summaries, biochemical measurements and targeted next generation sequencing (tNGS) data from the IVD gene were compared in 13 Mexican patients. The main symptoms were vomiting, feeding refusal, abdominal pain, impaired alertness, lethargy, stupor, coma; hypotonia, ataxia, hallucinations, seizures; anemia, neutropenia and pancytopenia. Mean blood concentration of isovalerylcarnintine was above the reference value (0.5 µM) in symptomatic patients (8.78 µM), as well as in the screen positive newborns (2.23 µM). The molecular spectrum of this cohort was heterogeneous, with 14 different variants identified, seven were previously-described, and seven were novel. The most frequent variant was c.158G > C (p.R53P). In this study, we found a long diagnostic delay (average of 44 months). Thus, it is essential to increase physician awareness of this treatable condition. Biochemical IVA NBS accompanied by molecular studies (e.g. tNGS) will permit identification of potentially asymptomatic forms of the disease, and improve genotype-phenotype relationship, management decisions and follow-up.

Accurate differential analysis of transcription factor activity from gene expression.

MOTIVATION: Activity of transcriptional regulators is crucial in elucidating the mechanism of phenotypes. However regulatory activity hypotheses are difficult to experimentally test. Therefore, we need accurate and reliable computational methods for regulator activity inference. There is extensive work in this area, however, current methods have difficulty with one or more of the following: resolving activity of TFs with overlapping regulons, reflecting known regulatory relationships, or flexible modeling of TF activity over the regulon. RESULTS: We present Effector and Perturbation Estimation Engine (EPEE), a method for differential analysis of transcription factor (TF) activity from gene expression data. EPEE addresses each of these principal challenges in the field. Firstly, EPEE collectively models all TF activity in a single multivariate model, thereby accounting for the intrinsic coupling among TFs that share targets, which is highly frequent. Secondly, EPEE incorporates context-specific TF-gene regulatory networks and therefore adapts the analysis to each biological context. Finally, EPEE can flexibly reflect different regulatory activity of a single TF among its potential targets. This allows the flexibility to implicitly recover other regulatory influences such as co-activators or repressors. We comparatively validated EPEE in 15 datasets from three well-studied contexts, namely immunology, cancer, and hematopoiesis. We show that addressing the aforementioned challenges enable EPEE to outperform alternative methods and reliably produce accurate results. AVAILABILITY AND IMPLEMENTATION: https://github.com/Cobanoglu-Lab/EPEE. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Correlation of abnormal histology with endoscopic findings among mycophenolate mofetil treated patients.

AIM: To describe all abnormal histological findings and their associated endoscopic presentation in patients using mycophenolate mofetil (MMF). METHODS: A retrospective review of all individuals prescribed MMF within 6 mo of a colonoscopy or flexible sigmoidoscopy between 07/2009 and 09/2015 was performed within Northwell Health system. Records were analyzed for age, gender, procedure indication, MMF indication, and both gross and microscopic findings. Only reports with abnormal histology were included. RESULTS: One hundred and eighty-four procedures from 170 patients were found, of which 39 met inclusion criteria. Fifty-one point three percent were female. MMF was used for solid organ transplant in 71.8%. Diarrhea was the indication for 71.8% of colonoscopies. Fifty-nine percent of reports revealed gross and microscopic abnormalities while 41.0% had only microscopic findings. Only 11 patients' reports (28.2%) indicated a specific histopathology of MMF colitis. Among the entire group, only 23.1% of abnormal histology was isolated proximal to the splenic flexure. CONCLUSION: Our results demonstrate a high rate of left sided disease and microscopic findings without gross mucosal abnormalities among patients using MMF. Also, a broader definition of MMF-colonopathy may be appropriate, with a majority of our abnormal histology falling outside of the more narrowly defined MMF-colitis category. Given the high frequency of isolated microscopic abnormalities and distal disease, sigmoidoscopy with random biopsies may be an appropriate, less invasive initial endoscopic examination in selected MMF patients.

Integrative analysis of 111 reference human epigenomes.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.

Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.

Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools.

BACKGROUND: Interactions between the epigenome and structural genomic variation are potentially bi-directional. In one direction, structural variants may cause epigenomic changes in cis. In the other direction, specific local epigenomic states such as DNA hypomethylation associate with local genomic instability. METHODS: To study these interactions, we have developed several tools and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. One key tool is Breakout, an algorithm for fast and accurate detection of structural variants from mate pair sequencing data. RESULTS: By applying Breakout and other Genboree Workbench tools we map breakpoints in breast and prostate cancer cell lines and tumors, discriminate between polymorphic breakpoints of germline origin and those of somatic origin, and analyze both types of breakpoints in the context of the Human Epigenome Atlas, ENCODE databases, and other sources of epigenomic profiles. We confirm previous findings that genomic instability in human germline associates with hypomethylation of DNA, binding sites of Suz12, a key member of the PRC2 Polycomb complex, and with PRC2-associated histone marks H3K27me3 and H3K9me3. Breakpoints in germline and in breast cancer associate with distal regulatory of active gene transcription. Breast cancer cell lines and tumors show distinct patterns of structural mutability depending on their ER, PR, or HER2 status. CONCLUSIONS: The patterns of association that we detected suggest that cell-type specific epigenomes may determine cell-type specific patterns of selective structural mutability of the genome.

Non-invasive detection of fatty liver in dairy cows by digital analyses of hepatic ultrasonograms.

During early lactation, many dairy cows develop fatty liver, which is associated with decreased health and reproductive performance. Currently, fatty liver can be detected reliably only by using liver biopsy followed by chemical or histological analysis, which is not practical in most on-farm situations. We tested whether digital analyses of hepatic ultrasonograms can be used to detect non-invasively fatty liver and estimate liver triacylglycerol content. A total of 49 liver biopsies and ultrasonograms were taken from 29 dairy cows within 2 weeks postpartum. The usefulness of 17 first- or second-order parameters from digital analysis of B-mode ultrasonograms were evaluated by discriminant, correlation, and regression analyses. A group of linear combinations of the 17 parameters correctly classified 40 of 49 samples into normal liver as well as mild, moderate and severe fatty liver when cut-off values were 1%, 5% and 10% and correctly classified 45 of 49 samples when cut-off values were 5% and 10% triacylglycerol of wet weight. A linear combination of 16 image parameters estimated triacylglycerol concentrations of 38 of the 39 liver samples below the cut-off value of 10% within 2.5% of liver wet weight, and a linear combination of 3 parameters estimated triacylglycerol concentrations of the 10 liver samples above the cut-off value of 10% within 2% of liver wet weight. Therefore, ultrasound imaging followed by digital analysis of sonograms has potential to non-invasively detect fatty liver and estimate liver triacylglycerol content.

Therapy planning and monitoring of tissue ablation by high intensity focused ultrasound (HIFU) using imaging and simulation.

High intensity focused ultrasound (HIFU) 'cooks' or ablates the target tissue at the focus of the ultrasound beam by thermal and cavitation effects. The HIFU is emerging as a non-invasive method for tumor ablation. The HIFU application for tissue ablation requires tools for dosimetry therapy planning, and real-time feedback of the intended and actual target tissues. Pretreatment planning is an important step for a successful HIFU therapy outcome. Typically, the therapy planning approach involves the use of pretreatment imaging data, defining the target and surrounding tissues by manual or semiautomatic segmentation, development of a 3-D anatomy model of the region of interest from segmentation or registration with a reference dataset, simulation of the HIFU beam and thermal dosimetry around the target tissue, display and 3-D visualization of imaging and simulation data, and review of the treatment plan options. Recent developments in therapy planning using imaging are targeted for specific applications such as prostate cancer using 3-D ultrasound images and uterine fibroids using MRI. However, significant developments have been accomplished in image guidance and feedback during the delivery of HIFU treatments. This talk reviews recent work towards therapy planning and presents approaches for developing strategies for HIFU therapy. It describes general and target-specific techniques and software tools for HIFU treatment planning using pretherapy imaging, and monitoring and controlling the HIFU delivery and tissue lesion using 1D, 2D and 3D ultrasound imaging. This aids development of optimized, high-precision HIFU applications for a controlled ablation of the target tumor. It also potentially reduces the overall treatment duration and exposure to non-target tissues.

Effects of extracorporeal shock wave therapy and radial pressure wave therapy on elasticity and microstructure of equine cortical bone.

OBJECTIVE: To measure changes in the modulus of elasticity (E) and describe histologic findings after extracorporeal shock wave therapy and radial pressure wave therapy on equine cortical bone specimens. SAMPLE POPULATION: 16 bone specimens from the proximodorsal cortex of an equine third metacarpal or metatarsal bone. PROCEDURE: Baseline E was determined by the density (p) and unidirectional ultrasound transmission velocity (C) of each specimen according to the equation E = pC2. Eight specimens were treated with 500 pulses of 0.15 mJ/mm2 of extracorporeal shock wave therapy, and 8 specimens were treated with 500 pulses of 0.16 mJ/mm2of radial pressure wave therapy. After treatment, C was determined again. Four treatment sessions resulted in 2,000 pulses and 5 C measurements. The p of each sample was measured again. Mean post-treatment E was calculated for each group. Nondecalcified sections of all specimens were stained with toluidine blue or basic fuchsin for histologic evaluation. RESULTS: Overall treatment group effect was not significant for C or E. Final E was not different from baseline values for extracorporeal shock wave therapy and radial pressure wave therapy. No histologic changes could be attributed to either treatment modality. CONCLUSIONS AND CLINICAL RELEVANCE: Extracorporeal shock wave therapy and radial pressure wave therapy did not affect the material properties of equine bone at the energy and pulse values used in this study.