Application of machine learning in screening for congenital heart diseases using fetal echocardiography

The International Journal of Cardiovascular Imaging - There is a growing body of literature supporting the utilization of machine learning (ML) to improve diagnosis and prognosis tools of...     

Maculopathy due to the R345W substitution in fibulin-3: distinct clinical features, disease variability, and extent of retinal dysfunction

PURPOSE: To determine (1) clinical features that distinguish maculopathy due to the R345W substitution in fibulin-3 from other forms of inherited or early-onset drusen, (2) the phenotypic variability, and (3) the extent of retinal disease in those with a positive molecular diagnosis. METHODS: Affected individuals underwent ophthalmic examination, digital color fundus photography, fundus autofluorescence (AF) imaging, and psychophysical testing with automated photopic and dark-adapted perimetry and fine matrix mapping. Blood samples were taken for DNA extraction and screening for the R345W mutation in fibulin-3. Patients were subsequently divided into mutation-positive and -negative groups, to compare the identified phenotypic findings in these two sets of subjects. RESULTS: Twenty-nine subjects from 19 families were ascertained with inherited or early-onset drusen. Twenty-four (83%) subjects from 15 families were found to harbor the R345W fibulin-3 mutation. Peripapillary deposition and a radial distribution of macular drusen were consistent, distinguishing signs in the mutation-positive group. Subretinal neovascular membrane (SRNVM) was a rare occurrence, affecting only 1 of 48 eyes, whereas hyperpigmentation and atrophy of the retinal pigment epithelium (RPE) were common in older mutation-positive patients. Increased AF corresponding to the drusen was detected in both the mutation-positive and -negative groups. The phenotype in the group of patients positive for the R345W mutation was extremely variable, with evidence of interocular, intrafamilial, and interfamilial variability in visual loss, natural history, ophthalmoscopic findings, autofluorescence imaging, and psychophysical data. The novel finding of nonpenetrance was observed in a 62-year-old asymptomatic, mutation-positive man. The findings from detailed perimetry performed on a subset of subjects were consistent with the presence of widespread retinal dysfunction not isolated to the macula. CONCLUSIONS: Marked inter- and intrafamilial variation associated with the fibulin-3 R345W mutation in terms of retinal appearance, severity, progression, and nonpenetrance were identified. It was noted that SRNVM is a rare occurrence in R345W fibulin-3 maculopathy. These findings are helpful for advice regarding prognosis and for genetic counseling. The findings established that the presence of peripapillary deposit is highly likely to indicate that a patient carries the R345W mutation.     

Assessment of rat and mouse RGC apoptosis imaging in vivo with different scanning laser ophthalmoscopes

PURPOSE: We have recently described a novel way of imaging apoptosing retinal ganglion cells in vivo in the rat. This study investigated if this technique could be used in the mouse, and whether the Heidelberg Retina Angiograph II (HRAII) was appropriate. METHODS: Retinal ganglion cell (RGC) death was induced by intravitreal injections in rat and mouse eyes using staurosporine. Fluorescent-labeled apoptosing cells were detected by imaging with both the HRAII and a prototype Zeiss confocal scanning laser ophthalmoscope (cSLO). Averaged in vivo images were analyzed and results compared with histologic analysis. RESULTS: Fluorescent points (FPs) used as a measure of RGC apoptosis in vivo were detected in the mouse eye but only with the HRAII and not the Zeiss cSLO. The HRAII was able to detect 62% more FPs in rat than the Zeiss cSLO. Both cSLOs showed peak FP counts at the 5- to 10-microm range in rat and mouse. Maximal FP counts were detected in the superior and superior temporal regions in the rat, with no obvious pattern of distribution in the mouse. The HRAII was found to have more FP correspondence with histologically identified apoptosing RGCs. CONCLUSIONS: To our knowledge, this is the first demonstration of visualized apoptosing RGC in vivo in a mouse. The improved image quality achieved with the HRAII compared with the Zeiss cSLO was validated by histology. This together with its enhanced maneuverability and the fact that it is already commercially available make the HRAII a potential tool for the early detection and diagnosis of glaucomatous disease in patients.     

Fanca deficiency reduces A/T transitions in somatic hypermutation and alters class switch recombination junctions in mouse B cells

Fanconi anemia is a rare genetic disorder that can lead to bone marrow failure, congenital abnormalities, and increased risk for leukemia and cancer. Cells with loss-of-function mutations in the FANC pathway are characterized by chromosome fragility, altered mutability, and abnormal regulation of the nonhomologous end-joining (NHEJ) pathway. Somatic hypermutation (SHM) and immunoglobulin (Ig) class switch recombination (CSR) enable B cells to produce high-affinity antibodies of various isotypes. Both processes are initiated after the generation of dG:dU mismatches by activation-induced cytidine deaminase. Whereas SHM involves an error-prone repair process that introduces novel point mutations into the Ig gene, the mismatches generated during CSR are processed to create double-stranded breaks (DSBs) in DNA, which are then repaired by the NHEJ pathway. As several lines of evidence suggest a possible role for the FANC pathway in SHM and CSR, we analyzed both processes in B cells derived from Fanca^−/− mice. Here we show that Fanca is required for the induction of transition mutations at A/T residues during SHM and that despite globally normal CSR function in splenic B cells, Fanca is required during CSR to stabilize duplexes between pairs of short microhomology regions, thereby impeding short-range recombination downstream of DSB formation.To respond to the enormous variety of pathogens they might encounter, B lymphocytes have evolved processes to alter their genetic material to assemble novel functional Ig genes through site-specific V(D)J recombination. Later, contact with antigens can induce two different activation-induced cytidine deaminase (AID)–dependent processes, which are known as somatic hypermutation (SHM) and class switch recombination (CSR). SHM is responsible for the targeted introduction of point mutations into the variable (V) region of the Ig gene, creating Ig variants with enhanced affinity for a particular antigen. CSR allows for exchange of the initial IgM constant region (Cμ) with a downstream constant region (Cδ, Cγ, Cε, or Cα) through deletional recombination to generate different classes of effector antibodies (Alt et al., 2013).AID, which converts cytosines into uracils, initiates both SHM and CSR by creating dU:dG mismatches (Alt et al., 2013). During SHM, mutations arise from these mismatches through several different mechanisms: (a) DNA replication across the uracil leads to transition mutations; (b) abasic sites generated by the base excision repair glycosylase UNG may be replicated in an error-prone manner by the translesional synthesis (TLS) polymerase REV1 to yield either transition or transversion mutations at the site of the C/G base pair; and (c) mismatch repair (MMR) proteins (MSH2/MSH6 and EXO1) can trigger excision and error-prone resynthesis of short stretches of DNA by the TLS polymerase Polη, thus spreading mutations to surrounding U/G base pairs (Liu and Schatz, 2009). In contrast, during CSR, both base excision repair and MMR proteins induce double-stranded breaks (DSBs) within the switch (S) regions situated upstream of each Ig C_H gene. These breaks are then repaired by either the classical nonhomologous end-joining (NHEJ) pathway, which directly rejoins DNA ends with minimal modification of the broken ends, or by the alternative NHEJ pathway, which makes use of sequence microhomologies (MHs) to associate and rejoin distal DSBs (Alt et al., 2013).Fanconi anemia (FA) is a rare, inherited chromosomal breakage disorder presenting bone marrow failure and cancer predisposition. FA is genetically heterogeneous, with 16 FANC genes (named A through Q) identified to date. After DNA damage or replicative stress, eight FANC proteins (FANCA, -B, -C, -E, -F, -G, -L, and -M) assemble into the FANCcore complex, which is necessary for the monoubiquitination and nuclear foci formation of both FANCD2 and FANCI. Monoubiquitinated FANCD2/FANCI heterodimer functionally or biochemically interacts with FANCD1/BRCA2, FANCN/PALB2, FANCJ/BRIP1, FANCO/RAD51C, FANCP/SXL4, and FANCQ/XPF to eliminate DNA lesions and rescue replication (Kottemann and Smogorzewska, 2013). FANC proteins promote homologous recombination and suppress NHEJ repair (Adamo et al., 2010; Pace et al., 2010). Moreover, FANC pathway disruption has been associated with abnormalities of several proteins involved in SHM or CSR, including the TLS polymerases REV1 and Polη (Kim et al., 2012; Fu et al., 2013; Renaud and Rosselli, 2013), the MMR protein MSH2 (Williams et al., 2011), the helicase BLM, and the DSB repair protein MRE11 (Pichierri et al., 2002, 2004; Naim and Rosselli, 2009). High levels of FANCD2 have been detected in germinal center (GC) cells in the spleen, tonsil, and reactive lymph nodes (Hölzel et al., 2003). Finally, expression of the Fanca mRNA, but not the Fancg mRNA, is specifically increased in GC B cells, which show high levels of SHM and CSR (Heng and Painter, 2008). In light of the above, we decided to analyze SHM and CSR in B cells derived from Fanca^−/− mice to determine a possible involvement of FANCA in the process of secondary Ig diversification.     

Multiple Tissue Biomarkers Independently and Additively Predict Prostate Cancer Pathology Outcomes

BackgroundDistinguishing indolent from aggressive prostate cancer remains a key challenge for decision making regarding prostate cancer management. A growing number of biomarkers are now available to help address this need, but these have rarely been examined together in the same patients to determine their potentially additive value.ObjectiveTo determine whether two previously validated plasma markers (transforming growth factor β1 [TGFβ1] and interleukin-6 soluble receptor [IL6-SR]) and two validated tissue scores (the Genomic Evaluators of Metastatic Prostate Cancer [GEMCaP] and cell cycle progression [CCP] scores) can improve on clinical parameters in predicting adverse pathology after prostatectomy, and how much they vary within tumors with heterogeneous Gleason grade.Design, setting, and participantsA case-control study was conducted among men with low-risk cancers defined by biopsy grade group (GG) 1, prostate-specific antigen (PSA) ≤10 ng/mL, and clinical stage ≤ T2 who underwent immediate prostatectomy. We collected paraffin-fixed prostatectomy tissue and presurgical plasma samples from 381 cases from the University of California, San Francisco, and 260 cases from the University of Washington.Outcome measurements and statistical analysisPathologic outcomes were minor upgrading/upstaging (GG 2 or pT3a) or major upgrading/upstaging (GG ≥ 3 or ≥ pT3b), and multinomial regression was performed to determine putative markers’ ability to predict these outcomes, controlling for PSA, percent of positive biopsy cores, age, and clinical site. For upgraded tumors, a secondary analysis of the GEMCaP and CCP scores from the higher-grade tumor was also performed to evaluate for heterogeneity.Results and limitationsOverall, 357 men had no upgrading/upstaging event at prostatectomy, 236 had a minor event, and 67 had a major event. Neither TGFβ1 nor IL6-SR was statistically significantly associated with any upgrading/upstaging. On the contrary, both the CCP and the GEMCaP score obtained from Gleason pattern 3 tissue were directly associated with minor and major upgrading/upstaging on univariate analysis. The two scores correlated with each other, but weakly. On multinomial analysis including both scores in the model, the CCP score predicted minor upgrading/upstaging (odds ratio [OR] 1.62, 95% confidence interval [CI] 1.05–2.49) and major upgrading/upstaging (OR 2.26, 95% CI 1.05–4.90), p = 0.04), and the GEMCaP score also predicted minor upgrading/upstaging (OR 1.05, 95% CI 1.03–1.08) and major upgrading/upstaging (OR 1.07, 95% CI 1.04–1.11), p < 0.01). The other clinical parameters were not significant in this model. Among upgraded tumors including both Gleason patterns 3 and 4, both the GEMCaP and the CCP score tended to be higher from the higher-grade tumor. The main limitation was the use of virtual biopsies from prostatectomy tissue as surrogates for prostate biopsies.ConclusionsBiomarker signatures based on analyses of both DNA and RNA significantly and independently predict adverse pathology among men with clinically low-risk prostate cancer undergoing prostatectomy.Patient summaryValidated biomarker scores derived from both prostate cancer DNA and prostate cancer RNA can add independent information to help predict outcomes after prostatectomy.     

Increased expression of p27 is associated with the cisplatin resistance in gastric cancer cell line YCC-3

The major obstacle of treating cancer patients is acquisition of chemoresistance, in which treated tumor cells become insensitive after chronic drug exposure. To study the mechanism of acquired cisplatin resistance, we established a cisplatin-resistant human gastric cancer cell line. The cisplatin-resistant cell line (YCC-3/R) was isolated after exposing the gastric cancer cell line, YCC-3, to a constant concentration (0.5 μg/mL) of cisplatin for 12 months. The expression of cell cycle regulatory proteins (p53, Bax, p21, p27) in the YCC-3/R were investigated by western blot analysis. The cisplatin treatment significantly down-regulated the p53 and p21 expression level, while up-regulated the p27 expression in the YCC-3/R cells compared to the parental cells. The Bax expression level was similar in both cells. These results suggest that the p27 dependent-cell cycle arrest may prevent cisplatin-induced apoptosis and give enough time to repair the DNA damage in the YCC-3/R cells.     

Multi-Modal Imaging with a Toolbox of Influenza A Reporter Viruses

Reporter viruses are useful probes for studying multiple stages of the viral life cycle. Here we describe an expanded toolbox of fluorescent and bioluminescent influenza A reporter viruses. The enhanced utility of these tools enabled kinetic studies of viral attachment, infection, and co-infection. Multi-modal bioluminescence and positron emission tomography–computed tomography (PET/CT) imaging of infected animals revealed that antiviral treatment reduced viral load, dissemination, and inflammation. These new technologies and applications will dramatically accelerate in vitro and in vivo influenza virus studies.     

Corpus callosum morphology and ventricular size in chromosome 22q11.2 deletion syndrome

In this paper, novel methods were used to map the corpus callosum morphology of children with chromosome 22q11.2 deletion syndrome in order to further investigate changes to that structure and to examine their possible effects on cognitive function. The callosal profiles were extracted from the centermost MRI midsagittal slice by supervised thresholding and the structure's boundary and midline were computed automatically. Difference analysis was based on non-rigid registration, in which a template image is warped to conform to the shape of each corpus callosum in the sample. Boundaries and midlines were registered to a template and the results used to determine the average callosal shapes for children with the deletion and for controls. Pointwise registration also enabled the detailed evaluation of callosal curvature, width, area and length. Significant differences between the two groups were found in shape, size and bending angle. Results showed group differences that were concentrated in the anterior part of the structure, more specifically in the rostrum, which was larger and longer in the group with the syndrome. Correlation analyses showed that ventricular enlargement does not fully account for callosal morphology differences in children with the deletion. However, areal measurements did reveal important relationships between changes in callosal morphology and cognitive function. These novel findings reveal intricate relationships between genetic and disease-specific factors in the callosal anatomy and the potential impact of those changes on cognitive functions.