From pixels to patient care: deep learning-enabled pathomics signature offers precise outcome predictions for immunotherapy in esophageal squamous cell cancer.

BACKGROUND: Immunotherapy has significantly improved survival of esophageal squamous cell cancer (ESCC) patients, however the clinical benefit was limited to only a small portion of patients. This study aimed to perform a deep learning signature based on H&E-stained pathological specimens to accurately predict the clinical benefit of PD-1 inhibitors in ESCC patients. METHODS: ESCC patients receiving PD-1 inhibitors from Shandong Cancer Hospital were included. WSI images of H&E-stained histological specimens of included patients were collected, and randomly divided into training (70%) and validation (30%) sets. The labels of images were defined by the progression-free survival (PFS) with the interval of 4 months. The pretrained ViT model was used for patch-level model training, and all patches were projected into probabilities after linear classifier. Then the most predictive patches were passed to RNN for final patient-level prediction to construct ESCC-pathomics signature (ESCC-PS). Accuracy rate and survival analysis were performed to evaluate the performance of ViT-RNN survival model in validation cohort. RESULTS: 163 ESCC patients receiving PD-1 inhibitors were included for model training. There were 486,188 patches of 1024*1024 pixels from 324 WSI images of H&E-stained histological specimens after image pre-processing. There were 120 patients with 227 images in training cohort and 43 patients with 97 images in validation cohort, with balanced baseline characteristics between two groups. The ESCC-PS achieved an accuracy of 84.5% in the validation cohort, and could distinguish patients into three risk groups with the median PFS of 2.6, 4.5 and 12.9 months (P < 0.001). The multivariate cox analysis revealed ESCC-PS could act as an independent predictor of survival from PD-1 inhibitors (P < 0.001). A combined signature incorporating ESCC-PS and expression of PD-L1 shows significantly improved accuracy in outcome prediction of PD-1 inhibitors compared to ESCC-PS and PD-L1 anlone, with the area under curve value of 0.904, 0.924, 0.610 for 6-month PFS and C-index of 0.814, 0.806, 0.601, respectively. CONCLUSIONS: The outcome supervised pathomics signature based on deep learning has the potential to enable superior prognostic stratification of ESCC patients receiving PD-1 inhibitors, which convert the images pixels to an effective and labour-saving tool to optimize clinical management of ESCC patients.

Prognostic Differences Between Surveillance and Active Treatment After Initial Orchiectomy in Patients With Stage I Mixed Germ Cell Tumors of the Testis: A Propensity Score Matching Analysis.

INTRODUCTION: The prognosis and optimal treatment approach for stage I mixed germ cell cancers of the testis are not well-established. This study aimed to assess contemporary treatment rates and their correlation with the cancer-specific mortality (CSM) and other-cause mortality (OCM) in patients with stage I testicular mixed germ cell tumors (TMGCT) who underwent orchiectomy, comparing surveillance with active treatment, including chemotherapy (CHT) and retroperitoneal lymph node dissection (RPLND). METHODS: Retrospective analysis of clinical data from stage I TMGCT patients who underwent orchiectomy was conducted using the Surveillance, Epidemiology, and End Results database from 2004 to 2019. The annual percentage change (APC) in the use of surveillance, postoperative CHT, and RPLND was examined. Propensity score matching (PSM) and cumulative incidence, analyses were employed to compare differences in CSM and OCM between surveillance and active treatment, as well as between CHT and RPLND. Multivariate competing-risks regression models were utilized to investigate independent factors affecting CSM and OCM among stage I TMGCT patients. RESULTS: The study included 5743 individuals with stage I TMGCT that underwent surveillance (61.6%), CHT(27.2%), or RPLND (11.2%). Among them, 82 deaths were attributed to TMGCT, and 82 deaths resulted from other causes. Surveillance rates increased over time (APC: 0.635%, P = 0.008), as did CHT rates (APC: 0.863%, P < 0.001), while RPLND rates declined (APC: -0.96%, P < 0.001). After PSM, multivariate competing-risks regression analysis showed that, active treatment, compared to surveillance, was not an independent factor for CSM and OCM. In contrast, when compared to CHT, RPLND was an independent factor associated with lower CSM (hazard ratio = 0.247, 95% confidence interval: 0.08-0.761; P = 0.015), but not OCM (hazard ratio = 0.946, 95% confidence interval: 0.377-2.37; P = 0.91). CONCLUSIONS: Surveillance and CHT rates have increased over time for patients with stage I TMGCT following initial orchiectomy, while RPLND utilization has decreased. There was no significant difference in CSM between surveillance and active treatment groups, but RPLND demonstrated significantly lower CSM than CHT in active treatment. Our findings suggest that the usage of RPLND in patients with stage I TMGCT should be reconsidered.

Outcome-Supervised Deep Learning on Pathologic Whole Slide Images for Survival Prediction of Immunotherapy in Patients with Non-Small Cell Lung Cancer.

Although programmed death-(ligand) 1 (PD-(L)1) inhibitors are marked by durable efficacy in patients with non-small cell lung cancer (NSCLC), approximately 60% of the patients still suffer from recurrence and metastasis after PD-(L)1 inhibitor treatment. To accurately predict the response to PD-(L)1 inhibitors, we presented a deep learning model using a Vision Transformer (ViT) network based on hematoxylin and eosin (H&E)-stained specimens of patients with NSCLC. Two independent cohorts of patients with NSCLC receiving PD-(L)1 inhibitors from Shandong Cancer Hospital and Institute and Shandong Provincial Hospital were enrolled for model training and external validation, respectively. Whole slide images (WSIs) of H&E-stained histologic specimens were obtained from these patients and patched into 1024 × 1024 pixels. The patch-level model was trained based on ViT to identify the predictive patches, and patch-level probability distribution was performed. Then, we trained a patient-level survival model based on the ViT-Recursive Neural Network framework and externally validated it in the Shandong Provincial Hospital cohort. A total of 291 WSIs of H&E-stained histologic specimens from 198 patients with NSCLC in Shandong Cancer Hospital and 62 WSIs from 30 patients with NSCLC in Shandong Provincial Hospital were included in the model training and validation. The model achieved an accuracy of 88.6% in the internal validation cohort and 81% in the external validation cohort. The survival model also remained a statistically independent predictor of survival from PD-(L)1 inhibitors. In conclusion, the outcome-supervised ViT-Recursive Neural Network survival model based on pathologic WSIs could be used to predict immunotherapy efficacy in patients with NSCLC.

Impact of nab-paclitaxel plus PD-1/PD-L1 inhibitor on chemorefractory relapsed small-cell lung cancer.

Background: The present study evaluated the efficacy and safety of nab-paclitaxel (nab-PTX) with a concurrent PD-1/PD-L1 inhibitor in patients with refractory relapsed small-cell lung cancer (SCLC). Patients & methods: We retrospectively analyzed 240 patients with refractory relapsed SCLC: 40 patients were treated with nab-PTX plus PD-1/PD-L1 inhibitor, and 200 received traditional chemotherapy. Results: Median progression-free survival in the nab-PTX plus PD-1/PD-L1 inhibitor and traditional chemotherapy groups was 3.6 and 2.5 months (p = 0.0021), respectively. The median overall survival was 8.0 and 5.2 months (p = 0.0002), respectively. No new safety issues were identified. Conclusion: Nab-PTX plus PD-1/PD-L1 inhibitor significantly improved survival in patients with refractory relapsed SCLC compared with traditional chemotherapy.

Most patients with refractory relapsed small-cell lung cancer (SCLC) have few treatment options and dismal survival rates. This study analyzed the clinical outcomes and safety profiles of patients treated with nab-paclitaxel (nab-PTX) plus PD-1/PD-L1 inhibitor compared with patients treated with conventional chemotherapy. Notably, treatment with nab-paclitaxel and PD-1/PD-L1 inhibitor was associated with more favorable clinical outcomes, including better overall response and disease control rates, as well as longer overall survival and progression-free survival. In terms of side effect profiles, the two groups were balanced and had a similar incidence of grade ≥3 adverse events, including depleted blood cells and hair loss. To the best of our knowledge, we are the first to report the use of nab-PTX plus PD-1/PD-L1 inhibitor in the treatment of refractory relapsed SCLC. In addition, nab-PTX plus PD-1/PD-L1 inhibitor showed more effective antitumor activity in patients with secondary tumors in the liver, further confirming that nab-PTX plus PD-1/PD-L1 inhibitor is effective for patients with refractory relapsed SCLC.

Pneumonitis with combined immune checkpoint inhibitors and chemoradiotherapy in locally advanced non-small-cell lung cancer: a systematic review and meta-analysis.

Aims: This study systematically evaluated cases of pneumonitis following combined immune checkpoint inhibitors (ICI) and chemoradiotherapy (CRT) for locally advanced non-small-cell lung cancer (LA-NSCLC). Methods: Studies from Embase, PubMed and the Cochrane Library on patients with LA-NSCLC who received CRT and ICIs were reviewed. The primary outcomes were rates of all-grade, grade 3-5 and grade 5 pneumonitis. Results: Overall, 35 studies involving 5000 patients were enrolled. The pooled rates of all-grade, grade 3-5 and grade 5 pneumonitis were 33.0% (95% CI: 23.5-42.6), 6.1% (95% CI: 4.7-7.4) and 0.8% (95% CI: 0.3-1.2), respectively, with 7.6% of patients discontinuing ICIs because of pneumonitis. Conclusion: The incidence rates of pneumonitis following combined CRT and ICIs for LA-NSCLC were acceptable. However, the pulmonary toxicity of concurrent CRT and nivolumab plus ipilimumab should be noted.

Combined immune checkpoint inhibitors (ICI) and chemoradiotherapy (CRT) may cause severe pneumonitis due to overlapped pulmonary toxicity. However, the safety data on pneumonitis are limited to a small number of prospective clinical trials and retrospective studies with limited evidence. Thus we conducted a systematic review of pneumonitis in relation to the combination treatment. A total of 35 studies, involving 5000 patients, were included for the final analysis. The pooled rates of all-grade, grade 3­5 and grade 5 pneumonitis were 33.0, 6.1 and 0.8%, respectively, and 7.6% of patients stopped taking ICIs because of pneumonitis. The pneumonitis rates following combined CRT and ICIs for LA-NSCLC were acceptable, but the pulmonary toxicity of concurrent CRT and nivolumab plus ipilimumab should be noted.

PM2.5 exposure and its interaction of oxidative balance score on ovarian cancer survival: A prospective cohort study.

Recent evidence advises particles with a diameter of 2.5 µm or less (PM2.5) might be a prognostic factor for ovarian cancer (OC) survival. The oxidative balance score (OBS) incorporates diet-lifestyle factors to estimate individuals' anti-oxidant exposure status which may be relevant to cancer prognosis. We aimed to investigate the roles of PM2.5, and OBS and their interaction in OC prognosis. 663 patients with OC were enrolled in the current study. Satellite-derived annual average exposures to PM2.5 based on patients' residential locations. The OBS was calculated based on 16 different diet-lifestyle components derived using an acknowledged self-reported questionnaire. The Cox regression model was performed to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival (OS). We also assessed the effect of modification between PM2.5 and OS by OBS via interaction terms. During a median follow-up of 37.57 (interquartile:35.27-40.17) months, 123 patients died. Compared to low-concentration PM2.5 exposure, high PM2.5 during 1 year before diagnosis was associated with worse OC survival (HR= 1.19, 95% CI = 1.01-1.42). We observed an improved OS with the highest compared with the lowest OBS (HR = 0.46, 95% CI = 0.27-0.79, P for trend < 0.05). Notably, we also found an additive interaction between low OBS and high exposure to PM2.5, with the corresponding associations of PM2.5 being more pronounced among participants with lower OBS (HR = 1.42, 95% CI = 1.09-1.86). PM2.5 may blunt OC survival, but high OBS represented an antioxidative performance that could alleviate the adverse association of PM2.5 and OS.

Prediction of a Narrow Exotic Hadronic State with Quantum Numbers J

Lots of charmonium-like structures have been observed in the last two decades. Most of them have quantum numbers that can be formed by a pair of charm and anticharm quarks, thus it is difficult to unambiguously identify the exotic ones among them. In this Letter, by exploiting heavy quark spin symmetry, we present a robust prediction of the hadronic molecular scenario, where the ψ(4230), ψ(4360) and ψ(4415) are identified as DD[over ¯]_{1}, D^{*}D[over ¯]_{1}, and D^{*}D[over ¯]_{2}^{*} bound states, respectively. We show that a flavor-neutral charmonium-like exotic state with quantum numbers J^{PC}=0^{--}, denoted as ψ_{0}(4360), should exist as a D^{*}D[over ¯]_{1} bound state. The mass and width of the ψ_{0}(4360) are predicted to be (4366±18) MeV and less than 10 MeV, respectively. The ψ_{0}(4360) is significant in two folds: no 0^{--} hadron has been observed so far, and a study of this state will enlighten the understanding of the mysterious vector mesons between 4.2 and 4.5 GeV, as well as the nature of previously observed exotic Z_{c} and P_{c} states. We propose that such an exotic state can be searched for in e^{+}e^{-}→ηψ_{0}(4360) and uniquely identified by measuring the angular distribution of the outgoing η meson.

Genome-wide DNA methylation signature predict clinical benefit of bevacizumab in non-small cell lung cancer.

BACKGROUND: The efficacy of bevacizumab in non-small cell lung cancer (NSCLC) patients is unsatisfactory, and the selection of suitable patients is still challenging. Given the epigenetic modifications can contribute to an aberrant regulation of angiogenesis and microenvironment, we investigated DNA methylation profiles to determine clinical benefit of bevacizumab in NSCLC patients. METHODS: Genome-wide DNA methylation profiling was performed in NSCLC patients treated with chemotherapy in combination with bevacizumab. Patients were divided into better prognosis group (A group) and inferior prognosis group (B group) based on their survival. The difference of methylation patterns and respective functional enrichment analysis were performed between two groups. Prognostic DNA methylation signature for bevacizumab was established with the least absolute shrinkage and selection operator regression analyses. TISIDB database was further used to infer immunological relationship for prognostic related DNA methylation. RESULTS: Twenty patients were included in this study, and significantly distinct methylation patterns were observed between patients with different prognosis. Related genes of different methylation regions were significantly enriched in the biological process of cell projection assembly, neutrophil mediated immunity, and pathway of VEGFA-VEGFR2 signaling pathway, neutrophil degranulation. A 10-gene DNA methylation signature for prognosis prediction was established with the C-index of 0.76. And host genes of signature were found to be related to the abundance of ActCD4, Th1, ActCD8, NKT and neutrophil cells. CONCLUSION: The 10-gene DNA methylation signature could serve as a novel biomarker to predict the clinical benefit of bevacizumab therapy and improve this anti-tumor approach for NSCLC patients.

[Radiation-Induced Heart Disease: Current Status and Challenges].

Being one of the major therapeutic measures for malignant tumors, radiation therapy, or radiotherapy, plays a particularly crucial role in the multidisciplinary integrated treatment of thoracic tumors. With the development in radiotherapy technology, the research focus has shifted from improving the overall survival of malignant tumor patients to reducing the incidence of radiation-related injuries. Currently, radiation-induced heart disease (RIHD) has become one of the leading non-cancer causes of death in thoracic tumor patients who have undergone radiotherapy, seriously affecting their quality of life and clinical prognosis. In recent years, there has been growing understanding of the pathogenesis of RIHD, and proposals have been made for some potential measures for the prevention and treatment of RIHD. Based on the clinical manifestations and pathological changes of RIHD that have been reported, we herein reviewed the biological mechanism and potential treatment options for RIHD. We also discussed existing challenges in the prevention and treatment of RIHD, intending to provide references for the prevention and treatment of RIHD.

Explaining the Many Threshold Structures in the Heavy-Quark Hadron Spectrum.

Tremendous progress has been made experimentally in the hadron spectrum containing heavy quarks in the last two decades. It is surprising that many resonant structures are around thresholds of a pair of heavy hadrons. There should be a threshold cusp at any S-wave threshold. By constructing a nonrelativistic effective field theory with open channels, we discuss the generalities of threshold behavior, and offer an explanation of the abundance of near-threshold peaks in the heavy quarkonium regime. We show that the threshold cusp can show up as a peak only for channels with attractive interaction, and the width of the cusp is inversely proportional to the reduced mass relevant for the threshold. We argue that there should be threshold structures at any threshold of a pair of heavy-quark and heavy-antiquark hadrons, which have attractive interaction at threshold, in the invariant mass distribution of a heavy quarkonium and light hadrons that couple to that open-flavor hadron pair. The structure becomes more pronounced if there is a near-threshold pole. Predictions of the possible pairs are also given for the ground state heavy hadrons. Precisely measuring the threshold structures will play an important role in revealing the heavy-hadron interactions, and thus understanding the puzzling hidden-charm and hidden-bottom structures.

A novel nomogram containing acute radiation esophagitis predicting radiation pneumonitis in thoracic cancer receiving radiotherapy.

BACKGROUND: Radiation-induced pneumonitis (RP) is a non-negligible and sometimes life-threatening complication among patients with thoracic radiation. We initially aimed to ascertain the predictive value of acute radiation-induced esophagitis (SARE, grade ≥ 2) to symptomatic RP (SRP, grade ≥ 2) among thoracic cancer patients receiving radiotherapy. Based on that, we established a novel nomogram model to provide individualized risk assessment for SRP. METHODS: Thoracic cancer patients who were treated with thoracic radiation from Jan 2018 to Jan 2019 in Shandong Cancer Hospital and Institute were enrolled prospectively. All patients were followed up during and after radiotherapy (RT) to observe the development of esophagitis as well as pneumonitis. Variables were analyzed by univariate and multivariate analysis using the logistic regression model, and a nomogram model was established to predict SRP by "R" version 3.6.0. RESULTS: A total of 123 patients were enrolled (64 esophageal cancer, 57 lung cancer and 2 mediastinal cancer) in this study prospectively. RP grades of 0, 1, 2, 3, 4 and 5 occurred in 29, 57, 31, 0, 3 and 3 patients, respectively. SRP appeared in 37 patients (30.1%). In univariate analysis, SARE was shown to be a significant predictive factor for SRP (P < 0.001), with the sensitivity 91.9% and the negative predictive value 93.5%. The incidence of SRP in different grades of ARE were as follows: Grade 0-1: 6.5%; Grade 2: 36.9%; Grade 3: 80.0%; Grade 4: 100%. Besides that, the dosimetric factors considering total lung mean dose, total lung V5, V20, ipsilateral lung mean dose, ipsilateral lung V5, and mean esophagus dose were correlated with SRP (all P < 0.05) by univariate analysis. The incidence of SRP was significantly higher in patients whose symptoms of RP appeared early. SARE, mean esophagus dose and ipsilateral mean lung dose were still significant in multivariate analysis, and they were included to build a predictive nomogram model for SRP. CONCLUSIONS: As an early index that can reflect the tissue's radiosensitivity visually, SARE can be used as a predictor for SRP in patients receiving thoracic radiation. And the nomogram containing SARE may be fully applied in future's clinical work.

[Methods of isothermal nucleic acid amplification-based microfluidic chips for pathogen microorganism detection].

Rapid detection of pathogenic microorganisms is key to the epidemiologic identification, prevention and control of disease in the field of public health. PCR-based pathogen detection methods have been widely used because they overcome the time-consuming issues that traditional culture-based methods required including the limited window required by immunological detection. However, the requirement on precision temperature-controlled thermal cyclers severely limits their use in resource-limited areas. The detection methods of pathogenic microorganisms based on isothermal amplification of nucleic acids are free of dependence on high-precision temperature control equipment, but requirements for nucleic acids extraction, amplification and detection must be defined. In recent years, a number of alternative methods for pathogenic microorganism detection have been developed by combining microfluidic technology with nucleic acid isothermal amplification technology. By designing the chip structures, optimizing the injection modes, and utilizing multiple detection and quantitative methods, the integration of pathogen nucleic acid extraction, amplification and detection is achieved. The method provides advantages of less instrument dependence, decreased operator requirements, smaller sample size, and higher automation which are suitable for the rapid detection of pathogenic microorganisms in various environments. In this review, we summarize several microfluidic detection methods based on nucleic acid isothermal amplification for pathogens including amplification principles, injection methods and detection methods. These methods provide more capability for the rapid screening of pathogenic microorganisms which enhances the management of infectious diseases in the field of public health.

Evidence for a direct cross-talk between malic enzyme and the pentose phosphate pathway via structural interactions.

Recent studies have revealed that the oxidative pentose phosphate pathway (PPP), malic enzyme (ME), and folate metabolism are the three major routes for generating cellular NADPH, a key cofactor involved in redox control and reductive biosynthesis. Many tumor cells exhibit altered NADPH metabolism to fuel their rapid proliferation. However, little is known about how NADPH metabolism is coordinated in tumor cells. Here we report that ME1 increases the PPP flux by forming physiological complexes with 6-phosphogluconate dehydrogenase (6PGD). We found that ME1 and 6PGD form a hetero-oligomer that increases the capability of 6PGD to bind its substrate 6-phosphogluconate. Through activating 6PGD, ME1 enhances NADPH generation, PPP flux, and tumor cell growth. Interestingly, although ME1 could bind either the dimer-defect mutant 6PGD (K294R) or the NADP+-binding defect 6PGD mutants, only 6PGD (K294R) activity was induced by ME1. Thus, ME1/6PGD hetero-complexes may mimic the active oligomer form of 6PGD. Together, these findings uncover a direct cross-talk mechanism between ME1 and PPP, may reveal an alternative model for signaling transduction via protein conformational simulation, and pave the way for better understanding how metabolic pathways are coordinated in cancer.

[Detection of UGT1A1*6 single nucleotide polymorphism in oral swap samples using the cascade invader assay-based real-time PCR].

The adverse reaction to irinotecan is related to the single nucleotide polymorphism (SNP) of UGT1A1*6 genotype. The current SNP detection methods have various disadvantages, including time-consuming procedures, high- risk cross-contamination, and cumbersome operation. Hence, it is necessary to establish a new method suitable for clinical application, which is easy and simple to detect SNP with minimal risk for cross-contamination. In this study, a cascade invader assay-based real-time PCR, for UGT1A1*6 genotyping has been established by optimizing reaction conditions with DNA samples of three genotypes. The sensitivity and accuracy of the method were evaluated with DNAs derived from oral swab samples. The results showed that the method could detect the UGT1A1*6 genotypes from the oral swab samples with a detection limit of 6 ng genomic DNA with 100% accuracy. Due to its convenient and non-invasive sampling, single close-tube operation, and minimal risk for cross-contamination, the method has the potential in clinical application for individualized detection of drug-related UGT1A1*6 polymorphism and reaction to irinotecan.

Knockdown of Long Non-Coding RNA-ZFAS1 Protects Cardiomyocytes Against Acute Myocardial Infarction Via Anti-Apoptosis by Regulating miR-150/CRP.

ZFAS1 is one of cardiac-specific or cardiac-related lncRNAs. This study was to explore the functional involvement of ZFAS1 and its regulatory role in AMI. In this study, the models of AMI rat and myocardial cell cultured under hypoxia were made. The expression of ZFAS1 and miR-150 of myocardial infarction tissue or cardiac myocytes was determined by quantitative real time PCR. The regulatory role of ZFAS1 on miR-150 was examined by RNA pull down assay. The effect of miR-150 or ZFAS1 expression on cell viability was analyzed by MTT assay. The relative expression of ZFAS1 in the myocardium infracted zone and border zone was significantly upregulated at 1-48 h of AMI rats, but it downregulated at 1 week and 2 weeks; miR-150 was significantly downregulated at AMI-1-48 h and upregulated at 1 and 2 weeks after model establishment. The result of RNA pull down assay indicated that ZFAS1 could interact directly with miR-150. C-reactive protein (CRP) was regulated by ZFAS1/miR-150 axis and negatively targeted by miR-150. Hypoxia caused the decrease of cell viability and the upregulation of CRP at mRNA and protein levels; whereas this upregulation could be attenuated by miR-150 mimic or si-ZFAS1 in H9C2 cells and cardiomyocytes. Knockdown of ZFAS1 or miR-150 overexpression effectively relieved AMI-induced myocardial infarction in AMI-1 week rats. The ZFAS1/miR-150 axis was involved in the molecular mechanism of AMI induced cardiomyocytes apoptosis via regulating CRP. J. Cell. Biochem. 118: 3281-3289, 2017. © 2017 Wiley Periodicals, Inc.

Two knockdown models of the autism genes SYNGAP1 and SHANK3 in zebrafish produce similar behavioral phenotypes associated with embryonic disruptions of brain morphogenesis.

Despite significant progress in the genetics of autism spectrum disorder (ASD), how genetic mutations translate to the behavioral changes characteristic of ASD remains largely unknown. ASD affects 1-2% of children and adults, and is characterized by deficits in verbal and non-verbal communication, and social interactions, as well as the presence of repetitive behaviors and/or stereotyped interests. ASD is clinically and etiologically heterogeneous, with a strong genetic component. Here, we present functional data from syngap1 and shank3 zebrafish loss-of-function models of ASD. SYNGAP1, a synaptic Ras GTPase activating protein, and SHANK3, a synaptic scaffolding protein, were chosen because of mounting evidence that haploinsufficiency in these genes is highly penetrant for ASD and intellectual disability (ID). Orthologs of both SYNGAP1 and SHANK3 are duplicated in the zebrafish genome and we find that all four transcripts (syngap1a, syngap1b, shank3a and shank3b) are expressed at the earliest stages of nervous system development with pronounced expression in the larval brain. Consistent with early expression of these genes, knockdown of syngap1b or shank3a cause common embryonic phenotypes including delayed mid- and hindbrain development, disruptions in motor behaviors that manifest as unproductive swim attempts, and spontaneous, seizure-like behaviors. Our findings indicate that both syngap1b and shank3a play novel roles in morphogenesis resulting in common brain and behavioral phenotypes.

A mutation in SLC22A4 encoding an organic cation transporter expressed in the cochlea strial endothelium causes human recessive non-syndromic hearing loss DFNB60.

The high prevalence/incidence of hearing loss (HL) in humans makes it the most common sensory defect. The majority of the cases are of genetic origin. Non-syndromic hereditary HL is extremely heterogeneous. Genetic approaches have been instrumental in deciphering genes that are crucial for auditory function. In this study, we first used NADf chip to exclude the implication of known North-African mutations in HL in a large consanguineous Tunisian family (FT13) affected by autosomal recessive non-syndromic HL (ARNSHL). We then performed genome-wide linkage analysis and assigned the deafness gene locus to ch:5q23.2-31.1, corresponding to the DFNB60 ARNSHL locus. Moreover, we performed whole exome sequencing on FT13 patient DNA and uncovered amino acid substitution p.Cys113Tyr in SLC22A4, a transporter of organic cations, cosegregating with HL in FT13 and therefore the cause of ARNSHL DFNB60. We also screened a cohort of small Tunisian HL families and uncovered an additional deaf proband of consanguineous parents that is homozygous for p.Cys113Tyr carried by the same microsatellite marker haplotype as in FT13, indicating that this mutation is ancestral. Using immunofluorescence, we found that Slc22a4 is expressed in stria vascularis (SV) endothelial cells of rodent cochlea and targets their apical plasma membrane. We also found Slc22a4 transcripts in our RNA-seq library from purified primary culture of mouse SV endothelial cells. Interestingly, p.Cys113Tyr mutation affects the trafficking of the transporter and severely alters ergothioneine uptake. We conclude that SLC22A4 is an organic cation transporter of the SV endothelium that is essential for hearing, and its mutation causes DFNB60 form of HL.

Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents.

Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.

[Histological changes in the circum-maxillary sutures during alternate maxillary expansions and constrictions in a rat model].

OBJECTIVE: To investigate changes in the circum-maxillary sutures during alternate maxillary expansions and constrictions in a rat model. METHODS: Twenty-two male Sprague-Dawley rats (6 weeks old) were used and divided into three groups. In maxillary expansion (ME) group (n=9), an expander was activated for 5 d, and then sacrificed. In alternate maxillary expansions and constrictions (Alt-MEC) group (9 animals), an alternate expansion and constriction protocol (5 d expansion and 5 d constriction for one cycle) was conducted for 2.5 cycles (25 d total), and then sacrificed. The control group comprised 4 animals with no appliances used, each of two sacrificed on day 5 and day 25, respectively. Circum-maxillary sutures (mid-palatal, maxillopalatine, premaxillary, zygomaticotemporal, and frontonasal suture) in each group were characterized histologically. RESULTS: Histological findings of circum-maxillary sutures: in control group, the normal sutures were divided into 5 zones, the center was polygon mesenchyme zone, the lateral was mature chondrocyte zone, the next lateral was bone tissue. In ME group, the mid-palatal suture was expanded after ME, the fibre and connective tissue were extracted and invaded into cartilage zone. Osteoblast hyperplasia and new bone formation occurred. The orientation of the new bone trabecula was consistent with force. The osteoclast appeared in some area. Findings of other sutures were similar with those of control group, osteogenesis was active in some area without obvious reconstruction in Alt-MEC group, mid-palatal suture and other sutures in some area were widened after Alt-MEC with much more osteoblast hyperplasia and new bone formation. Fibre and connective tissue were extracted, distorted or even broken. Sutures in some areas were narrowed with osteoblast cytopenia and osteoclast hyperplasia. Fibre and connective tissue compressed because of the different force and orientation. Osteoclast count results showed that compared with the control group, the number of the osteoclast was increased only in the palatal suture in ME group (P<0.05). Other sutures did not show obvious changes (P>0.05). In Alt-MEC group, the numbers of the osteoclast in circum-maxillary sutures were the most, and had statistical significances (P<0.05). CONCLUSION: These RESULTS suggested that circum -maxillary sutures were actively reconstructed after Alt-MEC. while only midpalatal suture had active reaction after ME.