The anaphase promoting complex impacts repair choice by protecting ubiquitin signalling at DNA damage sites

Double-strand breaks (DSBs) are repaired through two major pathways, homology-directed recombination (HDR) and non-homologous end joining (NHEJ). While HDR can only occur in S/G2, NHEJ can happen in all cell cycle phases (except mitosis). How then is the repair choice made in S/G2 cells? Here we provide evidence demonstrating that APCCdh1 plays a critical role in choosing the repair pathways in S/G2 cells. Our results suggest that the default for all DSBs is to recruit 53BP1 and RIF1. BRCA1 is blocked from being recruited to broken ends because its recruitment signal, K63-linked poly-ubiquitin chains on histones, is actively destroyed by the deubiquitinating enzyme USP1. We show that the removal of USP1 depends on APCCdh1 and requires Chk1 activation known to be catalysed by ssDNA-RPA-ATR signalling at the ends designated for HDR, linking the status of end processing to RIF1 or BRCA1 recruitment.We thank S.-Y. Lin (MD Anderson Cancer Center) for cell lines; J. Rosen (Baylor College of Medicine) for reagents; H. Masai (Tokyo Metropolitan Institute of Medical Science) for U2OS-Fucci cell line; D. Durocher (University of Toronto) for HeLa-Fucci cell line; E. Citterio (Netherlands Cancer Institute) for GFP-USP3 construct; M.S.Y. Huen (The University of Hong Kong) for RNF168 antibody. This work was performed with facilities and instruments in the Imaging Core of National Center for Protein Science (Beijing), the Cytometry and Cell Sorting Core at Baylor College of Medicine with funding from the NIH (P30 AI036211, P30 CA125123 and S10 RR024574), the Integrated Microscopy Core at Baylor College of Medicine with funding from the NIH (HD007495, DK56338 and CA125123), and the John S. Dunn Gulf Coast Consortium for Chemical Genomics. We also thank other members of the Zhang lab for helpful discussion and support. This work was supported in part by an international collaboration grant (# 2013DFB30210) and a 973 Project grant (# 2013CB910300) from Chinese Minister of Science and Technology, in part by a Chinese National Natural Science Foundation grant (# 81171920), in part by a grant from The Committee of Science and Technology of Beijing Municipality, China (# Z141100000214015), and in part by NIH grants CA116097 and CA122623 to P.Z. J.J. is supported by grants from National Institutes of Health (R01GM102529) and the Welch Foundation (AU-1711). S.H. is supported by grants (# 81272488 and 81472795) from Chinese National Natural Science Foundation. Y.Z. is supported by grants from the National Natural Scientific Foundation of China (No. 81430055), Programs for Changjiang Scholars and Innovative Research Team in University (No. IRT_15R13).S

Steric Clash in the SET Domain of Histone Methyltransferase NSD1 as a Cause of Sotos Syndrome and Its Genetic Heterogeneity in a Brazilian Cohort

Most histone methyltransferases (HMTase) harbor a predicted Su(var)3–9, Enhancer-of-zeste, Trithorax (SET) domain, which transfers a methyl group to a lysine residue in their substrates. Mutations of the SET domains were reported to cause intellectual disability syndromes such as Sotos, Weaver, or Kabuki syndromes. Sotos syndrome is an overgrowth syndrome with intellectual disability caused by haploinsufficiency of the nuclear receptor binding SET domain protein 1 (NSD1) gene, an HMTase at 5q35.2–35.3. Here, we analyzed NSD1 in 34 Brazilian Sotos patients and identified three novel and eight known mutations. Using protein modeling and bioinformatic approaches, we evaluated the effects of one novel (I2007F) and 21 previously reported missense mutations in the SET domain. For the I2007F mutation, we observed conformational change and loss of structural stability in Molecular Dynamics (MD) simulations which may lead to loss-of-function of the SET domain. For six mutations near the ligand-binding site we observed in simulations steric clashes with neighboring side chains near the substrate S-Adenosyl methionine (SAM) binding site, which may disrupt the enzymatic activity of NSD1. These results point to a structural mechanism underlying the pathology of the NSD1 missense mutations in the SET domain in Sotos syndrome. NSD1 mutations were identified in only 32% of the Brazilian Sotos patients in our study cohort suggesting other genes (including unknown disease genes) underlie the molecular etiology for the majority of these patients. Our studies also found NSD1 expression to be profound in human fetal brain and cerebellum, accounting for prenatal onset and hypoplasia of cerebellar vermis seen in Sotos syndrome

Lung cancer in never-smoker Asian females is driven by oncogenic mutations, most often involving EGFR

The aim of this study was to determine the distribution of known oncogenic driver mutations in female never-smoker Asian patients with lung adenocarcinoma. We analyzed 214 mutations across 26 lung cancer-associated genes and three fusion genes using the MassARRAY® LungCarta Panel and the ALK, ROS1, and RET fusion assays in 198 consecutively resected lung adenocarcinomas from never-smoker females at a single institution. EGFR mutation, which was the most frequent driver gene mutation, was detected in 124 (63%) cases. Mutation of ALK, KRAS, PIK3CA, ERBB2, BRAF, ROS1, and RET genesoccurred in 7%, 4%, 2.5%, 1.5%, 1%, 1%, and 1% of cases, respectively. Thus, 79% of lung adenocarcinomas from never-smoker females harbored well-known oncogenic mutations. Mucinous adenocarcinomas tended to have a lower frequency of known driver gene mutations than other histologic subtypes. EGFR mutation was associated with older age and a predominantly acinar pattern, while ALK rearrangement was associated with younger age and a predominantly solid pattern. Lung cancer in never-smoker Asian females is a distinct entity, with the majority of these cancers developing from oncogenic mutations

Steric Clash in the SET Domain of Histone Methyltransferase NSD1 as a Cause of Sotos Syndrome and Its Genetic Heterogeneity in a Brazilian Cohort

Most histone methyltransferases (HMTase) harbor a predicted Su(var)3–9, Enhancer-of-zeste, Trithorax (SET) domain, which transfers a methyl group to a lysine residue in their substrates. Mutations of the SET domains were reported to cause intellectual disability syndromes such as Sotos, Weaver, or Kabuki syndromes. Sotos syndrome is an overgrowth syndrome with intellectual disability caused by haploinsufficiency of the nuclear receptor binding SET domain protein 1 (NSD1) gene, an HMTase at 5q35.2–35.3. Here, we analyzed NSD1 in 34 Brazilian Sotos patients and identified three novel and eight known mutations. Using protein modeling and bioinformatic approaches, we evaluated the effects of one novel (I2007F) and 21 previously reported missense mutations in the SET domain. For the I2007F mutation, we observed conformational change and loss of structural stability in Molecular Dynamics (MD) simulations which may lead to loss-of-function of the SET domain. For six mutations near the ligand-binding site we observed in simulations steric clashes with neighboring side chains near the substrate S-Adenosyl methionine (SAM) binding site, which may disrupt the enzymatic activity of NSD1. These results point to a structural mechanism underlying the pathology of the NSD1 missense mutations in the SET domain in Sotos syndrome. NSD1 mutations were identified in only 32% of the Brazilian Sotos patients in our study cohort suggesting other genes (including unknown disease genes) underlie the molecular etiology for the majority of these patients. Our studies also found NSD1 expression to be profound in human fetal brain and cerebellum, accounting for prenatal onset and hypoplasia of cerebellar vermis seen in Sotos syndrome

Dream to Generalize: Zero-Shot Model-Based Reinforcement Learning for Unseen Visual Distractions

Model-based reinforcement learning (MBRL) has been used to efficiently solve vision-based control tasks in high-dimensional image observations. Although recent MBRL algorithms perform well in trained observations, they fail when faced with visual distractions in observations. These task-irrelevant distractions (e.g., clouds, shadows, and light) may be constantly present in real-world scenarios. In this study, we propose a novel self-supervised method, Dream to Generalize (Dr. G), for zero-shot MBRL. Dr. G trains its encoder and world model with dual contrastive learning which efficiently captures task-relevant features among multi-view data augmentations. We also introduce a recurrent state inverse dynamics model that helps the world model to better understand the temporal structure. The proposed methods can enhance the robustness of the world model against visual distractions. To evaluate the generalization performance, we first train Dr. G on simple backgrounds and then test it on complex natural video backgrounds in the DeepMind Control suite, and the randomizing environments in Robosuite. Dr. G yields a performance improvement of 117% and 14% over prior works, respectively. Our code is open-sourced and available at https://github.com/JeongsooHa/DrG.gi

Pneumothorax after CT-guided transthoracic lung biopsy: A comparison between immediate and delayed occurrence.

BackgroundIn CT-guided transthoracic lung biopsy (CTLB), pneumothorax can occur as a late complication (delayed pneumothorax). The incidence, risk factors, and clinical significance of delayed pneumothorax are not well known.ObjectivesTo compare the risk factors for immediate and delayed pneumothorax after CTLB and to know their clinical significance.MethodsImages and medical records of 536 consecutive patients who underwent CTLB were reviewed. All biopsies were performed as inpatient procedures. Follow-up chest radiographs were obtained at least twice at 4 h after procedure and before discharge. Risk factors for immediate and delayed pneumothorax were assessed based on patient-, lesion-, and procedure-related variables. Rates of chest tube insertion were also compared.ResultsPneumothorax developed in 161 patients (30.0%) including 135 (25.2%) immediate and 26 (4.9%) delayed cases. Lesion size was an independent risk factor for both immediate and delayed pneumothorax (OR = 0.813; CI = 0.717-0.922 and OR = 0.610; CI = 0.441-0.844, respectively). While emphysema, lower lobe location, and long intrapulmonary biopsy track were risk factors (OR = 1.981; CI = 1.172-3.344, OR = 3.505; CI = 2.718-5.650, and OR = 1.330; CI = 1.132-1.563, respectively) for immediate pneumothorax, upper lobe location and increased number of pleural punctures were independent risk factors (OR = 5.756; CI = 1.634-20.274 and OR = 3.738; CI = 1.860-7.511, respectively) for delayed pneumothorax. The rate of chest tube insertion was significantly (p ConclusionPneumothorax tends to occur immediately after CTLB in patients with emphysema, lower lobe lesion, and long intrapulmonary biopsy track. Further attention and warnings are needed for those with multiple punctures of small lesions involving upper lobes due to the possibility of delayed development of pneumothorax and higher requirement for chest tube drainage