Summary DNA double strand breaks (DSBs) initiate extensive local and global alterations in chromatin structure, many of which depend on the ATM kinase. Histone H2A ubiquitylation (uH2A) on chromatin surrounding DSBs is one example, thought to be important for recruitment of repair proteins. uH2A is also implicated in transcriptional repression; an intriguing yet untested hypothesis is that this function is conserved in the context of DSBs. Using a novel reporter that allows for visualization of repair protein recruitment and local transcription in single cells, we describe an ATM-dependent transcriptional silencing program in cis to DSBs. ATM prevents RNA polymerase II elongation dependent chromatin decondensation at regions distal to DSBs. Silencing is partially dependent on E3 ubiquitin ligases RNF8 and RNF168, while reversal of silencing relies on the uH2A deubiquitylating enzyme USP16. These findings give insight into the role of post-translational modifications in mediating cross talk between diverse processes occurring on chromatin.

The pathogenic sequelae of BRCA1 mutation in human and mouse cells are mitigated by concomitant deletion of 53BP1, which binds histone H4 dimethylated at Lys20 (H4K20me2) to promote nonhomologous end-joining, suggesting a balance between BRCA1 and 53BP1 regulates DNA double-strand break (DSB) repair mechanism choice. Here, we document that acetylation is a key determinant of this balance. TIP60 acetyltransferase deficiency reduced BRCA1 at DSB chromatin with commensurate increases in 53BP1, while HDAC inhibition yielded the opposite effect. TIP60 -dependent H4 acetylation diminished 53BP1 binding to H4K20me2 in part through disruption of a salt bridge between H4K16 and Glu1551 in the 53BP1 Tudor domain. Moreover, TIP60 deficiency impaired HR and conferred sensitivity to PARP inhibition in a 53BP1-dependent manner. These findings demonstrate that acetylation in cis to H4K20me2 regulates relative BRCA1 and 53BP1 DSB chromatin occupancy to direct DNA repair mechanism.

Identifying infectious causes of subacute or chronic meningitis can be challenging. Enhanced, unbiased diagnostic approaches are needed. OBJECTIVE To present a case series of patients with diagnostically challenging subacute or chronic meningitis using metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) supported by a statistical framework generated from mNGS of control samples from the environment and from patients who were noninfectious. DESIGN, SETTING, AND PARTICIPANTS In this case series, mNGS data obtained from the CSF of 94 patients with noninfectious neuroinflammatory disorders and from 24 water and reagent control samples were used to develop and implement a weighted scoring metric based on z scores at the species and genus levels for both nucleotide and protein alignments to prioritize and rank the mNGS results. Total RNA was extracted for mNGS from the CSF of 7 participants with subacute or chronic meningitis who were recruited between September 2013 and March 2017 as part of a multicenter study of mNGS pathogen discovery among patients with suspected neuroinflammatory conditions. The neurologic infections identified by mNGS in these 7 participants represented a diverse array of pathogens. The patients were referred from the University of California, San Francisco Medical Center (n = 2), Zuckerberg San Francisco General Hospital and Trauma Center (n = 2), Cleveland Clinic (n = 1), University of Washington (n = 1), and Kaiser Permanente (n = 1). A weighted z score was used to filter out environmental contaminants and facilitate efficient data triage and analysis. MAIN OUTCOMES AND MEASURES Pathogens identified by mNGS and the ability of a statistical model to prioritize, rank, and simplify mNGS results. RESULTS The 7 participants ranged in age from 10 to 55 years, and 3 (43%) were female. A parasitic worm (Taenia solium, in 2 participants), a virus (HIV-1), and 4 fungi (Cryptococcus neoformans, Aspergillus oryzae, Histoplasma capsulatum, and Candida dubliniensis) were identified among the 7 participants by using mNGS. Evaluating mNGS data with a weighted z score-based scoring algorithm reduced the reported microbial taxa by a mean of 87% (range, 41%-99%) when taxa with a combined score of 0 or less were removed, effectively separating bona fide pathogen sequences from spurious environmental sequences so that, in each case, the causative pathogen was found within the top 2 scoring microbes identified using the algorithm. CONCLUSIONS AND RELEVANCE Diverse microbial pathogens were identified by mNGS in the CSF of patients with diagnostically challenging subacute or chronic meningitis, including a case of subarachnoid neurocysticercosis that defied diagnosis for 1 year, the first reported case of CNS vasculitis caused by Aspergillus oryzae, and the fourth reported case of C dubliniensis meningitis. Prioritizing metagenomic data with a scoring algorithm greatly clarified data interpretation and highlighted the problem of attributing biological significance to organisms present in contr...

Rap80 targets the breast cancer suppressor protein BRCA1 along with Abraxas and the BRCC36 deubiquitinating enzyme (DUB) to polyubiquitin structures at DNA double-strand breaks (DSBs). These DSB targeting events are essential for BRCA1-dependent DNA damage response-induced checkpoint and repair functions. Here, we identify MERIT40 (Mediator of Rap80 Interactions and Targeting 40 kD)/(C19orf62) as a Rap80-associated protein that is essential for BRCA1-Rap80 complex protein interactions, stability, and DSB targeting. Moreover, MERIT40 is required for Rap80-associated lysine 63 -ubiquitin DUB activity, a critical component of BRCA1-Rap80 G2 checkpoint and viability responses to ionizing radiation. Thus, MERIT40 represents a novel factor that links BRCA1-Rap80 complex integrity, DSB recognition, and ubiquitin chain hydrolytic activities to the DNA damage response. These findings provide new molecular insights into how BRCA1 associates with independently assembled core protein complexes to maintain genome integrity.[Keywords: C19orf62; HSPC142; MERIT40; BRCA1; Rap80; Abraxas; BRCC36] Supplemental material is available at http://www.genesdev.org.

The maintenance of genomic integrity is essential for normal cellular functions. However, it is difficult to maintain over a lifetime in postmitotic cells such as neurons, in which DNA damage increases with age and is exacerbated by multiple neurological disorders, including Alzheimer’s disease (AD). Here we used immunohistochemical staining to detect DNA double strand breaks (DSBs), the most severe form of DNA damage, in postmortem brain tissues from patients with mild cognitive impairment (MCI) or AD and from cognitively unimpaired controls. Immunostaining for γH2AX—a post-translational histone modification that is widely used as a marker of DSBs—revealed increased proportions of γH2AX-labeled neurons and astrocytes in the hippocampus and frontal cortex of MCI and AD patients, as compared to age-matched controls. In contrast to the focal pattern associated with DSBs, some neurons and glia in humans and mice showed diffuse pan-nuclear patterns of γH2AX immunoreactivity. In mouse brains and primary neuronal cultures, such pan-nuclear γH2AX labeling could be elicited by increasing neuronal activity. To assess whether pan-nuclear γH2AX represents DSBs, we used a recently developed technology, DNA damage in situ ligation followed by proximity ligation assay, to detect close associations between γH2AX sites and free DSB ends. This assay revealed no evidence of DSBs in neurons or astrocytes with prominent pan-nuclear γH2AX labeling. These findings suggest that focal, but not pan-nuclear, increases in γH2AX immunoreactivity are associated with DSBs in brain tissue and that these distinct patterns of γH2AX formation may have different causes and consequences. We conclude that AD is associated with an accumulation of DSBs in vulnerable neuronal and glial cell populations from early stages onward. Because of the severe adverse effects this type of DNA damage can have on gene expression, chromatin stability and cellular functions, DSBs could be an important causal driver of neurodegeneration and cognitive decline in this disease. Electronic supplementary material The online version of this article (10.1186/s40478-019-0723-5) contains supplementary material, which is available to authorized users.

Objective Identification of a particular cause of meningoencephalitis can be challenging due to the myriad bacteria, viruses, fungi, and parasites that can produce overlapping clinical phenotypes, frequently delaying diagnosis and therapy. Metagenomic deep sequencing (MDS) approaches to infectious disease diagnostics are known for their ability to identify unusual or novel viruses and thus are well suited for investigating possible etiologies of meningoencephalitis. Methods We present the case of a 74 year-old woman with endophthalmitis followed by meningoencephalitis. MDS of her cerebrospinal fluid (CSF) was performed to identify an infectious agent. Results Sequences aligning to Balamuthia mandrillaris ribosomal RNA genes were identified in the CSF via MDS. Polymerase chain reaction (PCR) subsequently confirmed the presence of B. mandrillaris in CSF, brain tissue, and vitreous fluid from the patient’s infected eye. B. mandrillaris serology and immunohistochemistry for free-living amoebas on the brain biopsy tissue were positive. Interpretation The diagnosis was made using MDS after the patient had been hospitalized for several weeks and subjected to costly and invasive testing. MDS a powerful diagnostic tool with the potential for rapid and unbiased pathogen identification leading to early therapeutic targeting.

Background: BCL11A is a key transcription factor that suppresses the production of fetal hemoglobin (HbF) in red blood cells (RBCs), leading to the production of adult Hb (HbA). In diseases with hemoglobin production defects such as b-thalassemia, or in sickle cell disease (SCD), HbF upregulation could ameliorate anemia and reduce transfusion requirements, such as in β-thalassemia, or reduce clinical complications, including vaso-occlusive crises (VOCs), in SCD. To induce potentially curative levels of HbF in erythrocytes, we used the ex vivo CRISPR-Cas9-based gene-editing platform to edit the erythroid enhancer region of BCL11A in hematopoietic stem and progenitor cells (HSPCs), producing CTX001. Aims: CLIMB THAL-111 (NCT03655678) and CLIMB SCD-121 (NCT03745287) are multi-center, first-in-human studies of CTX001 for transfusion-dependent b-thalassemia (TDT) and SCD, respectively. Here, we present available safety and efficacy results from all patients with at least 3 months of follow-up from both studies as of July 2020. Methods: Patients (aged 18 to 35 years) with TDT receiving packed red blood cell (pRBC) transfusions of ≥100 mL/kg/year or ≥10 units/year in the previous 2 years, and those with severe SCD, defined as ≥2 VOCs/year requiring medical care in the previous 2 years, were eligible. Peripheral CD34+ HSPCs were collected by apheresis after mobilization with G-CSF (filgrastim) and plerixafor (for TDT) or plerixafor alone (SCD). The erythroid enhancer region of BCL11A was edited in CD34+ cells using a specific CRISPR guide RNA and Cas9 nuclease. Prior to CTX001 infusion on Day +1, patients received myeloablation with 4 days of busulfan. Patients were monitored for stem cell engraftment and hematopoietic recovery, adverse events, total Hb and HbF production, hemolysis, F-cells, pRBC transfusion requirements (TDT), and VOCs (SCD) during follow-up. Results: Data are presented for patients with TDT (N=5; RBC transfusion history range: 23.5 to 61 units/year; CTX001 post-infusion follow-up through Months 15, 6, 4, 4, and 3, respectively) and with SCD (N=2; 7 VOCs/year and 7.5 VOCs/year, respectively, annualized over 2 years prior to consent; CTX001 post-infusion follow-up through Months 12 and 3, respectively). In the patients with TDT, median neutrophil engraftment occurred on Day +32 (range: +27 to +36); median platelet engraftment occurred on Day +37 (range: +34 to +52). In the patients with SCD, neutrophil engraftment occurred on Day +30 and Day +22 and platelet engraftment occurred on Day +30 and Day +33, respectively. All patients demonstrated increases in total Hb and HbF over time (Figure). Patients with TDT ceased receiving pRBC transfusions soon after CTX001 infusion, with the last pRBC transfusion occurring between 0.9 and 1.9 months after CTX001 infusion. The first patient with TDT who received CTX001 has remained transfusion-free for over 15 months. Patients with SCD have had no VOCs since CTX001 infusion. The first SCD patient who received CTX001 has remained free of VOCs for over 1 year. In all 7 patients, the safety profile after CTX001 infusion was generally consistent with busulfan myeloablation. Four serious adverse events (SAEs) related or possibly related to CTX001 were reported in 1 patient with TDT: headache, haemophagocytic lymphohistiocytosis (HLH), acute respiratory distress syndrome, and idiopathic pneumonia syndrome. All 4 of these SAEs occurred in the context of HLH and were either resolved or clinically improving at the time of this analysis. No other CTX001-related SAEs were reported in the other patients with TDT or in any patients with SCD. Conclusions: These data demonstrate that CTX001, a first-in-human, CRISPR-Cas9-modified autologous HSPC product, has resulted in increases in HbF and total Hb in the first 7 patients infused. All patients infused with CTX001 demonstrated hematopoietic engraftment with a post-infusion safety profile generally consistent with myeloablation. All 5 patients with TDT have been transfusion-free since ~2 months after CTX001 infusion and the 2 patients with severe SCD have had no VOCs during follow-up after CTX001 infusion. These early data demonstrate that CTX001 is a potential functional cure for the treatment of TDT and SCD. Data will be updated for the presentation. Data from these ongoing studies were submitted on behalf of the CLIMB THAL-111 and CLIMB SCD-121 Investigators. Figure Disclosures Frangoul: Vertex Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Bobruff:CRISPR Therapeutics: Current Employment, Current equity holder in publicly-traded company. Cappellini:BMS: Honoraria; CRISPR Therapeutics, Novartis, Vifor Pharma: Membership on an entity's Board of Directors or advisory committees; Genzyme/Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees. Fernandez:CRISPR Therapeutics: Current Employment, Current equity holder in publicly-traded company. Grupp:Juno/BMS: Other; Cellectis: Other; TCR2: Other: SAB; Servier: Research Funding; Janssen/JnJ: Consultancy; CBMG: Consultancy; Humanigen: Consultancy; GlaxoSmithKline: Consultancy; Roche: Consultancy; CRISPR Therapeutics/Vertex Pharmaceuticals: Other; Allogene: Other; Kite/Gilead: Research Funding; Novartis: Consultancy, Other: SSC, Research Funding; Adaptimmune: Other: SAB; Jazz: Other: SSC. Handgretinger:Amgen: Honoraria. Ho:CRISPR Therapeutics: Current Employment, Current equity holder in publicly-traded company. Imren:Vertex Pharmaceuticals Incorporated: Current Employment, Current equity holder in publicly-traded company. Kattamis:Agios: Consultancy; Vertex: Membership on an entity's Board of Directors or advisory committees; Ionis: Membership on an entity's Board of Directors or advisory committees; Genesis Pharma SA: Membership on an entity's Board of Directors or advisory committees; Vifor: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Celgene/BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Apopharma/Chiesi: Honoraria, Speakers Bureau. Lekstrom-Himes:Vertex Pharmaceuticals Incorporated: Current Employment, Current equity holder in publicly-traded company. Locatelli:Medac: Speakers Bureau; Miltenyi: Speakers Bureau; Bellicum Pharmaceutical: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Amgen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz Pharmaceeutical: Speakers Bureau. Lu:Vertex Pharmaceuticals Incorporated: Current Employment, Current equity holder in publicly-traded company. de Montalembert:Bluebird bio: Honoraria, Membership on an entity's Board of Directors or advisory committees; Vertex: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Addmedica: Honoraria, Membership on an entity's Board of Directors or advisory committees. Mulcahey:Vertex Pharmaceuticals Incorporated: Current Employment, Current equity holder in publicly-traded company. Shanbhag:Vertex Pharmaceuticals Incorporated: Current Employment, Current equity holder in publicly-traded company. Sheth:Agios: Consultancy, Research Funding; Celgene/BMS: Consultancy, Research Funding; La Jolla: Research Funding; Acceleron: Consultancy; Bluebird Bio: Consultancy; Novartis: Consultancy, Research Funding; DisperSol Technologies: Research Funding; Terumo: Research Funding; Vertex Pharmaceuticals/CRISPR Therapeutics: Membership on an entity's Board of Directors or advisory committees. Soni:CRISPR Therapeutics: Current Employment, Current equity holder in private company. Steinberg:Vertex Pharmaceuticals/CRISPR Therapeutics: Membership on an entity's Board of Directors or advisory committees; Fulcrum Therapeutics: Membership on an entity's Board of Directors or advisory committees; DSMB: Membership on an entity's Board of Directors or advisory committees; Imara: Membership on an entity's Board of Directors or advisory committees. Weinstein:CRISPR Therapeutics: Current Employment, Current equity holder in publicly-traded company. Wu:Bayer: Research Funding; Novo Nordisk: Membership on an entity's Board of Directors or advisory committees; Octapharma: Membership on an entity's Board of Directors or advisory committees; CSL Behring: Membership on an entity's Board of Directors or advisory committees; Bioverativ: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Roche: Membership on an entity's Board of Directors or advisory committees.

ObjectiveTo describe the features of 2 unrelated adults with xeroderma pigmentosum complementation group F (XP-F) ascertained in a neurology care setting.MethodsWe report the clinical, imaging, molecular, and nucleotide excision repair (NER) capacity of 2 middle-aged women with progressive neurodegeneration ultimately diagnosed with XP-F.ResultsBoth patients presented with adult-onset progressive neurologic deterioration involving chorea, ataxia, hearing loss, cognitive deficits, profound brain atrophy, and a history of skin photosensitivity, skin freckling, and/or skin neoplasms. We identified compound heterozygous pathogenic mutations in ERCC4 and confirmed deficient NER capacity in skin fibroblasts from both patients.ConclusionsThese cases illustrate the role of NER dysfunction in neurodegeneration and how adult-onset neurodegeneration could be the major symptom bringing XP-F patients to clinical attention. XP-F should be considered by neurologists in the differential diagnosis of patients with adult-onset progressive neurodegeneration accompanied by global brain atrophy and a history of heightened sun sensitivity, excessive freckling, and skin malignancies.