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Apelt et al. identify patients with inherited ERCC1 mutations that impede DNA damage repair through protein instability and reduced recruitment to DNA repair machineries. Together, this results in a phenotype comprising short stature, photosensitivity, and severe liver and kidney impairment., ERCC1-XPF is a multifunctional endonuclease involved in nucleotide excision repair (NER), interstrand cross-link (ICL) repair, and DNA double-strand break (DSB) repair. Only two patients with bi-allelic ERCC1 mutations have been reported, both of whom had features of Cockayne syndrome and died in infancy. Here, we describe two siblings with bi-allelic ERCC1 mutations in their teenage years. Genomic sequencing identified a deletion and a missense variant (R156W) within ERCC1 that disrupts a salt bridge below the XPA-binding pocket. Patient-derived fibroblasts and knock-in epithelial cells carrying the R156W substitution show dramatically reduced protein levels of ERCC1 and XPF. Moreover, mutant ERCC1 weakly interacts with NER and ICL repair proteins, resulting in diminished recruitment to DNA damage. Consequently, patient cells show strongly reduced NER activity and increased chromosome breakage induced by DNA cross-linkers, while DSB repair was relatively normal. We report a new case of ERCC1 deficiency that severely affects NER and considerably impacts ICL repair, which together result in a unique phenotype combining short stature, photosensitivity, and progressive liver and kidney dysfunction., Graphical Abstract

Supplemental Digital Content is available in the text., Background: Approximately 25% of patients with pulmonary arterial hypertension (PAH) have been found to harbor rare mutations in disease-causing genes. To identify missing heritability in PAH, we integrated deep phenotyping with whole-genome sequencing data using Bayesian statistics. Methods: We analyzed 13 037 participants enrolled in the NBR study (NIHR BioResource—Rare Diseases), of which 1148 were recruited to the PAH domain. To test for genetic associations between genes and selected phenotypes of pulmonary hypertension, we used the Bayesian rare variant association method BeviMed. Results: Heterozygous, high impact, likely loss-of-function variants in the kinase insert domain receptor (KDR) gene were strongly associated with significantly reduced transfer coefficient for carbon monoxide (posterior probability=0.989) and older age at diagnosis (posterior probability=0.912). We also provide evidence for familial segregation of a rare nonsense KDR variant with these phenotypes. On computed tomographic imaging of the lungs, a range of parenchymal abnormalities were observed in the 5 patients harboring these predicted deleterious variants in KDR. Four additional PAH cases with rare likely loss-of-function variants in KDR were independently identified in the US PAH Biobank cohort with similar phenotypic characteristics. Conclusions: The Bayesian inference approach allowed us to independently validate KDR, which encodes for the VEGFR2 (vascular endothelial growth factor receptor 2), as a novel PAH candidate gene. Furthermore, this approach specifically associated high impact likely loss-of-function variants in the genetically constrained gene with distinct phenotypes. These findings provide evidence for KDR being a clinically actionable PAH gene and further support the central role of the vascular endothelium in the pathobiology of PAH.

Osteogenesis imperfecta (OI) is characterized primarily by susceptibility to fractures with or without bone deformation. OI is genetically heterogeneous: over 20 genetic causes are recognized. We identified bi-allelic pathogenic KDELR2 variants as a cause of OI in four families. KDELR2 encodes KDEL endoplasmic reticulum protein retention receptor 2, which recycles ER-resident proteins with a KDEL-like peptide from the cis-Golgi to the ER through COPI retrograde transport. Analysis of patient primary fibroblasts showed intracellular decrease of HSP47 and FKBP65 along with reduced procollagen type I in culture media. Electron microscopy identified an abnormal quality of secreted collagen fibrils with increased amount of HSP47 bound to monomeric and multimeric collagen molecules. Mapping the identified KDELR2 variants onto the crystal structure of G. gallus KDELR2 indicated that these lead to an inactive receptor resulting in impaired KDELR2-mediated Golgi-ER transport. Therefore, in KDELR2-deficient individuals, OI most likely occurs because of the inability of HSP47 to bind KDELR2 and dissociate from collagen type I. Instead, HSP47 remains bound to collagen molecules extracellularly, disrupting fiber formation. This highlights the importance of intracellular recycling of ER-resident molecular chaperones for collagen type I and bone metabolism and a crucial role of HSP47 in the KDELR2-associated pathogenic mechanism leading to OI., Dimitra Micha is funded by the Amsterdam Movement Sciences Innovation call grant. The work of Dimitra Micha, Gerard Pals and Lauria Claeys is funded by the kind donation of Hans Horsting and Mary Horsting-Stuit of the Horstingstuit foundation. The Netherlands Organisation for Scientific Research (NWO‐Middelgroot project number 91116017) is acknowledged for support of the mass spectrometry infrastructure. The work of Julia Etich, Mirko Rehberg, Oliver Semler and Frank Zaucke was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through RU2722 – 407168728 to OS and FZ and 407164210 to RW and by “Deutsche Gesellschaft für Osteogenesis imperfecta – Stiftung Baden-Württemberg” to OS. The Cologne Center for Genomics (CCG) is acknowledged for performing WES sequencing of P1. Christian Netzer would like to thank Florian Erger (Institute of Human Genetics, Cologne) for bioinformatics support with NGS data analysis. The work from Juan A Jimenez-Estrada, Julian Nevado, Karen E Heath, Pablo Lapunzina and Victor L Ruiz-Perez was supported by the Fundación AHUCE, CIBERER (ACCI 2017) and grants from the Spanish Ministry of Economy and Competitiveness (MINECO) to Victor L Ruiz-Perez (SAF2016‐ 75434‐R (AEI/FEDER, UE) and PID2019-105620RB-I00/AEI/10.13039/501100011033) and to Karen Heath (SAF2017-84646-R). They would also like to thank Dr. Pilar Gutierrez for clinical advice and Julia Piniella (Fundacion Ahuce) for coordination tasks during this project. We are grateful to the staff in the BioEM Lab, Biozentrum, University of Basel, and the Core Facility for Integrated Microscopy (CFIM), Panum Institute, University of Copenhagen, for providing highly innovative environments for electron microscopy. We thank Carola Alampi (BioEM lab), Mohamed Chami (BioEM lab) and Klaus Qvortrup (CFIM) for practical help with electron microscopy. We thank the technical expertise of Ferdy K Cayami at the Clinical Genetics department of the Amsterdam UMC whose work was funded by the High Reputation of International Publication Grant of Diponegoro University, Republic of Indonesia (No.329‐113/UN7.P4.3/PP/2019). Recruitment of affected individuals to this study was aided by the use of GeneMatcher.

Cockayne syndrome is caused by biallelic ERCC8 (CSA) or ERCC6 (CSB) mutations and is characterized by growth restriction, microcephaly, developmental delay, and premature pathological aging. Typically affected patients also have dermal photosensitivity. Although Cockayne syndrome is considered a DNA repair disorder, patients with UV-sensitive syndrome, with ERCC8 (CSA) or ERCC6 (CSB) mutations have indistinguishable DNA repair defects, but none of the extradermal features of Cockayne syndrome. We report novel missense mutations affecting a conserved loop in the ERCC6 (CSB) protein, associated with the Cockayne syndrome phenotype. Indeed, the amino acid sequence of this loop is more highly conserved than the adjacent helicase motifs V and VI, suggesting that this is a crucial structural component of the SWI/SNF family of proteins, to which ERCC6 (CSB) belongs. These comprise two RecA-like domains, separated by an interdomain linker, which interact through helicase motif VI. As the observed mutations are likely to act through destabilizing the tertiary protein structure, this prompted us to re-evaluate ERCC6 (CSB) mutation data in relation to the structure of SWI/SNF proteins. Our analysis suggests that antimorphic mutations cause Cockayne syndrome and that biallelic interdomain linker deletions produce more severe phenotypes. Based on our observations, we propose that further investigation of the pathogenic mechanisms underlying Cockayne syndrome should focus on the effect of antimorphic rather than null ERCC6 (CSB) mutations.

Item does not contain fulltext Histone lysine methylation, mediated by mixed-lineage leukemia (MLL) proteins, is now known to be critical in the regulation of gene expression, genomic stability, cell cycle and nuclear architecture. Despite MLL proteins being postulated as essential for normal development, little is known about the specific functions of the different MLL lysine methyltransferases. Here we report heterozygous variants in the gene KMT2B (also known as MLL4) in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance and characteristic brain magnetic resonance imaging findings. Over time, the majority of affected individuals developed prominent cervical, cranial and laryngeal dystonia. Marked clinical benefit, including the restoration of independent ambulation in some cases, was observed following deep brain stimulation (DBS). These findings highlight a clinically recognizable and potentially treatable form of genetic dystonia, demonstrating the crucial role of KMT2B in the physiological control of voluntary movement.

Background: Patients with malignant pleural effusions (MPEs) generally have advanced disease with poor survival and few therapeutic options. Cells within MPEs may be used to stratify patients for targeted therapy. Targeted therapy with poly(ADP ribose) polymerase inhibitors (PARPi) depends on identifying homologous recombination DNA repair (HRR)-defective cancer cells. We aimed to determine the feasibility of assaying HRR status in MPE cells. Methods: A total of 15 MPE samples were collected from consenting patients with non-small-cell lung cancer (NSCLC), mesothelioma and ovarian and breast cancer. Primary cultures were confirmed as epithelial by pancytokeratin, and HRR status was determined by the detection of γH2AX and RAD51 foci following a 24-h exposure to rucaparib, by immunofluorescence microscopy. Massively parallel next-generation sequencing of DNA repair genes was performed on cultured MPE cells. Results: From 15 MPE samples, 13 cultures were successfully established, with HRR function successfully determined in 12 cultures. Four samples – three NSCLC and one mesothelioma – were HRR defective and eight samples – one NSCLC, one mesothelioma, one sarcomatoid, one breast and four ovarian cancers – were HRR functional. No mutations in DNA repair genes were associated with HRR status, but there was probable loss of heterozygosity of FANCG, RPA1 and PARP1. Conclusions: HRR function can be successfully detected in MPE cells demonstrating the potential to stratify patients for targeted therapy with PARPi.

Uterine carcinosarcoma/malignant mixed Mullerian tumor (UC/MMMT) is an uncommon and aggressive gynecological malignancy with poor prognosis. Tumors arise from monoclonal carcinoma cells derived from embryonal mesoderm, which exhibit sarcomatous metaplasia. UC/MMMT usually occurs in postmenopausal women and accounts for 2%-5% of all uterine malignancies [1,2]. The five-year survival rates are particularly poor (21%-39%). Several case reports and case series describe UC/MMMT occurring after tamoxifen therapy for breast cancer [3,4,5,6,7,8,9]. Retrospective studies suggest that the increased incidence of these high-risk malignancies is greater than the observed increase in incidence of endometrial tumors generally following tamoxifen therapy [10,11,12,13], though the number of subjects with UC/MMMT in any of these studies is small. The increase in uterine cancers generally following tamoxifen therapy is thought to be driven by the estrogen receptor alpha (ERα) through a positive trophic effect on the uterine corpus. Although tamoxifen binds ERβ with equal affinity, there is no observed activation of this receptor [14,15]. Whether ER activation exerts any positive effect on UC/MMMTs remains equivocal. Other studies suggest that tamoxifen may upregulate expression of the HER2/neu oncogene in UC/MMMT cells [16,17], although any potential effect on the behavior of these malignancies is far from clear. As tamoxifen metabolites can covalently bind DNA, principally forming (E)- and (Z)-α-(deoxyguanosin-N2-yl)-4-hydroxytamoxifen adducts [18], the possibility that tamoxifen therapy is inherently carcinogenic has also been considered. However, tamoxifen-DNA adduct formation in uterine tissues following oral administration occurs at levels too low to be consistent with this being the mechanism driving such endometrial cancers [19]. We identified two unrelated women who developed UC/MMMT as a second primary malignancy following BRCA1-associated breast cancer. Neither of these women received hormone therapy, as their tumors were histologically determined to be unresponsive to hormone therapy (i.e., ER-/progesterone receptor [PR]-). Patient 1 had BRCA1 c.5503C>T (p.Arg1835*), developed breast cancer at 36 years, which was managed with lumpectomy and local radiotherapy, and subsequently developed UC/MMMT at 48 years. Patient 2 had BRCA1 c.2560_2561dupGC (p.Gln855fs), developed breast cancer at 34 years, again treated with lumpectomy and local radiotherapy, and was found to have UC/MMMT at 56 years. Although BRCA1 mutation carriers are at increased risk of developing endometrial cancers compared to the general population, most of this risk is attributable to tamoxifen use [20]. It has also been suggested that BRCA1 mutations may predispose carriers to uterine papillary serous carcinoma specifically [21,22]. However, UC/MMMT is not recognized as part of the BRCA1 phenotype. Prompted by this unexpected finding, we conducted a retrospective population-based study to establish whether an association exists between breast cancer and UC/MMMT generally and whether a breast tumor being ER-/PR- has any bearing on this.

Background Cell lines provide a powerful model to study cancer and here we describe a new spontaneously immortalised epithelial ovarian cancer cell line (NUOC-1) derived from the ascites collected at a time of primary debulking surgery for a mixed endometrioid / clear cell / High Grade Serous (HGS) histology. Results This spontaneously immortalised cell line was found to maintain morphology and epithelial markers throughout long-term culture. NUOC-1 cells grow as an adherent monolayer with a doubling time of 58 hours. The cells are TP53 wildtype, positive for PTEN, HER2 and HER3 expression but negative for oestrogen, progesterone and androgen receptor expression. NUOC-1 cells are competent in homologous recombination and non-homologous end joining, but base excision repair defective. Karyotype analysis demonstrated a complex tetraploid karyotype. SNP array analysis of parent and derived subpopulations (NUOC-1-A1 and NUOC-1-A2) cells demonstrated heterogeneous cell populations with numerous copy number alterations and a pro-amplification phenotype. The characteristics of this new cell line lends it to be an excellent model for investigation of a number of the identified targets. Materials and Methods The cell line has been characterised for growth, drug sensitivity, expression of common ovarian markers and mutations, clonogenic potential and ability to form xenografts in SCID mice. Copy number changes and clonal evolution were assessed by SNP arrays.

PURPOSE: Cockayne syndrome (CS) is a rare, autosomal-recessive disorder characterized by microcephaly, impaired postnatal growth, and premature pathological aging. It has historically been considered a DNA repair disorder; fibroblasts from classic patients often exhibit impaired transcription-coupled nucleotide excision repair. Previous studies have largely been restricted to case reports and small series, and no guidelines for care have been established.METHODS: One hundred two study participants were identified through a network of collaborating clinicians and the Amy and Friends CS support groups. Families with a diagnosis of CS could also self-recruit. Comprehensive clinical information for analysis was obtained directly from families and their clinicians.RESULTS AND CONCLUSION: We present the most complete evaluation of Cockayne syndrome to date, including detailed information on the prevalence and onset of clinical features, achievement of neurodevelopmental milestones, and patient management. We confirm that the most valuable prognostic factor in CS is the presence of early cataracts. Using this evidence, we have created simple guidelines for the care of individuals with CS. We aim to assist clinicians in the recognition, diagnosis, and management of this condition and to enable families to understand what problems they may encounter as CS progresses.Genet Med advance online publication 23 July 2015Genetics in Medicine (2015); doi:10.1038/gim.2015.110.

Nat. Genet. 49, 223–237 (2017); published online 19 December 2016; corrected after print 20 April 2017 Following publication of this article, the authors were asked to remove a clinical image and some video footage of one of the affected individuals. Although consent was obtained, in keeping with their ethical consent framework, the authors allow for withdrawal of consent and are carrying out the wishes of the research subjects under their consent process.