Structural basis of TFIIH activation for nucleotide excision repair.

Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a 'plug' element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway

Ion therapy within the trimodal management of superior sulcus tumors: the INKA trial

Background: The standard trimodal treatment concept in locally advanced and non-metastasized non-small-cell superior sulcus tumors consists of a preoperative chemoradiation followed by surgical resection. High linear energy transfer (LET) radiation as, for example, C12 heavy-ion beam therapy theoretically offers biological advantages compared to high energy x-ray therapy as, for example, higher biological efficiency. Methods/Design: In the present prospective, single-armed, open pilot study performed at the Heidelberg Ion-Beam Therapy Center (HIT) in Heidelberg, the radiation treatment within the standard trimodal concept will be exchanged against C12 heavy-ion beam treatment and apply 39GyE in 13 single fractions in combination with a chemotherapy consisting of cisplatin and vinorelbine (local standard). The primary endpoint is feasibility and safety measured by the incidence of NCI-CTCAE grade 3/4 toxicity and/or discontinuation due to any reason. Secondary endpoint is the degree of regression in the histological specimen. The main inclusion criteria are histologically confirmed non-small-cell superior sulcus tumor, nodal disease stage ≤ N2, Karnofsky performance score ≥70%, patient age between 18 and 75 years as well as written informed consent. The main exclusion criteria include medical contraindications against elements of the trimodal treatment concept, PET confirmed nodal disease stage N3, stage IV disease, prior thoracic irradiation and decompensated diseases of the lung, cardio-vascular system, metabolism, hematopoietic and coagulation system and renal function. Furthermore, patients with implanted active medical devices without certification for ion-beam therapy are not allowed to take part in the study. Trial registration number: DRKS00006323 (www.drks.de)

A randomized phase II study of radiation induced immune boost in operable non-small cell lung cancer (RadImmune trial)

Background: Lung cancer is the leading cause of cancer deaths worldwide. Surgery, radiotherapy at conventional and high dose and chemotherapy are the mainstay for lung cancer treatment. Insufficient migration and activation of tumour specific effector T cells seem to be important reasons for inadequate host anti-tumour immune response. Ionizing radiation can induce a variety of immune responses. The goal of this randomized trial is to assess if a preoperative single fraction low dose radiation is able to improve anti-tumour immune response in operable early stage lung cancer. Methods/Design: This trial has been designed as an investigator-initiated, prospective, randomized, 2-armed phase II trial. Patients who are candidates for elective resection of early stage non-small cell lung cancer will be randomized into 2 arms. A total of 36 patients will be enrolled. The patients receive either 2 Gy or no radiation prescribed to their primary tumour. Radiation will be delivered by external beam radiotherapy using 3D radiotherapy or intensity-modulated radiation technique (IMRT) 7 days prior to surgical resection. The primary objective is to compare CD8+ T cell counts detected by immunohistochemistry in resected tumours following preoperative radiotherapy versus no radiotherapy. Secondary objectives include the association between CD8+ T cell counts and progression free survival, the correlation of CD8+ T cell counts quantified by immunohistochemistry and flow cytometry, local tumour control and recurrence patterns, survival, radiogenic treatment toxicity and postoperative morbidity and mortality. Further, frequencies of tumour reactive T cells in blood and bone marrow as well as whole blood cell transcriptomics and plasma-proteomics will be correlated with clinical outcome. Discussion: This unique intervention combining preoperative low dose radiation and surgical removal of early stage non-small cell lung cancer is designed to address the problem of inadequate host anti-tumour immune response. If successful, this study may affect the role of radiotherapy in lung cancer treatment. Trial registration: NCT02319408; Registration: December 29, 2014

Differential diagnostic value of CD5 and CD117 expression in thoracic tumors: A large scale study of 1465 non-small cell lung cancer cases

Background: Thoracic pathologists are frequently faced with tissue specimens from intrathoracic/mediastinal tumors. Specifically the differentiation between thymic and pulmonary squamous cell carcinomas (SqCC) can be challenging. In order to clarify the differential diagnostic value of CD5 and CD117 in this setting, we performed a large scale expression study of both markers in 1465 non-small cell lung cancer (NSCLC) cases. Methods: Tissue microarrays of formalin-fixed paraffin-embedded resection specimens of 1465 NSCLC were stained with antibodies against CD117 and CD5. Positivity of both markers was correlated with clinicopathological variables. Results: CD117 was positive in 145 out of 1457 evaluable cases (9.9 %) and CD5 was positive in 133 out of 1427 evaluable cases (9.3 %). 28 cases (1.9 %) showed coexpression of CD117 and CD5. Among the 145 cases that were positive for CD117, 97 (66.8 %) were adenocarcinomas (ADC), 34 (23.4 %) were SqCC, 5 (3.4 %) were adenosquamous carcinomas (ADSqCC), 8 (5.5 %) were large cell carcinomas (LC), and one (0.6 %) was a pleomorphic carcinoma (PC). In the CD5 positive group consisting of 133 cases, 123 (92.4 %) were ADC, 0 (0 %) were SqCC, 4 (3.0 %) were ADSqCC, 3 (2.2 %) LC and 3 (2.2 %) were PC. None of the 586 SqCC showed expression of CD5. No association of CD117- or CD5 positivity to patients’ age, pathological stages or to T-, N-, or M- categories was observed. Conclusions: A substantial subset of NSCLC exhibit positivity of CD117 and CD5. Since CD5 expression was not observed in pulmonary SqCC, but is expressed in the majority of thymic squamous cell carcinomas, the application of this immunomarker is a valuable tool in the differential diagnosis of thoracic neoplasms

Simultaneous computed tomography-guided biopsy and radiofrequency ablation of solitary pulmonary malignancy in high-risk patients

Background: In recent years experience has been accumulated in percutaneous radiofrequency ablation (RFA) of lung malignancies in nonsurgical patients. Objectives: In this study, we retrospectively evaluated a simultaneous diagnostic and therapeutic approach including CT-guided biopsy followed immediately by RFA of solitary malignant pulmonary lesions. Methods: CT-guided transthoracic core needle biopsy of solitary pulmonary lesions suspicious for malignancy was performed and histology was proven based on immediate frozen sections. RFA probes were placed into the pulmonary tumors under CT guidance and the ablation was performed subsequently. The procedure-related morbidity was analyzed. Follow-up included a CT scan and pulmonary function parameters. Results: A total of 33 CT-guided biopsies and subsequent RFA within a single procedure were performed. Morbidity of CT-guided biopsy included pulmonary hemorrhage (24%) and a mild pneumothorax (12%) without need for further interventions. The RFA procedure was not aggravated by the previous biopsy. The rate of pneumothorax requiring chest tube following RFA was 21%. Local tumor control was achieved in 77% with a median follow-up of 12 months. The morbidity of the CT-guided biopsy had no statistical impact on the local recurrence rate. Conclusions: The simultaneous diagnostic and therapeutic approach including CT-guided biopsy followed immediately by RFA of solitary malignant pulmonary lesions is a safe procedure. The potential of this combined approach is to avoid unnecessary therapies and to perform adequate therapies based on histology. Taking the local control rate into account, this approach should only be performed in those patients who are unable to undergo or who refuse surgery. Copyright (C) 2012 S. Karger AG, Base

a global network of chronic kidney disease cohorts

Background Chronic kidney disease (CKD) is a global health burden, yet it is still underrepresented within public health agendas in many countries. Studies focusing on the natural history of CKD are challenging to design and conduct, because of the long time-course of disease progression, a wide variation in etiologies, and a large amount of clinical variability among individuals with CKD. With the difference in health-related behaviors, healthcare delivery, genetics, and environmental exposures, this variability is greater across countries than within one locale and may not be captured effectively in a single study. Methods Studies were invited to join the network. Prerequisites for membership included: 1) observational designs with a priori hypotheses and defined study objectives, patient-level information, prospective data acquisition and collection of bio-samples, all focused on predialysis CKD patients; 2) target sample sizes of 1,000 patients for adult cohorts and 300 for pediatric cohorts; and 3) minimum follow-up of three years. Participating studies were surveyed regarding design, data, and biosample resources. Results Twelve prospective cohort studies and two registries covering 21 countries were included. Participants age ranges from >2 to >70 years at inclusion, CKD severity ranges from stage 2 to stage 5. Patient data and biosamples (not available in the registry studies) are measured yearly or biennially. Many studies included multiple ethnicities; cohort size ranges from 400 to more than 13,000 participants. Studies’ areas of emphasis all include but are not limited to renal outcomes, such as progression to ESRD and death. Conclusions iNET-CKD (International Network of CKD cohort studies) was established, to promote collaborative research, foster exchange of expertise, and create opportunities for research training. Participating studies have many commonalities that will facilitate comparative research; however, we also observed substantial differences. The diversity we observed across studies within this network will be able to be leveraged to identify genetic, behavioral, and health services factors associated with the course of CKD. With an emerging infrastructure to facilitate interactions among the investigators of iNET-CKD and a broadly defined research agenda, we are confident that there will be great opportunity for productive collaborative investigations involving cohorts of individuals with CKD

Investigating the release of coprecipitated uranium from iron oxides

The removal of uranium (VI) from zerovalent iron permeable reactive barriers and wetlands can be explained by its association with iron oxides. The long term stability of immobilized U is yet to be addressed. The present study investigates the remobilization of U(VI) from iron oxides via diverse reaction pathways (acidification, reduction, complex formation). Prior, uranium coprecipitation experiments were conducted under various conditions. The addition of various amounts of a pH-shifting agents (pyrite), an iron complexing agent (EDTA) or iron (III) reduction agent (TiCl3) yielded in uranium remobilization, concentrations above the US EPA allowedmaximum contaminant level(MCL=30 æg/l). This study demonstrates that U(VI) release in nature strongly depends on the conditions and the mechanism of its fixation by geological materials.researc

Structure of an inactive RNA polymerase II dimer

Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two other RNA polymerases dimerize. Here we present the cryo-electron microscopy (cryo-EM) structure of a mammalian Pol II dimer at 3.5 Å resolution. The structure differs from the Pol I dimer and reveals that one Pol II copy uses its RPB4-RPB7 stalk to penetrate the active centre cleft of the other copy, and vice versa, giving rise to a molecular handshake. The polymerase clamp domain is displaced and mobile, and the RPB7 oligonucleotide-binding fold mimics the DNA–RNA hybrid that occupies the cleft during active transcription. The Pol II dimer is incompatible with nucleic acid binding as required for transcription and may represent an inactive storage form of the polymerase

Die Bedeutung der subzellulären Lokalisierung von Cyclin A in Drosophila melanogaster

Cyclin A ist in Drosophila das einzige essentielle mitotische Cyclin. Die Cyclin A Mutation führt zu einem Arrest in der G2-Phase von Zellzyklus 16 und resultiert in embryonaler Letalität. Neben dieser mitotischen Funktion kann Cyclin A auch den G1-S Übergang induzieren. Cyclin A zeigt eine dynamische, zellzyklusabhängige Lokalisierung. In der Interphase ist es zytoplasmatisch und akkumuliert in der Prophase im Kern. Das Ziel dieser Arbeit war es, die Bedeutung der subzelluläre Lokalisierung zu untersuchen. Die vorliegende Arbeit zeigt, dass der LMB-sensitive Crm1-abhängige Kernexport zur zytoplasmatischen Lokalisierung von Cyclin A während der Interphase beiträgt. Die Lokalisierung von Cyclin A ist somit ein aktiver und regulierter Prozess. Deletionsstudien zeigten, dass diese Lokalisierung von der C-terminalen Hälfte in Cyclin A vermittelt wird. Es konnte weiterhin gezeigt werden, dass die Kernakkumulierung von Cyclin A während der Prophase graduell verläuft und mit der voranschreitenden DNA-Kondensierung korreliert. Prophasespezifische Vorgänge im Kern könnten somit von der Menge an Cyclin A-assoziierter Kinaseaktivität abhängen. In funktionellen in vivo Analysen wurde jedoch gefunden, dass die Lokalisierung von Cyclin A weder für den Eintritt in die Mitose noch für die Induktion von ektopischen S-Phasen eine essentielle oder regulatorische Bedeutung hat. Dies konnte mit Cyclin A-Konstrukten, die durch heterologe Lokalisierungssignale verändert waren, gezeigt werden. Die Expression von zytoplasmatischem, membranverankertem oder nukleärem Cyclin A konnte die Cyclin A Mutation überwinden, Mitosen induzieren und Adulte enstehen lassen oder ektopische S-Phasen induzieren. Die essentielle Funktion von Cyclin A während des Zellzyklus hängt also nicht mit der Lokalisierung zusammen, sondern ist wahrscheinlich durch die Substratspezifität charakterisiert, die auch nicht durch Überexpression von Cyclin B übergangen werden kann. Als Substrate kommen sogenannte Vermittler-Kinasen in Frage, die nach Aktivierung von Cyclin A S-Phase- oder mitosespezifische Vorgänge im Kern katalysieren. Aufgrund der Abhängigkeit von Cyclin A, scheint die Aktivität der Vermittler-Kinasen im Verlauf der Mitose in Drosophila anscheinend nur durch Cyclin A aufrechterhalten werden zu können. In diesem Zusammenhang ist es möglich, dass die Kernakkumulierung von Cyclin A während der Prophase einen effizienteren und schnelleren Ablauf der Kernprozesse garantiert und dadurch einen Einfluß auf den zeitlichen Ablauf der Mitose hat