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Vázquez Rosas T, Cazap E, Delgado L, Ismael J, Bejarano S, Castro C, Castro H, Müller B, Gutiérrez-Delgado F, Santini LA, Vallejos Sologuren C. Social Distancing and Economic Crisis During COVID-19 Pandemic Reduced Cancer Control in Latin America and Will Result in Increased Late-Stage Diagnoses and Expense. JCO Glob Oncol 2021; 7:694-703. [PMID: 33999696 PMCID: PMC8162975 DOI: 10.1200/go.21.00016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Since December 2019, the world has been mired in an infectious pandemic that has displaced other health priorities for 21st century populations. Concerned about this situation, Latin American experts on cancer decided to evaluate the impact of the pandemic on cancer control in the region. The analysis was based on information obtained from public sources and scientific publications and included the characteristics of the health care and cancer control prior to the pandemic, the COVID-19 pandemic and measures implemented by the governments of the region, and the regional impact of the pandemic on cancer control together with the costs of cancer care and possible impact of the pandemic on cancer expense. We compared 2019 and 2020 data corresponding to the period March 16-June 30 and found a significant reduction in the number of first-time visits to oncology services (variable depending on the country between –28% and –38%) and a corresponding reduction in pathology (between –6% and –50%), cancer surgery (between –28% and –70%), and chemotherapy (between –2% and –54%). Furthermore, a significant reduction in cancer screening tests was found (PAP smear test studies: between –46% and –100%, mammography: between –32% and –100%, and fecal occult blood test: –73%). If this situation becomes a trend, the health and economic impact will be compounded in the postpandemic period, with an overload of demand on health services to ensure diagnostic tests and consequent treatments. On the basis of this information, a set of prevention and mitigation measures to be immediately implemented and also actions to progressively strengthen health systems are proposed.
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Singh A, Müller B, Schnürer A. Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP. Sci Rep 2021; 11:13298. [PMID: 34168213 PMCID: PMC8225771 DOI: 10.1038/s41598-021-92658-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.
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Haas GC, Müller B, Osiander C, Schmidtke J, Trahms A, Volkert M, Zins S. Development of a new COVID-19 panel survey: the IAB high-frequency online personal panel (HOPP). JOURNAL FOR LABOUR MARKET RESEARCH 2021; 55:16. [PMID: 34179683 PMCID: PMC8220878 DOI: 10.1186/s12651-021-00295-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/05/2021] [Indexed: 05/23/2023]
Abstract
Since January 2020, the COVID-19 crisis has affected everyday life around the world, and rigorous government lockdown restrictions have been implemented to prevent the further spread of the pandemic. The consequences of the corona crisis and the associated lockdown policies for public health, social life, and the economy are vast. In view of the rapidly changing situation during this crisis, policymakers require timely data and research results that allow for informed decisions. Addressing the requirement for adequate databases to assess people's life and work situations during the pandemic, the Institute for Employment Research (IAB) developed the High-frequency Online Personal Panel (HOPP). The HOPP study started in May 2020 and is based on a random sample of individuals drawn from the administrative data of the Federal Employment Agency in Germany, containing information on all labour market participants except civil servants and self-employed. The main goal of the HOPP study is to assess the short-term as well as long-term changes in people's social life and working situation in Germany due to the corona pandemic. To assess individual dynamics the HOPP collected data on a monthly (wave one to four) and bi-monthly (wave five to seven) basis. Furthermore, respondents were divided into four groups. The different groups of a new wave were invited to the survey at weekly intervals (wave two to four) or bi-weekly intervals (wave five to seven). This gives us the advantage of being able to provide weekly data while each participant only had to participate on a monthly or bi-monthly basis. In this article, we delineate the HOPP study in terms of its main goals and features, topics, and survey design. Furthermore, we provide a summary of results derived from HOPP and the future prospects of the study.
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Müller B, García C, Sola JA, Fernandez W, Werner P, Cerda M, Slater J, Benavides C, Arancibia J, Ascui R, Reyes F, Stevens MA, Miranda JP, Buchholtz M, Corvalan AH. Perioperative chemotherapy in locally advanced gastric cancer in Chile: from evidence to daily practice. Ecancermedicalscience 2021; 15:1244. [PMID: 34267800 PMCID: PMC8241457 DOI: 10.3332/ecancer.2021.1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Indexed: 11/04/2022] Open
Abstract
Gastric cancer (GC) is a leading cause of cancer death in Chile. Although recommended in international guidelines since 2006, perioperative chemotherapy was not available to patients in the public health system in Chile until 2016. We conducted an observational study to assess the feasibility of this strategy in public hospitals in Chile (Observational Study of Perioperative Chemotherapy in Locally Advanced Gastric Cancer – PRECISO). Patients with locally advanced, operable GC were offered to receive preoperative chemotherapy with Epirubicin + Cisplatin + Capecitabine (ECX) for three cycles followed by curative surgery. Staging included abdominal CT scan and laparoscopy if peritoneal carcinomatosis was suspected. Postoperative ECX for three cycles was recommended. Between August 2010 and March 2013, 110 patients were screened and 61 enrolled. Median age was 62 years (23–76 years) and most patients had good performance status at baseline (Eastern Cooperative Oncology Group performance status score (ECOG) 0: 42, ECOG 1: 19). Tumour site was proximal in 32 (52%) and medial and distal in 29 (48%) patients. All but four patients (n = 57, 93%) completed three cycles of preoperative chemotherapy. Fifty-six patients were operated and 54 (89%) had a curative resection. Thirty-three patients (54%) had pT0-2, and 18 (30%) had pN0 tumours, with two patients achieving a complete response. As of 20 December 2020, 39 patients died, 32 due to GC, one within 30 days of surgery, two due to intestinal obstruction at 5 and 3 months after surgery and four due to other causes. Five-year survival rate was 38%. We conclude that perioperative chemotherapy is feasible in public hospitals in Chile and should be offered to patients with locally advanced GC.
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Brägelmann J, Barahona Ponce C, Marcelain K, Roessler S, Goeppert B, Gallegos I, Colombo A, Sanhueza V, Morales E, Rivera MT, de Toro G, Ortega A, Müller B, Gabler F, Scherer D, Waldenberger M, Reischl E, Boekstegers F, Garate-Calderon V, Umu SU, Rounge TB, Popanda O, Lorenzo Bermejo J. Epigenome-Wide Analysis of Methylation Changes in the Sequence of Gallstone Disease, Dysplasia, and Gallbladder Cancer. Hepatology 2021; 73:2293-2310. [PMID: 33020926 DOI: 10.1002/hep.31585] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Gallbladder cancer (GBC) is a highly aggressive malignancy of the biliary tract. Most cases of GBC are diagnosed in low-income and middle-income countries, and research into this disease has long been limited. In this study we therefore investigate the epigenetic changes along the model of GBC carcinogenesis represented by the sequence gallstone disease → dysplasia → GBC in Chile, the country with the highest incidence of GBC worldwide. APPROACH AND RESULTS To perform epigenome-wide methylation profiling, genomic DNA extracted from sections of formalin-fixed, paraffin-embedded gallbladder tissue was analyzed using Illumina Infinium MethylationEPIC BeadChips. Preprocessed, quality-controlled data from 82 samples (gallstones n = 32, low-grade dysplasia n = 13, high-grade dysplasia n = 9, GBC n = 28) were available to identify differentially methylated markers, regions, and pathways as well as changes in copy number variations (CNVs). The number and magnitude of epigenetic changes increased with disease development and predominantly involved the hypermethylation of cytosine-guanine dinucleotide islands and gene promoter regions. The methylation of genes implicated in Wnt signaling, Hedgehog signaling, and tumor suppression increased with tumor grade. CNVs also increased with GBC development and affected cyclin-dependent kinase inhibitor 2A, MDM2 proto-oncogene, tumor protein P53, and cyclin D1 genes. Gains in the targetable Erb-B2 receptor tyrosine kinase 2 gene were detected in 14% of GBC samples. CONCLUSIONS Our results indicate that GBC carcinogenesis comprises three main methylation stages: early (gallstone disease and low-grade dysplasia), intermediate (high-grade dysplasia), and late (GBC). The identified gradual changes in methylation and CNVs may help to enhance our understanding of the mechanisms underlying this aggressive disease and eventually lead to improved treatment and early diagnosis of GBC.
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Müller B, von Hagen A, Vannini N, Büttner G. Measurement of the Effects of School Psychological Services: A Scoping Review. Front Psychol 2021; 12:606228. [PMID: 33935862 PMCID: PMC8085380 DOI: 10.3389/fpsyg.2021.606228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
School psychologists are asked to systematically evaluate the effects of their work to ensure quality standards. Given the different types of methods applied to different users of school psychology measuring the effects of school psychological services is a complex task. Thus, the focus of our scoping review was to systematically investigate the state of past research on the measurement of the effects of school psychological services published between 1998 and 2018 in eight major school psychological journals. Of the 5,048 peer-reviewed articles published within this period, 623 were coded by two independent raters as explicitly refering to school psychology or counseling in the school context in their titles or abstracts. However, only 22 included definitions of effects of school psychological services or described outcomes used to evaluate school psychological services based on full text screening. These findings revealed that measurement of the effects of school psychological services has not been a focus of research despite its' relevance in guidelines of school psychological practice.
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Barahona Ponce C, Scherer D, Brinster R, Boekstegers F, Marcelain K, Gárate-Calderón V, Müller B, de Toro G, Retamales J, Barajas O, Ahumada M, Morales E, Rojas A, Sanhueza V, Loader D, Rivera MT, Gutiérrez L, Bernal G, Ortega A, Montalvo D, Portiño S, Bertrán ME, Gabler F, Spencer L, Olloquequi J, Fischer C, Jenab M, Aleksandrova K, Katzke V, Weiderpass E, Bonet C, Moradi T, Fischer K, Bossers W, Brenner H, Hveem K, Eklund N, Völker U, Waldenberger M, Fuentes Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, Ruiz-Linares A, Rothhammer F, Lorenzo Bermejo J. Gallstones, Body Mass Index, C-Reactive Protein, and Gallbladder Cancer: Mendelian Randomization Analysis of Chilean and European Genotype Data. Hepatology 2021; 73:1783-1796. [PMID: 32893372 DOI: 10.1002/hep.31537] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 07/10/2020] [Accepted: 07/31/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND AIMS Gallbladder cancer (GBC) is a neglected disease with substantial geographical variability: Chile shows the highest incidence worldwide, while GBC is relatively rare in Europe. Here, we investigate the causal effects of risk factors considered in current GBC prevention programs as well as C-reactive protein (CRP) level as a marker of chronic inflammation. APPROACH AND RESULTS We applied two-sample Mendelian randomization (MR) using publicly available data and our own data from a retrospective Chilean and a prospective European study. Causality was assessed by inverse variance weighted (IVW), MR-Egger regression, and weighted median estimates complemented with sensitivity analyses on potential heterogeneity and pleiotropy, two-step MR, and mediation analysis. We found evidence for a causal effect of gallstone disease on GBC risk in Chileans (P = 9 × 10-5 ) and Europeans (P = 9 × 10-5 ). A genetically elevated body mass index (BMI) increased GBC risk in Chileans (P = 0.03), while higher CRP concentrations increased GBC risk in Europeans (P = 4.1 × 10-6 ). European results suggest causal effects of BMI on gallstone disease (P = 0.008); public Chilean data were not, however, available to enable assessment of the mediation effects among causal GBC risk factors. CONCLUSIONS Two risk factors considered in the current Chilean program for GBC prevention are causally linked to GBC risk: gallstones and BMI. For Europeans, BMI showed a causal effect on gallstone risk, which was itself causally linked to GBC risk.
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Van Damme R, Hölzer M, Viehweger A, Müller B, Bongcam-Rudloff E, Brandt C. Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PLoS Comput Biol 2021; 17:e1008716. [PMID: 33561126 PMCID: PMC7899367 DOI: 10.1371/journal.pcbi.1008716] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 02/22/2021] [Accepted: 01/17/2021] [Indexed: 01/12/2023] Open
Abstract
Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analyses complex. We, therefore, developed MUFFIN, a complete metagenomic workflow that uses short and long reads to produce high-quality bins and their annotations. The workflow is written by using Nextflow, a workflow orchestration software, to achieve high reproducibility and fast and straightforward use. This workflow also produces the taxonomic classification and KEGG pathways of the bins and can be further used for quantification and annotation by providing RNA-Seq data (optionally). We tested the workflow using twenty biogas reactor samples and assessed the capacity of MUFFIN to process and output relevant files needed to analyze the microbial community and their function. MUFFIN produces functional pathway predictions and, if provided de novo metatranscript annotations across the metagenomic sample and for each bin. MUFFIN is available on github under GNUv3 licence: https://github.com/RVanDamme/MUFFIN.
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Müller M, Kaegi-Braun N, Schuetz P, Müller B, Kutz A. Association of nutritional support with in-hospital mortality in malnourished medical patients. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Hersberger L, Bürgler H, Dietz A, Schuetz P, Müller B, Bargetzi L, Bargetzi A. Individualized nutritional support in congestive heart failure inpatients at nutritional risk secondary analysis of a randomized clinical trial. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bargetzi L, Schütz P, Müller B, Bargetzi M, Brack C, Herrmann J, Bargetzi A, Hersberger L. Association of different cancer types and benefit from nutritional support in patients at nutritional risk: secondary analysis of a prospective randomized trial. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Guerini-Rocco E, Gray KP, Fumagalli C, Reforgiato MR, Leone I, Rafaniello Raviele P, Munzone E, Kammler R, Neven P, Hitre E, Jerusalem G, Simoncini E, Gombos A, Deleu I, Karlsson P, Aebi S, Chirgwin J, Di Lauro V, Thompson A, Graas MP, Barber M, Fontaine C, Loibl S, Gavilá J, Kuroi K, Müller B, O'Reilly S, Di Leo A, Goldhirsch A, Viale G, Barberis M, Regan MM, Colleoni M. Genomic Aberrations and Late Recurrence in Postmenopausal Women with Hormone Receptor-positive Early Breast Cancer: Results from the SOLE Trial. Clin Cancer Res 2020; 27:504-512. [PMID: 33082214 DOI: 10.1158/1078-0432.ccr-20-0126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 06/10/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Women with hormone receptor-positive early breast cancers have a persistent risk of relapse and biomarkers for late recurrence are needed. We sought to identify tumor genomic aberrations associated with increased late-recurrence risk. EXPERIMENTAL DESIGN In a secondary analysis of Study of Letrozole Extension trial, a case-cohort-like sampling selected 598 primary breast cancers for targeted next-generation sequencing analysis of gene mutations and copy-number gains (CNGs). Correlations of genomic aberrations with clinicopathologic factors and breast and distant recurrence-free intervals (BCFIs and DRFIs) were analyzed using weighted Cox models. RESULTS Analysis of mutations and CNGs was successfully performed for 403 and 350 samples, including 148 and 134 patients with breast cancer recurrences (median follow-up time, 5.2 years), respectively. The most frequent alterations were PIK3CA mutations (42%) and CNGs of CCND1 (15%), ERBB2 (10%), FGFR1 (8%), and MYC (8%). PIK3CA mutations and MYC CNGs were associated with lower (P = 0.03) and higher (P = 0.004) tumor grade, respectively; a higher Ki-67 was seen in tumor with CCND1, ERBB2, and MYC CNGs (P = 0.01, P < 0.001, and P = 0.03, respectively). FGFR1 CNG was associated with an increased risk of late events in univariate analyses [17/29 patients; BCFI: HR, 3.2; 95% confidence interval (CI), 1.48-6.92; P = 0.003 and DRFI: HR, 3.5; 95% CI, 1.61-7.75; P = 0.002) and in multivariable models adjusted for clinicopathologic factors. CONCLUSIONS Postmenopausal women with hormone receptor-positive early breast cancer harboring FGFR1 CNG had an increased risk of late recurrence despite extended therapy. FGFR1 CNG may represent a useful prognostic biomarker for late recurrence and a therapeutic target.
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Gronbach M, Mitrach F, Lidzba V, Müller B, Möller S, Rother S, Salbach-Hirsch J, Hofbauer LC, Schnabelrauch M, Hintze V, Hacker MC, Schulz-Siegmund M. Scavenging of Dickkopf-1 by macromer-based biomaterials covalently decorated with sulfated hyaluronan displays pro-osteogenic effects. Acta Biomater 2020; 114:76-89. [PMID: 32673749 DOI: 10.1016/j.actbio.2020.07.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 12/27/2022]
Abstract
Dickkopf-1 (DKK1), a Wnt inhibitor secreted by bone marrow stromal cells (MSC), is known to play an important role in long-term non-union bone fracture defects and glucocorticoid induced osteoporosis. Mitigating its effects in early bone defects could improve osteogenesis and bone defect healing. Here, we applied a biomaterial strategy to deplete a defect environment from DKK1 by scavenging the protein via a macromer-based biomaterial covalently decorated with sulfated hyaluronan (sHA3). The material consisted of cross-copolymerized three-armed macromers with a small anchor molecule. Using the glycidyl anchor, polyetheramine (ED900) could be grafted to the material to which sHA3 was efficiently coupled in a separate step. For thorough investigation of material modification, flat material surfaces were generated by fabricating them on glass discs. The binding capability of sHA3 for DKK1 was demonstrated in this study by surface plasmon resonance measurements. Furthermore, the surfaces demonstrated the ability to scavenge and inactivate pathologic amounts of DKK1 from complex media. In a combinatory approach with Wnt3a, we were able to demonstrate that DKK1 is the preferred binding partner of our sHA3-functionalized surfaces. We validated our findings in a complex in vitro setting of differentiating SaOS-2 cells and primary hMSC. Here, endogenous DKK-1 was scavenged resulting in increased osteogenic differentiation indicating that this is a consistent biological effect irrespective of the model system used. Our study provides insights in the mechanisms and efficiency of sHA3 surface functionalization for DKK1 scavenging, which may be used in a clinical context in the future.
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Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B. High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure. Front Microbiol 2020; 11:2066. [PMID: 32983047 PMCID: PMC7481360 DOI: 10.3389/fmicb.2020.02066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline “AcetoScan” presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.
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Cunningham JL, Bramstång L, Singh A, Jayarathna S, Rasmusson AJ, Moazzami A, Müller B. Impact of time and temperature on gut microbiota and SCFA composition in stool samples. PLoS One 2020; 15:e0236944. [PMID: 32745090 PMCID: PMC7398539 DOI: 10.1371/journal.pone.0236944] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/16/2020] [Indexed: 01/08/2023] Open
Abstract
Gut dysbiosis has been implicated in the pathophysiology of a growing number of non-communicable diseases. High through-put sequencing technologies and short chain fatty acid (SCFA) profiling enables surveying of the composition and function of the gut microbiota and provide key insights into host-microbiome interactions. However, a methodological problem with analyzing stool samples is that samples are treated and stored differently prior to submission for analysis potentially influencing the composition of the microbiota and its metabolites. In the present study, we simulated the sample acquisition of a large-scale study, in which stool samples were stored for up to two days in the fridge or at room temperature before being handed over to the hospital. To assess the influence of time and temperature on the microbial community and on SCFA composition in a controlled experimental setting, the stool samples of 10 individuals were exposed to room and fridge temperatures for 24 and 48 hours, respectively, and analyzed using 16S rRNA gene amplicon sequencing, qPCR and nuclear magnetic resonance spectroscopy. To best of our knowledge, this is the first study to investigate the influence of storage time and temperature on the absolute abundance of methanogens, and of Lactobacillus reuteri. The results indicate that values obtained for methanogens, L. reuteri and total bacteria are still representative even after storage for up to 48 hours at RT (20°C) or 4°C. The overall microbial composition and structure appeared to be influenced more by laboratory errors introduced during sample processing than by the actual effects of temperature and time. Although microbial activity was demonstrated by elevated SCFA at both 4°C and RT, SCFAs ratios were more stable over the different conditions and may be considered as long as samples are come from similar storage conditions.
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Vedham V, Henderson MK, Podhajcer O, Llera A, Breitenbach MD, Abdelhay E, Müller B, Ordenes JF, Navarro AD, Del Toro-Arreola A, Velazquez CA, Delgado L, Artagaveytia N, Gross TG. The US–Latin America Cancer Research Network. JCO Glob Oncol 2020. [DOI: 10.1200/go.20.52000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The National Cancer Institute (NCI) Center for Global Health promotes global oncology research to reduce cancer burden worldwide. In 2009, NCI launched the Latin American Cancer Research Network (LACRN) to support a clinical cancer research network in Latin America. LACRN was started by a coalition of research institutions through bilateral collaborative agreements between the US Department of Health and Human Services and the governments of Argentina, Brazil, Chile, Mexico, and Uruguay. The LACRN is supported through a research contract to a study coordination center and subcontracts to 6 low- and middle-income country sites. The participating countries have a shared goal that meets the specific research needs of the regions. The overarching purpose of this endeavor is to implement high-quality standards for conducting clinical research studies and developing collaborative cancer research projects. METHODS NCI supported a clinical breast cancer project for LACRN, “Molecular profiling of breast cancer (MPBC) in Latin American women with stage II and III breast cancer receiving standard neo-adjuvant chemotherapy.” The molecular profiling of breast cancer study was conducted in 40 hospitals and research institutions across 5 countries with a study population of approximately 1,400 patients. RESULTS AND CONCLUSION Establishing a comprehensive network in Latin America and their research institutions yielded an incredible research resource that can be used in future studies, driven by the network. Throughout the process of developing and implementing studies, LACRN helped identify key elements of the functionality of research networks, such as the pivotal role of institutional and government commitment for sustainability; the importance of building multidisciplinary teams, transparent communications, and training; the ability to combine translational, epidemiology, and clinical research to close research gaps; and the application of new technologies to standard cancer clinical care.
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Müller B, Ruby L, Jordan S, Rominger MB, Mazza E, Distler O. Validation of the suction device Nimble for the assessment of skin fibrosis in systemic sclerosis. Arthritis Res Ther 2020; 22:128. [PMID: 32493508 PMCID: PMC7268280 DOI: 10.1186/s13075-020-02214-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/12/2020] [Indexed: 01/04/2023] Open
Abstract
Objectives Skin fibrosis is a main hallmark of systemic sclerosis (SSc). Clinical assessment is done semi-quantitatively using the modified Rodnan skin score (mRSS). Objective measurements for quantifying skin fibrosis could complement the mRSS to achieve higher reproducibility. The aim of this study was to explore the potential of suction measurements to detect structural changes in the skin that are associated with skin fibrosis. Methods This clinical trial included 30 SSc patients and 30 healthy volunteers (HC). We validated a novel suction device—the Nimble—to quantify skin stiffness in comparison to the Cutometer using the OMERACT filter. Results A significant difference (p < 0.05) between the skin stiffness of HC and SSc patient groups was found for each location measured. The correlation between the measurements of forearm skin stiffness and the mRSS values was high for the Nimble (r = 0.82) and moderate for the Cutometer (r = 0.58). A ROC analysis showed good ability for the Nimble to distinguish between SSc patients with and without skin involvement (AUC = 0.82). Both suction devices provided excellent reliability in all measurements on HC and SSc patients and proved face validity and feasibility. Conclusion Suction devices assessing skin stiffness, such as the Nimble, show clear potential to objectively quantify skin fibrosis in SSc patients and might be promising outcome measures complementing established methods such as the mRSS. Trial registration Clinicaltrials.gov, NCT03644225, Registered 23 August 2018—Retrospectively registered, http://www.clinicaltrials.gov
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Wietecha MS, Pensalfini M, Cangkrama M, Müller B, Jin J, Brinckmann J, Mazza E, Werner S. Activin-mediated alterations of the fibroblast transcriptome and matrisome control the biomechanical properties of skin wounds. Nat Commun 2020; 11:2604. [PMID: 32451392 PMCID: PMC7248062 DOI: 10.1038/s41467-020-16409-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Matrix deposition is essential for wound repair, but when excessive, leads to hypertrophic scars and fibrosis. The factors that control matrix deposition in skin wounds have only partially been identified and the consequences of matrix alterations for the mechanical properties of wounds are largely unknown. Here, we report how a single diffusible factor, activin A, affects the healing process across scales. Bioinformatics analysis of wound fibroblast transcriptome data combined with biochemical and histopathological analyses of wounds and functional in vitro studies identify that activin promotes pro-fibrotic gene expression signatures and processes, including glycoprotein and proteoglycan biosynthesis, collagen deposition, and altered collagen cross-linking. As a consequence, activin strongly reduces the wound and scar deformability, as identified by a non-invasive in vivo method for biomechanical analysis. These results provide mechanistic insight into the roles of activin in wound repair and fibrosis and identify the functional consequences of alterations in the wound matrisome at the biomechanical level. The relationship between histopathology, gene expression, and biochemical and mechanical properties of wounds is largely unknown. Here, the authors show that activin A alters wound healing at multiple levels by promoting pro-fibrotic gene expression and matrix deposition, thereby affecting biomechanical properties of skin wounds.
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Boekstegers F, Marcelain K, Barahona Ponce C, Baez Benavides PF, Müller B, de Toro G, Retamales J, Barajas O, Ahumada M, Morales E, Rojas A, Sanhueza V, Loader D, Rivera MT, Gutiérrez L, Bernal G, Ortega A, Montalvo D, Portiño S, Bertrán ME, Gabler F, Spencer L, Olloquequi J, González Silos R, Fischer C, Scherer D, Jenab M, Aleksandrova K, Katzke V, Weiderpass E, Moradi T, Fischer K, Bossers W, Brenner H, Hveem K, Eklund N, Völker U, Waldenberger M, Fuentes Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Canizales S, Gallo C, Ruiz Linares A, Rothhammer F, Lorenzo Bermejo J. ABCB1/4 gallbladder cancer risk variants identified in India also show strong effects in Chileans. Cancer Epidemiol 2020; 65:101643. [PMID: 32058310 DOI: 10.1016/j.canep.2019.101643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The first large-scale genome-wide association study of gallbladder cancer (GBC) recently identified and validated three susceptibility variants in the ABCB1 and ABCB4 genes for individuals of Indian descent. We investigated whether these variants were also associated with GBC risk in Chileans, who show the highest incidence of GBC worldwide, and in Europeans with a low GBC incidence. METHODS This population-based study analysed genotype data from retrospective Chilean case-control (255 cases, 2042 controls) and prospective European cohort (108 cases, 181 controls) samples consistently with the original publication. RESULTS Our results confirmed the reported associations for Chileans with similar risk effects. Particularly strong associations (per-allele odds ratios close to 2) were observed for Chileans with high Native American (=Mapuche) ancestry. No associations were noticed for Europeans, but the statistical power was low. CONCLUSION Taking full advantage of genetic and ethnic differences in GBC risk may improve the efficiency of current prevention programs.
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Jerusalem G, Farah S, Chirgwin J, Aebi S, Karlsson P, Neven P, Hitre E, Graas MP, Simoncini E, Kamby C, Thompson A, Loibl S, Gavilá J, Kuroi K, Marth C, Müller B, O'Reilly S, Gombos A, Ruhstaller T, Burstein H, Rabaglio M, Ruepp B, Viale G, Gelber RD, Coates AS, Leo AD, Goldhirsch A, Regan M, Colleoni M. Abstract P5-12-01: SOLE (study of letrozole extension), a phase 3 randomized clinical trial of continuous vs intermittent letrozole in postmenopausal women who have received 4-6 years of adjuvant endocrine therapy for lymph node-positive, early breast cancer (BC): Final analysis and sole estrogen substudy (SOLE-EST). Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p5-12-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: In animal models of hormone receptor positive (HR+) breast cancer, acquired resistance to continued letrozole was shown to be reversed by estrogen-induced apoptosis. We hypothesized that the rise in estrogen levels during short treatment interruptions would resensitize breast cancer cells to letrozole and improve treatment outcome. SOLE tested the hypothesis that 3 mos treatment-free intervals during extended adjuvant therapy will improve disease-free survival (DFS). We previously reported the primary endpoint after 60 mos median follow-up: extended intermittent letrozole did not improve DFS vs extended continuous letrozole. However, only 9% of pts had breast cancer events, justifying updating the analysis with longer follow-up. The dynamic of recovery of estrogen levels after stopping letrozole therapy has not been previously reported.
Methods: SOLE enrolled 4884 postmenopausal women with HR+ lymph node-positive BC who had completed 4-6 yrs of adjuvant endocrine therapy (19% SERM, 43% AI, 38% both; stratification factor). Pts were randomized to an additional 5 yrs continuous letrozole (2.5 mg daily; n=2441) vs 5 yrs intermittent letrozole (taken for the first 9 mos of yrs 1-4, and 12 mos in yr 5; n=2443). We report the final analysis of the SOLE trial after 84 mos median follow-up. In SOLE-EST, levels of estradiol (E2), estrone (E1) and estrone sulphate (E1S) at 0, 9, 10.5 and 12 mos after randomization were determined using a highly sensitive assay in a subgroup of 90 evaluable patients (21 in the continuous and 69 in the intermittent group).
Results: There were 923 DFS events. 7 yr DFS was 81.5% in both groups. More pts had distant metastases in the continuous group (8.7% vs 7.5%) while second (non-breast) malignancies were more frequent in the intermittent group (5.5% vs 4.7%). Similar outcomes were observed for breast cancer-free interval (BCFI) (88.6% vs 88.0%), distant recurrence-free interval (DRFI) (91.6% vs 90.4%), and overall survival (OS) (90.6% vs 89.6%) for pts assigned intermittent vs continuous letrozole. In the intermittent group, median E2, E1 and E1S levels more than doubled compared with levels at 9 mos after randomization in the first 6 weeks after stopping letrozole during the treatment free interval while levels were stable for the 21 pts tested in the continuous group.
Conclusions: Among postmenopausal women with HR+ BC, extended intermittent letrozole did not improve DFS vs continuous letrozole. Similar outcome was consistently observed for BCFI, DRFI and OS. The SOLE-EST substudy indicates an important increase in estrogen levels as soon as 6 weeks after stopping letrozole therapy in the intermittent group. Further investigation of prior exposure to aromatase inhibitors in relation with outcome and with E2, E1 and E1S levels in SOLE-EST are underway.
Citation Format: Guy Jerusalem, Subrina Farah, Jacquie Chirgwin, Stefan Aebi, Per Karlsson, Patrick Neven, Erika Hitre, Marie-Pascale Graas, Edda Simoncini, Claus Kamby, Alastair Thompson, Sibylle Loibl, Joaquín Gavilá, Katsumasa Kuroi, Christian Marth, Bettina Müller, Seamus O'Reilly, Andrea Gombos, Thomas Ruhstaller, Harold Burstein, Manuela Rabaglio, Barbara Ruepp, Giuseppe Viale, Richard D Gelber, Alan S Coates, Angelo Di Leo, Aron Goldhirsch, Meredith Regan, Marco Colleoni. SOLE (study of letrozole extension), a phase 3 randomized clinical trial of continuous vs intermittent letrozole in postmenopausal women who have received 4-6 years of adjuvant endocrine therapy for lymph node-positive, early breast cancer (BC): Final analysis and sole estrogen substudy (SOLE-EST) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-12-01.
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Martínez-Pérez MJ, Müller B, Lin J, Rodriguez LA, Snoeck E, Kleiner R, Sesé J, Koelle D. Magnetic vortex nucleation and annihilation in bi-stable ultra-small ferromagnetic particles. NANOSCALE 2020; 12:2587-2595. [PMID: 31939948 DOI: 10.1039/c9nr08557b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Vortex-mediated magnetization reversal in individual ultra-small (∼100 nm) ferromagnetic particles at low temperatures is studied by nanoSQUID magnetometry. At zero applied bias field, the flux-closure magnetic state (vortex) and the quasi uniform configuration are bi-stable. This stems from the extremely small size of the nanoparticles that lies very close to the limit of single-domain formation. The analysis of the temperature-dependent (from 0.3 to 70 K) hysteresis of the magnetization allows us to infer the nature of the ground state magnetization configuration. The latter corresponds to a vortex state as also confirmed by electron holography experiments. Based on the simultaneous analysis of the vortex nucleation and annihilation data, we estimate the magnitude of the energy barriers separating the quasi single-domain and the vortex state and their field dependence. For this purpose, we use a modified power-law scaling of the energy barriers as a function of the applied bias field. These studies are essential to test the thermal and temporal stability of flux-closure states stabilized in ultra-small ferromagnets.
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Brandes K, Leuzinger K, Rogge G, Müller B, Teifke J. Conjunctival Papillomas and Corneal Squamous Cell Carcinomas After Long-term Ciclosporin Treatment in Four Brachycephalic Dogs with Chronic Keratitis. J Comp Pathol 2020. [DOI: 10.1016/j.jcpa.2019.10.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Paula FS, Chin JP, Schnürer A, Müller B, Manesiotis P, Waters N, Macintosh KA, Quinn JP, Connolly J, Abram F, McGrath JW, O'Flaherty V. The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei. Sci Rep 2019; 9:17101. [PMID: 31745137 PMCID: PMC6864096 DOI: 10.1038/s41598-019-53168-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a > 5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical phosphate starvation control.
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McCarthy K, Hischenhuber C, Joyce N, Cherix G, Hischenhuber C, Joyce N, Kuhr S, McDonald J, McKnight S, McNamee P, Mevissen L, Müller B, Revitt S. Determination of Total Taurine in Pet Foods by Liquid Chromatography of the Dansyl Derivative: Collaborative Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/83.4.784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
A liquid chromatographic (LC) method for the determination of total taurine in pet foods was evaluated in a collaborative study. Ten laboratories assayed 6 blind duplicate pairs of wet and dry pet foods. The taurine in the 6 sample pairs ranged from low (170 mg/kg) to high (2250 mg/kg) concentrations as is. Collaborators also assayed a sample of known taurine concentration for familiarization purposes. Samples were hydrolyzed to release bound taurine, which was subsequently converted to the dansyl derivative and quantitated by gradient-elution LC with fluorescence detection. Repeatability relative standard deviations, RSDr, ranged from 3.2 to 10.0%; reproducibility relative standard deviations, RSDR, ranged from 6.1 to 16.1%. The method has been adopted Official First Action status by AOAC INTERNATIONAL.
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Elrod J, Müller B, Mohr C, Meuli M, Mazza E, Schiestl C. An effective procedure for skin stiffness measurement to improve Paediatric Burn Care. Burns 2019; 45:1102-1111. [DOI: 10.1016/j.burns.2019.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/16/2019] [Accepted: 02/07/2019] [Indexed: 12/31/2022]
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