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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 5. |
- Holmström, Margareta, et al.
(author)
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SWEDISH NATIONAL REGISTRY FOR BLEEDING DISORDERS – A SECOND REPORT
- 2019
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In: EAHAD 2019.
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Conference paper (peer-reviewed)abstract
- Introduction: Hemophilia Care in Sweden is centralized to three different and certified European Hemophilia Care Centers (EHCCs) (Stockholm, Gothenburg and Malmö[f1]). A recent web- based National registry has been set up for patients with bleeding disorders in Sweden. The registry is mainly funded by Swedish authorities. Methods: A multi- professional steering committee is running the registry with representatives from all three centers including physicians, nurses, physiotherapist and also a patient representative. A web- based platform, Real- Q, is used for the registry. Results: By the 31st Dec 2017, a total number of 1030 patients with bleeding disorders were included in the registry, mainly patients with hemophilia A, B and Von Willebrand disease. Data regarding bleedings, treatment modality and type of product, inhibitor status, viral infections are collected. Likewise patient reported outcome measurements (PROM)- such as pain and quality of life[.The number of patients with hemophilia A, B and Von Willebrand disease in 2016 resp 2017 were as follows:Hemophilia A; n = 243 in 2016 and n= 691 in 2017.Hemophilia B: n = 49 in 2016 and n = 191 in 2017.Von Willebrand disease: n = 11 in 2016 and n = 152 in 2017.[LMW1] are registered.[LMW2] are registered on a regular basis? Discussion/Conclusion: The number of patients in the Swedish National Registry for bleeding disorders has increased significantly during the last year; from a total of 308 Dec 31st 2016 to 1030 in Dec 31st 2017. Increasing amount of data will enable further evaluation of treatment data and also joint status, quality of life and bleeding reports.
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| 6. |
- Holmström, Margareta, et al.
(author)
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Swedish national registry for bleeding disorders - first report
- 2018
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In: 11th Annual Congress of the European Association for Haemophilia and Allied Disorders 2018, 7–9 February 2018, Madrid, Spain. Haemophilia, 24 (S1). - : Wiley. - 1365-2516.
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Conference paper (other academic/artistic)abstract
- Introduction : Hemophilia care in Sweden is centralized to 3 centers localized in Gothenburg, Malmö and Stockholm. All centers are certi-fied as European Hemophilia Comprehensive Care Centers (EHCCs). Recently a web- based Swedish national registry has been established with funding from Swedish authorities. Methods : One of the conclusions from the earlier reports from the Swedish agency for health technology assessment and assessment of social services (SBU) and the Dental and Pharmaceutical benefits agency (TLV) was that a national registry for hemophilia and other bleeding disorders was needed to be able to follow the long- term effects of the disease and treatment strategies. An application was submitted in 2012 to apply for funding from Swedenʹs municipali-ties and count councils (SKL). The registry was validated as an official national registry. A multi- professional steering committee is running the registry with representatives from all 3 hemophilia centers includ-ing physicians, nurses, physiotherapist and a patient representative. Support regarding legal aspects, IT- solutions, statistics and economy is provided by QRC Stockholm. Results : By now, 780 patients with bleeding disorders are included in the Swedish national Registry and data regarding bleedings, treat-ment with factor concentrate, inhibitor status, mutations, viral infections such as hepatitis C and HIV are collected. Patient reported outcome measurements (PROM)- such as pain and quality of life - HJHS and target joints are followed continuously. Discussion/Conclusion : The establishment of a Swedish National Registry enables us to perform national annual reports, have a close follow- up of our patients and perform clinical research. Currently are working on an on- line patient treatment application recording directly into the registry. Data from the registry will be an important tool for further evaluation of the treatment of hemophilia and how it affects the long- term consequences of the disease.
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| 7. |
- Jönsson, Göran B, et al.
(author)
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The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer.
- 2012
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In: Cancer Research. - 1538-7445. ; 72:16, s. 4028-4036
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Journal article (peer-reviewed)abstract
- Breast tumors from BRCA1 germ line mutation carriers typically exhibit features of the basal-like molecular subtype. However, the specific genes recurrently mutated as a consequence of BRCA1 dysfunction have not been fully elucidated. In this study, we utilized gene expression profiling to molecularly subtype 577 breast tumors, including 72 breast tumors from BRCA1/2 mutation carriers. Focusing on the RB1 locus, we analyzed 33 BRCA1-mutated, 36 BRCA2-mutated and 48 non-BRCA1/2-mutated breast tumors using a custom-designed high-density oligomicroarray covering the RB1 gene. We found a strong association between the basal-like subtype and BRCA1-mutated breast tumors and the luminal B subtype and BRCA2-mutated breast tumors. RB1 was identified as a major target for genomic disruption in tumors arising in BRCA1 mutation carriers and in sporadic tumors with BRCA1 promoter-methylation, but rarely in other breast cancers. Homozygous deletions, intragenic breaks, or microdeletions were found in 33% of BRCA1-mutant tumors, 36% of BRCA1 promoter-methylated basal-like tumors, 13% of non-BRCA1 deficient basal-like tumors, and 3% of BRCA2-mutated tumors. In conclusion, RB1 was frequently inactivated by gross gene disruption in BRCA1-related hereditary breast cancer and BRCA1-methylated sporadic basal-like breast cancer, but rarely in BRCA2-hereditary breast cancer and non-BRCA1-deficient sporadic breast cancers. Together, our findings demonstrate the existence of genetic heterogeneity within the basal-like breast cancer subtype that is based upon BRCA1-status.
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- Machiela, Mitchell J., et al.
(author)
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Characterization of Large Structural Genetic Mosaicism in Human Autosomes
- 2015
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In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497
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Journal article (peer-reviewed)abstract
- Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
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| 9. |
- Machiela, Mitchell J, et al.
(author)
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Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
- 2016
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In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7
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Journal article (peer-reviewed)abstract
- To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
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