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Tafavvoghi M, Bongo LA, Shvetsov N, Busund LTR, Møllersen K. Publicly available datasets of breast histopathology H&E whole-slide images: A scoping review. J Pathol Inform 2024; 15:100363. [PMID: 38405160 PMCID: PMC10884505 DOI: 10.1016/j.jpi.2024.100363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/24/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024] Open
Abstract
Advancements in digital pathology and computing resources have made a significant impact in the field of computational pathology for breast cancer diagnosis and treatment. However, access to high-quality labeled histopathological images of breast cancer is a big challenge that limits the development of accurate and robust deep learning models. In this scoping review, we identified the publicly available datasets of breast H&E-stained whole-slide images (WSIs) that can be used to develop deep learning algorithms. We systematically searched 9 scientific literature databases and 9 research data repositories and found 17 publicly available datasets containing 10 385 H&E WSIs of breast cancer. Moreover, we reported image metadata and characteristics for each dataset to assist researchers in selecting proper datasets for specific tasks in breast cancer computational pathology. In addition, we compiled 2 lists of breast H&E patches and private datasets as supplementary resources for researchers. Notably, only 28% of the included articles utilized multiple datasets, and only 14% used an external validation set, suggesting that the performance of other developed models may be susceptible to overestimation. The TCGA-BRCA was used in 52% of the selected studies. This dataset has a considerable selection bias that can impact the robustness and generalizability of the trained algorithms. There is also a lack of consistent metadata reporting of breast WSI datasets that can be an issue in developing accurate deep learning models, indicating the necessity of establishing explicit guidelines for documenting breast WSI dataset characteristics and metadata.
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Affiliation(s)
- Masoud Tafavvoghi
- Department of Community Medicine, Uit The Arctic University of Norway, Tromsø, Norway
| | - Lars Ailo Bongo
- Department of Computer Science, Uit The Arctic University of Norway, Tromsø, Norway
| | - Nikita Shvetsov
- Department of Computer Science, Uit The Arctic University of Norway, Tromsø, Norway
| | | | - Kajsa Møllersen
- Department of Community Medicine, Uit The Arctic University of Norway, Tromsø, Norway
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2
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Wang Z, Zhao N, Zhang S, Wang D, Wang S, Liu N. YEATS domain-containing protein GAS41 regulates nuclear shape by working in concert with BRD2 and the mediator complex in colorectal cancer. Pharmacol Res 2024; 206:107283. [PMID: 38964523 DOI: 10.1016/j.phrs.2024.107283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
The maintenance of nuclear shape is essential for cellular homeostasis and disruptions in this process have been linked to various pathological conditions, including cancer, laminopathies, and aging. Despite the significance of nuclear shape, the precise molecular mechanisms controlling it are not fully understood. In this study, we have identified the YEATS domain-containing protein 4 (GAS41) as a previously unidentified factor involved in regulating nuclear morphology. Genetic ablation of GAS41 in colorectal cancer cells resulted in significant abnormalities in nuclear shape and inhibited cancer cell proliferation both in vitro and in vivo. Restoration experiments revealed that wild-type GAS41, but not a YEATS domain mutant devoid of histone H3 lysine 27 acetylation or crotonylation (H3K27ac/cr) binding, rescued the aberrant nuclear phenotypes in GAS41-deficient cells, highlighting the importance of GAS41's binding to H3K27ac/cr in nuclear shape regulation. Further experiments showed that GAS41 interacts with H3K27ac/cr to regulate the expression of key nuclear shape regulators, including LMNB1, LMNB2, SYNE4, and LEMD2. Mechanistically, GAS41 recruited BRD2 and the Mediator complex to gene loci of these regulators, promoting their transcriptional activation. Disruption of GAS41-H3K27ac/cr binding caused BRD2, MED14 and MED23 to dissociate from gene loci, leading to nuclear shape abnormalities. Overall, our findings demonstrate that GAS41 collaborates with BRD2 and the Mediator complex to control the expression of crucial nuclear shape regulators.
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Affiliation(s)
- Zhengmin Wang
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, China
| | - Nan Zhao
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Siwei Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Deyu Wang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Shuai Wang
- Bethune Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun 130021, China
| | - Nan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130021, China.
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van der Zijden CJ. International Expert Consensus on Semantics of Multimodal Esophageal Cancer Treatment: Delphi Study. Ann Surg Oncol 2024; 31:5075-5082. [PMID: 38717548 PMCID: PMC11236823 DOI: 10.1245/s10434-024-15367-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 07/13/2024]
Abstract
BACKGROUND Recent developments in esophageal cancer treatment, including studies exploring active surveillance following chemoradiotherapy, have led to a need for clear terminology and definitions regarding different multimodal treatment options. OBJECTIVE The aim of this study was to reach worldwide consensus on the definitions and semantics of multimodal esophageal cancer treatment. METHODS In total, 72 experts working in the field of multimodal esophageal cancer treatment were invited to participate in this Delphi study. The study comprised three Delphi surveys sent out by email and one online meeting. Input for the Delphi survey consisted of terminology obtained from a systematic literature search. Participants were asked to respond to open questions and to indicate whether they agreed or disagreed with different statements. Consensus was reached when there was ≥75% agreement among respondents. RESULTS Forty-nine of 72 invited experts (68.1%) participated in the first online Delphi survey, 45 (62.5%) in the second survey, 21 (46.7%) of 45 in the online meeting, and 39 (86.7%) of 45 in the final survey. Consensus on neoadjuvant and definitive chemoradiotherapy with or without surgery was reached for 27 of 31 items (87%). No consensus was reached on follow-up after treatment with definitive chemoradiotherapy. CONCLUSION(S) Consensus was reached on most statements regarding terminology and definitions of multimodal esophageal cancer treatment. Implementing uniform criteria facilitates comparison of studies and promotes international research collaborations.
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Affiliation(s)
- Charlène J van der Zijden
- Department of Surgery, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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4
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Hogenhout R, Remmers S, van Slooten-Midderigh ME, de Vos II, Roobol MJ. From Screening to Mortality Reduction: An Overview of Empirical Data on the Patient Journey in European Randomized Study of Screening for Prostate Cancer Rotterdam After 21 Years of Follow-up and a Reflection on Quality of Life. Eur Urol Oncol 2024; 7:713-720. [PMID: 37690917 DOI: 10.1016/j.euo.2023.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/13/2023] [Accepted: 08/23/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Previous research quantified the effect of prostate-specific antigen (PSA)-based prostate cancer (PCa) screening on quality-adjusted life years using 11-yr follow-up data from the European Randomized Study of Screening for Prostate Cancer (ERSPC) extrapolated by the Microsimulation Screening Analysis (MISCAN). ERSPC data now matured to 21 yr of follow-up. OBJECTIVE To provide an overview of the effect of PSA-based screening on tumour characteristics and PCa treatment using long-term, detailed, empirical ERSPC data. DESIGN, SETTING, AND PARTICIPANTS Men were included from the ERSPC Rotterdam who were randomised to a PSA-based screening (S) or control (C) arm. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We assessed the effects of PSA-based screening on the number of PCa diagnoses, tumour characteristics, treatments, and cumulative incidence of disease progression. We also evaluated the changes in tumour characteristics and treatments over time for both study arms. RESULTS AND LIMITATIONS Among PCa patients in the S-arm, fewer patients were diagnosed with advanced tumour stages (T3/T4: 12% vs 23%; relative risk [RR] = 0.50; 95% confidence interval [CI] 0.44-0.57), less disease progression was observed, and less secondary treatment (30% vs 48%; RR = 0.61; 95% CI 0.57-0.66; p < 0.001) and less palliative treatment were needed (21% vs 55%; RR = 0.38; 95% CI 0.35-0.42) than among those in the C-arm. This was at the cost of overdiagnosis and increased local treatments (eg, radical prostatectomy: 32% vs 14%; RR = 2.18; 95% CI 1.92-2.48). Over time, the number of local treatments decreased, whereas expectant management strategies increased. The RRs of treatments were slightly different from those of the MISCAN. CONCLUSIONS After 21 yr of follow-up, empirical data of the ERSPC showed that PSA-based screening reduces advanced PCa stages, disease progression, and extensive treatments at the cost of more overdiagnosis and probably more overtreatment. Our data showed reduced local treatments and increased expectant management strategies over time. PATIENT SUMMARY Prostate-specific antigen-based screening reduces the number of invasive prostate cancer treatments needed, however, at the cost of more overdiagnosis and probably more overtreatment. Limiting these costs remains crucial to benefit optimally from prostate cancer screening.
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Affiliation(s)
- Renée Hogenhout
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Sebastiaan Remmers
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Ivo I de Vos
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Monique J Roobol
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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5
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Bourgeois JS, You SS, Clendenen LH, Shrestha M, Petnicki-Ocwieja T, Telford SR, Hu LT. Comparative reservoir competence of Peromyscus leucopus, C57BL/6J, and C3H/HeN for Borrelia burgdorferi B31. Appl Environ Microbiol 2024; 90:e0082224. [PMID: 38899883 PMCID: PMC11267898 DOI: 10.1128/aem.00822-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Borrelia burgdorferi, a Lyme disease spirochete, causes a range of acute and chronic maladies in humans. However, a primary vertebrate reservoir in the United States, the white-footed deermouse Peromyscus leucopus, is reported not to have reduced fitness following infection. Although laboratory strains of Mus musculus mice have successfully been leveraged to model acute human Lyme disease, the ability of these rodents to model B. burgdorferi-P. leucopus interactions remains understudied. Here, we compared infection of P. leucopus with B. burgdorferi B31 with infection of the traditional B. burgdorferi murine models-C57BL/6J and C3H/HeN Mus musculus, which develop signs of inflammation akin to human disease. We find that B. burgdorferi was able to reach much higher burdens (10- to 30-times higher) in multiple M. musculus skin sites and that the overall dynamics of infection differed between the two rodent species. We also found that P. leucopus remained transmissive to larval Ixodes scapularis for a far shorter period than either M. musculus strain. In line with these observations, we found that P. leucopus does launch a modest but sustained inflammatory response against B. burgdorferi in the skin, which we hypothesize leads to reduced bacterial viability and rodent-to-tick transmission in these hosts. Similarly, we also observe evidence of inflammation in infected P. leucopus hearts. These observations provide new insight into reservoir species and the B. burgdorferi enzootic cycle.IMPORTANCEA Lyme disease-causing bacteria, Borrelia burgdorferi, must alternate between infecting a vertebrate host-usually rodents or birds-and ticks. In order to be successful in that endeavor, the bacteria must avoid being killed by the vertebrate host before it can infect a new larval tick. In this work, we examine how B. burgdorferi and one of its primary vertebrate reservoirs, Peromyscus leucopus, interact during an experimental infection. We find that B. burgdorferi appears to colonize its natural host less successfully than conventional laboratory mouse models, which aligns with a sustained seemingly anti-bacterial response by P. leucopus against the microbe. These data enhance our understanding of P. leucopus host-pathogen interactions and could potentially serve as a foundation to uncover ways to disrupt the spread of B. burgdorferi in nature.
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Affiliation(s)
- Jeffrey S. Bourgeois
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
- Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Stephanie S. You
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
- Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Luke H. Clendenen
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
- Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Muskan Shrestha
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
- Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Tanja Petnicki-Ocwieja
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
- Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
| | - Sam R. Telford
- Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts, USA
| | - Linden T. Hu
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
- Tufts University, Tufts Lyme Disease Initiative, Boston, Massachusetts, USA
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Múrria C, Wangensteen OS, Somma S, Väisänen L, Fortuño P, Arnedo MA, Prat N. Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173243. [PMID: 38761946 DOI: 10.1016/j.scitotenv.2024.173243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 04/04/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.
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Affiliation(s)
- Cesc Múrria
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Zoological Systematics & Evolution (ZooSysEvo), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Owen S Wangensteen
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Simona Somma
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Leif Väisänen
- Stream Ecology Research Group, Department of Ecology and Genetics, University of Oulu, Finland
| | - Pau Fortuño
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Miquel A Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Zoological Systematics & Evolution (ZooSysEvo), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Narcís Prat
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Universitat de Barcelona, Barcelona, Catalonia, Spain
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7
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Bangma C, Doan P, Zhu L, Remmers S, Nieboer D, Helleman J, Roobol MJ, Sugimoto M, Chung BH, Lee LS, Frydenberg M, Klotz L, Peacock M, Perry A, Bjartell A, Rannikko A, Van Hemelrijck M, Dasgupta P, Moore C, Trock BJ, Pavlovich C, Steyerberg E, Carroll P, Koo KC, Hayen A, Thompson J. Has Active Surveillance for Prostate Cancer Become Safer? Lessons Learned from a Global Clinical Registry. Eur Urol Oncol 2024:S2588-9311(24)00176-7. [PMID: 39025687 DOI: 10.1016/j.euo.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/02/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND AND OBJECTIVE Active surveillance (AS) has evolved into a widely applied treatment strategy for many men around the world with low-risk prostate cancer (or in selected cases intermediate-risk disease). Here, we report on the safety and acceptability of AS, and treatment outcomes for low- and intermediate-risk tumours over time in 14 623 men with follow-up of over 6 yr. METHODS Clinical data from 26 999 men on AS from 25 cohorts in 15 countries have been collected in an international database from 2000 onwards. KEY FINDINGS AND LIMITATIONS Across our predefined four time periods of 4 yr each (covering the period 2000-2016), there was no significant change in overall survival (OS). However, metastasis-free survival (MFS) rates have improved since the second period and were excellent (>99%). Treatment-free survival rates for earlier periods showed a slightly more rapid shift to radical treatment. Over time, there was a constant proportion of 5% of men for whom anxiety was registered as the reason for treatment alteration. There was, however, also a subset of 10-15% in whom treatment was changed, for which no apparent reason was available. In a subset of men (10-15%), tumour progression was the trigger for treatment. In men who opted for radical treatment, surgery was the most common treatment modality. In those men who underwent radical treatment, 90% were free from biochemical recurrence at 5 yr after treatment. CONCLUSIONS AND CLINICAL IMPLICATIONS Our study confirms that AS was a safe management option over the full duration in this large multicentre cohort with long-term follow-up, given the 84.1% OS and 99.4% MFS at 10 yr. The probability of treatment at 10 yr was 20% in men with initial low-risk tumours and 31% in men with intermediate-risk tumours. New diagnostic modalities may improve the acceptability of follow-up using individual risk assessments, while safely broadening the use of AS in higher-risk tumours. PATIENT SUMMARY Active surveillance (AS) has evolved into a widely applied treatment strategy for many men with prostate cancer around the world. In this report, we show the long-term safety of following AS for men with low- and intermediate-risk prostate cancer. Our study confirms AS as a safe management option for low- and intermediate-risk prostate cancer. New diagnostic modalities may improve the acceptability of follow-up using individual risk assessments, while safely broadening the use of AS in higher-risk tumours.
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Affiliation(s)
- Chris Bangma
- Department of Urology, Erasmus Medical Centre Cancer Institute, University Medical Center, Rotterdam, The Netherlands.
| | - Paul Doan
- St Vincent's Prostate Cancer Research Centre, Department of Urology, Sydney, Australia
| | - Lin Zhu
- University of Technology Sydney, Department of Public Health, Sydney, Australia
| | - Sebastiaan Remmers
- Department of Urology, Erasmus Medical Centre Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Daan Nieboer
- Department of Urology, Erasmus Medical Centre Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Jozien Helleman
- Department of Urology, Erasmus Medical Centre Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Monique J Roobol
- Department of Urology, Erasmus Medical Centre Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | | | - Byung Ha Chung
- Yonsei University, College of Medicine, Seoul, Republic of Korea
| | - Lui Shiong Lee
- Department of Urology, Sengkang General Hospital and Singapore General Hospital, Singapore
| | - Mark Frydenberg
- Department of Surgery, Monash University, Clayton, VIC, Australia; Cabrini Health, Cabrini Institute, Melbourne, Australia
| | - Laurence Klotz
- University of Toronto, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Michael Peacock
- University of British Columbia, BC Cancer Agency, Vancouver, Canada
| | | | - Anders Bjartell
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | | | | | - Prokar Dasgupta
- King's College London, London, UK; Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Caroline Moore
- University College London, London, UK; University College London Hospitals Trust, London, UK
| | - Bruce J Trock
- Johns Hopkins University, The James Buchanan Brady Urological Institute, Baltimore, MD, USA
| | - Christian Pavlovich
- Johns Hopkins University, The James Buchanan Brady Urological Institute, Baltimore, MD, USA
| | - Ewout Steyerberg
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Carroll
- University of California San Francisco, Department of Urology, San Francisco, USA
| | - Kyo Chul Koo
- Yonsei University, College of Medicine, Seoul, Republic of Korea
| | - Andrew Hayen
- University of Technology Sydney, Department of Public Health, Sydney, Australia
| | - James Thompson
- St Vincent's Prostate Cancer Research Centre, Department of Urology, Sydney, Australia
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8
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Costacurta M, Sandow JJ, Maher B, Susanto O, Vervoort SJ, Devlin JR, Garama D, Condina MR, Steele JR, Kahrood HV, Gough D, Johnstone RW, Shortt J. Mapping the IMiD-dependent cereblon interactome using BioID-proximity labelling. FEBS J 2024. [PMID: 38975872 DOI: 10.1111/febs.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/17/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
Immunomodulatory imide drugs (IMiDs) are central components of therapy for multiple myeloma (MM). IMiDs bind cereblon (CRBN), an adaptor for the CUL4-DDB1-RBX1 E3 ligase to change its substrate specificity and induce degradation of 'neosubstrate' transcription factors that are essential to MM cells. Mechanistic studies to date have largely focussed on mediators of therapeutic activity and insight into clinical IMiD toxicities is less developed. We adopted BioID2-dependent proximity labelling (BioID2-CRBN) to characterise the CRBN interactome in the presence and absence of various IMiDs and the proteasome inhibitor, bortezomib. We aimed to leverage this technology to further map CRBN interactions beyond what has been achieved by conventional proteomic techniques. In support of this approach, analysis of cells expressing BioID2-CRBN following IMiD treatment displayed biotinylation of known CRBN interactors and neosubstrates. We observed that bortezomib alone significantly modifies the CRBN interactome. Proximity labelling also suggested that IMiDs augment the interaction between CRBN and proteins that are not degraded, thus designating 'neointeractors' distinct from previously disclosed 'neosubstrates'. Here we identify Non-Muscle Myosin Heavy Chain IIA (MYH9) as a putative CRBN neointeractor that may contribute to the haematological toxicity of IMiDs. These studies provide proof of concept for proximity labelling technologies in the mechanistic profiling of IMiDs and related E3-ligase-modulating drugs.
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Affiliation(s)
- Matteo Costacurta
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Belinda Maher
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Olivia Susanto
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Stephin J Vervoort
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Jennifer R Devlin
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Daniel Garama
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Mark R Condina
- Mass Dynamics, Melbourne, Australia
- Clinical & Health Sciences, University of South Australia, Adelaide, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Hossein V Kahrood
- Monash Proteomics and Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Daniel Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Ricky W Johnstone
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Jake Shortt
- Monash Haematology, Monash Health, Clayton, Australia
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
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9
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Yan H, Tang W. Programmed RNA editing with an evolved bacterial adenosine deaminase. Nat Chem Biol 2024:10.1038/s41589-024-01661-x. [PMID: 38969862 DOI: 10.1038/s41589-024-01661-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
Programmed RNA editing presents an attractive therapeutic strategy for genetic disease. In this study, we developed bacterial deaminase-enabled recoding of RNA (DECOR), which employs an evolved Escherichia coli transfer RNA adenosine deaminase, TadA8e, to deposit adenosine-to-inosine editing to CRISPR-specified sites in the human transcriptome. DECOR functions in a variety of cell types, including human lung fibroblasts, and delivers on-target activity similar to ADAR-overexpressing RNA-editing platforms with 88% lower off-target effects. High-fidelity DECOR further reduces off-target effects to basal level. We demonstrate the clinical potential of DECOR by targeting Van der Woude syndrome-causing interferon regulatory factor 6 (IRF6) insufficiency. DECOR-mediated RNA editing removes a pathogenic upstream open reading frame (uORF) from the 5' untranslated region of IRF6 and rescues primary ORF expression from 12.3% to 36.5%, relative to healthy transcripts. DECOR expands the current portfolio of effector proteins and opens new territory in programmed RNA editing.
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Affiliation(s)
- Hao Yan
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Weixin Tang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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10
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Dimet-Wiley AL, Latham CM, Brightwell CR, Neelakantan H, Keeble AR, Thomas NT, Noehren H, Fry CS, Watowich SJ. Nicotinamide N-methyltransferase inhibition mimics and boosts exercise-mediated improvements in muscle function in aged mice. Sci Rep 2024; 14:15554. [PMID: 38969654 PMCID: PMC11226645 DOI: 10.1038/s41598-024-66034-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Human hallmarks of sarcopenia include muscle weakness and a blunted response to exercise. Nicotinamide N-methyltransferase inhibitors (NNMTis) increase strength and promote the regenerative capacity of aged muscle, thus offering a promising treatment for sarcopenia. Since human hallmarks of sarcopenia are recapitulated in aged (24-month-old) mice, we treated mice from 22 to 24 months of age with NNMTi, intensive exercise, or a combination of both, and compared skeletal muscle adaptations, including grip strength, longitudinal running capacity, plantarflexor peak torque, fatigue, and muscle mass, fiber type, cross-sectional area, and intramyocellular lipid (IMCL) content. Exhaustive proteome and metabolome analyses were completed to identify the molecular mechanisms underlying the measured changes in skeletal muscle pathophysiology. Remarkably, NNMTi-treated aged sedentary mice showed ~ 40% greater grip strength than sedentary controls, while aged exercised mice only showed a 20% increase relative to controls. Importantly, the grip strength improvements resulting from NNMTi treatment and exercise were additive, with NNMTi-treated exercised mice developing a 60% increase in grip strength relative to sedentary controls. NNMTi treatment also promoted quantifiable improvements in IMCL content and, in combination with exercise, significantly increased gastrocnemius fiber CSA. Detailed skeletal muscle proteome and metabolome analyses revealed unique molecular mechanisms associated with NNMTi treatment and distinct molecular mechanisms and cellular processes arising from a combination of NNMTi and exercise relative to those given a single intervention. These studies suggest that NNMTi-based drugs, either alone or combined with exercise, will be beneficial in treating sarcopenia and a wide range of age-related myopathies.
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Affiliation(s)
| | - Christine M Latham
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Camille R Brightwell
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | | | - Alexander R Keeble
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Nicholas T Thomas
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Haley Noehren
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Christopher S Fry
- Center for Muscle Biology, College of Health Sciences, University of Kentucky, Lexington, KY, USA
| | - Stanley J Watowich
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
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11
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Dias AB, Woo S, Leni R, Rajwa P, Kasivisvanathan V, Ghai S, Haider M, Gandaglia G, Brembilla G. Is MRI ready to replace biopsy during active surveillance? Eur Radiol 2024:10.1007/s00330-024-10863-9. [PMID: 38965093 DOI: 10.1007/s00330-024-10863-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/15/2024] [Accepted: 05/25/2024] [Indexed: 07/06/2024]
Abstract
Active surveillance (AS) is a conservative management option recommended for patients diagnosed with low-risk prostate cancer (PCa) and selected cases with intermediate-risk PCa. The adoption of prostate MRI in the primary diagnostic setting has sparked interest in its application during AS. This review aims to examine the role and performance of multiparametric MRI (mpMRI) across the entire AS pathway, from initial stratification to follow-up, also relative to the utilization of the Prostate Cancer Radiological Estimation of Change in Sequential Evaluation (PRECISE) criteria. Given the high negative predictive value of mpMRI in detecting clinically significant PCa (csPCa), robust evidence supports its use in patient selection and risk stratification at the time of diagnosis or confirmatory biopsy. However, conflicting results have been observed when using MRI in evaluating disease progression during follow-up. Key areas requiring clarification include addressing the clinical significance of MRI-negative csPCa, optimizing MRI quality, determining the role of biparametric MRI (bpMRI) or mpMRI protocols, and integrating artificial intelligence (AI) for improved performance. CLINICAL RELEVANCE STATEMENT: MRI plays an essential role in the selection, stratification, and follow up of patients in active surveillance (AS) for prostate cancer. However, owing to existing limitations, it cannot fully replace biopsies in the context of AS. KEY POINTS: Multiparametric MRI (mpMRI) has become a crucial tool in active surveillance (AS) for prostate cancer (PCa). Conflicting results have been observed regarding multiparametric MRI efficacy in assessing disease progression. Standardizing MRI-guided protocols will be critical in addressing current limitations in active surveillance for prostate cancer.
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Affiliation(s)
- Adriano B Dias
- University Medical Imaging Toronto; Joint Department of Medical Imaging; University Health Network-Sinai Health System-Women's College Hospital, University of Toronto, Toronto, ON, Canada
| | - Sungmin Woo
- Department of Radiology, NYU Langone Health, New York, NY, USA
| | - Riccardo Leni
- Division of Experimental Oncology, Department of Urology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Pawel Rajwa
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Urology, Medical University of Silesia, Zabrze, Poland
| | - Veeru Kasivisvanathan
- Division of Surgery & Interventional Science, University College London, London, UK; Department of Urology, University College London Hospital NHS Foundation Trust, London, UK
| | - Sangeet Ghai
- University Medical Imaging Toronto; Joint Department of Medical Imaging; University Health Network-Sinai Health System-Women's College Hospital, University of Toronto, Toronto, ON, Canada
| | - Masoom Haider
- University Medical Imaging Toronto; Joint Department of Medical Imaging; University Health Network-Sinai Health System-Women's College Hospital, University of Toronto, Toronto, ON, Canada
| | - Giorgio Gandaglia
- Division of Experimental Oncology, Department of Urology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giorgio Brembilla
- Vita-Salute San Raffaele University, Milan, Italy.
- Department of Radiology, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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12
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Yang J, Xiao L, Zhou M, Li Y, Cai Y, Gan Y, Tang Y, Hu S. [ 68Ga]Ga‑PSMA‑617 PET-based radiomics model to identify candidates for active surveillance amongst patients with GGG 1-2 prostate cancer at biopsy. Cancer Imaging 2024; 24:86. [PMID: 38965552 PMCID: PMC11229016 DOI: 10.1186/s40644-024-00735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
PURPOSE To develop a radiomics-based model using [68Ga]Ga-PSMA PET/CT to predict postoperative adverse pathology (AP) in patients with biopsy Gleason Grade Group (GGG) 1-2 prostate cancer (PCa), assisting in the selection of patients for active surveillance (AS). METHODS A total of 75 men with biopsy GGG 1-2 PCa who underwent radical prostatectomy (RP) were enrolled. The patients were randomly divided into a training group (70%) and a testing group (30%). Radiomics features of entire prostate were extracted from the [68Ga]Ga-PSMA PET scans and selected using the minimum redundancy maximum relevance algorithm and the least absolute shrinkage and selection operator regression model. Logistic regression analyses were conducted to construct the prediction models. Receiver operating characteristic (ROC) curve, decision curve analysis (DCA), and calibration curve were employed to evaluate the diagnostic value, clinical utility, and predictive accuracy of the models, respectively. RESULTS Among the 75 patients, 30 had AP confirmed by RP. The clinical model showed an area under the curve (AUC) of 0.821 (0.695-0.947) in the training set and 0.795 (0.603-0.987) in the testing set. The radiomics model achieved AUC values of 0.830 (0.720-0.941) in the training set and 0.829 (0.624-1.000) in the testing set. The combined model, which incorporated the Radiomics score (Radscore) and free prostate-specific antigen (FPSA)/total prostate-specific antigen (TPSA), demonstrated higher diagnostic efficacy than both the clinical and radiomics models, with AUC values of 0.875 (0.780-0.970) in the training set and 0.872 (0.678-1.000) in the testing set. DCA showed that the net benefits of the combined model and radiomics model exceeded those of the clinical model. CONCLUSION The combined model shows potential in stratifying men with biopsy GGG 1-2 PCa based on the presence of AP at final pathology and outperforms models based solely on clinical or radiomics features. It may be expected to aid urologists in better selecting suitable patients for AS.
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Affiliation(s)
- Jinhui Yang
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
| | - Ling Xiao
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
| | - Ming Zhou
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
| | - Yujia Li
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
| | - Yi Cai
- Department of Urology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu Gan
- Department of Urology, Disorders of Prostate Cancer Multidisciplinary Team, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yongxiang Tang
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Department of Nuclear Medicine, Inselspital, University Hospital Bern, Bern, Switzerland.
| | - Shuo Hu
- Department of Nuclear Medicine, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Biological, Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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13
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Zhang K, Teoh J, Zhu G, Ng CF, Suberville M, Laguna P, de la Rosette J. Irreversible Electroporation for the Focal Treatment of Prostate Cancer: A Systematic Review. World J Mens Health 2024; 42:42.e65. [PMID: 39028129 DOI: 10.5534/wjmh.240012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/24/2024] [Accepted: 04/23/2024] [Indexed: 07/20/2024] Open
Abstract
PURPOSE Irreversible electroporation (IRE) is a promising alternative treatment for low-intermediate-risk localized prostate cancer. In this systematic review we aim to evaluate the safety profile and functional and oncological outcomes of this new technique. MATERIALS AND METHODS A systematic review of the literature was performed on PubMed, EMBASE, and Scopus up to 24 August 2023. Nineteen studies were analyzed, including 12 prospective studies and 7 retrospective studies. A total of 1,452 patients underwent IRE as the sole primary treatment modality. RESULTS The in-field clinically significant prostate cancer rate was reported between 0%-15.6% in the repeat biopsy. The retreatment rate was reported from 8% to 36.6%. The 3 years failure-free survival was presented between 90%-96.8%. The post-operative pad-free rate ranged between 96.7%-100%. Greater heterogeneity exists considering the change in erectile function. The most common reported complications were urinary tract infection and hematuria. Major complications were rare. CONCLUSIONS These results underline that IRE achieves favorable oncological control with an excellent safety profile, in the meantime preserving patients' urinary and erectile function.
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Affiliation(s)
- Kai Zhang
- Department of Urology, Beijing United Family Hospital and Clinics, Beijing, China
| | - Jeremy Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Gang Zhu
- Department of Urology, Beijing United Family Hospital and Clinics, Beijing, China
| | - Chi-Fai Ng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Michel Suberville
- Department of Urology, Pôle Saint Germain Centre Hospitalier de BRIVE, Brive la Gaillarde, France
| | - Pilar Laguna
- Department of Urology, Medipol Mega Hospital, Istanbul Medipol University, Istanbul, Türkiye
| | - Jean de la Rosette
- Department of Urology, Medipol Mega Hospital, Istanbul Medipol University, Istanbul, Türkiye.
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14
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Mateus P, Moonen J, Beran M, Jaarsma E, van der Landen SM, Heuvelink J, Birhanu M, Harms AGJ, Bron E, Wolters FJ, Cats D, Mei H, Oomens J, Jansen W, Schram MT, Dekker A, Bermejo I. Data harmonization and federated learning for multi-cohort dementia research using the OMOP common data model: A Netherlands consortium of dementia cohorts case study. J Biomed Inform 2024; 155:104661. [PMID: 38806105 DOI: 10.1016/j.jbi.2024.104661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Establishing collaborations between cohort studies has been fundamental for progress in health research. However, such collaborations are hampered by heterogeneous data representations across cohorts and legal constraints to data sharing. The first arises from a lack of consensus in standards of data collection and representation across cohort studies and is usually tackled by applying data harmonization processes. The second is increasingly important due to raised awareness for privacy protection and stricter regulations, such as the GDPR. Federated learning has emerged as a privacy-preserving alternative to transferring data between institutions through analyzing data in a decentralized manner. METHODS In this study, we set up a federated learning infrastructure for a consortium of nine Dutch cohorts with appropriate data available to the etiology of dementia, including an extract, transform, and load (ETL) pipeline for data harmonization. Additionally, we assessed the challenges of transforming and standardizing cohort data using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM) and evaluated our tool in one of the cohorts employing federated algorithms. RESULTS We successfully applied our ETL tool and observed a complete coverage of the cohorts' data by the OMOP CDM. The OMOP CDM facilitated the data representation and standardization, but we identified limitations for cohort-specific data fields and in the scope of the vocabularies available. Specific challenges arise in a multi-cohort federated collaboration due to technical constraints in local environments, data heterogeneity, and lack of direct access to the data. CONCLUSION In this article, we describe the solutions to these challenges and limitations encountered in our study. Our study shows the potential of federated learning as a privacy-preserving solution for multi-cohort studies that enhance reproducibility and reuse of both data and analyses.
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Affiliation(s)
- Pedro Mateus
- Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, Netherlands.
| | - Justine Moonen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, Netherlands; Amsterdam Neuroscience, Neurodegeneration, Amsterdam, Netherlands
| | - Magdalena Beran
- Department of Internal Medicine, School for Cardiovascular Diseases (CARIM), Maastricht University, Maastricht, Netherlands; Department of Epidemiology and Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Eva Jaarsma
- Center for Nutrition, Prevention, and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands; Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, Netherlands
| | - Sophie M van der Landen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, Netherlands; Amsterdam Neuroscience, Neurodegeneration, Amsterdam, Netherlands
| | - Joost Heuvelink
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, Netherlands
| | - Mahlet Birhanu
- Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Alexander G J Harms
- Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Esther Bron
- Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Frank J Wolters
- Erasmus MC - University Medical Centre Rotterdam, Departments of Epidemiology and Radiology & Nuclear Medicine, Netherlands
| | - Davy Cats
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Netherlands
| | - Julie Oomens
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Center Limburg, Maastricht University, Netherlands
| | - Willemijn Jansen
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Center Limburg, Maastricht University, Netherlands
| | - Miranda T Schram
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands; Department of Internal Medicine, Maastricht University Medical Centre, Maastricht, Netherlands; MHeNS School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands; Heart and Vascular Center, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Andre Dekker
- Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Inigo Bermejo
- Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, Netherlands
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Walshe J, Elphinstone B, Nicol D, Taylor M. A systematic literature review of the 'commercialisation effect' on public attitudes towards biobank and genomic data repositories. PUBLIC UNDERSTANDING OF SCIENCE (BRISTOL, ENGLAND) 2024; 33:548-567. [PMID: 38389329 PMCID: PMC11264570 DOI: 10.1177/09636625241230864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Initiatives that collect and share genomic data to advance health research are widespread and accelerating. Commercial interests in these efforts, while vital, may erode public trust and willingness to provide personal genomic data, upon which these initiatives depend. Understanding public attitudes towards providing genomic data for health research in the context of commercial involvement is critical. A PRISMA-guided search of six online academic databases identified 113 quantitative and qualitative studies using primary data pertaining to public attitudes towards commercial actors in the management, collection, access, and use of biobank and genomic data. The presence of commercial interests yields interrelated public concerns around consent, privacy and data security, trust in science and scientists, benefit sharing, and the ownership and control of health data. Carefully considered regulatory and data governance and access policies are therefore required to maintain public trust and support for genomic health initiatives.
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16
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Molnar C, Heinen JP, Reina J, Llamazares S, Palumbo E, Pollarolo G, Gonzalez C. TrxT and dhd are dispensable for Drosophila brain development but essential for l(3)mbt brain tumour growth. EMBO Rep 2024; 25:2842-2860. [PMID: 38750349 PMCID: PMC11239866 DOI: 10.1038/s44319-024-00154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 07/13/2024] Open
Abstract
Expression of the Drosophila cancer-germline (CG), X-linked, head-to-head gene pair TrxT and dhd is normally germline-specific but becomes upregulated in brain tumours caused by mutation in l(3)mbt. Here, we show that TrxT and dhd play a major synergistic role in the emergence of l(3)mbt tumour-linked transcriptomic signatures and tumour development, which is remarkable, taking into account that these two genes are never expressed together under normal conditions. We also show that TrxT, but not dhd, is crucial for the growth of l(3)mbt allografts, hence suggesting that the initial stages of tumour development and long-term tumour growth may depend on different molecular pathways. In humans, head-to-head inverted gene pairs are abundant among CG genes that map to the X chromosome. Our results identify a first example of an X-linked, head-to-head CG gene pair in Drosophila, underpinning the potential of such CG genes, dispensable for normal development and homoeostasis of somatic tissue, as targets to curtail malignant growth with minimal impact on overall health.
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Affiliation(s)
- Cristina Molnar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Jan Peter Heinen
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Jose Reina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Salud Llamazares
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Giulia Pollarolo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028, Barcelona, Spain
- ISGlobal, Carrer del Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Cayetano Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028, Barcelona, Spain.
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Pg Lluis Companys 23, 08010, Barcelona, Spain.
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17
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van Harten MJ, Roobol MJ, van Leeuwen PJ, Willemse PPM, van den Bergh RCN. Evolution of European prostate cancer screening protocols and summary of ongoing trials. BJU Int 2024; 134:31-42. [PMID: 38469728 DOI: 10.1111/bju.16311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Population-based organised repeated screening for prostate cancer has been found to reduce disease-specific mortality, but with substantial overdiagnosis leading to overtreatment. Although only very few countries have implemented a screening programme on a national level, individual prostate-specific antigen (PSA) testing is common. This opportunistic testing may have little favourable impact, while stressing the side-effects. The classic early detection protocols as were state-of-the-art in the 1990s applied a PSA and digital rectal examination threshold for sextant systematic prostate biopsy, with a fixed interval for re-testing, and limited indication for expectant management. In the three decades since these trials were started, different important improvements have become available in the cascade of screening, indication for biopsy, and treatment. The main developed aspects include: better identification of individuals at risk (using early/baseline PSA, family history, and/or genetic profile), individualised re-testing interval, optimised and individualised starting and stopping age, with gradual invitation at a fixed age rather than invitation of a wider range of age groups, risk stratification for biopsy (using PSA density, risk calculator, magnetic resonance imaging, serum and urine biomarkers, or combinations/sequences), targeted biopsy, transperineal biopsy approach, active surveillance for low-risk prostate cancer, and improved staging of disease. All these developments are suggested to decrease the side-effects of screening, while at least maintaining the advantages, but Level 1 evidence is lacking. The knowledge gained and new developments on early detection are being tested in different prospective screening trials throughout Europe. In addition, the European Union-funded PRostate cancer Awareness and Initiative for Screening in the European Union (PRAISE-U) project will compare and evaluate different screening pilots throughout Europe. Implementation and sustainability will also be addressed. Modern screening approaches may reduce the burden of the second most frequent cause of cancer-related death in European males, while minimising side-effects. Also, less efficacious opportunistic early detection may be indirectly reduced.
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Affiliation(s)
- Meike J van Harten
- Cancer Center, Department of Urology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monique J Roobol
- Cancer Institute, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | | | - Peter-Paul M Willemse
- Cancer Center, Department of Urology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roderick C N van den Bergh
- Cancer Institute, Erasmus University Medical Centre, Rotterdam, The Netherlands
- St Antonius Hospital, Utrecht, The Netherlands
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Ciordia S, Santos FM, Dias JML, Lamas JR, Paradela A, Alvarez-Sola G, Ávila MA, Corrales F. Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Talanta 2024; 274:125988. [PMID: 38569368 DOI: 10.1016/j.talanta.2024.125988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (μg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 μg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 μg of beads for sample preparation and long-term digestion (16h) with 0.15 μg Lys-C and 2.5 μg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.
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Affiliation(s)
- Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - João M L Dias
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom; Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - José Ramón Lamas
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Gloria Alvarez-Sola
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Matías A Ávila
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
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19
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Doerfler P, Schoefmann N, Cabral G, Bauer W, Berli MC, Binder B, Borst C, Botter S, French LE, Goerge T, Hafner J, Hartmann D, Høgh A, Hoetzenecker W, Holzer-Geissler JCJ, Kamolz LP, Kofler K, Luger T, Nischwitz SP, Popovits M, Rappersberger K, Restivo G, Schlager JG, Schmuth M, Stingl G, Stockinger T, Stroelin A, Stuetz A, Umlauft J, Weninger WP, Wolff-Winiski B. Development of a cellular assay as a personalized model for testing chronic wound therapeutics. J Invest Dermatol 2024:S0022-202X(24)01866-9. [PMID: 38960086 DOI: 10.1016/j.jid.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/19/2024] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Exudates of non-healing wounds contain drivers of pathogenicity. We utilized >800 exudates from non-healing and healing wounds of diverse etiologies, collected by three different methods, to develop a wound-specific, cell-based functional biomarker assay. Human dermal fibroblast proliferation served as readout to a) to differentiate between healing and non-healing wounds, b) follow the healing process of individual patients, and c) assess the effects of therapeutics for chronic wounds ex vivo. We observed a strong correlation between wound chronicity and inhibitory effects of individual exudates on fibroblast proliferation, with good diagnostic sensitivity (76-90%, depending on the sample collection method). Transition of a clinically non-healing to a healing phenotype restored fibroblast proliferation and extracellular matrix formation while reducing inflammatory cytokine production. Transcriptional analysis of fibroblasts exposed to ex vivo non-healing wound exudates revealed an induction of inflammatory cytokine- and chemokine pathways and the unfolded protein response, indicating that these changes may contribute to the pathology of non-healing wounds. Testing the wound therapeutics platelet derived growth factor and silver sulfadiazine yielded responses in line with clinical experience and indicate the usefulness of the assay to search for and profile new therapeutics.
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Affiliation(s)
| | | | | | - Wolfgang Bauer
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Martin C Berli
- University Hospital Balgrist, Zurich, Switzerland; Present address: Technical orthopedics, diabetic foot consultation, wound outpatient clinic and plaster room, Spital Limmattal, Schlieren, Switzerland
| | - Barbara Binder
- Medical University of Graz, Department of Dermatology and Venerology, Graz, Austria
| | - Carina Borst
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Sander Botter
- Swiss Center for Musculoskeletal Biobanking, Balgrist Campus AG, Zurich, Switzerland
| | - Lars E French
- Ludwig-Maximilians-University Munich, Department of Dermatology and Allergology, Munich, Germany
| | - Tobias Goerge
- University of Münster, Department of Dermatology, Muenster, Germany
| | - Juerg Hafner
- University Hospital of Zurich, Department of Dermatology, Zurich, Switzerland
| | - Daniela Hartmann
- Ludwig-Maximilians-University Munich, Department of Dermatology and Allergology, Munich, Germany
| | - Annette Høgh
- Regionshospitalet Viborg, Department of Vascular Surgery, Viborg, Denmark
| | | | - Judith C J Holzer-Geissler
- Medical University of Graz, Department of Surgery, Division of Plastic, Aesthetic and Reconstructive Surgery, Graz, Austria
| | - Lars P Kamolz
- Medical University of Graz, Department of Surgery, Division of Plastic, Aesthetic and Reconstructive Surgery, Graz, Austria
| | - Katrin Kofler
- Medical University of Tübingen, Department of Dermatology, Tuebingen, Germany
| | - Thomas Luger
- University of Münster, Department of Dermatology, Muenster, Germany
| | - Sebastian P Nischwitz
- Medical University of Graz, Department of Surgery, Division of Plastic, Aesthetic and Reconstructive Surgery, Graz, Austria
| | - Michael Popovits
- Barmherzige Brueder Hospital, Graz, Department of Surgery, Graz, Austria; Present address: Privatklinik Graz Ragnitz, Graz, Austria
| | | | - Gaetana Restivo
- University Hospital of Zurich, Department of Dermatology, Zurich, Switzerland
| | - Justin G Schlager
- Ludwig-Maximilians-University Munich, Department of Dermatology and Allergology, Munich, Germany
| | - Matthias Schmuth
- Medical University of Innsbruck, Department of Dermatology, Venerology and Allergology, Innsbruck, Austria; Present address of JU: Zellmed Medalp, Dermatology, Zell am Ziller, Austria
| | - Georg Stingl
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | | | - Anke Stroelin
- Medical University of Tübingen, Department of Dermatology, Tuebingen, Germany
| | | | - Julian Umlauft
- Medical University of Innsbruck, Department of Dermatology, Venerology and Allergology, Innsbruck, Austria; Present address of JU: Zellmed Medalp, Dermatology, Zell am Ziller, Austria
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20
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Dixon CW, Gschwend AR. Trichomes and unique gene expression confer insect herbivory resistance in Vitis labrusca grapevines. BMC PLANT BIOLOGY 2024; 24:609. [PMID: 38926877 PMCID: PMC11209964 DOI: 10.1186/s12870-024-05260-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Grapevine (Vitis) is one of the world's most valuable fruit crops, but insect herbivory can decrease yields. Understanding insect herbivory resistance is critical to mitigating these losses. Vitis labrusca, a wild North American grapevine species, has been leveraged in breeding programs to generate hybrid grapevines with enhanced abiotic and biotic stress resistance, rendering it a valuable genetic resource for sustainable viticulture. This study assessed the resistance of V. labrusca acc. 'GREM4' and Vitis vinifera cv. 'PN40024' grapevines to Popillia japonica (Japanese beetle) herbivory and identified morphological and genetic adaptations underlying this putative resistance. RESULTS 'GREM4' displayed greater resistance to beetle herbivory compared to 'PN40024' in both choice and no-choice herbivory assays spanning periods of 30 min to 19 h. 'GREM4' had significantly higher average leaf trichome densities than 'PN40024' and beetles preferred to feed on the side of leaves with fewer trichomes. When leaves from each species that specifically did not differ in trichome densities were fed on by beetles, significantly less leaf area was damaged in 'GREM4' (3.29mm2) compared to 'PN40024' (9.80mm2), suggesting additional factors beyond trichomes contributed to insect herbivory resistance in 'GREM4'. Comparative transcriptomic analyses revealed 'GREM4' exhibited greater constitutive (0 h) expression of defense response and secondary metabolite biosynthesis genes compared to 'PN40024', indicative of heightened constitutive defenses. Upon herbivory, 'GREM4' displayed a greater number of differentially expressed genes (690) compared to 'PN40024' (502), suggesting a broader response. Genes up-regulated in 'GREM4' were enriched in terpene biosynthesis, flavonoid biosynthesis, phytohormone signaling, and disease defense-related functions, likely contributing to heighted insect herbivory defense, while genes differentially expressed in 'PN40024' under herbivory were enriched in xyloglucan, cell wall formation, and calcium ion binding. The majority of genes implicated in insect herbivory defense were orthologs with specific expression patterns in 'GREM4' and 'PN40024', but some paralogous and genome-specific genes also likely contributed to conferring resistance. CONCLUSIONS Our findings suggest that 'GREM4' insect herbivory resistance was attributed to a combination of factors, including trichomes and unique constitutive and inducible expression of genes implicated in terpene, flavonoid, and phenylpropanoid biosynthesis, as well as pathogen defense.
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Affiliation(s)
- Cullen W Dixon
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Andrea R Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA.
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21
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Huang WP, Ellis BCS, Hodgson RE, Sanchez Avila A, Kumar V, Rayment J, Moll T, Shelkovnikova TA. Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion. Cell Rep 2024; 43:114421. [PMID: 38941189 DOI: 10.1016/j.celrep.2024.114421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/04/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024] Open
Abstract
TDP-43 protein is dysregulated in several neurodegenerative diseases, which often have a multifactorial nature and may have extrinsic stressors as a "second hit." TDP-43 undergoes reversible nuclear condensation in stressed cells including neurons. Here, we demonstrate that stress-inducible nuclear TDP-43 condensates are RNA-depleted, non-liquid assemblies distinct from the known nuclear bodies. Their formation requires TDP-43 oligomerization and ATP and is inhibited by RNA. Using a confocal nanoscanning assay, we find that amyotrophic lateral sclerosis (ALS)-linked mutations alter stress-induced TDP-43 condensation by changing its affinity to liquid-like ribonucleoprotein assemblies. Stress-induced nuclear condensation transiently inactivates TDP-43, leading to loss of interaction with its protein binding partners and loss of function in splicing. Splicing changes are especially prominent and persisting for STMN2 RNA, and STMN2 protein becomes rapidly depleted early during stress. Our results point to early pathological changes to TDP-43 in the nucleus and support therapeutic modulation of stress response in ALS.
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Affiliation(s)
- Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Brittany C S Ellis
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Anna Sanchez Avila
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Vedanth Kumar
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Jessica Rayment
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK.
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22
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Scott-Hewitt N, Mahoney M, Huang Y, Korte N, Yvanka de Soysa T, Wilton DK, Knorr E, Mastro K, Chang A, Zhang A, Melville D, Schenone M, Hartigan C, Stevens B. Microglial-derived C1q integrates into neuronal ribonucleoprotein complexes and impacts protein homeostasis in the aging brain. Cell 2024:S0092-8674(24)00639-1. [PMID: 38942014 DOI: 10.1016/j.cell.2024.05.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/08/2024] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Abstract
Neuroimmune interactions mediate intercellular communication and underlie critical brain functions. Microglia, CNS-resident macrophages, modulate the brain through direct physical interactions and the secretion of molecules. One such secreted factor, the complement protein C1q, contributes to complement-mediated synapse elimination in both developmental and disease models, yet brain C1q protein levels increase significantly throughout aging. Here, we report that C1q interacts with neuronal ribonucleoprotein (RNP) complexes in an age-dependent manner. Purified C1q protein undergoes RNA-dependent liquid-liquid phase separation (LLPS) in vitro, and the interaction of C1q with neuronal RNP complexes in vivo is dependent on RNA and endocytosis. Mice lacking C1q have age-specific alterations in neuronal protein synthesis in vivo and impaired fear memory extinction. Together, our findings reveal a biophysical property of C1q that underlies RNA- and age-dependent neuronal interactions and demonstrate a role of C1q in critical intracellular neuronal processes.
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Affiliation(s)
- Nicole Scott-Hewitt
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Matthew Mahoney
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Youtong Huang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nils Korte
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - T Yvanka de Soysa
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel K Wilton
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Emily Knorr
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kevin Mastro
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Allison Chang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Allison Zhang
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - David Melville
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Monica Schenone
- The Broad Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Christina Hartigan
- The Broad Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Beth Stevens
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Investigator, Boston Children's Hospital, Boston, MA 02115, USA.
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23
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Picavet LW, Samat AAK, Calis J, Nijhuis L, Scholman R, Mokry M, Tough DF, Prinjha RK, Vastert SJ, van Loosdregt J. CBP/P300 Inhibition Impairs CD4+ T Cell Activation: Implications for Autoimmune Disorders. Biomedicines 2024; 12:1344. [PMID: 38927552 PMCID: PMC11202127 DOI: 10.3390/biomedicines12061344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
T cell activation is critical for an effective immune response against pathogens. However, dysregulation contributes to the pathogenesis of autoimmune diseases, including Juvenile Idiopathic Arthritis (JIA). The molecular mechanisms underlying T cell activation are still incompletely understood. T cell activation promotes the acetylation of histone 3 at Lysine 27 (H3K27ac) at enhancer and promoter regions of proinflammatory cytokines, thereby increasing the expression of these genes which is essential for T cell function. Co-activators E1A binding protein P300 (P300) and CREB binding protein (CBP), collectively known as P300/CBP, are essential to facilitate H3K27 acetylation. Presently, the role of P300/CBP in human CD4+ T cells activation remains incompletely understood. To assess the function of P300/CBP in T cell activation and autoimmune disease, we utilized iCBP112, a selective inhibitor of P300/CBP, in T cells obtained from healthy controls and JIA patients. Treatment with iCBP112 suppressed T cell activation and cytokine signaling pathways, leading to reduced expression of many proinflammatory cytokines, including IL-2, IFN-γ, IL-4, and IL-17A. Moreover, P300/CBP inhibition in T cells derived from the inflamed synovium of JIA patients resulted in decreased expression of similar pathways and preferentially suppressed the expression of disease-associated genes. This study underscores the regulatory role of P300/CBP in regulating gene expression during T cell activation while offering potential insights into the pathogenesis of autoimmune diseases. Our findings indicate that P300/CBP inhibition could potentially be leveraged for the treatment of autoimmune diseases such as JIA in the future.
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Affiliation(s)
- Lucas Wilhelmus Picavet
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (A.A.K.S.); (J.C.); (L.N.); (R.S.); (S.J.V.)
| | - Anoushka A. K. Samat
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (A.A.K.S.); (J.C.); (L.N.); (R.S.); (S.J.V.)
| | - Jorg Calis
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (A.A.K.S.); (J.C.); (L.N.); (R.S.); (S.J.V.)
| | - Lotte Nijhuis
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (A.A.K.S.); (J.C.); (L.N.); (R.S.); (S.J.V.)
| | - Rianne Scholman
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (A.A.K.S.); (J.C.); (L.N.); (R.S.); (S.J.V.)
| | - Michal Mokry
- Department of Experimental Cardiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
| | - David F. Tough
- Immunology Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (D.F.T.); (R.K.P.)
| | - Rabinder K. Prinjha
- Immunology Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (D.F.T.); (R.K.P.)
| | - Sebastiaan J. Vastert
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (A.A.K.S.); (J.C.); (L.N.); (R.S.); (S.J.V.)
- Department of Pediatric Rheumatology and Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (L.W.P.); (A.A.K.S.); (J.C.); (L.N.); (R.S.); (S.J.V.)
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24
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Kato T, Matsumoto R, Yokomizo A, Tohi Y, Fukuhara H, Fujii Y, Mori K, Sato T, Inokuchi J, Hashine K, Sakamoto S, Kinoshita H, Inoue K, Tanikawa T, Utsumi T, Goto T, Hara I, Okuno H, Kakehi Y, Sugimoto M. Outcomes of active surveillance for Japanese patients with prostate cancer (PRIAS-JAPAN). BJU Int 2024. [PMID: 38886979 DOI: 10.1111/bju.16436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
OBJECTIVE To report the outcomes of repeat biopsies, metastasis and survival in the Prostate Cancer Research International: Active Surveillance (PRIAS)-JAPAN study, a prospective observational study for Japanese patients, initiated in 2010. PATIENTS AND METHODS At the beginning, inclusion criteria were initially low-risk patients, prostate-specific antigen (PSA) density (PSAD) <0.2, and ≤2 positive biopsy cores. As from 2014, GS3+4 has also been allowed for patients aged 70 years and over. Since January 2021, the age limit for Gleason score (GS) 3 + 4 cases was removed, and eligibility criteria were expanded to PSA ≤20 ng/mL, PSAD <0.25 nd/mL/cc, unlimited number of positive GS 3 + 3 cores, and positive results for fewer than half of the total number of cores for GS 3 + 4 cases if magnetic resonance imaging fusion biopsy was performed at study enrolment or subsequent follow-up. For patients eligible for active surveillance, PSA tests were performed every 3 months, rectal examination every 6 months, and biopsies at 1, 4, 7 and 10 years, followed by every 5 years thereafter. Patients with confirmed pathological reclassification were recommended for secondary treatments. RESULTS As of February 2024, 1302 patients were enrolled in AS; 1274 (98%) met the eligibility criteria. The median (interquartile range) age, PSA level, PSAD, and number of positive cores were 69 (64-73) years, 5.3 (4.5-6.6) ng/mL, 0.15 (0.12-0.17) ng/mL, and 1 (1-2), respectively. The clinical stage was T1c in 1089 patients (86%) and T2 in 185 (15%). The rates of acceptance by patients for the first, second, third and fourth re-biopsies were 83%, 64%, 41% and 22%, respectively. The pathological reclassification rates for the first, second, third and fourth re-biopsies were 29%, 30%, 35% and 25%, respectively. The 1-, 5- and 10-year persistence rates were 77%, 45% and 23%, respectively. Six patients developed metastasis, and one patient died from prostate cancer. CONCLUSION Pathological reclassification was observed in approximately 30% of the patients during biopsy; however, biopsy acceptance rates decreased over time. Although metastasis occurred in six patients, only one death from prostate cancer was recorded.
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Affiliation(s)
- Takuma Kato
- Department of Urology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, Japan
| | - Ryuji Matsumoto
- Department of Renal and Genito-Urinary Surgery, Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Akira Yokomizo
- Department of Urology, Harasanshin Hospital, Fukuoka, Japan
| | - Yoichiro Tohi
- Department of Urology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, Japan
| | - Hiroshi Fukuhara
- Department of Urology, Faculty of Medicine, Kyorin University, Tokyo, Japan
| | - Yoichi Fujii
- Department of Urology, Faculty of Medicine, Tokyo University, Tokyo, Japan
| | - Keiichiro Mori
- Department of Urology, Jikei University School of Medicine, Tokyo, Japan
| | - Takuma Sato
- Department of Urology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Junichi Inokuchi
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuyoshi Hashine
- Department of Urology, NHO Shikoku Cancer Center, Matsuyama, Ehime, Japan
| | - Shinichi Sakamoto
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidefumi Kinoshita
- Department of Urology, Faculty of Medicine, Kansai Medical University, Osaka, Japan
| | - Koji Inoue
- Department of Urology, Kurashiki Central Hospital, Kurashiki, Okayama, Japan
| | - Toshiki Tanikawa
- Department of Urology, Niigata Cancer Center Hospital, Niigata, Japan
| | - Takanobu Utsumi
- Department of Urology, Toho University Sakura Medical Center, Chiba, Japan
| | - Takayuki Goto
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Isao Hara
- Department of Urology, Wakayama Medical University, Wakayama, Japan
| | - Hiroshi Okuno
- Department of Urology, Kyoto Medical Center, Kyoto, Japan
| | - Yoshiyuki Kakehi
- Department of Urology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, Japan
| | - Mikio Sugimoto
- Department of Urology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, Japan
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25
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Gottardelli B, Gatta R, Nucciarelli L, Tudor AM, Tavazzi E, Vallati M, Orini S, Di Giorgi N, Damiani A. GEN-RWD Sandbox: bridging the gap between hospital data privacy and external research insights with distributed analytics. BMC Med Inform Decis Mak 2024; 24:170. [PMID: 38886772 PMCID: PMC11184891 DOI: 10.1186/s12911-024-02549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Artificial intelligence (AI) has become a pivotal tool in advancing contemporary personalised medicine, with the goal of tailoring treatments to individual patient conditions. This has heightened the demand for access to diverse data from clinical practice and daily life for research, posing challenges due to the sensitive nature of medical information, including genetics and health conditions. Regulations like the Health Insurance Portability and Accountability Act (HIPAA) in the U.S. and the General Data Protection Regulation (GDPR) in Europe aim to strike a balance between data security, privacy, and the imperative for access. RESULTS We present the Gemelli Generator - Real World Data (GEN-RWD) Sandbox, a modular multi-agent platform designed for distributed analytics in healthcare. Its primary objective is to empower external researchers to leverage hospital data while upholding privacy and ownership, obviating the need for direct data sharing. Docker compatibility adds an extra layer of flexibility, and scalability is assured through modular design, facilitating combinations of Proxy and Processor modules with various graphical interfaces. Security and reliability are reinforced through components like Identity and Access Management (IAM) agent, and a Blockchain-based notarisation module. Certification processes verify the identities of information senders and receivers. CONCLUSIONS The GEN-RWD Sandbox architecture achieves a good level of usability while ensuring a blend of flexibility, scalability, and security. Featuring a user-friendly graphical interface catering to diverse technical expertise, its external accessibility enables personnel outside the hospital to use the platform. Overall, the GEN-RWD Sandbox emerges as a comprehensive solution for healthcare distributed analytics, maintaining a delicate equilibrium between accessibility, scalability, and security.
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Affiliation(s)
- Benedetta Gottardelli
- Department of Diagnostic Imaging, Oncological Radiotherapy and Hematology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roberto Gatta
- Department of Clinical and Experimental Sciences, Università degli Studi di Brescia, Brescia, Italy
| | - Leonardo Nucciarelli
- Department of Diagnostic Imaging, Oncological Radiotherapy and Hematology, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Andrada Mihaela Tudor
- Department of Diagnostic Imaging, Oncological Radiotherapy and Hematology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Erica Tavazzi
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Mauro Vallati
- School of Computing and Engineering, University of Huddersfield, Huddersfield, UK
| | - Stefania Orini
- Department of Clinical and Experimental Sciences, Università degli Studi di Brescia, Brescia, Italy
- Alzheimer Operative Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | - Andrea Damiani
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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Carraro C, Montgomery JV, Klimmt J, Paquet D, Schultze JL, Beyer MD. Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs. Front Mol Neurosci 2024; 17:1414886. [PMID: 38952421 PMCID: PMC11215216 DOI: 10.3389/fnmol.2024.1414886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024] Open
Abstract
Drug discovery is a generally inefficient and capital-intensive process. For neurodegenerative diseases (NDDs), the development of novel therapeutics is particularly urgent considering the long list of late-stage drug candidate failures. Although our knowledge on the pathogenic mechanisms driving neurodegeneration is growing, additional efforts are required to achieve a better and ultimately complete understanding of the pathophysiological underpinnings of NDDs. Beyond the etiology of NDDs being heterogeneous and multifactorial, this process is further complicated by the fact that current experimental models only partially recapitulate the major phenotypes observed in humans. In such a scenario, multi-omic approaches have the potential to accelerate the identification of new or repurposed drugs against a multitude of the underlying mechanisms driving NDDs. One major advantage for the implementation of multi-omic approaches in the drug discovery process is that these overarching tools are able to disentangle disease states and model perturbations through the comprehensive characterization of distinct molecular layers (i.e., genome, transcriptome, proteome) up to a single-cell resolution. Because of recent advances increasing their affordability and scalability, the use of omics technologies to drive drug discovery is nascent, but rapidly expanding in the neuroscience field. Combined with increasingly advanced in vitro models, which particularly benefited from the introduction of human iPSCs, multi-omics are shaping a new paradigm in drug discovery for NDDs, from disease characterization to therapeutics prediction and experimental screening. In this review, we discuss examples, main advantages and open challenges in the use of multi-omic approaches for the in vitro discovery of targets and therapies against NDDs.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jessica V. Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
| | - Julien Klimmt
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
| | - Marc D. Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
- PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn and West German Genome Center, Bonn, Germany
- Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), Bonn, Germany
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27
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Popovic MM, Balas M, Sadda SR, Sarraf D, Huang R, Bakri SJ, Berrocal A, Chang A, Gemmy Cheung CM, Garg S, Hillier RJ, Holz FG, Johnson MW, Kaiser PK, Kertes PJ, Lai TYY, Noble J, Park SS, Paulus YM, Querques G, Rachitskaya A, Ruamviboonsuk P, Saidkasimova S, Sandinha MT, Steel DH, Terasaki H, Weng CY, Williams BK, Wu L, Muni RH. International Classification System for Ocular Complications of Anti-VEGF Agents in Clinical Trials. Ophthalmology 2024:S0161-6420(24)00366-X. [PMID: 38878904 DOI: 10.1016/j.ophtha.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 04/10/2024] [Accepted: 06/06/2024] [Indexed: 07/25/2024] Open
Abstract
PURPOSE Complications associated with intravitreal anti-VEGF therapies are reported inconsistently in the literature, thus limiting an accurate evaluation and comparison of safety between studies. This study aimed to develop a standardized classification system for anti-VEGF ocular complications using the Delphi consensus process. DESIGN Systematic review and Delphi consensus process. PARTICIPANTS Twenty-five international retinal specialists participated in the Delphi consensus survey. METHODS A systematic literature search was conducted to identify complications of intravitreal anti-VEGF agent administration based on randomized controlled trials (RCTs) of anti-VEGF therapy. A comprehensive list of complications was derived from these studies, and this list was subjected to iterative Delphi consensus surveys involving international retinal specialists who voted on inclusion, exclusion, rephrasing, and addition of complications. Furthermore, surveys determined specifiers for the selected complications. This iterative process helped to refine the final classification system. MAIN OUTCOME MEASURES The proportion of retinal specialists who choose to include or exclude complications associated with anti-VEGF administration. RESULTS After screening 18 229 articles, 130 complications were categorized from 145 included RCTs. Participant consensus via the Delphi method resulted in the inclusion of 91 complications (70%) after 3 rounds. After incorporating further modifications made based on participant suggestions, such as rewording certain phrases and combining similar terms, 24 redundant complications were removed, leaving a total of 67 complications (52%) in the final list. A total of 14 complications (11%) met exclusion thresholds and were eliminated by participants across both rounds. All other remaining complications not meeting inclusion or exclusion thresholds also were excluded from the final classification system after the Delphi process terminated. In addition, 47 of 75 proposed complication specifiers (63%) were included based on participant agreement. CONCLUSIONS Using the Delphi consensus process, a comprehensive, standardized classification system consisting of 67 ocular complications and 47 unique specifiers was established for intravitreal anti-VEGF agents in clinical trials. The adoption of this system in future trials could improve consistency and quality of adverse event reporting, potentially facilitating more accurate risk-benefit analyses. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Marko M Popovic
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Michael Balas
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - SriniVas R Sadda
- Doheny Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - David Sarraf
- Stein Eye Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Ryan Huang
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Sophie J Bakri
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Audina Berrocal
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Leonard M. Miller School of Medicine, Miami, Florida
| | - Andrew Chang
- Sydney Retina Clinic, Sydney Eye Hospital, University of New South Wales, Sydney, Australia
| | - Chui Ming Gemmy Cheung
- Department of Ophthalmology, National University of Singapore, Singapore, Republic of Singapore
| | - Sunir Garg
- Mid Atlantic Retina, The Retina Service of Wills Eye Hospital, Wills Eye Hospital, Philadelphia, Pennsylvania
| | - Roxane J Hillier
- Newcastle Eye Centre, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Frank G Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Mark W Johnson
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan
| | | | - Peter J Kertes
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Timothy Y Y Lai
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong, China
| | - Jason Noble
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Susanna S Park
- Department of Ophthalmology & Vision Science, University of California Davis Eye Center, Sacramento, California
| | - Yannis M Paulus
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan
| | - Giuseppe Querques
- Department of Ophthalmology, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | | | - Paisan Ruamviboonsuk
- Department of Ophthalmology, College of Medicine, Rangsit University, Rajavithi Hospital, Bangkok, Thailand
| | | | - Maria Teresa Sandinha
- Department of Eye and Visual Science, University of Liverpool, Merseyside, United Kingdom
| | - David H Steel
- Sunderland Eye Infirmary, Sunderland, United Kingdom
| | | | - Christina Y Weng
- Cullen Eye Institute, Baylor College of Medicine, Houston, Texas
| | - Basil K Williams
- Cincinnati Eye Institute, Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Lihteh Wu
- Department of Ophthalmology, Asociados de Mácula Vitreo y Retina de Costa Rica, San José, Costa Rica
| | - Rajeev H Muni
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada.
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Bazant J, Weiss A, Baldauf J, Schermuly RT, Hain T, Lucas R, Mraheil MA. Pneumococcal hydrogen peroxide regulates host cell kinase activity. Front Immunol 2024; 15:1414195. [PMID: 38903521 PMCID: PMC11188345 DOI: 10.3389/fimmu.2024.1414195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Protein kinases are indispensable reversible molecular switches that adapt and control protein functions during cellular processes requiring rapid responses to internal and external events. Bacterial infections can affect kinase-mediated phosphorylation events, with consequences for both innate and adaptive immunity, through regulation of antigen presentation, pathogen recognition, cell invasiveness and phagocytosis. Streptococcus pneumoniae (Spn), a human respiratory tract pathogen and a major cause of community-acquired pneumoniae, affects phosphorylation-based signalling of several kinases, but the pneumococcal mediator(s) involved in this process remain elusive. In this study, we investigated the influence of pneumococcal H2O2 on the protein kinase activity of the human lung epithelial H441 cell line, a generally accepted model of alveolar epithelial cells. Methods We performed kinome analysis using PamGene microarray chips and protein analysis in Western blotting in H441 lung cells infected with Spn wild type (SpnWT) or with SpnΔlctOΔspxB -a deletion mutant strongly attenuated in H2O2 production- to assess the impact of pneumococcal hydrogen peroxide (H2O2) on global protein kinase activity profiles. Results Our kinome analysis provides direct evidence that kinase activity profiles in infected H441 cells significantly vary according to the levels of pneumococcal H2O2. A large number of kinases in H441 cells infected with SpnWT are significantly downregulated, whereas this no longer occurs in cells infected with the mutant SpnΔlctOΔspxB strain, which lacks H2O2. In particular, we describe for the first time H2O2-mediated downregulation of Protein kinase B (Akt1) and activation of lymphocyte-specific tyrosine protein kinase (Lck) via H2O2-mediated phosphorylation.
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Affiliation(s)
- Jasmin Bazant
- Institute of Medical Microbiology, German Centre for Infection Giessen-Marburg-Langen Site, Justus-Liebig University Giessen, Giessen, Germany
| | - Astrid Weiss
- Department of Internal Medicine, Cardio–Pulmonary Institute (CPI), Member of German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Julia Baldauf
- Department of Internal Medicine, Cardio–Pulmonary Institute (CPI), Member of German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Ralph Theo Schermuly
- Department of Internal Medicine, Cardio–Pulmonary Institute (CPI), Member of German Center for Lung Research (DZL), Justus-Liebig University Giessen, Giessen, Germany
| | - Torsten Hain
- Institute of Medical Microbiology, German Centre for Infection Giessen-Marburg-Langen Site, Justus-Liebig University Giessen, Giessen, Germany
| | - Rudolf Lucas
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, GA, United States
- Division of Pulmonary, Sleep and Critical Care Medicine, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Mobarak Abu Mraheil
- Institute of Medical Microbiology, German Centre for Infection Giessen-Marburg-Langen Site, Justus-Liebig University Giessen, Giessen, Germany
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Kang S, Ko EY, Andrews AE, Shin JE, Nance KJ, Barman PK, Heeger PS, Freeman WM, Benayoun BA, Goodridge HS. Microglia undergo sex-dimorphic transcriptional and metabolic rewiring during aging. J Neuroinflammation 2024; 21:150. [PMID: 38840206 PMCID: PMC11155174 DOI: 10.1186/s12974-024-03130-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Microglia, the brain's resident macrophages, maintain brain homeostasis and respond to injury and infection. During aging they undergo functional changes, but the underlying mechanisms and their contributions to neuroprotection versus neurodegeneration are unclear. Previous studies suggested that microglia are sex dimorphic, so we compared microglial aging in mice of both sexes. RNA-sequencing of hippocampal microglia revealed more aging-associated changes in female microglia than male microglia, and more sex differences in old microglia than young microglia. Pathway analyses and subsequent validation assays revealed a stronger AKT-mTOR-HIF1α-driven shift to glycolysis among old female microglia and indicated that C3a production and detection was elevated in old microglia, especially in females. Recombinant C3a induced AKT-mTOR-HIF1α signaling and increased the glycolytic and phagocytic activity of young microglia. Single cell analyses attributed the aging-associated sex dimorphism to more abundant disease-associated microglia (DAM) in old female mice than old male mice, and evaluation of an Alzheimer's Disease mouse model revealed that the metabolic and complement changes are also apparent in the context of neurodegenerative disease and are strongest in the neuroprotective DAM2 subset. Collectively, our data implicate autocrine C3a-C3aR signaling in metabolic reprogramming of microglia to neuroprotective DAM during aging, especially in females, and also in Alzheimer's Disease.
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Affiliation(s)
- Seokjo Kang
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Emily Y Ko
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Amelia E Andrews
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Juliana E Shin
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Karina J Nance
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Pijus K Barman
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Peter S Heeger
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Willard M Freeman
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Molecular and Computational Biology Department, Arts and Sciences, USC Dornsife College of Letters, University of Southern California, Los Angeles, CA, 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Helen S Goodridge
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Research Division of Immunology in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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30
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Schäfer Y, Palitzsch K, Leptin M, Whiteley AR, Wiehe T, Suurväli J. Copy number variation and population-specific immune genes in the model vertebrate zebrafish. eLife 2024; 13:e98058. [PMID: 38832644 PMCID: PMC11192531 DOI: 10.7554/elife.98058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024] Open
Abstract
Copy number variation in large gene families is well characterized for plant resistance genes, but similar studies are rare in animals. The zebrafish (Danio rerio) has hundreds of NLR immune genes, making this species ideal for studying this phenomenon. By sequencing 93 zebrafish from multiple wild and laboratory populations, we identified a total of 1513 NLRs, many more than the previously known 400. Approximately half of those are present in all wild populations, but only 4% were found in 80% or more of the individual fish. Wild fish have up to two times as many NLRs per individual and up to four times as many NLRs per population than laboratory strains. In contrast to the massive variability of gene copies, nucleotide diversity in zebrafish NLR genes is very low: around half of the copies are monomorphic and the remaining ones have very few polymorphisms, likely a signature of purifying selection.
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Affiliation(s)
| | | | - Maria Leptin
- Institute for Genetics, University of CologneCologneGermany
| | - Andrew R Whiteley
- WA Franke College of Forestry and Conservation, University of MontanaMissoulaUnited States
| | - Thomas Wiehe
- Institute for Genetics, University of CologneCologneGermany
| | - Jaanus Suurväli
- Institute for Genetics, University of CologneCologneGermany
- Department of Biological Sciences, University of ManitobaWinnipegCanada
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31
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Zhong X, Peddada N, Moresco JJ, Wang J, Jiang Y, Rios JJ, Moresco EMY, Choi JH, Beutler B. Viable mutations of mouse midnolin suppress B cell malignancies. J Exp Med 2024; 221:e20232132. [PMID: 38625151 PMCID: PMC11022886 DOI: 10.1084/jem.20232132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/20/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
In a genetic screen, we identified two viable missense alleles of the essential gene Midnolin (Midn) that were associated with reductions in peripheral B cells. Causation was confirmed in mice with targeted deletion of four of six MIDN protein isoforms. MIDN was expressed predominantly in lymphocytes where it augmented proteasome activity. We showed that purified MIDN directly stimulated 26S proteasome activity in vitro in a manner dependent on the ubiquitin-like domain and a C-terminal region. MIDN-deficient B cells displayed aberrant activation of the IRE-1/XBP-1 pathway of the unfolded protein response. Partial or complete MIDN deficiency strongly suppressed Eμ-Myc-driven B cell leukemia and the antiapoptotic effects of Eμ-BCL2 on B cells in vivo and induced death of Sp2/0 hybridoma cells in vitro, but only partially impaired normal lymphocyte development. Thus, MIDN is required for proteasome activity in support of normal lymphopoiesis and is essential for malignant B cell proliferation over a broad range of differentiation states.
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Affiliation(s)
- Xue Zhong
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nagesh Peddada
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James J. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yiao Jiang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eva Marie Y. Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Ersoy B, Herzog ML, Pan W, Schilling S, Endres M, Göttert R, Kronenberg GD, Gertz K. The atypical antidepressant tianeptine confers neuroprotection against oxygen-glucose deprivation. Eur Arch Psychiatry Clin Neurosci 2024; 274:777-791. [PMID: 37653354 PMCID: PMC11127858 DOI: 10.1007/s00406-023-01685-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Proregenerative and neuroprotective effects of antidepressants are an important topic of inquiry in neuropsychiatric research. Oxygen-glucose deprivation (OGD) mimics key aspects of ischemic injury in vitro. Here, we studied the effects of 24-h pretreatment with serotonin (5-HT), citalopram (CIT), fluoxetine (FLU), and tianeptine (TIA) on primary mouse cortical neurons subjected to transient OGD. 5-HT (50 μM) significantly enhanced neuron viability as measured by MTT assay and reduced cell death and LDH release. CIT (10 μM) and FLU (1 μM) did not increase the effects of 5-HT and neither antidepressant conferred neuroprotection in the absence of supplemental 5-HT in serum-free cell culture medium. By contrast, pre-treatment with TIA (10 μM) resulted in robust neuroprotection, even in the absence of 5-HT. Furthermore, TIA inhibited mRNA transcription of candidate genes related to cell death and hypoxia and attenuated lipid peroxidation, a hallmark of neuronal injury. Finally, deep RNA sequencing of primary neurons subjected to OGD demonstrated that OGD induces many pathways relating to cell survival, the inflammation-immune response, synaptic dysregulation and apoptosis, and that TIA pretreatment counteracted these effects of OGD. In conclusion, this study highlights the comparative strength of the 5-HT independent neuroprotective effects of TIA and identifies the molecular pathways involved.
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Affiliation(s)
- Burcu Ersoy
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marie-Louise Herzog
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
| | - Wen Pan
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
| | - Simone Schilling
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Endres
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
- Einstein Center for Neurosciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
- DZNE (German Center for Neurodegenerative Diseases), Partner site, Berlin, Germany
- DZPG (German Center for Mental Health), Partner site, Berlin, Germany
| | - Ria Göttert
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany
| | - Golo D Kronenberg
- Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry Zürich, Lenggstrasse 31, P.O. Box 363, 8032, Zurich, Switzerland
| | - Karen Gertz
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Center for Stroke Research Berlin, Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research), Partner site, Berlin, Germany.
- Einstein Center for Neurosciences, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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33
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Rebak AS, Hendriks IA, Elsborg JD, Buch-Larsen SC, Nielsen CH, Terslev L, Kirsch R, Damgaard D, Doncheva NT, Lennartsson C, Rykær M, Jensen LJ, Christophorou MA, Nielsen ML. A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nat Struct Mol Biol 2024; 31:977-995. [PMID: 38321148 PMCID: PMC11189309 DOI: 10.1038/s41594-024-01214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/04/2024] [Indexed: 02/08/2024]
Abstract
Despite the importance of citrullination in physiology and disease, global identification of citrullinated proteins, and the precise targeted sites, has remained challenging. Here we employed quantitative-mass-spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites within the HL60 leukemia cell line following differentiation into neutrophil-like cells. We identified 14,056 citrullination sites within 4,008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. With this resource, we provide quantitative and site-specific information on thousands of PADI4 substrates, including signature histone marks and transcriptional regulators. Additionally, using peptide microarrays, we demonstrate the potential clinical relevance of certain identified sites, through distinct reactivities of antibodies contained in synovial fluid from anti-CCP-positive and anti-CCP-negative people with rheumatoid arthritis. Collectively, we describe the human citrullinome at a systems-wide level, provide a resource for understanding citrullination at the mechanistic level and link the identified targeted sites to rheumatoid arthritis.
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Affiliation(s)
- Alexandra S Rebak
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas D Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lene Terslev
- Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rebecca Kirsch
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dres Damgaard
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nadezhda T Doncheva
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Lennartsson
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Rykær
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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34
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Jauhiainen S, Onyeogaziri FC, Lazzaroni F, Conze LL, Laakkonen JP, Laham-Karam N, Laakso A, Niemelä M, Rezai Jahromi B, Magnusson PU. Proteomics on human cerebral cavernous malformations reveals novel biomarkers in neurovascular dysfunction for the disease pathology. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167139. [PMID: 38537685 DOI: 10.1016/j.bbadis.2024.167139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Cerebral cavernous malformation (CCM) is a disease associated with an elevated risk of focal neurological deficits, seizures, and hemorrhagic stroke. The disease has an inflammatory profile and improved knowledge of CCM pathology mechanisms and exploration of candidate biomarkers will enable new non-invasive treatments. METHODS We analyzed protein signatures in human CCM tissue samples by using a highly specific and sensitive multiplexing technique, proximity extension assay. FINDINGS Data analysis revealed CCM specific proteins involved in endothelial dysfunction/inflammation/activation, leukocyte infiltration/chemotaxis, hemostasis, extracellular matrix dysfunction, astrocyte and microglial cell activation. Biomarker expression profiles matched bleeding status, especially with higher levels of inflammatory markers and activated astrocytes in ruptured than non-ruptured samples, some of these biomarkers are secreted into blood or urine. Furthermore, analysis was also done in a spatially resolving manner by separating the lesion area from the surrounding brain tissue. Our spatial studies revealed that although appearing histologically normal, the CCM border areas were pathological when compared to control brain tissues. Moreover, the functional relevance of CD93, ICAM-1 and MMP9, markers related to endothelial cell activation and extracellular matrix was validated by a murine pre-clinical CCM model. INTERPRETATION Here we present a novel strategy for proteomics analysis on human CCMs, offering a possibility for high-throughput protein screening acquiring data on the local environment in the brain. Our data presented here describe CCM relevant brain proteins and specifically those which are secreted can serve the need of circulating CCM biomarkers to predict cavernoma's risk of bleeding.
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Affiliation(s)
- Suvi Jauhiainen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Favour C Onyeogaziri
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Francesca Lazzaroni
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lei Liu Conze
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johanna P Laakkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nihay Laham-Karam
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Aki Laakso
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mika Niemelä
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Behnam Rezai Jahromi
- Department of Neurosurgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peetra U Magnusson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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35
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Hwang SP, Denicourt C. The impact of ribosome biogenesis in cancer: from proliferation to metastasis. NAR Cancer 2024; 6:zcae017. [PMID: 38633862 PMCID: PMC11023387 DOI: 10.1093/narcan/zcae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
The dysregulation of ribosome biogenesis is a hallmark of cancer, facilitating the adaptation to altered translational demands essential for various aspects of tumor progression. This review explores the intricate interplay between ribosome biogenesis and cancer development, highlighting dynamic regulation orchestrated by key oncogenic signaling pathways. Recent studies reveal the multifaceted roles of ribosomes, extending beyond protein factories to include regulatory functions in mRNA translation. Dysregulated ribosome biogenesis not only hampers precise control of global protein production and proliferation but also influences processes such as the maintenance of stem cell-like properties and epithelial-mesenchymal transition, contributing to cancer progression. Interference with ribosome biogenesis, notably through RNA Pol I inhibition, elicits a stress response marked by nucleolar integrity loss, and subsequent G1-cell cycle arrest or cell death. These findings suggest that cancer cells may rely on heightened RNA Pol I transcription, rendering ribosomal RNA synthesis a potential therapeutic vulnerability. The review further explores targeting ribosome biogenesis vulnerabilities as a promising strategy to disrupt global ribosome production, presenting therapeutic opportunities for cancer treatment.
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Affiliation(s)
- Sseu-Pei Hwang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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36
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Fernandez A, Hoq MR, Hallinan GI, Li D, Bharath SR, Vago FS, Zhang X, Ozcan KA, Newell KL, Garringer HJ, Jiang W, Ghetti B, Vidal R. Cryo-EM structures of amyloid-β and tau filaments in Down syndrome. Nat Struct Mol Biol 2024; 31:903-909. [PMID: 38553642 PMCID: PMC11189299 DOI: 10.1038/s41594-024-01252-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/09/2024] [Indexed: 04/10/2024]
Abstract
Adult individuals with Down syndrome (DS) develop Alzheimer disease (AD). Whether there is a difference between AD in DS and AD regarding the structure of amyloid-β (Aβ) and tau filaments is unknown. Here we report the structure of Aβ and tau filaments from two DS brains. We found two Aβ40 filaments (types IIIa and IIIb) that differ from those previously reported in sporadic AD and two types of Aβ42 filaments (I and II) identical to those found in sporadic and familial AD. Tau filaments (paired helical filaments and straight filaments) were identical to those in AD, supporting the notion of a common mechanism through which amyloids trigger aggregation of tau. This knowledge is important for understanding AD in DS and assessing whether adults with DS could be included in AD clinical trials.
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Affiliation(s)
- Anllely Fernandez
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Md Rejaul Hoq
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Grace I Hallinan
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Daoyi Li
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Sakshibeedu R Bharath
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Frank S Vago
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Xiaoqi Zhang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Kadir A Ozcan
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA.
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
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37
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Johansen A, Thiede B, Anonsen JH, Nilsson GE. Phosphoproteomic changes in response to anoxia are tissue-specific in the anoxia-tolerant crucian carp ( Carassius carassius). Front Physiol 2024; 15:1407834. [PMID: 38872833 PMCID: PMC11170284 DOI: 10.3389/fphys.2024.1407834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024] Open
Abstract
Crucian carp (Carassius carassius), a freshwater fish, can survive chronic anoxia for several months at low temperatures. Consequently, anoxia-related physiological and biochemical adaptations in this species have been studied for more than half a century. Still, despite for the well-known role of protein phosphorylation in regulating cellular processes, no studies have comprehensively characterized the phosphoproteome in crucian carp. In this study, we report the global phosphoproteome in crucian carp brain and liver during anoxia and reoxygenation. By applying a bottom-up proteomic approach on enriched phosphopeptides we found that the brain phosphoproteome shows surprisingly few changes during anoxia-reoxygenation exposure with only 109 out of 4200 phosphopeptides being differentially changed compared to normoxic controls. By contrast, in the liver 395 out of 1287 phosphopeptides changed. Although most changes occurred in the liver phosphoproteome, the pattern of changes indicated metabolic depression and decreased translation in both brain and liver. We also found changes in phosphoproteins involved in apoptotic regulation and reactive oxygen species handling in both tissues. In the brain, some of the most changed phosphopeptides belonged to proteins involved in central nervous system development and neuronal activity at the synaptic cleft. Changed phosphoproteins specific for liver tissue were related to glucose metabolism, such as glycolytic flux and glycogenolysis. In conclusion, protein phosphorylation in response to anoxia and reoxygenation showed both common and tissue-specific changes related to the functional differences between brain and liver.
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Affiliation(s)
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jan Haug Anonsen
- Department of Biosciences, University of Oslo, Oslo, Norway
- Norwegian Research Centre AS, Climate and Environment Department, Stavanger, Norway
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38
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Tomić G, Sheridan C, Refermat AY, Baggelaar MP, Sipthorp J, Sudarshan B, Ocasio CA, Suárez-Bonnet A, Priestnall SL, Herbert E, Tate EW, Downward J. Palmitoyl transferase ZDHHC20 promotes pancreatic cancer metastasis. Cell Rep 2024; 43:114224. [PMID: 38733589 DOI: 10.1016/j.celrep.2024.114224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/04/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Metastasis is one of the defining features of pancreatic ductal adenocarcinoma (PDAC) that contributes to poor prognosis. In this study, the palmitoyl transferase ZDHHC20 was identified in an in vivo short hairpin RNA (shRNA) screen as critical for metastatic outgrowth, with no effect on proliferation and migration in vitro or primary PDAC growth in mice. This phenotype is abrogated in immunocompromised animals and animals with depleted natural killer (NK) cells, indicating that ZDHHC20 affects the interaction of tumor cells and the innate immune system. Using a chemical genetics platform for ZDHHC20-specific substrate profiling, a number of substrates of this enzyme were identified. These results describe a role for palmitoylation in enabling distant metastasis that could not have been detected using in vitro screening approaches and identify potential effectors through which ZDHHC20 promotes metastasis of PDAC.
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Affiliation(s)
- Goran Tomić
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Clare Sheridan
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Marc P Baggelaar
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, UK
| | - James Sipthorp
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, UK
| | | | - Cory A Ocasio
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alejandro Suárez-Bonnet
- The Royal Veterinary College, Department of Pathobiology & Population Sciences, Hawkshead Lane, Hatfield AL9 7TA, UK; Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Simon L Priestnall
- The Royal Veterinary College, Department of Pathobiology & Population Sciences, Hawkshead Lane, Hatfield AL9 7TA, UK; Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eleanor Herbert
- The Royal Veterinary College, Department of Pathobiology & Population Sciences, Hawkshead Lane, Hatfield AL9 7TA, UK; Experimental Histopathology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Edward W Tate
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, UK
| | - Julian Downward
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Tian X, Teo WFA, Yang Y, Dong L, Wong A, Chen L, Ahmed H, Choo SW, Jakubovics NS, Tan GYA. Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity. BMC Microbiol 2024; 24:185. [PMID: 38802738 PMCID: PMC11131293 DOI: 10.1186/s12866-024-03346-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences. RESULTS Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24. CONCLUSIONS Based on these findings, strain NCTC 9931T (= ATCC 17982T = DSM 43331T = CIP 104728T = CCUG 18309T = NCTC 14978T = CGMCC 1.90328T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24T (= NCTC 14980T = CGMCC 1.90329T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health. SIGNIFICANCE This research reveals two Schaalia strains, NCTC 9931 T and C24T, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics.
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Affiliation(s)
- Xuechen Tian
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Yixin Yang
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Linyinxue Dong
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
| | - Aloysius Wong
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Li Chen
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Halah Ahmed
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4BW, UK
| | - Siew Woh Choo
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA.
| | - Nicholas S Jakubovics
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4BW, UK.
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
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Abou Nader N, Charrier L, Meisnsohn MC, Banville L, Deffrennes B, St-Jean G, Boerboom D, Zamberlam G, Brind'Amour J, Pépin D, Boyer A. Lats1 and Lats2 regulate YAP and TAZ activity to control the development of mouse Sertoli cells. FASEB J 2024; 38:e23633. [PMID: 38690712 DOI: 10.1096/fj.202400346r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Recent reports suggest that the Hippo signaling pathway regulates testis development, though its exact roles in Sertoli cell differentiation remain unknown. Here, we examined the functions of the main Hippo pathway kinases, large tumor suppressor homolog kinases 1 and 2 (Lats1 and Lats2) in developing mouse Sertoli cells. Conditional inactivation of Lats1/2 in Sertoli cells resulted in the disorganization and overgrowth of the testis cords, the induction of a testicular inflammatory response and germ cell apoptosis. Stimulated by retinoic acid 8 (STRA8) expression in germ cells additionally suggested that germ cells may have been preparing to enter meiosis prior to their loss. Gene expression analyses of the developing testes of conditional knockout animals further suggested impaired Sertoli cell differentiation, epithelial-to-mesenchymal transition, and the induction of a specific set of genes associated with Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ)-mediated integrin signaling. Finally, the involvement of YAP/TAZ in Sertoli cell differentiation was confirmed by concomitantly inactivating Yap/Taz in Lats1/2 conditional knockout model, which resulted in a partial rescue of the testicular phenotypic changes. Taken together, these results identify Hippo signaling as a crucial pathway for Sertoli cell development and provide novel insight into Sertoli cell fate maintenance.
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Affiliation(s)
- Nour Abou Nader
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Laureline Charrier
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Marie-Charlotte Meisnsohn
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Laurence Banville
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Bérengère Deffrennes
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- École Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Guillaume St-Jean
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Derek Boerboom
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Gustavo Zamberlam
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Julie Brind'Amour
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - David Pépin
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexandre Boyer
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
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41
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Xu J, Bock CH, Janisse J, Woo J, Cher ML, Ginsburg K, Yacoub R, Goodman M. Determinants of active surveillance uptake in a diverse population-based cohort of men with low-risk prostate cancer: The Treatment Options in Prostate Cancer Study (TOPCS). Cancer 2024; 130:1797-1806. [PMID: 38247317 DOI: 10.1002/cncr.35190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Active surveillance (AS) is the preferred strategy for low-risk prostate cancer (LRPC); however, limited data on determinants of AS adoption exist, particularly among Black men. METHODS Black and White newly diagnosed (from January 2014 through June 2017) patients with LRPC ≤75 years of age were identified through metro-Detroit and Georgia population-based cancer registries and completed a survey evaluating factors influencing AS uptake. RESULTS Among 1688 study participants, 57% chose AS (51% of Black participants, 61% of White) over definitive treatment. In the unadjusted analysis, patient factors associated with initial AS uptake included older age, White race, and higher education. However, after adjusting for covariates, none of these factors was significant predictors of AS uptake. The strongest determinant of AS uptake was the AS recommendation by a urologist (adjusted prevalence ratio, 6.59, 95% CI, 4.84-8.97). Other factors associated with the decision to undergo AS included a shared patient-physician treatment decision, greater prostate cancer knowledge, and residence in metro-Detroit compared with Georgia. Conversely, men whose decision was strongly influenced by the desire to achieve "cure" or "live longer" with treatment and those who perceived their LRPC diagnosis as more serious were less likely to choose AS. CONCLUSIONS In this contemporary sample, the majority of patients with newly diagnosed LRPC chose AS. Although the input from their urologists was highly influential, several patient decisional and psychological factors were independently associated with AS uptake. These data shed new light on potentially modifiable factors that can help further increase AS uptake among patients with LRPC.
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Affiliation(s)
- Jinping Xu
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Cathryn H Bock
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - James Janisse
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Justin Woo
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Michael L Cher
- Department of Urology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Kevin Ginsburg
- Department of Urology, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Rami Yacoub
- Department of Epidemiology, School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Michael Goodman
- Department of Epidemiology, School of Public Health, Emory University, Atlanta, Georgia, USA
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42
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Vermassen T, Lumen N, Van Praet C, Callewaert N, Delanghe J, Rottey S. The Association between Urine N-Glycome and Prognosis after Initial Therapy for Primary Prostate Cancer. Biomedicines 2024; 12:1039. [PMID: 38791001 PMCID: PMC11118943 DOI: 10.3390/biomedicines12051039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Next to prostate-specific antigen, no biochemical biomarkers have been implemented to guide patient follow-up after primary therapy for localized prostate cancer (PCa). We evaluated the prognostic potential of urine N-glycome in terms of event-free survival (EFS) in patients undergoing primary therapy for PCa. The prognostic features of the urine N-glycosylation profile at diagnosis, assessed in 77 PCa patients, were determined in terms of EFS next to standard clinical parameters. The majority of patients were diagnosed with International Society of Urological Pathology grade ≤ 3 (82%) T1-2 tumors (79%) and without pelvic lymph node invasion (96%). The patients underwent active surveillance (14%), robot-assisted laparoscopic prostatectomy (48%), or external beam radiotherapy (37%). Decreased ratios of biantennary core-fucosylation were noted in patients who developed an event, which was linked to a shorter EFS in both the intention-to-treat cohort and all subcohort analyses. Combining the urine N-glycan biomarker with the D'Amico Risk Classification for PCa resulted in an improved nomogram for patient classification after primary therapy. The rate of urine N-glycan biantennary core-fucosylation, typically linked to more aggressive disease status, is lower in patients who eventually developed an event following primary therapy and subsequently in patients with a worse EFS. The combination of urine N-glycan biomarkers together with clinical parameters could, therefore, improve the post-therapy follow-up of patients with PCa.
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Affiliation(s)
- Tijl Vermassen
- Department Medical Oncology, Ghent University Hospital, 9000 Ghent, Belgium
- Biomarkers in Cancer, Department Basic and Applied Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
| | - Nicolaas Lumen
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department Urology (ERN eUROGEN Accredited Centre), Ghent University Hospital, 9000 Ghent, Belgium
- Uro-Oncology Research Group, Department Human Structure and Repair, Ghent University, 9000 Ghent, Belgium
| | - Charles Van Praet
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department Urology (ERN eUROGEN Accredited Centre), Ghent University Hospital, 9000 Ghent, Belgium
- Uro-Oncology Research Group, Department Human Structure and Repair, Ghent University, 9000 Ghent, Belgium
| | - Nico Callewaert
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department Molecular Biomedical Research, VIB-UGent Center for Medical Biotechnology, 9052 Ghent, Belgium
- Department Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Joris Delanghe
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sylvie Rottey
- Department Medical Oncology, Ghent University Hospital, 9000 Ghent, Belgium
- Biomarkers in Cancer, Department Basic and Applied Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Drug Research Unit Ghent, Ghent University Hospital, 9000 Ghent, Belgium
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Selheim F, Aasebø E, Reikvam H, Bruserud Ø, Hernandez-Valladares M. Monocytic Differentiation of Human Acute Myeloid Leukemia Cells: A Proteomic and Phosphoproteomic Comparison of FAB-M4/M5 Patients with and without Nucleophosmin 1 Mutations. Int J Mol Sci 2024; 25:5080. [PMID: 38791118 PMCID: PMC11121526 DOI: 10.3390/ijms25105080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Even though morphological signs of differentiation have a minimal impact on survival after intensive cytotoxic therapy for acute myeloid leukemia (AML), monocytic AML cell differentiation (i.e., classified as French/American/British (FAB) subtypes M4/M5) is associated with a different responsiveness both to Bcl-2 inhibition (decreased responsiveness) and possibly also bromodomain inhibition (increased responsiveness). FAB-M4/M5 patients are heterogeneous with regard to genetic abnormalities, even though monocytic differentiation is common for patients with Nucleophosmin 1 (NPM1) insertions/mutations; to further study the heterogeneity of FAB-M4/M5 patients we did a proteomic and phosphoproteomic comparison of FAB-M4/M5 patients with (n = 13) and without (n = 12) NPM1 mutations. The proteomic profile of NPM1-mutated FAB-M4/M5 patients was characterized by increased levels of proteins involved in the regulation of endocytosis/vesicle trafficking/organellar communication. In contrast, AML cells without NPM1 mutations were characterized by increased levels of several proteins involved in the regulation of cytoplasmic translation, including a large number of ribosomal proteins. The phosphoproteomic differences between the two groups were less extensive but reflected similar differences. To conclude, even though FAB classification/monocytic differentiation are associated with differences in responsiveness to new targeted therapies (e.g., Bcl-2 inhibition), our results shows that FAB-M4/M5 patients are heterogeneous with regard to important biological characteristics of the leukemic cells.
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Affiliation(s)
- Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Elise Aasebø
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
| | - Håkon Reikvam
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Øystein Bruserud
- Acute Leukemia Research Group, Department of Clinical Science, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway; (E.A.); (H.R.); (Ø.B.)
- Section for Hematology, Department of Medicine, Haukeland University Hospital, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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44
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Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D’Eustachio P, Wu G. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. Database (Oxford) 2024; 2024:baae031. [PMID: 38713862 PMCID: PMC11184451 DOI: 10.1093/database/baae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/23/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024]
Abstract
Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting changes to normal biology. A disease reaction is defined as an aberrant reaction in which a variant protein participates. A disease pathway is defined as a pathway that contains a disease reaction. Annotation of disease variants as participants of disease reactions and disease pathways can provide a standardized overview of molecular phenotypes of pathogenic variants that is amenable to computational mining and mathematical modeling. Reactome (https://reactome.org/), an open source, manually curated, peer-reviewed database of human biological pathways, in addition to providing annotations for >11 000 unique human proteins in the context of ∼15 000 wild-type reactions within more than 2000 wild-type pathways, also provides annotations for >4000 disease variants of close to 400 genes as participants of ∼800 disease reactions in the context of ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, described in wild-type reactions and pathways, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Reactome's data model enables mapping of disease variant datasets to specific disease reactions within disease pathways, providing a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity. Database URL: https://reactome.org/.
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Affiliation(s)
- Marija Orlic-Milacic
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Karen Rothfels
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Lisa Matthews
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Adam Wright
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Bijay Jassal
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Veronica Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Quang Trinh
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Marc E Gillespie
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
- College of Pharmacy and Health Sciences, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Cristoffer Sevilla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Krishna Tiwari
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eliot Ragueneau
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Chuqiao Gong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ralf Stephan
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
- Institute for Globally Distributed Open Research and Education (IGDORE)
| | - Bruce May
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Robin Haw
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Joel Weiser
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
| | - Deidre Beavers
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239, USA
| | - Patrick Conley
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239, USA
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Lincoln D Stein
- Adaptive Oncology, Ontario Institute for Cancer Research, 661 University Avenue Suite 510, Toronto, ON M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Room 4386, Toronto, ON M5S 1A8, Canada
| | - Peter D’Eustachio
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Guanming Wu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239, USA
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45
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Crowson MG, Nwosu OI. The Integration and Impact of Artificial Intelligence in Otolaryngology-Head and Neck Surgery: Navigating the Last Mile. Otolaryngol Clin North Am 2024:S0030-6665(24)00058-6. [PMID: 38705741 DOI: 10.1016/j.otc.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Incorporating artificial Intelligence and machine learning into otolaryngology requires careful data handling, security, and ethical considerations. Success depends on interdisciplinary cooperation, consistent innovation, and regulatory compliance to improve clinical outcomes, provider experience, and operational effectiveness.
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Affiliation(s)
- Matthew G Crowson
- Department of Otolaryngology-Head & Neck Surgery, Massachusetts Eye & Ear Hospital, Boston, MA, USA; Department of Otolaryngology-Head & Neck Surgery, Harvard Medical School, Boston, MA, USA.
| | - Obinna I Nwosu
- Department of Otolaryngology-Head & Neck Surgery, Massachusetts Eye & Ear Hospital, Boston, MA, USA; Department of Otolaryngology-Head & Neck Surgery, Harvard Medical School, Boston, MA, USA
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46
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Guglielmi V, Dalle Grave R, Leonetti F, Solini A. Female obesity: clinical and psychological assessment toward the best treatment. Front Endocrinol (Lausanne) 2024; 15:1349794. [PMID: 38765954 PMCID: PMC11099266 DOI: 10.3389/fendo.2024.1349794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
Obesity is a heterogeneous condition which results from complex interactions among sex/gender, sociocultural, environmental, and biological factors. Obesity is more prevalent in women in most developed countries, and several clinical and psychological obesity complications show sex-specific patterns. Females differ regarding fat distribution, with males tending to store more visceral fat, which is highly correlated to increased cardiovascular risk. Although women are more likely to be diagnosed with obesity and appear more motivated to lose weight, as confirmed by their greater representation in clinical trials, males show better outcomes in terms of body weight and intra-abdominal fat loss and improvements in the metabolic risk profile. However, only a few relatively recent studies have investigated gender differences in obesity, and sex/gender is rarely considered in the assessment and management of the disease. This review summarizes the evidence of gender differences in obesity prevalence, contributing factors, clinical complications, and psychological challenges. In addition, we explored gender differences in response to obesity treatments in the specific context of new anti-obesity drugs.
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Affiliation(s)
- Valeria Guglielmi
- Unit of Internal Medicine and Obesity Center, Department of Systems Medicine, Policlinico Tor Vergata, University of Rome Tor Vergata, Rome, Italy
| | - Riccardo Dalle Grave
- Department of Eating and Weight Disorders, Villa Garda Hospital, Garda, VR, Italy
| | - Frida Leonetti
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Anna Solini
- Department of Surgical, Medical, Molecular and Critical Area Pathology, University of Pisa, Pisa, Italy
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47
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Wang HE, Triebkorn P, Breyton M, Dollomaja B, Lemarechal JD, Petkoski S, Sorrentino P, Depannemaecker D, Hashemi M, Jirsa VK. Virtual brain twins: from basic neuroscience to clinical use. Natl Sci Rev 2024; 11:nwae079. [PMID: 38698901 PMCID: PMC11065363 DOI: 10.1093/nsr/nwae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 05/05/2024] Open
Abstract
Virtual brain twins are personalized, generative and adaptive brain models based on data from an individual's brain for scientific and clinical use. After a description of the key elements of virtual brain twins, we present the standard model for personalized whole-brain network models. The personalization is accomplished using a subject's brain imaging data by three means: (1) assemble cortical and subcortical areas in the subject-specific brain space; (2) directly map connectivity into the brain models, which can be generalized to other parameters; and (3) estimate relevant parameters through model inversion, typically using probabilistic machine learning. We present the use of personalized whole-brain network models in healthy ageing and five clinical diseases: epilepsy, Alzheimer's disease, multiple sclerosis, Parkinson's disease and psychiatric disorders. Specifically, we introduce spatial masks for relevant parameters and demonstrate their use based on the physiological and pathophysiological hypotheses. Finally, we pinpoint the key challenges and future directions.
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Affiliation(s)
- Huifang E Wang
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Paul Triebkorn
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Martin Breyton
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
- Service de Pharmacologie Clinique et Pharmacosurveillance, AP–HM, Marseille, 13005, France
| | - Borana Dollomaja
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Jean-Didier Lemarechal
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Spase Petkoski
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Pierpaolo Sorrentino
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Damien Depannemaecker
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Meysam Hashemi
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
| | - Viktor K Jirsa
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106; Marseille 13005, France
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48
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Gandaglia G, Pellegrino F, Golozar A, De Meulder B, Abbott T, Achtman A, Imran Omar M, Alshammari T, Areia C, Asiimwe A, Beyer K, Bjartell A, Campi R, Cornford P, Falconer T, Feng Q, Gong M, Herrera R, Hughes N, Hulsen T, Kinnaird A, Lai LYH, Maresca G, Mottet N, Oja M, Prinsen P, Reich C, Remmers S, Roobol MJ, Sakalis V, Seager S, Smith EJ, Snijder R, Steinbeisser C, Thurin NH, Hijazy A, van Bochove K, Van den Bergh RCN, Van Hemelrijck M, Willemse PP, Williams AE, Zounemat Kermani N, Evans-Axelsson S, Briganti A, N'Dow J. Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management: A PIONEER Analysis Based on Big Data. Eur Urol 2024; 85:457-465. [PMID: 37414703 DOI: 10.1016/j.eururo.2023.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Conservative management is an option for prostate cancer (PCa) patients either with the objective of delaying or even avoiding curative therapy, or to wait until palliative treatment is needed. PIONEER, funded by the European Commission Innovative Medicines Initiative, aims at improving PCa care across Europe through the application of big data analytics. OBJECTIVE To describe the clinical characteristics and long-term outcomes of PCa patients on conservative management by using an international large network of real-world data. DESIGN, SETTING, AND PARTICIPANTS From an initial cohort of >100 000 000 adult individuals included in eight databases evaluated during a virtual study-a-thon hosted by PIONEER, we identified newly diagnosed PCa cases (n = 527 311). Among those, we selected patients who did not receive curative or palliative treatment within 6 mo from diagnosis (n = 123 146). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Patient and disease characteristics were reported. The number of patients who experienced the main study outcomes was quantified for each stratum and the overall cohort. Kaplan-Meier analyses were used to estimate the distribution of time to event data. RESULTS AND LIMITATIONS The most common comorbidities were hypertension (35-73%), obesity (9.2-54%), and type 2 diabetes (11-28%). The rate of PCa-related symptomatic progression ranged between 2.6% and 6.2%. Hospitalization (12-25%) and emergency department visits (10-14%) were common events during the 1st year of follow-up. The probability of being free from both palliative and curative treatments decreased during follow-up. Limitations include a lack of information on patients and disease characteristics and on treatment intent. CONCLUSIONS Our results allow us to better understand the current landscape of patients with PCa managed with conservative treatment. PIONEER offers a unique opportunity to characterize the baseline features and outcomes of PCa patients managed conservatively using real-world data. PATIENT SUMMARY Up to 25% of men with prostate cancer (PCa) managed conservatively experienced hospitalization and emergency department visits within the 1st year after diagnosis; 6% experienced PCa-related symptoms. The probability of receiving therapies for PCa decreased according to time elapsed after the diagnosis.
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Affiliation(s)
- Giorgio Gandaglia
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands; Department of Urology and Division of Experimental Oncology, Urological Research Institute, IRCCS San Raffaele Hospital, Milan, Italy.
| | - Francesco Pellegrino
- Department of Urology and Division of Experimental Oncology, Urological Research Institute, IRCCS San Raffaele Hospital, Milan, Italy
| | - Asieh Golozar
- Odysseus Data Services, New York, NY, USA; OHDSI Center, Northeastern University, Boston, MA, USA
| | | | | | | | - Muhammad Imran Omar
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands; Academic Urology Unit, University of Aberdeen, Scotland, UK
| | | | | | | | - Katharina Beyer
- Translational Oncology and Urology Research, King's College London, London, UK
| | - Anders Bjartell
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Riccardo Campi
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands; Unit of Urological Robotic Surgery and Renal Transplantation, University of Florence, Careggi Hospital, Florence, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Thomas Falconer
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Qi Feng
- Astellas Pharma, Inc., Northbrook, IL, USA
| | - Mengchun Gong
- Nanfang Hospital, Southern Medical University, Guangzhou, China; DHC Technologies, Beijing, China
| | | | | | - Tim Hulsen
- Philips Research, Department of Hospital Services & Informatics, Eindhoven, The Netherlands
| | | | | | | | - Nicolas Mottet
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands
| | - Marek Oja
- Institute of Computer Science, University of Tartu, Tartu, Estonia; STACC, Tartu, Estonia
| | - Peter Prinsen
- Netherlands Comprehensive Cancer Organization, Eindhoven, The Netherlands
| | | | - Sebastiaan Remmers
- Erasmus University Medical Centre, Cancer Institute, Rotterdam, The Netherlands
| | - Monique J Roobol
- Erasmus University Medical Centre, Cancer Institute, Rotterdam, The Netherlands
| | - Vasileios Sakalis
- Department of Urology, General Hospital of Thessaloniki Agios Pavlos, Thessaloniki, Greece
| | | | - Emma J Smith
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands
| | | | | | - Nicolas H Thurin
- INSERM CIC-P 1401, Bordeaux PharmacoEpi, Université de Bordeaux, Bordeaux, France
| | | | | | | | | | - Peter-Paul Willemse
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands; Department of Urology, Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andrew E Williams
- The Institute for Clinical Research and Health Policy Studies at Tufts Medical Center, Boston, MA, USA
| | | | | | - Alberto Briganti
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands; Department of Urology and Division of Experimental Oncology, Urological Research Institute, IRCCS San Raffaele Hospital, Milan, Italy
| | - James N'Dow
- Guidelines Office, European Association of Urology, Arnhem, The Netherlands; Academic Urology Unit, University of Aberdeen, Scotland, UK
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Jurkovic CM, Raisch J, Tran S, Nguyen HD, Lévesque D, Scott MS, Campos EI, Boisvert FM. Replisome Proximal Protein Associations and Dynamic Proteomic Changes at Stalled Replication Forks. Mol Cell Proteomics 2024; 23:100767. [PMID: 38615877 PMCID: PMC11101681 DOI: 10.1016/j.mcpro.2024.100767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024] Open
Abstract
DNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events, we can better grasp the complex and dynamic molecular mechanisms that facilitate DNA replication and repair. Proximity-dependent biotin identification was used to identify associations with 17 proteins within four core replication components, namely the CDC45/MCM2-7/GINS helicase that unwinds DNA, the DNA polymerases, replication protein A subunits, and histone chaperones needed to disassemble and reassemble chromatin. We further investigated the impact of genotoxic stress on these interactions. This analysis revealed a vast proximity association network with 108 nuclear proteins further modulated in the presence of hydroxyurea; 45 being enriched and 63 depleted. Interestingly, hydroxyurea treatment also caused a redistribution of associations with 11 interactors, meaning that the replisome is dynamically reorganized when stressed. The analysis identified several poorly characterized proteins, thereby uncovering new putative players in the cellular response to DNA replication arrest. It also provides a new comprehensive proteomic framework to understand how cells respond to obstacles during DNA replication.
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Affiliation(s)
- Carla-Marie Jurkovic
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jennifer Raisch
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Stephanie Tran
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Hoang Dong Nguyen
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Lévesque
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
| | - François-Michel Boisvert
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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Leni R, Roscigno M, Barzaghi P, La Croce G, Catellani M, Saccà A, de Angelis M, Montorsi F, Briganti A, Da Pozzo LF. Medium-term follow up of active surveillance for early prostate cancer at a non-academic institution. BJU Int 2024; 133:614-621. [PMID: 38093673 DOI: 10.1111/bju.16259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
OBJECTIVES To report oncological outcomes of active surveillance (AS) at a single non-academic institution adopting the standardised Prostate Cancer Research International Active Surveillance (PRIAS) protocol. PATIENTS AND METHODS Competing risk analyses estimated the incidence of overall mortality, metastases, conversion to treatment, and grade reclassification. The incidence of reclassification and adverse pathological findings at radical prostatectomy were compared between patients fulfilling all PRIAS inclusion criteria vs those not fulfilling at least one. RESULTS We analysed 341 men with Grade Group 1 prostate cancer (PCa) followed on AS between 2010 and 2022. There were no PCa deaths, two patients developed distant metastases and were alive at the end of the study period. The 10-year cumulative incidence of metastases was 1.9% (95% confidence interval [CI] 0.33-6.4%). A total of 111 men were reclassified, and 127 underwent definitive treatment. Men not fulfilling at least one PRIAS inclusion criteria (n = 43) had a higher incidence of reclassification (subdistribution hazards ratio 1.73, 95% CI 1.07-2.81; P = 0.03), but similar rates of adverse pathological findings at radical prostatectomy. CONCLUSION Metastases in men on AS at a non-academic institution are as rare as those reported in established international cohorts. Men followed without stringent inclusion criteria should be counselled about the higher incidence of reclassification and reassured they can expect rates of adverse pathological findings comparable to those fulfilling all criteria. Therefore, AS should be proposed to all men with low-grade PCa regardless of whether they are followed at academic institutions or smaller community hospitals.
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Affiliation(s)
- Riccardo Leni
- Division of Experimental Oncology, Department of Urology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Marco Roscigno
- University of Milano-Bicocca, Milan, Italy
- Department of Urology, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Paolo Barzaghi
- Department of Urology, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | | | - Antonino Saccà
- Department of Urology, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Mario de Angelis
- Division of Experimental Oncology, Department of Urology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesco Montorsi
- Division of Experimental Oncology, Department of Urology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Alberto Briganti
- Division of Experimental Oncology, Department of Urology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Luigi Filippo Da Pozzo
- University of Milano-Bicocca, Milan, Italy
- Department of Urology, ASST Papa Giovanni XXIII, Bergamo, Italy
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