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Article ; Online: Stress granules and P-bodies - New ideas and experimental models worth exploring.

Buchan, J Ross

Seminars in cell & developmental biology

2024 Volume 158, Page(s) 1–2

MeSH term(s)	Stress Granules ; Processing Bodies ; Protein Biosynthesis ; RNA, Messenger/metabolism ; Models, Theoretical ; Cytoplasmic Granules ; Stress, Physiological
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2024-01-16
Publishing country	England
Document type	Editorial
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2024.01.003
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Article ; Online: Stress granule and P-body clearance: Seeking coherence in acts of disappearance.

Buchan, J Ross

Seminars in cell & developmental biology

2024 Volume 159-160, Page(s) 10–26

Abstract: Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into ...

Abstract	Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
MeSH term(s)	Processing Bodies ; Stress Granules ; Cytoplasmic Granules ; RNA Helicases ; Cytoplasm
Chemical Substances	RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2024-01-25
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2024.01.002
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Article ; Online: HARLEY mitigates user bias and facilitates efficient quantification and co-localization analyses of foci in yeast fluorescence images.

Shabanov, Ilya / Buchan, J Ross

Scientific reports

2022 Volume 12, Issue 1, Page(s) 12238

Abstract: Quantification of cellular structures in fluorescence microscopy data is a key means of understanding cellular function. Unfortunately, numerous cellular structures present unique challenges in their ability to be unbiasedly and accurately detected and ... ...

Abstract	Quantification of cellular structures in fluorescence microscopy data is a key means of understanding cellular function. Unfortunately, numerous cellular structures present unique challenges in their ability to be unbiasedly and accurately detected and quantified. In our studies on stress granules in yeast, users displayed a striking variation of up to 3.7-fold in foci calls and were only able to replicate their results with 62-78% accuracy, when re-quantifying the same images. To facilitate consistent results we developed HARLEY (Human Augmented Recognition of LLPS Ensembles in Yeast), a customizable software for detection and quantification of stress granules in S. cerevisiae. After a brief model training on ~ 20 cells the detection and quantification of foci is fully automated and based on closed loops in intensity contours, constrained only by the a priori known size of the features of interest. Since no shape is implied, this method is not limited to round features, as is often the case with other algorithms. Candidate features are annotated with a set of geometrical and intensity-based properties to train a kernel Support Vector Machine to recognize features of interest. The trained classifier is then used to create consistent results across datasets. For less ambiguous foci datasets, a parametric selection is available. HARLEY is an intuitive tool aimed at yeast microscopy users without much technical expertise. It allows batch processing of foci detection and quantification, and the ability to run various geometry-based and pixel-based colocalization analyses to uncover trends or correlations in foci-related data. HARLEY is open source and can be downloaded from https://github.com/lnilya/harley .
MeSH term(s)	Algorithms ; Humans ; Image Processing, Computer-Assisted/methods ; Microscopy, Fluorescence/methods ; Saccharomyces cerevisiae ; Software
Language	English
Publishing date	2022-07-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-16381-2
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Article: RNAs as Regulators of Cellular Matchmaking.

Fernandes, Nikita / Buchan, J Ross

Frontiers in molecular biosciences

2021 Volume 8, Page(s) 634146

Abstract: RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the ... ...

Abstract	RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.
Language	English
Publishing date	2021-04-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2021.634146
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Article ; Online: RNAs as Regulators of Cellular Matchmaking

Nikita Fernandes / J. Ross Buchan

Frontiers in Molecular Biosciences, Vol

2021 Volume 8

Abstract	RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.
Keywords	RNA scaffolds ; RNA decoys ; 3′UTR ; nascent protein interactions ; lncRNA ; mRNA ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: RPS28B mRNA acts as a scaffold promoting cis-translational interaction of proteins driving P-body assembly.

Fernandes, Nikita / Buchan, J Ross

Nucleic acids research

2020 Volume 48, Issue 11, Page(s) 6265–6279

Abstract: P-bodies (PBs) are cytoplasmic mRNA-protein (mRNP) granules conserved throughout eukaryotes which are implicated in the repression, storage and degradation of mRNAs. PB assembly is driven by proteins with self-interacting and low-complexity domains. Non- ... ...

Abstract	P-bodies (PBs) are cytoplasmic mRNA-protein (mRNP) granules conserved throughout eukaryotes which are implicated in the repression, storage and degradation of mRNAs. PB assembly is driven by proteins with self-interacting and low-complexity domains. Non-translating mRNA also stimulates PB assembly, however no studies to date have explored whether particular mRNA transcripts are more critical than others in facilitating PB assembly. Previous work revealed that rps28bΔ (small ribosomal subunit-28B) mutants do not form PBs under normal growth conditions. Here, we demonstrate that the RPS28B 3'UTR is important for PB assembly, consistent with it harboring a binding site for the PB assembly protein Edc3. However, expression of the RPS28B 3'UTR alone is insufficient to drive PB assembly. Intriguingly, chimeric mRNA studies revealed that Rps28 protein, translated in cis from an mRNA bearing the RPS28B 3'UTR, physically interacts more strongly with Edc3 than Rps28 protein synthesized in trans. This Edc3-Rps28 interaction in turn facilitates PB assembly. Our work indicates that PB assembly may be nucleated by specific RNA 'scaffolds'. Furthermore, this is the first description in yeast to our knowledge of a cis-translated protein interacting with another protein in the 3'UTR of the mRNA which encoded it, which in turn stimulates assembly of cellular structures.
MeSH term(s)	3' Untranslated Regions/genetics ; Cytoplasmic Structures/metabolism ; Gene Deletion ; Protein Binding ; Protein Biosynthesis ; RNA Stability ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribosomal Proteins/deficiency ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	3' Untranslated Regions ; EDC3 protein, S cerevisiae ; RNA, Messenger ; RPS28A protein, S cerevisiae ; RPS28B protein, S cerevisiae ; Ribosomal Proteins ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2020-05-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa352
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Article ; Online: mRNP granules. Assembly, function, and connections with disease.

Buchan, J Ross

RNA biology

2014 Volume 11, Issue 8, Page(s) 1019–1030

Abstract: Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is ... ...

Abstract	Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is far reaching, ranging from precise spatial-temporal control of mRNAs that drive developmental programs in oocytes and embryos, to similarly exquisite control of mRNAs in neurons that underpin synaptic plasticity, and thus, memory formation. Analysis of mRNP granules in their various contexts has revealed common themes of assembly, disassembly, and modes of mRNA regulation, yet new studies continue to reveal unexpected and important findings, such as links between aberrant mRNP granule assembly and neurodegenerative disease. Continued study of these enigmatic structures thus promises fascinating new insights into cellular function, and may also suggest novel therapeutic strategies in various disease states.
MeSH term(s)	Cytoplasmic Granules/genetics ; Cytoplasmic Granules/metabolism ; Gene Expression Regulation ; Humans ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/pathology ; Neuronal Plasticity/genetics ; Neurons/metabolism ; Neurons/pathology ; Protein Biosynthesis/genetics ; RNA Transport/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribonucleoproteins/genetics ; Ribonucleoproteins/metabolism ; Synapses/genetics ; Synapses/metabolism ; Synapses/pathology
Chemical Substances	RNA, Messenger ; Ribonucleoproteins ; messenger ribonucleoprotein
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.4161/15476286.2014.972208
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Article ; Online: Role of overnight oximetry in assessing the severity of obstructive sleep apnoea in typically developing children: a multicentre study.

Selby, Anna / Buchan, Elise / Davies, Matthew / Hill, Catherine M / Kingshott, Ruth N / Langley, Ross J / McGovern, Julia / Presslie, Callum / Senior, Emily / Shinde, Supriya Suresh / Yuen, Ho Ming / Samuels, Martin / Evans, Hazel J

Archives of disease in childhood

2024 Volume 109, Issue 4, Page(s) 308–313

Abstract: Background and objective: Cardiorespiratory polygraphy (CRP) is the predominant technology used to diagnose obstructive sleep apnoea (OSA) in tertiary centres in the UK. Nocturnal pulse oximetry (NPO) is, however, cheaper and more accessible. This study ...

Abstract	Background and objective: Cardiorespiratory polygraphy (CRP) is the predominant technology used to diagnose obstructive sleep apnoea (OSA) in tertiary centres in the UK. Nocturnal pulse oximetry (NPO) is, however, cheaper and more accessible. This study evaluated the ability of NPO indices to predict OSA in typically developing (TD) children. Methods: Indices from simultaneous NPO and CRP recordings were compared in TD children (aged 1-16 years) referred to evaluate OSA in three tertiary centres. OSA was defined as an obstructive apnoea-hypopnoea index (OAHI) ≥1 event/hour. Receiver operating characteristic curves assessed the diagnostic accuracy of NPO indices including ODI3 (3% Oxygen Desaturation Index, ODI4 (4% Oxygen Desaturation Index), delta 12 s index and minimum oxygen saturation. Two-by-two tables were generated to determine the sensitivities and specificities of whole number cut-off values for predicting OAHIs ≥1, 5 and 10 events/hour. Results: Recordings from 322 TD children, 197 male (61.2%), median age 4.9 years (range 1.1-15.6), were reviewed. OAHI was ≥1/hour in 144 (44.7%), ≥5/hour in 61 (18.9%) and ≥10/hour in 28 (8.7%) cases. ODI3 and ODI4 had the best diagnostic accuracy. ODI3 ≥7/hour and ODI4 ≥4/hour predicted OSA in TD children with sensitivities/specificities of 57.6%/85.4% and 46.2%/91.6%, respectively. ODI3 ≥8/hour was the best predictor of OAHI ≥5/hour (sensitivity 82.0%, specificity 84.3%). Conclusion: Raised ODI3 and ODI4 predict OSA in TD children with high specificity but variable sensitivity. NPO may be an alternative to diagnose moderate-severe OSA if access to CRP is limited. Low sensitivities to detect mild OSA mean that confirmatory CRP is needed if NPO is normal.
MeSH term(s)	Child ; Humans ; Male ; Infant ; Child, Preschool ; Adolescent ; Polysomnography ; Sleep Apnea, Obstructive/diagnosis ; Oximetry ; Oxygen ; Sensitivity and Specificity
Chemical Substances	Oxygen (S88TT14065)
Language	English
Publishing date	2024-03-19
Publishing country	England
Document type	Multicenter Study ; Journal Article
ZDB-ID	524-1
ISSN	1468-2044 ; 0003-9888 ; 1359-2998
ISSN (online)	1468-2044
ISSN	0003-9888 ; 1359-2998
DOI	10.1136/archdischild-2023-326191
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Article ; Online: Increased Mortality in Patients With Acutely Decompensated Heart Failure During the COVID-19 Pandemic in Toronto, Canada.

Buchan, Tayler A / Kugathasan, Lakshmi / Kobulnik, Jeremy / Poon, Stephanie / Runeckles, Kyle / Fan, Steve / Ross, Heather J / Alba, Ana C

CJC open

2022 Volume 4, Issue 9, Page(s) 772–781

Abstract: Background: Coronavirus disease 2019 (COVID-19) has resulted in a reduction in patients seeking timely consultation for illnesses that are not related to COVID-19. Previously, we reported a decline in the number of emergency department (ED) visits and ... ...

Abstract	Background: Coronavirus disease 2019 (COVID-19) has resulted in a reduction in patients seeking timely consultation for illnesses that are not related to COVID-19. Previously, we reported a decline in the number of emergency department (ED) visits and hospitalizations for acute decompensated heart failure (ADHF) during the 2020 COVID-19 pandemic vs that in 2019. We aimed to determine the consequences of these early trends on ADHF-patient morbidity and mortality. Methods: We compared consecutive patients presenting with ADHF to 3 academic medical centres in Toronto, Canada from March 1-September 28, 2020, vs those from the same time period in 2019. We used multivariate logistic regression models to evaluate whether the odds of hospitalization after presenting to the ED, recurrent ED visits or readmission within 30 days, and in-hospital all-cause mortality differed by timeframe. Results: We observed that, during the COVID-19 pandemic, a lower total number of patients presented to the hospital with ADHF, vs that in 2019. Despite this difference, the probability of being admitted to the hospital did not differ for patients seen in 2020 vs 2019. Among ADHF patients admitted to the hospital, however, we observed a significantly higher proportion being admitted to the intensive care unit, and a relative 66% increase in in-hospital mortality during the 2020 COVID-19 era, compared to that in 2019. Conclusions: Our findings suggest that improved messaging may be needed for patients living with chronic health conditions, including HF, during the pandemic, to educate and encourage them to present to hospital services when in need.
Language	English
Publishing date	2022-06-22
Publishing country	United States
Document type	Journal Article
ISSN	2589-790X
ISSN (online)	2589-790X
DOI	10.1016/j.cjco.2022.06.006
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Article ; Online: Factors Impacting Physician Prognostic Accuracy in Heart Failure Patients With Reduced Left Ventricular Ejection Fraction.

Alba, Ana C / Buchan, Tayler A / Saha, Sudipta / Fan, Steve / Poon, Stephanie / Mak, Susanna / Al-Hesayen, Abdul / Toma, Mustafa / Zieroth, Shelley / Anderson, Kim / Demers, Catherine / Amin, Faizan / Porepa, Liane / Chih, Sharon / Giannetti, Nadia / Rac, Valeria / Ross, Heather J / Guyatt, Gordon H

JACC. Heart failure

2024

Abstract: Background: A recent study showed that the accuracy of heart failure (HF) cardiologists and family doctors to predict mortality in outpatients with HF proved suboptimal, performing less well than models.: Objectives: The authors sought to evaluate ... ...

Abstract	Background: A recent study showed that the accuracy of heart failure (HF) cardiologists and family doctors to predict mortality in outpatients with HF proved suboptimal, performing less well than models. Objectives: The authors sought to evaluate patient and physician factors associated with physician accuracy. Methods: The authors included outpatients with HF from 11 HF clinics. Family doctors and HF cardiologists estimated patient 1-year mortality. They calculated predicted mortality using the Seattle HF Model and followed patients for 1 year to record mortality (or urgent heart transplant or ventricular assist device implant as mortality-equivalent events). Using multivariable logistic regression, the authors evaluated associations among physician experience and confidence in estimates, duration of patient-physician relationship, patient-physician sex concordance, patient race, and predicted risk, with concordant results between physician and model predictions. Results: Among 1,643 patients, 1-year event rate was 10% (95% CI: 8%-12%). One-half of the estimates showed discrepant results between model and physician predictions, mainly owing to physician risk overestimation. Discrepancies were more frequent with increasing patient risk from 38% in low-risk to ∼75% in high-risk patients. When making predictions on male patients, female HF cardiologists were 26% more likely to have discrepant predictions (OR: 0.74; 95% CI: 0.58-0.94). HF cardiologist estimates in Black patients were 33% more likely to be discrepant (OR: 0.67; 95% CI: 0.45-0.99). Low confidence in predictions was associated with discrepancy. Analyses restricted to high-confidence estimates showed inferior calibration to the model, with risk overestimation across risk groups. Conclusions: Discrepant physician and model predictions were more frequent in cases with perceived increased risk. Model predictions outperform physicians even when they are confident in their predictions. (Predicted Prognosis in Heart Failure [INTUITION]; NCT04009798).
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2705621-1
ISSN	2213-1787 ; 2213-1779
ISSN (online)	2213-1787
ISSN	2213-1779
DOI	10.1016/j.jchf.2024.02.009
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