Small nucleolar RNAs (snoRNAs) are non-coding RNAs vital for ribosomal RNA (rRNA) maturation. The U8 snoRNA, encoded by the SNORD118 gene in humans, is an atypical C/D box snoRNA as it promotes rRNA ...cleavage rather than 2′-O-methylation and is unique to vertebrates. The U8 snoRNA is critical for cleavage events that produce the mature 5.8S and 28S rRNAs of the large ribosomal subunit. Unexpectedly, single nucleotide polymorphisms (SNPs) in the SNORD118 gene were recently found causal to the neurodegenerative disease leukoencephalopathy, brain calcifications, and cysts (LCC; aka Labrune syndrome), but its molecular pathogenesis is unclear. Here, we will review current knowledge on the function of the U8 snoRNA in ribosome biogenesis, and connect it to the preservation of brain function in humans as well as to its dysregulation in inherited white matter disease.
Long noncoding RNAs (lncRNAs), defined as nontranslated transcripts greater than 200 nucleotides in length, are often differentially expressed throughout developmental stages, tissue types, and ...disease states. The identification, visualization, and suppression/overexpression of these sequences have revealed impacts on a wide range of biological processes, including epigenetic regulation. Biochemical investigations on select systems have revealed striking insight into the biological roles of lncRNAs and lncRNA:protein complexes, which in turn prompt even more unanswered questions. To begin, multiple protein- and RNA-centric technologies have been employed to isolate lncRNA:protein and lncRNA:chromatin complexes. LncRNA interactions with the multi-subunit protein complex PRC2, which acts as a transcriptional silencer, represent some of the few cases where the binding affinity, selectivity, and activity of a lncRNA:protein complex have been investigated. At the same time, recent reports of full-length lncRNA secondary structures suggest the formation of complex structures with multiple independent folding domains and pave the way for more detailed structural investigations and predictions of lncRNA three-dimensional structure. This review will provide an overview of the methods and progress made to date as well as highlight new methods that promise to further inform the molecular recognition, specificity, and function of lncRNAs.
Ribosome biogenesis occurs in the nucleolus and relies upon RNA Polymerase I (Pol I) transcription of the rDNA into rRNA. This process is critical for normal cells but is dysregulated in diseases ...such as Alzheimer’s disease and cancer. To date, however, we have not yet explored the potential relationship between nucleoli and mitochondria. Mitochondria are critical for cellular energy and mitochondrial disorders exhibit dysregulation of nutrient and energy homeostasis. Like nucleoli, mitochondria are also dysregulated in Alzheimer’s disease and cancer, suggesting we may have overlooked a regulatory relationship between these two organelles.
In pursuing novel regulators of nucleoli number and function, we have identified a mitochondrial protein that when individually depleted by siRNA in breast epithelial cells (MCF10As) causes a change in nucleolar number – sulfite oxidase (SUOX). Upon SUOX depletion, the nucleolar number decreases from the typical 2‐3 nucleoli to 1 nucleolus. SiRNA‐mediated SUOX depletion reduces nucleolar rRNA levels in a high‐throughput 5‐EU assay (Bryant et al. 2021) and reduces global protein translation by a puromycin incorporation assay, indicating defective nucleolar function. Furthermore, combined metabolomic and transcriptomic analyses following siRNA‐mediated SUOX depletion reveal disruption in the activated methyl cycle, consistent with aberrant ribosome biogenesis. Experiments are underway to validate defective methylation experimentally at specific steps in ribosome biogenesis. The glutamate cycle is also disrupted, congruent with the presentation of the recessive nervous system disorder Isolated Sulfite Oxidase Deficiency (ISOD). Thus, we have defined a novel mitochondrial regulator of nucleolar number and function, nucleolar rRNA biogenesis, and protein translation with implications in human disease. Our work will open up a new avenue of nucleolus‐mitochondria relationships and regulation, and potentially connect mitochondrial disorders with ribosome biogenesis as well as identify how mitochondrial homeostasis is critical for nucleolar function.
It is plausible that night shift work could affect breast cancer risk, possibly by melatonin suppression or circadian clock disruption, but epidemiological evidence is inconclusive.
Using serial ...questionnaires from the Generations Study cohort, we estimated hazard ratios (HR) and 95% confidence intervals (95%CI) for breast cancer in relation to being a night shift worker within the last 10 years, adjusted for potential confounders.
Among 102,869 women recruited in 2003-2014, median follow-up 9.5 years, 2059 developed invasive breast cancer. The HR in relation to night shift work was 1.00 (95%CI: 0.86-1.15). There was a significant trend with average hours of night work per week (P = 0.035), but no significantly raised risks for hours worked per night, nights worked per week, average hours worked per week, cumulative years of employment, cumulative hours, time since cessation, type of occupation, age starting night shift work, or age starting in relation to first pregnancy.
The lack of overall association, and no association with all but one measure of dose, duration, and intensity in our data, does not support an increased risk of breast cancer from night shift work in women.
Advances in deep sequencing technologies have facilitated the identification and annotation of thousands of long noncoding RNAs (lncRNAs) across the transcriptome. LncRNAs are documented to play ...critical housekeeping roles within the cell and are implicated in a wide variety of diseases, including cancer. While studies into lncRNA function in cancer abound, there are limited examples to date of detailed lncRNA structural analyses to enable understanding of structure‐function relationships. Understanding structure‐function relationships would increase our insight into the noncoding transcriptome and yield potential avenues for targeting lncRNAs implicated in disease. The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) has been identified in multiple clinical studies as a predictive biomarker and molecular driver of aggressive prostate cancer. While several protein interactors have been identified for SChLAP1 to date, structural insight into SChLAP1:protein recognition has not yet been explored. We believe that structural analysis of SChLAP1 will assist in designing specific therapeutic strategies to inhibit SChLAP1:protein interactions implicated in prostate cancer. To this end, we performed Selective 2′‐Hydroxyl Acylation analyzed by Primer Extension with Mutational Profiling (SHAPE‐MaP) and dimethyl sulfate (DMS)‐MaP in vitroand in cellulo. This approach yielded the first secondary structure model of SChLAP1, which revealed a complex architecture with a wide variety of secondary structures throughout the length of the transcript. Analyzing our in‐cell probing data with the ΔSHAPE algorithm, we identified protein binding regions within SChLAP1 and mapped them to non‐human primate‐conserved exons within the transcript. Finally, we identified a smaller, highly structured fragment of SChLAP1 that houses multiple putative protein binding sites implicated in prostate cancer. We believe that this region of SChLAP1 is amenable to therapeutic targeting and may be used as a smaller construct for in vitrodevelopment of SChLAP1‐targeting therapeutics. We also believe this fragment may be amenable to 3D biophysical analyses, such as X‐ray crystallography or cryo‐EM, to further enhance structural understanding of SChLAP1:protein complexation. Ongoing work is focused on determining the sufficiency of this fragment for protein recognition and characterizing potential magnesium‐dependent tertiary structures. We believe this work will facilitate the development of specific therapeutic strategies for SChLAP1 and contribute to the growing need of characterizing structure‐function relationships within lncRNAs.
Breast development and hormonal changes at puberty might affect breast cancer risk, but epidemiological analyses have focussed largely on age at menarche and not at other pubertal stages.
We ...investigated associations between the timing of pubertal stages and breast cancer risk using data from a cohort study of 104,931 women (Breakthrough Generations Study, UK, 2003-2013). Pubertal variables were reported retrospectively at baseline. Breast cancer risk was analysed using Cox regression models with breast cancer diagnosis as the outcome of interest, attained age as the underlying time variable, and adjustment for potentially confounding variables.
During follow-up (mean = 4.1 years), 1094 breast cancers (including ductal carcinoma in situ) occurred. An increased breast cancer risk was associated with earlier thelarche (age when breast growth begins; HR 95% CI = 1.23 1.02, 1.48, 1 referent and 0.80 0.69, 0.93 for ≤10, 11-12 and ≥13 years respectively), menarche (initiation of menses; 1.06 0.93, 1.21, 1 referent and 0.78 0.62, 0.99 for ≤12, 13-14 and ≥15 years), regular periods (0.99 0.83, 1.18, 1 referent and 0.74 0.59, 0.92 for ≤12, 13-14 and ≥15 years) and age reached adult height (1.25 1.03, 1.52, 1 referent and 1.07 0.87, 1.32 for ≤14, 15-16 and ≥17 years), and with increased time between thelarche and menarche (0.87 0.65, 1.15, 1 referent, 1.14 0.96, 1.34 and 1.27 1.04, 1.55 for <0, 0, 1 and ≥2 years), and shorter time between menarche and regular periods (1 referent, 0.87 0.73, 1.04 and 0.66 0.50, 0.88 for 0, 1 and ≥2 years). These associations were generally similar when considered separately for premenopausal and postmenopausal breast cancer.
Breast duct development may be a time of heightened susceptibility to risk of carcinogenesis, and greater attention needs to be given to the relation of breast cancer risk to the different stages of puberty.
The majority of patients with chronic kidney disease are diagnosed and monitored in primary care. Glomerular filtration rate (GFR) is a key marker of renal function, but direct measurement is ...invasive; in routine practice, equations are used for estimated GFR (eGFR) from serum creatinine. We systematically assessed bias and accuracy of commonly used eGFR equations in populations relevant to primary care.
MEDLINE, EMBASE, and the Cochrane Library were searched for studies comparing measured GFR (mGFR) with eGFR in adult populations comparable to primary care and reporting both the Modification of Diet in Renal Disease (MDRD) and the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equations based on standardized creatinine measurements. We pooled data on mean bias (difference between eGFR and mGFR) and on mean accuracy (proportion of eGFR within 30% of mGFR) using a random-effects inverse-variance weighted metaanalysis. We included 48 studies of 26875 patients that reported data on bias and/or accuracy. Metaanalysis of within-study comparisons in which both formulae were tested on the same patient cohorts using isotope dilution-mass spectrometry-traceable creatinine showed a lower mean bias in eGFR using CKD-EPI of 2.2 mL/min/1.73 m
(95% CI, 1.1-3.2; 30 studies;
= 74.4%) and a higher mean accuracy of CKD-EPI of 2.7% (1.6-3.8; 47 studies;
= 55.5%). Metaregression showed that in both equations bias and accuracy favored the CKD-EPI equation at higher mGFR values.
Both equations underestimated mGFR, but CKD-EPI gave more accurate estimates of GFR.
To examine long-term complications in women with stress urinary incontinence (SUI) and pelvic organ prolapse (POP), with and without surgical mesh implants.
Longitudinal open cohort study from 1 ...April 2006 (or 1 April 2012) to 30 November 2018.
The Clinical Practice Research Datalink (CPRD) Gold database, which is linked to Hospital Episodes Statistics (HES) inpatient data, the HES Diagnostic Imaging Dataset (DID), Office for National Statistics mortality data and Index of Multiple Deprivation socio-economic status data.
Women aged ≥18 years with a diagnostic SUI/POP Read code.
Rates are estimated using negative binomial regression.
Rates of referrals for: psychological and pain services; urinalysis, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) testing; and pelvic ultrasound, computed tomography (CT) and magnetic resonance imaging (MRI) scans.
A cohort of 220 544 women were eligible for inclusion; 74% (n = 162 687) had SUI, 37% (n = 82 123) had POP and 11% (n = 24 266) had both. Rates of psychological referrals and CT scans were lower in women with SUI mesh surgery, but this was offset by higher rates of CRP testing in women with SUI or POP mesh, MRI scans in women with SUI mesh, and urinalysis testing and referrals to pain clinics for women with POP mesh.
Our results suggest a higher burden of morbidity in women with SUI/POP mesh surgery, and that these women may require ongoing follow-up in the primary care setting.
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