ОПРЕДЕЛЕНИЕ СРОКОВ НАЧАЛА ГЕМОДИАЛИЗА: РАЗРАБОТКА И ПОДТВЕРЖДЕНИЕ ШКАЛЫ START

Aim. The optimal time for initiating of chronic dialysis remains unknown. The scale for mortality risk assessment could help in decision-making concerning dialysis start timing.Methods. We randomly divided 1856 patients started dialysis in 2009–2016 into developmental and validation group (1:1) to create and validate scoring system «START» predicting mortality risk at dialysis initiation in order to fi nd unmodifi able and modifi able factors which could help in the decision-making of dialysis start. In the series of univariate regression models in the developmental set, we evaluated the mortality risk linked with available parameters: age, eGFR, serum phosphate, total calcium, hemoglobin, Charlson comorbidity index, diabetes status, urgency of start (turned to be signifi cant) and gender, serum sodium, potassium, blood pressure (without impact on survival). Similar hazard ratios were converted to score points.Results. The START score was highly predictive of death: C-statistic was 0.82 (95% CI 0.79–0.85) for the developmental dataset and 0.79 (95% CI 0.74–0.84) for validation dataset (both p < 0.001). On applying the cutoff between 7–8 points in the developmental dataset, the risk score was highly sensitive 81.1% and specifi c 67.9%; for validation dataset, the sensitivity was 78.9%, specifi city 67.9%. We confi rmed the similarity in survival prediction in the validation set to developmental set in low, medium and high START score groups. The difference in survival between three levels of START-score in validation set remained similar to that of developmental set: Wilcoxon = 8.78 (p = 0.02) vs 15.31 (p < 0.001) comparing low–medium levels and 25.18 (p < 0.001) vs 39.21 (p < 0.001) comparing medium–high levels.Conclusion. Developed START score system including modifi able factors showed good mortality prediction and could be used in dialysis start decision-making. Цель. Оптимальное время начала лечения гемодиализом (ГД) остается неопределенным. Создание шкалы для оценки рисков для пациента, начинающего диализ, поможет в принятии решения о сроках его начала.Методы. По данным регистра пациентов на заместительной почечной терапии проанализированы результаты лечения 1856 пациентов, начавших диализ в 2009–2016 гг. Случайным образом их разделили в соотношении 1:1 на группу разработки и группу подтверждения для создания прогностической шкалы оценки вероятности летального исхода при лечении программным гемодиализом (шкала START). При этом учитывали модифицируемые и немодифицируемые факторы риска. В серии регрессионных моделей с одной переменной в группе разработки шкалы мы оценивали риски смерти, связанные с доступными для анализа модифицируемыми и немодифицируемыми параметрами. Среди них значимыми оказались возраст, расчетная скорость клубочковой фильтрации (рСКФ), уровни фосфатов, общего кальция, гемоглобина, индекс коморбидности Чарлсон, наличие сахарного диабета, экстренность старта диализа. Пол, уровни натрия, калия, артериального давления не оказали влияния на выживаемость. Близкие по величине риски были преобразованы в баллы шкалы.Результаты. Шкала START продемонстрировала высокую предсказательную ценность в отношении риска смерти: AUC 0,82 (95% ДИ 0,79–0,85) для группы разработки шкалы и 0,79 (95% ДИ 0,74–0,84) для группы подтверждения (для обеих p < 0,001). Для точки отсечения 7–8 баллов чувствительность метода составила 81,1%, специфичность 69,9% для группы разработки и 78,9 и 67,9% соответственно – для группы подтверждения. Мы подтвердили близкие значения выживаемости пациентов в обеих группах для низких, средних и высоких значений шкалы START. Различия в выживаемости для подгрупп с тремя уровнями шкалы были близкими для групп разработки и подтверждения: критерий Wilcoxon = 8,78 (p = 0,02) vs 15,31 (p < 0,001) при сравнении выживаемости подгрупп низких и средних величин шкалы и 25,18 (p < 0,001) vs 39,21 (p < 0,001) при сравнении выживаемости подгрупп средних и высоких величин шкалы.Заключение. Разработанная шкала START, включающая модифицируемые факторы риска, продемонстрировала хорошую предсказательную ценность в отношении 5-летней летальности и может использоваться при принятии решения о времени старта диализа.

Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

Tracking of ancestral histone proteins over multiple generations of genome replication in yeast reveals that old histones move along genes from 3′ toward 5′ over time, and that maternal histones move up to around 400 bp during genomic replication

The 3-Base Periodicity and Codon Usage of Coding Sequences Are Correlated with Gene Expression at the Level of Transcription Elongation

Background: Gene transcription is regulated by DNA transcriptional regulatory elements, promoters and enhancers that are located outside the coding regions. Here, we examine the characteristic 3-base periodicity of the coding sequences and analyse its correlation with the genome-wide transcriptional profile of yeast. Principal Findings: The analysis of coding sequences by a new class of indices proposed here identified two different sources of 3-base periodicity: the codon frequency and the codon sequence. In exponentially growing yeast cells, the codon-frequency component of periodicity accounts for 71.9 % of the variability of the cellular mRNA by a strong association with the density of elongating mRNA polymerase II complexes. The mRNA abundance explains most of the correlation between the codon-frequency component of periodicity and protein levels. Furthermore, pyrimidine-ending codons of the four-fold degenerate small amino acids alanine, glycine and valine are associated with genes with double the transcription rate of those associated with purine-ending codons. Conclusions: We demonstrate that the 3-base periodicity of coding sequences is higher than expected by the codon usage frequency (CUF) and that its components, associated with codon bias and amino acid composition, are correlated with gene expression, principally at the level of transcription elongation. This indicates a role of codon sequences in maximising the transcription efficiency in exponentially growing yeast cells. Moreover, the results contrast with the common Darwinia

Cell type-specific over-expression of chromosome 21 genes in fibroblasts and fetal hearts with trisomy 21

BACKGROUND: Down syndrome (DS) is caused by trisomy 21 (+21), but the aberrations in gene expression resulting from this chromosomal aneuploidy are not yet completely understood. METHODS: We used oligonucleotide microarrays to survey mRNA expression in early- and late-passage control and +21 fibroblasts and mid-gestation fetal hearts. We supplemented this analysis with northern blotting, western blotting, real-time RT-PCR, and immunohistochemistry. RESULTS: We found chromosome 21 genes consistently over-represented among the genes over-expressed in the +21 samples. However, these sets of over-expressed genes differed across the three cell/tissue types. The chromosome 21 gene MX1 was strongly over-expressed (mean 16-fold) in senescent +21 fibroblasts, a result verified by northern and western blotting. MX1 is an interferon target gene, and its mRNA was induced by interferons present in +21 fibroblast conditioned medium, suggesting an autocrine loop for its over-expression. By immunohistochemistry the p78(MX1 )protein was induced in lesional tissue of alopecia areata, an autoimmune disorder associated with DS. We found strong over-expression of the purine biosynthesis gene GART (mean 3-fold) in fetal hearts with +21 and verified this result by northern blotting and real-time RT-PCR. CONCLUSION: Different subsets of chromosome 21 genes are over-expressed in different cell types with +21, and for some genes this over-expression is non-linear (>1.5X). Hyperactive interferon signaling is a candidate pathway for cell senescence and autoimmune disorders in DS, and abnormal purine metabolism should be investigated for a potential role in cardiac defects

Spt6 is a maintenance factor for centromeric CENP-A

Replication and transcription of genomic DNA requires partial disassembly of nucleosomes to allow progression of polymerases. This presents both an opportunity to remodel the underlying chromatin and a danger of losing epigenetic information. Centromeric transcription is required for stable incorporation of the centromere-specific histone dCENP-A in M/G1 phase, which depends on the eviction of previously deposited H3/H3.3-placeholder nucleosomes. Here we demonstrate that the histone chaperone and transcription elongation factor Spt6 spatially and temporarily coincides with centromeric transcription and prevents the loss of old CENP-A nucleosomes in both Drosophila and human cells. Spt6 binds directly to dCENP-A and dCENP-A mutants carrying phosphomimetic residues alleviate this association. Retention of phosphomimetic dCENP-A mutants is reduced relative to wildtype, while non-phosphorylatable dCENP-A retention is increased and accumulates at the centromere. We conclude that Spt6 acts as a conserved CENP-A maintenance factor that ensures long-term stability of epigenetic centromere identity during transcription-mediated chromatin remodeling

Interaction of SET domains with histones and nucleic acid structures in active chromatin

Changes in the normal program of gene expression are the basis for a number of human diseases. Epigenetic control of gene expression is programmed by chromatin modifications—the inheritable “histone code”—the major component of which is histone methylation. This chromatin methylation code of gene activity is created upon cell differentiation and is further controlled by the “SET” (methyltransferase) domain proteins which maintain this histone methylation pattern and preserve it through rounds of cell division. The molecular principles of epigenetic gene maintenance are essential for proper treatment and prevention of disorders and their complications. However, the principles of epigenetic gene programming are not resolved. Here we discuss some evidence of how the SET proteins determine the required states of target genes and maintain the required levels of their activity. We suggest that, along with other recognition pathways, SET domains can directly recognize the nucleosome and nucleic acids intermediates that are specific for active chromatin regions

Effects of DNA supercoiling on chromatin architecture

Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales. This supercoiling changes the properties of the DNA helix in a manner that substantially alters the binding specificity of DNA binding proteins and complexes, including nucleosomes, polymerases, topoisomerases and transcription factors. For example, transient over-wound DNA destabilises nucleosome core particles ahead of a transcribing polymerase, whereas under-wound DNA facilitates pre-initiation complex formation, transcription factor binding and nucleosome core particle association behind the transcribing polymerase. Importantly, DNA supercoiling can also dissipate through DNA, even in a chromatinised context, to influence both local elements and large chromatin domains. We propose a model in which changes in unconstrained DNA supercoiling influences higher levels of chromatin organisation through the additive effects of DNA supercoiling on both DNA-protein and DNA-nucleosome interactions. This model links small-scale changes in DNA and chromatin to the higher-order fibre and large-scale chromatin structures, providing a mechanism relating gene regulation to chromatin architecture in vivo