Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed.MethodsTen CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.ResultsAn average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value <0.05, minimum inclusion level difference >0.1).ConclusionThe RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis

Inhibition of MicroRNA miR-222 with LNA Inhibitor Can Reduce Cell Proliferation in B Chronic Lymphoblastic Leukemia

MicroRNAs (miRNAs) are small regulatory molecules that negatively regulate gene expression by base-pairing with their target mRNAs. miRNAs have contribute significantly to cancer biology and recent studies have demonstrated the oncogenic or tumor-suppressing role in cancer cells. In many tumors up-regulation miRNAs has been reported especially miR-222 has been shown to be up-regulated in B chronic lymphocytic leukemia (B-CLL). In this study we assessed the effected inhibition of miR-222 in cell viability of B-CLL. We performed inhibition of mir-222 in B-CLL cell line (183-E95) using locked nucleic acid (LNA) antagomir. At different time points after LNA-anti-mir-222 transfection, miR-222 quantitation and cell viability were assessed by qRT-real time polymerase chain reaction and MTT assays. The data were analyzed by independent t test and one way ANOVA. Down-regulation of miR-222 in B-CLL cell line (183-E95) with LNA antagomir decreased cell viability in B-CLL. Cell viability gradually decreased over time as the viability of LNA-anti-mir transfected cells was <47 % of untreated cells at 72 h post-transfection. The difference in cell viability between LNA-anti-miR and control groups was statistically significant (p < 0.042). Based on our findings, the inhibition of miR-222 speculate represent a potential novel therapeutic approach for treatment of B-CLL

ДИНАМИКА СОСТОЯНИЯ УГЛЕВОДНОГО ОБМЕНА ПОСЛЕ РЕНАЛЬНОЙ ДЕНЕРВАЦИИ У БОЛЬНЫХ РЕЗИСТЕНТНОЙ АРТЕРИАЛЬНОЙ ГИПЕРТОНИЕЙ В СОЧЕТАНИИ С САХАРНЫМ ДИАБЕТОМ 2-ГО ТИПА

The aim of the study was to evaluatetheglycemic control dynamics depending on degree of blood pressure (BP) reduction and dynamic of TNF-α after 6 and 12 months of Tran catheter renal denervation (TRD) of patients with true resistant hypertension (RH) and type 2 diabetes mellitus (T2DM). Material and methods. Thirty two essentially hypertensive patients with type 2 diabetes mellitus (T2DM) and resistant hypertension were included in single-arm prospective interventional study. Office BP measurement, ambulatory 24-h BP, renal Doppler ultrasound and assessment of renal function (proteinuria, creatinine, eGFR), HbА1c and fasting plasma glucose (FPG) levels, activity of TNF-α were performed at baseline and 6 and 12 months after TRD. On average, patients were taking 4 (3–6) antihypertensive drugs. None of the patients changed the antihypertensive treatments during follow-up. A 6 months follow-up was completed by 27 patients (43–75 years old, 14 male), 12 months follow-up was completed by 26 patients. Results. Renal denervation significantly reduced the systolic office BP (SBP) as well as 24-h SBP (– 27.2/–10.7 mm Hg and–13.4/–10 mm Hg, respectively, p &lt; 0.01 after 6-month follow-up, and –31,7/–12,8 mmHg and –13.4/–10 mm Hg, respectively, p &lt; 0.01 after 12-month follow-up) without any negative effect on renal function. The number of responders with reduction of SBP &gt;10 mmHg according to ABPM were 56% (15/27) after 6-month and 61.5% (16/26) after 12-month follow-up. There were significant reduction of the average HbA1c levels (from (6.9 ± 1.8)% to (5.8 ± 1.5)%, p = 0.04) and nonsignificant decreasing of FPG levels (from 8.7 ± 2.8 to 7.7 ± 2.1 mmol/L, p = 0.07) after 6-month followup. Conspicuously, the responders according to ABPM had significantly higher mean dynamics of HbA1c than the non-responders after 6-month follow-up (–2.4 ± 1.9 and –0.1 ± 0.8%, p = 0.02, respectively) as well as after 12-month follow-up (–0.12 ± 0.98 and 1,26 ± 1.11%, p = 0.04 for HbA1c, and – 0.89 ± 1.9 и 0.85 mmol/L ± 1.19, p = 0.02 for FPG levels). There were significant decreasing of TNF-α after 12-monthfollow-up (from 2.21 (1.54–3.65) to 1.4 (1.11–1.47pg/ml), p = 0.007), without relation to BP and HbA1c dynamics, and response to TRD. There were not the correlations between dynamics of HbA1c and FPG levels with BP reduction and change of TNF-α after 12-month follow-up. Conclusions. Renal denervation of patients with true resistant hypertension and diabetes mellitus type 2 after 6 and 12 months was followed by improved glycemic control, BP reduction and decreasing of mean levels of TNF-α. Glycemic control improvement after the renal denervation was more expressive in the responders. Цель исследования – оценить изменение состояния углеводного обмена через 6 мес и 1 год после ренальной денервации (РД) в зависимости от степени антигипертензивного эффекта и динамики фактора некроза опухолей α (ФНО-α) у больных резистентной артериальной гипертонией (РАГ) в сочетании с сахарным диабетом (СД) 2-го типа (СД-2).Материал и методы. Ренальная денервация почечных артерий проведена у 32 больных истинно резистентной АГ в сочетании с СД-2. Полугодовой период наблюдения закончили 27 пациентов (14 мужчин и 13 женщин (возраст 43–75 лет)), годовое наблюдение – 26 человек. Всем больным проводили общеклиническое обследование, измерение офисного артериального давления (АД), 24-часовое амбулаторное мониторирование АД (АМАД), допплерографию почечных артерий, оценивали состояние углеводного обмена (базальная гликемия, гликированный гемоглобин (HbA1c), концентрацию в плазме крови ФНО-α и почечную функцию (протеинурия, креатинин сыворотки крови, расчетная скорость клубочковой фильтрации (по формуле MDRD). Пациенты получали в среднем 4 (3–6) антигипертензивных препарата. Антигипертензивная и сахароснижающая терапия оставались стабильными в течение всего периода наблюдения. Результаты. Через 6 мес после РД отмечался значимый антигипертензивный эффект (–27,2/–10,7 мм рт. ст. для офисного АД и –13,4/–10,0 мм рт. ст. для АД–24-ч, p &lt; 0,01), остававшийся стабильным в течение всего года (–31,7/–12,8 мм рт. ст. и –13,4/–10,0 мм рт. ст., соответственно,p &lt; 0,01). Снижение систолического АД (САД) более 10 мм рт. ст от исходных значений (группа респондеров) по результатам АМАД через 6 мес зарегистрировано у 56% больных (15 из 27 пациентов), через год – 61,5% (16 из 26 человек). Через 6 мес после вмешательства установлено статистически значимое уменьшение среднего уровня HbA1c (от (6,9 ± 1,8) до (5,8 ± 1,5)%, p = 0,04) и тенденция к снижению базальной гликемии (от 8,7 ± 2,8 до (7,7 ± 2,1) ммоль/л, p = 0,07). При этом снижение HbA1c было более выраженным у респондеров (по САД–24 ч), чем у нереспондеров  (–2,4 ± 1,9 и –0,1 ± 0,8 соответственно, p = 0,02). Различие динамики HbA1c между респондерами и нереспондерами cохранялось и через год наблюдения (–0,1 ± 1,0 и 1,3 ± 1,1, p = 0,04), также как и динамики базальной гликемии (–0,9 ± 1,9 и 0,8 ± 1,2, p = 0,02). Через год после РД было обнаружено статистически значимое снижение уровня ФНО-α (от 2,21 (1,54–3,65) до 1,40 (1,11–1,47) пг/мл),p = 0,007), не зависящее от выраженности снижения АД и ответа на вмешательства. Прямой связи между снижением показателей углеводного обмена и динамикой концентрации ФНО-α, а также степенью антигипертензивного эффекта через год также не отмечено. Выводы. Ренальная денервация у больных резистентной АГ, ассоциированной с СД-2, оказывала благоприятное влияние на состояние углеводного обмена на фоне выраженного и стабильного в течение года антигипертензивного эффекта, а также снижения активности ФНО-α. При этом статистически значимое улучшение гликемического контроля отмечалось при снижении среднесуточного систолического АД более 10 мм рт. ст. от исходных значений

Accurate molecular classification of cancer using simple rules

<p>Abstract</p> <p>Background</p> <p>One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often hampers the interpretability of the models. For a better understanding of the classification results, it is desirable to develop simpler rule-based models with as few marker genes as possible.</p> <p>Methods</p> <p>We screened a small number of informative single genes and gene pairs on the basis of their depended degrees proposed in rough sets. Applying the decision rules induced by the selected genes or gene pairs, we constructed cancer classifiers. We tested the efficacy of the classifiers by leave-one-out cross-validation (LOOCV) of training sets and classification of independent test sets.</p> <p>Results</p> <p>We applied our methods to five cancerous gene expression datasets: leukemia (acute lymphoblastic leukemia [ALL] vs. acute myeloid leukemia [AML]), lung cancer, prostate cancer, breast cancer, and leukemia (ALL vs. mixed-lineage leukemia [MLL] vs. AML). Accurate classification outcomes were obtained by utilizing just one or two genes. Some genes that correlated closely with the pathogenesis of relevant cancers were identified. In terms of both classification performance and algorithm simplicity, our approach outperformed or at least matched existing methods.</p> <p>Conclusion</p> <p>In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction.</p

MicroRNA Expression Profiling Identifies Activated B Cell Status in Chronic Lymphocytic Leukemia Cells

Chronic lymphocytic leukemia (CLL) is thought to be a disease of resting lymphocytes. However, recent data suggest that CLL cells may more closely resemble activated B cells. Using microRNA (miRNA) expression profiling of highly-enriched CLL cells from 38 patients and 9 untransformed B cells from normal donors before acute CpG activation and 5 matched B cells after acute CpG activation, we demonstrate an activated B cell status for CLL. Gene set enrichment analysis (GSEA) identified statistically-significant similarities in miRNA expression between activated B cells and CLL cells including upregulation of miR-34a, miR-155, and miR-342-3p and downregulation of miR-103, miR-181a and miR-181b. Additionally, decreased levels of two CLL signature miRNAs miR-29c and miR-223 are associated with ZAP70+ and IgVH unmutated status and with shorter time to first therapy. These data indicate an activated B cell status for CLL cells and suggest that the direction of change of individual miRNAs may predict clinical course in CLL

Dissecting Oct3/4-Regulated Gene Networks in Embryonic Stem Cells by Expression Profiling

POU transcription factor Pou5f1 (Oct3/4) is required to maintain ES cells in an undifferentiated state. Here we show that global expression profiling of Oct3/4-manipulated ES cells delineates the downstream target genes of Oct3/4. Combined with data from genome-wide chromatin-immunoprecipitation (ChIP) assays, this analysis identifies not only primary downstream targets of Oct3/4, but also secondary or tertiary targets. Furthermore, the analysis also reveals that downstream target genes are regulated either positively or negatively by Oct3/4. Identification of a group of genes that show both activation and repression depending on Oct3/4 expression levels provides a possible mechanism for the requirement of appropriate Oct3/4 expression to maintain undifferentiated ES cells. As a proof-of-principle study, one of the downstream genes, Tcl1, has been analyzed in detail. We show that Oct3/4 binds to the promoter region of Tcl1 and activates its transcription. We also show that Tcl1 is involved in the regulation of proliferation, but not differentiation, in ES cells. These findings suggest that the global expression profiling of gene-manipulated ES cells can help to delineate the structure and dynamics of gene regulatory networks

At Least Ten Genes Define the Imprinted Dlk1-Dio3 Cluster on Mouse Chromosome 12qF1

Background: Genomic imprinting is an exception to Mendelian genetics in that imprinted genes are expressed monoallelically, dependent on parental origin. In mammals, imprinted genes are critical in numerous developmental and physiological processes. Aberrant imprinted gene expression is implicated in several diseases including Prader-Willi/ Angelman syndromes and cancer. Methodology/Principal Findings: To identify novel imprinted genes, transcription profiling was performed on two uniparentally derived cell lines, androgenetic and parthenogenetic primary mouse embryonic fibroblasts. A maternally expressed transcript termed Imprinted RNA near Meg3/Gtl2 (Irm) was identified and its expression studied by Northern blotting and whole mounts in situ hybridization. The imprinted region that contains Irm has a parent of origin effect in three mammalian species, including the sheep callipyge locus. In mice and humans, both maternal and paternal uniparental disomies (UPD) cause embryonic growth and musculoskeletal abnormalities, indicating that both alleles likely express essential genes. To catalog all imprinted genes in this chromosomal region, twenty-five mouse mRNAs in a 1.96Mb span were investigated for allele specific expression. Conclusions/Significance: Ten imprinted genes were elucidated. The imprinting of three paternally expressed protein coding genes (Dlk1, Peg11, and Dio3) was confirmed. Seven noncoding RNAs (Meg3/Gtl2, Anti-Peg11, Meg8, Irm/‘‘Rian’’