Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility.

Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibility regions (ASTAR-seq), for simultaneous measurement of whole-cell transcriptome and chromatin accessibility within the same single cell. To show the utility of ASTAR-seq, we profiled 384 mESCs under naive and primed pluripotent states as well as a two-cell like state, 424 human cells of various lineage origins (BJ, K562, JK1, and Jurkat), and 480 primary cord blood cells undergoing erythroblast differentiation. With the joint profiles, we configured the transcriptional and chromatin accessibility landscapes of discrete cell states, uncovered linked sets of cis-regulatory elements and target genes unique to each state, and constructed interactome and transcription factor (TF)-centered upstream regulatory networks for various cell states.

The lupus autoantigen La/Ssb is an Xist-binding protein involved in Xist folding and cloud formation.

Using the programmable RNA-sequence binding domain of the Pumilio protein, we FLAG-tagged Xist (inactivated X chromosome specific transcript) in live mouse cells. Affinity pulldown coupled to mass spectrometry was employed to identify a list of 138 candidate Xist-binding proteins, from which, Ssb (also known as the lupus autoantigen La) was validated as a protein functionally critical for X chromosome inactivation (XCI). Extensive XCI defects were detected in Ssb knockdown cells, including chromatin compaction, death of female mouse embryonic stem cells during in vitro differentiation and chromosome-wide monoallelic gene expression pattern. Live-cell imaging of Xist RNA reveals the defining XCI defect: Xist cloud formation. Ssb is a ubiquitous and versatile RNA-binding protein with RNA chaperone and RNA helicase activities. Functional dissection of Ssb shows that the RNA chaperone domain plays critical roles in XCI. In Ssb knockdown cells, Xist transcripts are unstable and misfolded. These results show that Ssb is critically involved in XCI, possibly as a protein regulating the in-cell structure of Xist.

IL-18R-dependent and independent pathways account for IL-18-enhanced antitumor ability of CAR-T cells.

Interleukin-18 (IL-18) has been demonstrated to augment the antitumor capacity of chimeric antigen receptor-T cells (CAR-T) but the underlying mechanisms are largely unknown. Here we explored the effects and mechanisms of exogenous IL-18 on the antitumor response of CAR-T cells. IL-18 boosted the cytotoxicity of human epidermal growth factor receptor-2 (HER2)-specific CAR-T cells ex vivo and enhanced the antitumor efficacy of the CAR-T cells in immunodeficient mice, moreover, IL-18 improved the antitumor capacity of OVA-specific T cells in immunocompetent mice, indicating the universal enhancing function of IL-18 for adoptive cell therapy. To address the roles of IL-18 receptor (IL-18R) in the enhancing function, we evaluated the effects of IL-18R knockout (IL-18R-/-) condition in immunocompetent host and CAR-T cells on the IL-18-enhanced antitumor activities. Interestingly, IL-18 persisted to improve the antitumor ability of IL-18R intact CAR-T cells in IL-18R-/- mice. For IL-18R-/- CAR-T cells, however, IL-18 still holds the enhancing ability to boost the antitumor efficacy in IL-18R-/- mice, albeit the ex vivo tumor-killing ability was lower than that of IL-18R intact CAR-T cells, indicating that IL-18R-independent pathway is involved in the enhancement. Furthermore, tagged IL-18 binded to the membrane of IL-18R-/- splenic and lymph node cells and IL-18R intact and IL-18R-/- CAR-T cells showed distinct transcriptomic profiles when stimulated by IL-18. These data demonstrate that IL-18R-independent pathways contribute to functions of IL-18.

Gamma Knife Radiosurgery for Cavernous Malformations of Basal Ganglia and Thalamus: A Retrospective Study of 53 Patients.

INTRODUCTION: Gamma Knife radiosurgery (GKRS) has been used to treat cavernous malformations (CMs) located in basal ganglia and thalamus. However, previous reports are limited by small patient population. METHODS: We retrospectively reviewed the clinical and radiological data of 53 patients with CMs of basal ganglia and thalamus who underwent GKRS at West China Hospital between May 2009 and July 2018. All patients suffered at least once bleeding before GKRS. The mean volume of these lesions was 1.77 cm3, and the mean marginal dose was 13.2 Gy. After treatment, patients were followed to determine the change in symptom and hemorrhage event. RESULTS: The mean follow-up period was 52.1 months (6.2-104.3 months). The calculated annual hemorrhage rate (AHR) was 48.5% prior to GKRS and 3.0% after treatment (p < 0.001). The Kaplan-Meier analysis revealed that 2-, 3-, and 5-year hemorrhage-free survival were 88, 80.9, and 80.9%, respectively. Preexisting symptoms were resolved in 11 patients, improved in 14, and stable in 5. Only 2 patients (3.8%) developed new neurological deficit. CONCLUSION: Our study suggests that AHR after GKRS was comparable to the recorded AHR of natural history (3.1-4.1%) in previous studies. GKRS is a safe and effective treatment modality for CMs of basal ganglia and thalamus. Considering the relative insufficient understanding of natural history of CMs, future study warrants longer follow-up.

Exploration of the core genes in ulcerative interstitial cystitis/bladder pain syndrome.

OBJECTIVE: Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a chronic inflammatory disease that can cause bladder pain and accompanying symptoms, such as long-term urinary frequency and urgency. IC/BPS can be ulcerative or non-ulcerative. The aim of this study was to explore the core genes involved in the pathogenesis of ulcerative IC, and thus the potential biomarkers for clinical treatment. MATERIALS AND METHODS: First, the gene expression dataset GSE11783 was downloaded using the Gene Expression Omnibus (GEO) database and analyzed using the limma package in R to identify differentially expressed genes (DEGs). Then, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for Gene Ontology (GO) functional analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for pathway enrichment analysis. Finally, the protein-protein interaction (PPI) network was constructed, and key modules and hub genes were determined using the STRING and Cytoscape software. The resulting key modules were then analyzed for tissue-specific gene expression using BioGPS. RESULTS: A total of 216 up-regulated DEGs and 267 down-regulated genes were identified, and three key modules and nine hub genes were obtained. CONCLUSION: The core genes (CXCL8, CXCL1, IL6) obtained in this study may be potential biomarkers of interstitial cystitis with guiding significance for clinical treatment.

The oncogenic role of MUC12 in RCC progression depends on c-Jun/TGF-ß signalling.

Renal cell carcinoma (RCC) is a common kidney cancer worldwide. Even though current treatments show promising therapeutic effectiveness, metastatic RCC still has limited therapeutic options so that novel treatments were urgently needed. Here, we identified that MUC12 was overexpressed in RCC patients and served as poor prognostic factor for RCC progression. Overexpression of MUC12 increased RCC cell growth and cell invasion while deficiency of MUC12 exerted opposite effects on RCC cells. Mechanistic dissection demonstrated that MUC12-mediated RCC cell growth and cell invasion were dependent of TGF-ß1 signalling because they could be blocked in the presence of TGF-ß1 inhibitor. Moreover, the regulation of TGF-ß1 by MUC12 relied on the transactivation of c-Jun. MUC12 promoted the recruitment of c-Jun on the promoter of TGF-ß1, leading to its transcription. Importantly, knockdown of c-Jun also attenuated MUC12-mediated TGF-ß1 induction and RCC cell invasion. In summary, our study defines the role of MUC12 in RCC progression and provides rational to develop novel targeted therapy to battle against RCC.

Association of C-reactive protein (CRP) rs1205 and rs2808630 variants and risk of cancer.

The correlation between rs1205, rs2808630 variants of C-reactive protein (CRP) gene and susceptibility of cancer has been assessed previously, but with conflicting results. We adopted odds ratios (ORs) with 95% confidence intervals (CIs), in silico tools and enzyme-linked immunosorbent assay (ELISA) analysis to evaluate this association. Totally, 10,614 cancer subjects and 33,294 controls were involved in the pooled analysis. When all the studies were pooled, no significant correlation was indicated between the two variants and cancer risk. However, in stratification analysis by ethnicity, we found that CRP rs1205 C>T polymorphism was associated with an elevated risk of cancer in Asians (T-allele vs. C-allele, OR = 1.20, 95% CI = 1.06-1.36, pheterogeneity = .226; TT vs. CC, OR = 1.48, 95% CI = 1.14-1.93, pheterogeneity = .089). Similar findings were observed for rs2808630 variant. In silico tools showed that lung adenocarcinoma participants with high CRP expression may have shorter overall survival time than low expression group. ELISA analysis indicated that CRP expression in prostate adenocarcinoma subjects with TT + TC genotypes was statistically higher than in those with CC genotypes. CRP rs1205 C>T and rs2808630 T>C polymorphism may be associated with cancer risk, especially for Asians.

Comparison of clinical outcomes in patients who underwent Gamma Knife radiosurgery for parasellar meningiomas with or without prior surgery.

BACKGROUND: Parasellar meningioma is a common benign tumour in brain. Both surgery and radiosurgery are important treatment modalities for this tumour. The study was designed to investigate whether prior surgery would affect treatment outcomes of patients with parasellar meningiomas after management with Gamma Knife radiosurgery. METHODS: A total of 93 patients who received Gamma Knife surgery were included in this retrospective study. There were 30 males and 63 females, with a median age of 48.6 years (range, 15.2-78.7 years). Prior surgery was performed in 45 patients. The median tumor volume was 5.02 cm3 (range 1.07-35.46 cm3) and median marginal dose was 12 Gy (range 10-15 Gy). The mean imaging follow-up and clinical follow-up periods were 40.7 and 52.7 months, respectively. RESULTS: In the group without prior surgery, 31 patients had improvement of preexisting symptoms; and in the group with prior surgery, 20 patients were noted to improve. The difference in symptom improvement between the two groups reached statistical significance (P = 0.009). Patients with prior surgery were more likely to have stable symptoms after Gamma Knife surgery (P = 0.012). Tumor recurrence was reported in 8 patients out of 45 patients with prior surgery, and 3 patients out of 48 patents without prior surgery (P = 0.085). After Gamma Knife surgery, 5 and 4 patients in two groups developed new neurological symptoms, respectively (P = 0.651). Cox regression analysis identified follow-up period as prognostic factor of progression-free survival. Ordinal logistic regression analysis identified surgery prior to Gamma Knife surgery as an unfavorable factor of symptom change. CONCLUSION: Gamma Knife radiosurgery provided long-term effective tumor control and better symptom recovery compared with those with prior surgery. Patients with surgery before Gamma Knife radiosurgery were more likely to have stable symptoms. Further analyses indicated that long follow-up is essential to determine the efficacy of radiosurgery for parasellar meningiomas. Further study needs to include more patients with longer follow-up to draw a more solid conclusion.

CDKN1B Val 109 Gly variant is not related to risk of prostate cancer.

Association between CDKN1B gene Val 109 Gly polymorphism and prostate cancer (PCa) susceptibility has been investigated in several studies but with inconsistent conclusions. We adopted odds ratios (ORs) and 95% confidence intervals (CIs) to assess the correlation between CDKN1B Val 109 Gly variant and PCa susceptibility. Moreover, we used in-silico tools to evaluate the relationship of CDKN1B expression and overall survival (OS) or disease free survival (DFS) time in PCa patients. The overall results demonstrated no association of the CDKN1B variant on PCa risk [allelic contrast (OR = 0.78, 95% CI = 0.45 - 1.35, Pheterogeneity = 0.038); GV vs VV (OR = 0.83, 95% CI = 0.56 - 1.25, Pheterogeneity = 0.253); GG vs VV (OR = 0.48, 95% CI = 0.23 - 1.01, Pheterogeneity = 0.161); GG+GV vs VV (OR = 0.75, 95% CI = 0.52 -1.08, Pheterogeneity = 0.132) and GG vs GV+VV (OR = 0.63, 95% CI = 0.25 - 1.11, Pheterogeneity = 0.152)]. In subgroup analysis by ethnicity and source of control, we also identified similar results. In-silico results showed that expression of CDKN1B was decreased in PCa tissue, especially in less advanced PCa (Gleason score = 6 or 7). No significant difference of OS or DFS time was indicated between the low and high expression of CDKN1B. Our present study showed evidence that CDKN1B Val 109 Gly variant is not related to PCa risk. Future studies with large sample size are needed to confirm this correlation in more details.

The association between three AXIN2 variants and cancer risk.

Plenty of epidemiological studies have assessed the effects of AXIN2 polymorphisms on the risk of developing cancer, but the available results were somewhat inconclusive. Odds ratios (ORs) with 95% confidence intervals (CIs) were utilized to investigate the relationship between three AXIN2 variants (rs2240308 C/T, rs1133683 C/T, and rs4791171 A/G) and overall cancer susceptibility. In silico tools were undertaken to investigate the correlation of AXIN2 expression with cancer risk and survival time. Furthermore, we explored the serum expression of AXIN2 by enzyme-linked immunosorbent assay. A total of 4167 cancer patients and 3515 control subjects were evaluated. The overall results demonstrated that there was no major association of these polymorphisms on cancer risk. However, stratified analysis by cancer type showed evidence that rs2240308 C/T polymorphism had a lower risk in lung cancer (OR, 0.76; 95% CI, 0.63-0.92; Pheterogeneity = 0.865) and prostate cancer (OR, 0.54; 95% CI, 0.35-0.84; Pheterogeneity = 0.088) by heterozygote comparison. Similar results were indicated in Asian descendants and population-based studies. In silico analysis showed evidence that AXIN2 expressions in lung cancer and prostate cancer were lower than that in normal counterpart. High expression of AXIN2 may have longer overall survival time than low expression group for lung cancer participants. In addition, individuals who were CC/TC carriers had a higher serum expression level than TT carriers. In conclusion, this pooled analysis suggested that AXIN2 rs2240308 C/T variant may decrease both lung and prostate cancer susceptibility, particularly in Asian descendants and population-based studies. Future large scale and well-designed research are required to validate these effects in more detail.

VEGF gene rs3025039C/T and rs833052C/A variants are associated with bladder cancer risk in Asian descendants.

INTRODUCTION: Polymorphisms of vascular endothelial growth factor (VEGF) gene were evaluated in a number of studies to evaluate bladder cancer (BCa) susceptibility but with controversial conclusions. MATERIAL AND METHODS: We performed a pooled analysis and used odds ratios (ORs) with corresponding 95% confidence intervals (95% CIs) to investigate the correlation between VEGF gene rs3025039C/T and rs833052C/A variants and risk of BCa. Furthermore, we utilized in silico tools to demonstrate the relationship of VEGF expression correlated with BCa susceptibility and survival time. RESULTS: A total of eight studies including 4359 BCa patients and 5417 control subjects were enrolled in our study. For VEGF rs3025039C/T, a significant association was indicated between this variant and BCa risk in homozygote comparison (OR = 1.51; 95% CI = 1.13-2.02; P heterogeneity = 0.815) and recessive genetic model (OR = 1.49; 95% CI = 1.12-1.99; P heterogeneity = 0.874), in particular in an Asian population subgroup. For VEGF rs833052C/A, we observed a positive association between this variant and BCa susceptibility in Asian descendants. Results from in silico tool showed evidence that VEGF expression in bladder carcinoma tissue is higher than that in normal counterpart (transcripts per kilobase million = 7.21 vs 6.85; P < 0.05). CONCLUSIONS: The VEGF gene rs3025039C/T and rs833052C/A variants may contribute to the risk of developing BCa, especially in Asian descendants. Future larger sample studies should be continued to focus on this issue in more detail.

MMP-8 C-799 T, Lys460Thr, and Lys87Glu variants are not related to risk of cancer.

BACKGROUND: Several studies have focused on the relationship between MMP-8 variants and cancer risk, but they have been unsuccessful in drawing reliable conclusions. METHODS: We employed odds ratio (OR) together with 95% confidence interval (CI) to assess the correlation between MMP-8 C-799 T, Lys460Thr, and Lys87Glu polymorphisms and cancer risk. We further employed in silico tools to evaluate the effect of MMP-8 expression on cancer susceptibility and overall survival time. RESULTS: A total of 8140 patients with malignant carcinoma and 10,529 healthy individuals (control) were enrolled. Overall, the analysis showed that the relationship between three MMP-8 variants and cancer susceptibility was not significant (allelic contrast, C-799 T: OR = 0.98, 95% CI = 0.92-1.04, Pheterogeneity = 0.068; Lys460Thr: OR = 0.94, 95% CI = 0.67-1.32, Pheterogeneity = 0.905; Lys87Glu: OR = 1.05, 95% CI = 0.93-1.18, Pheterogeneity = 0.968). Similar results were observed in subgroup analysis by ethnicity, cancer type, and source of control. In silico analysis indicated that MMP-8 expression was elevated in bladder cancer tissue compared to that in the control. However, both the higher and lower MMP-8 expression groups did not show an impact on the overall survival time of the patients. CONCLUSIONS: MMP-8 C-799 T, Lys460Thr, and Lys87Glu variants are not participant with the susceptibility of cancer.

Reducing the carbon footprint per unit of economic benefit is a new method to accomplish low-carbon agriculture. A case study: adjustment of the planting structure in Zhangbei County, China.

BACKGROUND: The development of low-carbon agriculture is promising for mitigating climate change. This study used adjustments to the planting structure in Zhangbei County, China, as an example to evaluate whether the carbon footprint per unit of economic benefit is a suitable indicator of low-carbon agriculture and to determine if low-carbon agriculture is not necessarily low-input non-intensive agriculture. RESULTS: The results showed that total greenhouse gas emissions increased; therefore, the adjustments to the planting structure were ostensibly not a low-carbon process. However, if we obtain the same economic benefit as the actual distribution of the planting industry by adopting the scenario of planting only grain crops, then the annual greenhouse gas emissions would be 1608.00 × 103  t CO2 eq, and 5769.94 × 103  ha of farmland would be required. However, if we adopt the scenario of planting only vegetable crops, then only 82.52 × 103  ha of farmland would be required, and the annual greenhouse gas emissions would be 323.52 × 103  t CO2 eq. CONCLUSIONS: These results indicated that the carbon footprint per unit of economic benefit is a suitable indicator to assess agricultural sustainability and that intensive agriculture with high input and high output is a form of low-carbon agriculture if the carbon footprint per unit of economic benefit is low. © 2019 Society of Chemical Industry.

Upregulation of Mineralocorticoid Receptor in the Hypothalamus Associated with a High Anxiety-like Level in Apolipoprotein E4 Transgenic Mice.

Anxiety symptoms occur in a large portion of Alzheimer's disease (AD) patients. ApolipoproteinE-4 (ApoE ε4 allele), a risk factor for AD, has been recognized as an important contributor to psychiatric disorders. In the present study, we aimed to investigate the corticosterone level in relation to anxiety-like behavior changes in transgenic male mice with different glial fibrillary acidic protein (GFAP)-ApoE isoforms. GFAP-ApoE4 transgenic mice aged 3 months showed higher anxiety-like behavior in open field, light-dark box and elevated plus maze tasks compared with that of age-matched GFAP-ApoE3 mice. However, corticotropin releasing factor levels in the hypothalamus and plasma corticosterone secretion were similar in GFAP-ApoE3 and GFAP-ApoE4 transgenic male mice. Additionally, increased expression of the mineralocorticoid receptor (MR) and unchanged expression of the glucocorticoid receptor were observed in the hypothalamus of GFAP-ApoE4 mice. However, no significant differences were found in the expression levels of the MR in GFAP-ApoE3 and GFAP-ApoE4 mice at postnatal day 2. In conclusion, we found that MR upregulation rather than corticosterone level changes in the early stage of adulthood was associated with the higher anxiety-like level measured in GFAP-ApoE4 mice.

[Effect of Scalp Electroacupuncture Combined Constraint-induced Movement Therapy on Move- ment Function of Ischemic Stroke Patients' Upper Limbs].

Objective To observe the effects of scalp electroacupuncture (SEA) combined con- straint-induced movement therapy ( CIMT) on movement function of ischemic stroke patients' upper limbs. Methods Totally 80 stroke patients were assigned to four groups according to random digit table, i.e., the routine rehabilitation group, the SEA group, the CIMT group, and the comprehensive intervention group. Patients in the routine rehabilitation group strengthened the training of upper limbs on the affected side by Bobath dominated technology and Brunnstrom assisted technology. Patients in the SEA group received Jiao's SEA combined EA therapy. Those in the CIMT group restricted the upper limbs of the healthy side and strengthened training of the affected side. Those in the comprehensive intervention group used SEA combined CIMT treatment. Fugl-Meyer assessment scale (FMA) , grading of hand function and range of wrist movement were observed before intervention, at week 4 and 12 after intervention, respectively. Results Compared with before treatment in the same group, FMA scores of upper limbs significantly increased, grading of hand function, and range of wrist movement were obviously improved in the 4 groups after 4-week treatment (P <0. 05, P <0. 01). There was no statistical difference in FMA scores of upper limbs or grading of hand function among the four groups. But dorsal expansion of wrist and radial deviation were more obviously improved in the comprehensive intervention group than in the routine rehabilitation group (P <0. 05). Compared with the routine rehabilitation group, FMA scores of up- per limbs increased, grading of hand function and range of wrist movement were obviously improved in the comprehensive intervention group (P <0. 05). Conclusions Routine rehabilitation, SEA, and CIMT showed better rehabilitation effect on movement function of ischemic stroke patients' upper limbs. But ESA combined CIMT showed most obvious effect with earliest effect shown.

Beneficial effects of enriched environment on behaviors were correlated with decreased estrogen and increased BDNF in the hippocampus of male mice.

OBJECTIVE: Previous studies reported that environmental enrichment might induce various beneficial effects in the central nervous system. However, the effect of environmental factors on endogenous estrogen level was not investigated. The present study was designed to examine the effect of enriched environment on endogenous estrogen in hippocampus and behavioral outcomes. METHODS: Behavioural measurements, including open field, elevated plus maze and Morris water maze, were used to evaluate anxiety and learning and memory of the male C57BL/6J mice that were housed in enriched environment for five months. In addition, the estrogen and brain-derived neurotrophic factor (BDNF) expression in the hippocampus were measured. RESULTS: We found that environmental enrichment decreased anxiety-like behaviors and facilitated spatial learning and memory in male C57BL/6J mice. In addition, the mice raised in enriched environment showed decreased endogenous estrogen levels both in the hippocampus and plasma compared to controls. Furthermore, our results indicated that environmental enrichment up-regulated BDNF mRNA expression level in the hippocampus. CONCLUSION: In conclusion, environmental enrichment decreased anxiety-like behaviors and facilitated spatial learning and memory in male C57BL/6J mice. Lastly, environmental enrichment up-regulated BDNF mRNA expression level in the hippocampus and decreased plasma estrogen level. The possible mechanism remained to be determined.

Microglial activation mediates host neuronal survival induced by neural stem cells.

The rational of neural stem cells (NSCs) in the therapy of neurological disease is either to replace dead neurons or to improve host neuronal survival, the latter of which has got less attention and the underlying mechanism is as yet little known. Using a transwell co-culture system, we reported that, in organotypic brain slice cultures, NSCs significantly improved host neuronal viability. Interestingly, this beneficial effect of NSCs was abrogated by a microglial inhibitor minocycline, while it was mimicked by a microglial agonist, Toll-like receptor 9 (TLR9) ligand CpG-ODN, which supports the pro-vital mediation by microglia on this NSCs-improved neuronal survival. Moreover, we showed that NSCs significantly induced host microglial movement and higher expression of a microglial marker IBA-1, the latter of which was positively correlated with TLR9 or extracellular-regulated protein kinases 1/2 (ERK1/2) activation. Real-time PCR revealed that NSCs inhibited the expression of pro-inflammatory molecules, but significantly increased the expression of molecules associated with a neuroprotective phenotype such as CX3CR1, triggering receptor expressed on myeloid cells-2 (TREM2) and insulin growth factor 1 (IGF-1). Similarly, in the microglia cells, NSCs induced the same microglial response as that in the slices. Further treatment with TLR9 ligand CpG-ODN, TLR9 inhibitor chloroquine (CQ) or ERK1/2 inhibitor U0126 demonstrated that TLR9-ERK1/2 pathway was involved in the NSCs-induced microglial activation. Collectively, this study indicated that NSCs improve host neuronal survival by switching microglia from a detrimental to a neuroprotective phenotype in adult mouse brain, and the microglial TLR9-ERK1/2 pathway seems to participate in this NSCs-mediated rescue action.

LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data.

BACKGROUND: With the advances in high-throughput DNA sequencing technologies, RNA-seq has rapidly emerged as a powerful tool for the quantitative analysis of gene expression and transcript variant discovery. In comparative experiments, differential expression analysis is commonly performed on RNA-seq data to identify genes/features that are differentially expressed between biological conditions. Most existing statistical methods for differential expression analysis are parametric and assume either Poisson distribution or negative binomial distribution on gene read counts. However, violation of distributional assumptions or a poor estimation of parameters often leads to unreliable results. RESULTS: In this paper, we introduce a new nonparametric approach called LFCseq that uses log fold changes as a differential expression test statistic. To test each gene for differential expression, LFCseq estimates a null probability distribution of count changes from a selected set of genes with similar expression strength. In contrast, the nonparametric NOISeq approach relies on a null distribution estimated from all genes within an experimental condition regardless of their expression levels. CONCLUSION: Through extensive simulation study and RNA-seq real data analysis, we demonstrate that the proposed approach could well rank the differentially expressed genes ahead of non-differentially expressed genes, thereby achieving a much improved overall performance for differential expression analysis.

Immunofluorescence protects RNA signals in simultaneous RNA-DNA FISH.

Cell research often requires combinational detection of RNA and DNA by fluorescence in situ hybridization (RNA-DNA FISH). However, it is difficult to preserve the fragile RNA signals through the harsh conditions used to denature the DNA template in DNA FISH. The current protocols of RNA-DNA FISH still cannot work robustly in all experiments. RNA-DNA FISH remains as a technically challenging and tedious experiment. By incorporating protein components into the signal detection steps of RNA FISH, which is then followed by a post-fixation step, we established an improved protocol of RNA-DNA FISH. The established method worked satisfyingly and robustly in our studies on Xist (inactivated X chromosome specific transcript) RNA and Terra (telomeric repeat-containing RNA). Our results provided the direct evidence to show that, not all the telomeres are associated with Terra, and a significant fraction of Terra foci do not overlap with telomere DNA in interphase cell nuclei. The improved method of simultaneous RNA-DNA FISH is reliable and time-efficient. It can be used in a variety of biological studies.

Splenic hamartomas in two children.

Hamartomas are extremely rare splenic benign tumours in children. We present two cases, both in boys (6 and 8 years old), with left upper quadrant abdominal pain that were otherwise asymptomatic. Both patients showed a splenic mass on preoperative ultrasonography and magnetic resonance imaging (MRI). One patient had a focal splenic mass that was identified preoperatively with contrasted computed tomography (CT) scans. Both patients underwent a total splenectomy. Although multi-modality imaging findings were described preoperatively, the final diagnosis in each case was splenic hamartoma based on histology and immunohistochemistry. The postoperative courses were uneventful.