Decoding the diagnostic potential of T cell repertoires in peripheral blood of patients from amnestic mild cognitive impairment to Alzheimer's disease.

Alzheimer's disease (AD) is currently an incurable neurodegenerative disorder and is the most common etiological cause of dementia. Consequently, it has severe burden on its patients and on their caregivers and represents a global health concern. Clinical investigations have indicated that a dysregulation of peripheral T cell immune homeostasis may be involved in the pathogenesis of AD, as well as in the early stages of AD, characterized by mild cognitive impairment (MCI). However, the characteristics and concomitant feasibility of the use of T-cell receptor (TCR) typing for disease diagnosis remains largely unknown. We employed a high-throughput sequencing and multidimensional bioinformatics analyses for the identification of TCR repertoires present in peripheral blood samples of 10 patients with amnestic MCI (aMCI), 10 patients with AD, and 10 healthy controls (HCs). Based on the characteristics of the TCR repertoires in the amount and diversity of combinations of V-J, the spectrum of immune defense, and differentially expressed genes (DEGs), single and specific TCR profiles were observed in the patient samples of aMCI and AD compared to profiles of HCs. In particular, the diversity of TCR clonotypes manifested a pattern of "decreased first and then increased" pattern during the progression from aMCI to AD, a pattern that was not observed in HC samples. Additionally, a total of 46 and 35 amino acid CDR3 sequences with consistent and reverse expressive abundance with diversity of TCR clonotypes were identified, respectively. Taken together, we provide novel and essential preliminary evidence demonstrating the presence of diversity of T cell repertoires from differentially expressed V-J gene segments and amino acid clonotypes using peripheral blood samples from patients with AD, aMCI, and from HC. Such findings have the potential to reveal potential mechanisms through which aMCI progresses to AD and provide a reference for the future development of immune-related diagnoses and therapies for AD.

Dispersion complexity-entropy curves: An effective method to characterize the structures of nonlinear time series.

The complexity-entropy curve (CEC) is a valuable tool for characterizing the structure of time series and finds broad application across various research fields. Despite its widespread usage, the original permutation complexity-entropy curve (PCEC), which is founded on permutation entropy (PE), exhibits a notable limitation: its inability to take the means and amplitudes of time series into considerations. This oversight can lead to inaccuracies in differentiating time series. In this paper, drawing inspiration from dispersion entropy (DE), we propose the dispersion complexity-entropy curve (DCEC) to enhance the capability of CEC in uncovering the concealed structures within nonlinear time series. Our approach initiates with simulated data including the logistic map, color noises, and various chaotic systems. The outcomes of our simulated experiments consistently showcase the effectiveness of DCEC in distinguishing nonlinear time series with diverse characteristics. Furthermore, we extend the application of DCEC to real-world data, thereby asserting its practical utility. A novel approach is proposed, wherein DCEC-based feature extraction is combined with multivariate support vector machine for the diagnosis of various types of bearing faults. This combination achieved a high accuracy rate in our experiments. Additionally, we employ DCEC to assess stock indices from different countries and periods, thereby facilitating an analysis of the complexity inherent in financial markets. Our findings reveal significant insights into the dynamic regularities and distinct structures of these indices, offering a novel perspective for analyzing financial time series. Collectively, these applications underscore the potential of DCEC as an effective tool for the nonlinear time series analysis.

Electrochemical Tandem Olefination and Hydrogenation Reaction with Ammonia.

An electrochemical Horner-Wadsworth-Emmons/hydrogenation tandem reaction was achieved using ammonia as electron and proton donors. The reaction could give two-carbon-elongated ester and nitrile from aldehyde or ketones directly. This reaction could proceed with a catalytic amount of base or even without a base. The ammonia provides both the electron and proton for this tandem reaction and enables the catalyst-free hydrogenation of an α,ß-unsaturated HWE intermediate. More than 40 examples were reported, and functional groups, including heterocycles and hydroxyl, were tolerated.

Novel SPEG variant cause centronuclear myopathy in China.

BACKGROUND: Centronuclear myopathy (CNM), a subtype of congenital myopathy (CM), is a group of clinical and genetically heterogeneous muscle disorders. Centronuclear myopathy is a kind of disease difficult to diagnose due to its genetic diversity. Since the discovery of the SPEG gene and disease-causing variants, only a few additional patients have been reported. METHODS: A radiograph test, ultrasonic test, and biochemical tests were applied to clinical diagnosis of CNM. We performed trio medical exome sequencing of the family and conservation analysis to identify variants. RESULTS: We report a pair of severe CNM twins with the same novel homozygous SPEG variant c. 8710A>G (p.Thr2904Ala) identified by clinical trio medical exome sequencing of the family and conservation analysis. The twins showed clinical symptoms of facial weakness, hypotonia, arthrogryposis, strephenopodia, patent ductus arteriosus, and pulmonary arterial hypertension. CONCLUSIONS: Our report expands the clinical and molecular repertoire of CNM and enriches the variant spectrum of the SPEG gene in the Chinese population and helps us further understand the pathogenesis of CNM.

Realization of parallel experiments in a diamond anvil cell and their application to water-mineral interactions at high-pressure and high-temperature conditions.

Parallel experiments are normally used to compare different chemical systems and conditions simultaneously. In the field of high-pressure experimental science, parallel experiments are hard to realize due to very limited reaction chamber size for the generation of high-pressure conditions, especially in diamond anvil cells (DACs). Multiple holes, instead of a single hole, can be drilled into a gasket (i.e., multihole gasket technique) to realize parallel experiments in a DAC. In this study, we conducted a series of systematic calibration experiments on multihole gasket techniques using statistical methods. Multiple (two or three or four) holes 100 µm in diameter were symmetrically drilled into a gasket by a laser drilling instrument with the help of a coded Python program. The pressure deviations among different holes in a gasket at average pressures below 10 GPa are constrained to less than 0.2 GPa in all calibration experiments at room temperature. We further checked the influences of the gasket material, hole number, pre-indented gasket thickness, and temperature on the pressure deviations among different holes in a gasket. Finally, we applied the multihole gasket technique in a DAC experiment and compared the solubility of calcite in different chemical environments at the same pressure and temperature conditions. The experimental results showed that the multihole gasket technique could be widely applied to study water-mineral interactions at high-P (<10 GPa) and high-T (<700 °C) conditions because multiple parallel experiments can be efficiently realized simultaneously.

Correction to: Downregulation of the long noncoding RNA TUG1 inhibits the proliferation, migration, invasion and promotes apoptosis of renal cell carcinoma.

In the original article, we realized that an error occurred when we grouped the separate photos to generate the combined Figure 4 The same image was accidentally pasted twice in one figure, while we were not fully aware of the error at that time. We immediately reviewed the original data again and made sure that no changes need to be made in other parts of the paper. We are sure that the published manuscript was published without prior knowledge of the error and that it does not alter the conclusions of the study.

LncRNA-p21 alters the antiandrogen enzalutamide-induced prostate cancer neuroendocrine differentiation via modulating the EZH2/STAT3 signaling.

While the antiandrogen enzalutamide (Enz) extends the castration resistant prostate cancer (CRPC) patients' survival an extra 4.8 months, it might also result in some adverse effects via inducing the neuroendocrine differentiation (NED). Here we found that lncRNA-p21 is highly expressed in the NEPC patients derived xenograft tissues (NEPC-PDX). Results from cell lines and human clinical sample surveys also revealed that lncRNA-p21 expression is up-regulated in NEPC and Enz treatment could increase the lncRNA-p21 to induce the NED. Mechanism dissection revealed that Enz could promote the lncRNA-p21 transcription via altering the androgen receptor (AR) binding to different androgen-response-elements, which switch the EZH2 function from histone-methyltransferase to non-histone methyltransferase, consequently methylating the STAT3 to promote the NED. Preclinical studies using the PDX mouse model proved that EZH2 inhibitor could block the Enz-induced NED. Together, these results suggest targeting the Enz/AR/lncRNA-p21/EZH2/STAT3 signaling may help urologists to develop a treatment for better suppression of the human CRPC progression.

Polymorphisms in ERCC2 and ERCC5 and Risk of Prostate Cancer: A Meta-Analysis and Systematic Review.

Background and Objective: Excision repair cross complementing (ERCC) group genes play important roles in the nucleotide excision repair (NER) way, which can effectively remove bulky lesions and reduce UV-caused DNA damage by environmental chemicals. Polymorphisms in ERCCs were thought to be related to prostate cancer (PCa) risk. However, it has been unclear whether this relationship is consistent. This study aimed to obtain the overall profile regarding the associations between ERCCs polymorphisms and PCa risk. Materials and Methods: We identified relevant studies by a systematic search of PubMed, Medline, Embase, Google Scholar databases, Web of Science and Wanfang databases up to April 8, 2018. Odds ratios (ORs) with 95% confidential intervals (95%CIs) were conducted to evaluate the associations. All the statistical analyses were conducted basing on STATA 12.0 software. Results: Finally, a total of 29 previous studies published in 17 publications were included for four polymorphisms in two DNA repair genes (ERCC2-rs1799793, ERCC2-rs238406, ERCC2-rs13181 and ERCC5-rs17655). Overall, we observed no significant connection between these four polymorphisms and PCa risk. However, after stratifying the studies by ethnicity, ERCC2-rs1799793 polymorphism was associated with an increased risk of PCa in Asian patients and the relationship was subsequently validated with the allelic model, the homozygous model and the recessive model when extracting the data of Asian patients for specific analyses (B vs. A: OR = 1.537, 95%CI: 1.240-1.906, PA< 0.001; BB vs. AA: OR = 2.089, 95%CI: 1.388-3.145, PA< 0.001 and BB vs. BA + AA: OR = 1.929, 95%CI: 1.313-2.835, PA= 0.020). Furthermore, subgroup analyses were also conducted by Hardy-Weinberg Equilibrium (HWE) and source of control, negative results were identified for ERCC2-rs238406, ERCC2-rs13181 and ERCC5-rs17655 polymorphisms (PA> 0.050). Conclusion: To sum up, our work demonstrated that ERCC2-rs1799793 polymorphism is positively associated with PCa risk in Asian population. Further larger-scale studies with subjects of the same ethnicity and biological characteristics are required to verify these findings.

Analyzing 37,900 samples shows significant association between HOTAIR polymorphisms and cancer susceptibility: a meta-analysis.

BACKGROUND AND OBJECTIVE: An increasing number of investigations are drawing attention to the relationship between polymorphisms in the HOTAIR gene and the risk of cancers, but the results obtained so far have been controversial and inconclusive. We performed an up-to-date meta-analysis to obtain a more precise estimate of the possible associations. METHODS: Crude odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the associations. RESULTS: Nine publications including 26 case-control studies comprising 37,900 individuals were enrolled for the 5 polymorphisms in HOTAIR. The overall analyses identified a significant association between the rs920778 polymorphism and increased susceptibility to cancer in homozygous and recessive models. We conducted a stratification analysis by cancer type and identified a significantly increased susceptibility to esophageal squamous cell carcinoma in all the genetic models and to gastric cancer in the dominant model. For the rs7958904 polymorphism we detected a significantly decreased susceptibility to overall cancer in all 5 genetic models rather than the heterogeneous model. However, no significant association was identified between the rs874945, rs4759314 and rs1899663 polymorphisms and cancer susceptibility. CONCLUSIONS: Our results demonstrate that the HOTAIR rs920778 polymorphism may represent a risk factor for cancer, whereas the rs7958904 polymorphism may play a protective role.

Downregulation of the long noncoding RNA TUG1 inhibits the proliferation, migration, invasion and promotes apoptosis of renal cell carcinoma.

Long non-coding RNAs, a newly discovered category of noncoding genes, play a leading role in various biological processes, including tumorigenesis. In our study, we aimed to examine the TUG1 expression, and explore the influence of TUG1 silencing on cell proliferation and apoptosis in renal cell carcinoma (RCC) cell lines. The TUG1 expression level was detected using quantitative real-time PCR reverse transcription-polymerase chain reaction in 40 paired clear cell renal cell carcinoma (ccRCC) and adjacent paired normal tissues, as well as four RCC cell lines and one normal human proximal tubule epithelial cell line HK-2. Small interfering RNA was applied to suppress the TUG1 expression in RCC cell lines (A489 and A704). In vitro assays were conducted to further deliberate its potential functions in RCC progression. The relative TUG1 expression was significantly higher in ccRCC tissues compared to the adjacent normal renal tissues. In addition, higher TUG1 expression was equally detected in RCC cell lines (particularly in A498 and A704) compared to HK-2. The ccRCC specimens with higher TUG1 expression had a higher Fuhrman grade and larger tumor size than those with lower TUG1 expression. In vitro assays results suggested that knockdown of TUG1 suppressed RCC cells migration, invasion and proliferation, while the apoptosis process was activated. Our results indicate that TUG1 is identified as a novel oncogene in the morbid state of RCC, which potentially acts as a therapeutic target/biomarker in RCC. The graphic abstract of the present work.

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells.

BACKGROUND: Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas. Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied. HeLa is a well characterized HPV+ cervical cancer cell line. RESULT: We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip. Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing. Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions. Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level. By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins. CONCLUSION: Our results reveal the heterogeneity of a virus-infected cell line. It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers.

A comparison of isolated circulating tumor cells and tissue biopsies using whole-genome sequencing in prostate cancer.

Previous studies have demonstrated focal but limited molecular similarities between circulating tumor cells (CTCs) and biopsies using isolated genetic assays. We hypothesized that molecular similarity between CTCs and tissue exists at the single cell level when characterized by whole genome sequencing (WGS). By combining the NanoVelcro CTC Chip with laser capture microdissection (LCM), we developed a platform for single-CTC WGS. We performed this procedure on CTCs and tissue samples from a patient with advanced prostate cancer who had serial biopsies over the course of his clinical history. We achieved 30X depth and ≥ 95% coverage. Twenty-nine percent of the somatic single nucleotide variations (SSNVs) identified were founder mutations that were also identified in CTCs. In addition, 86% of the clonal mutations identified in CTCs could be traced back to either the primary or metastatic tumors. In this patient, we identified structural variations (SVs) including an intrachromosomal rearrangement in chr3 and an interchromosomal rearrangement between chr13 and chr15. These rearrangements were shared between tumor tissues and CTCs. At the same time, highly heterogeneous short structural variants were discovered in PTEN, RB1, and BRCA2 in all tumor and CTC samples. Using high-quality WGS on single-CTCs, we identified the shared genomic alterations between CTCs and tumor tissues. This approach yielded insight into the heterogeneity of the mutational landscape of SSNVs and SVs. It may be possible to use this approach to study heterogeneity and characterize the biological evolution of a cancer during the course of its natural history.

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing.

BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. RESULTS: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2). CONCLUSIONS: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.