SPCS: A Spatial and Pattern Combined Smoothing Method of Spatial Transcriptomic Expression

The recently developed spatial transcriptomics (ST) technique has made it possible to view spatial transcriptional heterogeneity in a high throughput manner. It is based on highly multiplexed sequence analysis and uses barcodes to split the sequenced reads into respective tissue locations. However, this type of sequencing technique suffers from high noise and drop-out events in the data, which makes smoothing a necessary step before performing downstream analysis. Traditional smoothing methods used in the similar single cell RNA sequencing (scRNA-seq) data are one-factor methods that can only utilize associations in transcriptome space. Since they do not account for associations in the Euclidean space, i.e. tissue location distances on the ST slide, these one-factor methods cannot take full advantage of all the knowledge in ST data. In this study, we present a novel two-factor smoothing technique, Spatial and Pattern Combined Smoothing (SPCS), that employs k-nearest neighbor technique to utilize associations from transcriptome and Euclidean space from the ST data. By performing SPCS on 10 ST slides from pancreatic ductal adenocarcinoma (PDAC), smoothed ST slides have better separability, partition accuracy, and biological interpretability than the ones smoothed by pre-existing one-factor smoothing methods. Source code of SPCS is provided in Github (https://github.com/Usos/SPCS).

Botanical Drug Puerarin Ameliorates Liposaccharide-Induced Depressive Behaviors in Mice via Inhibiting RagA/mTOR/p70S6K Pathways

Background. The depressive symptom hallmarks the progression of the neurodegenerative diseases, especially Alzheimer’s disease. Bacterial infection is related to inflammation and depression. The present project thereby examined whether botanical drug puerarin could attenuate liposaccharide- (LPS-) induced depressive behaviors in mice. Methods. Adult male C57BL/6N mice were sequentially treated with LPS and puerarin and evaluated for the depressive behaviors by tail suspension test and forced swim test. The brain tissues were profiled for the molecular targets of puerarin by next-generation RNA sequencing technique. Candidate targets were further verified in LPS-treated mice, neural stem cells, and highly differentiated PC12 cell line. Results. Puerarin ameliorated LPS-induced depression in the mice. RNA sequencing profiles revealed that puerarin altered the expression of 16 genes while markedly downregulated Ras-related GTP-binding protein A (RagA) in LPS-treated mice. The effect of puerarin on RagA expression was confirmed by immunostaining, Western blot, and quantitative real-time PCR (qRT-PCR). Biochemical studies showed that puerarin inhibited RagA/mTOR/p70S6K pathway, attenuated the accumulation of mTORC1 in close proximity to lysosome, and reduced the production of proinflammatory cytokines. Conclusions. Botanical drug puerarin attenuated inflammation and depressive behaviors in LPS-challenged mice by inhibiting RagA/mTOR/p70S6K pathways. Puerarin may be a lead compound for the new antidepressant drugs.

The value of bacterial metagenomic analysis in post-surgical examination of gallstones

Gallstone disease is one of the most common causes of hospitalization for gastrointestinal diseases in the world. Recent studies have examined the presence of bacteria in the formation of stones. Our main goal was to determine the overall composition of gallstone microflora. Gallstones were obtained from 24 patients during laparoscopic cholecystectomy from which DNA were extracted. Composition of bacterial flora was evaluated on 16 s rDNA sequencing technique. In the vast majority of samples, bacteria were present, and four groups could be differentiated regarding the flora. Overall composition shows that 87% of the stones were cholesterol/mixed type of gallstone. Additionally, potentially harmful microorganisms (Streptococcus, Clostridium and Kocuria) that could cause post-surgery complications were identified in several patients. The obtained results indicate that this technique may be useful in analyzing the type of stones and in pinpointing the presence of pathogenic bacteria.

Common and Unique Genetic Background between Attention-Deficit/Hyperactivity Disorder and Excessive Body Weight

Comorbidity studies show that children with ADHD have a higher risk of being overweight and obese than healthy children. This study aimed to assess the genetic alternations that differ between and are shared by ADHD and excessive body weight (EBW). The sample consisted of 743 Polish children aged between 6 and 17 years. We analyzed a unique set of genes and polymorphisms selected for ADHD and/or obesity based on gene prioritization tools. Polymorphisms in the KCNIP1, SLC1A3, MTHFR, ADRA2A, and SLC6A2 genes proved to be associated with the risk of ADHD in the studied population. The COMT gene polymorphism was one that specifically increased the risk of EBW in the ADHD group. Using the whole-exome sequencing technique, we have shown that the ADHD group contains rare and protein-truncating variants in the FBXL17, DBH, MTHFR, PCDH7, RSPH3, SPTBN1, and TNRC6C genes. In turn, variants in the ADRA2A, DYNC1H1, MAP1A, SEMA6D, and ZNF536 genes were specific for ADHD with EBW. In this way, we confirmed, at the molecular level, the existence of genes specifically predisposing to EBW in ADHD patients, which are associated with the biological pathways involved in the regulation of the reward system, intestinal microbiome, and muscle metabolism.

Simpler and Faster Development of Tumor Phylogeny Pipelines

In the recent years there has been an increasing amount of single-cell sequencing (SCS) studies, producing a considerable number of new datasets. This has particularly affected the field of cancer analysis, where more and more papers are published using this sequencing technique that allows for capturing more detailed information regarding the specific genetic mutations on each individually sampled cell. As the amount of information increases, it is necessary to have more sophisticated and rapid tools for analyzing the samples. To this goal we developed *plastic*, an easy-to-use and quick to adapt pipeline that integrates three different steps: (1) to simplify the input data; (2) to infer tumor phylogenies; and (3) to compare the phylogenies. We have created a pipeline submodule for each of those steps, and developed new in-memory data structures that allow for easy and transparent sharing of the information across the tools implementing the above steps. While we use existing open source tools for those steps, we have extended the tool used for simplifying the input data, incorporating two machine learning procedures --- which greatly reduce the running time without affecting the quality of the downstream analysis. Moreover, we have introduced the capability of producing some plots to quickly visualize results.

Neurosecretory protein GL-induced fat accumulation is accompanied by repressing the immune-inflammatory response in the adipose tissue of mice

We have recently identified neurosecretory protein GL (NPGL), a small secretory protein expressed in the vertebrate hypothalamus, as an orexigenic factor with remarkable fat accumulation by overexpression of the NPGL precursor gene (Npgl) for two months. In the present study, we analyzed the effects of short-term Npgl overexpression for 18 days as the early stage of obesity to address the mechanisms underlying obese-like phenotype. Similar to previous studies, short-term Npgl overexpression stimulated food intake and fat accumulation in the white adipose tissues (WAT), whereas the masses of the brown adipose tissue, testis, liver, heart, and muscle remained unchanged. In addition, we observed increased blood insulin and leptin levels due to Npgl overexpression, while little changes were induced in blood glucose, free fatty acids, triglyceride, and cholesterol levels. Furthermore, transcriptome analysis of the inguinal WAT using RNA-sequencing technique revealed that overexpression of Npgl upregulated the genes involved in cytoskeleton regulation, whereas it decreased those involved in immune-inflammatory responses. These results suggest that NPGL plays a crucial role in enlarging adipocytes and suppressing inflammation to avoid metabolic abnormalities, eventually contributing to accelerating energy storage.

HERON: A Novel Tool Enables Identification of Long, Weakly Enriched Genomic Domains in ChIP-seq Data

The explosive development of next-generation sequencing-based technologies has allowed us to take an unprecedented look at many molecular signatures of the non-coding genome. In particular, the ChIP-seq (Chromatin ImmunoPrecipitation followed by sequencing) technique is now very commonly used to assess the proteins associated with different non-coding DNA regions genome-wide. While the analysis of such data related to transcription factor binding is relatively straightforward, many modified histone variants, such as H3K27me3, are very important for the process of gene regulation but are very difficult to interpret. We propose a novel method, called HERON (HiddEn MaRkov mOdel based peak calliNg), for genome-wide data analysis that is able to detect DNA regions enriched for a certain feature, even in difficult settings of weakly enriched long DNA domains. We demonstrate the performance of our method both on simulated and experimental data.

Molecular Analysis of β-Globin Mutations Among β-Thalassemia Patients in Hamadan

Background: β-Thalassemia (βT) is one of the most common genetic diseases. The specific mutation profile of that region can be identified by determining the specific mutations of each region and ethnicity. Objectives: This study investigated the β-globin mutations in patients with βT in Hamadan. Methods: This cross-sectional study was performed on 47 βT carriers. In the present study, the polymerase chain reaction (PCR)-sequencing technique was used to confirm βT carriers, and data were analyzed with SPSS-16 at a 95% confidence level. Results: In general, 164 individuals (81 men and 83 women) suspected of having thalassemia were examined, where 28.7 % (n=47) of them were identified by PCR-sequencing with βT carriers (48.8% male and 53.2% females). Hemoglobin beta (HBβ): c.251 del, HBβ: c.27dupG, and HBβ: c.92+5G>A mutations had the greatest effect on mean corpuscular volume (MCV) reduction, mean corpuscular HB (MCH) reduction, and HbA2 increment, respectively. The most common mutation in both males and females was the same (HBβ: c.315+1G>A). Conclusion: According to the results, the most common mutations in the diagnosis of βT in Hamadan were serially HBβ: c.315+1G>A mutation and HBβ: c.25-26del, HBβ: c.112del, HBβ: c.20A>T, HBβ: 92+6T>C, and HBβ: c.316-106C>G.

Author Correction: Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

An amendment to this paper has been published and can be accessed via a link at the top of the paper.