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We have developed ComplexBrowser, an open source, online platform for supervised analysis of quantitative proteomic data (label free and isobaric mass tag based) that focuses on protein complexes. The software uses manually curated information from CORUM and Complex Portal databases to identify protein complex components. For the first time, we provide a Complex Fold Change (CFC) factor that identifies up- and downregulated complexes based on the level of complex subunits coregulation. The software provides interactive visualization of protein complexes' composition and expression for exploratory analysis and incorporates a quality control step that includes normalization and statistical analysis based on the limma package. ComplexBrowser was tested on two published studies identifying changes in protein expression within either human adenocarcinoma tissue or activated mouse T-cells. The analysis revealed 1519 and 332 protein complexes, of which 233 and 41 were found coordinately regulated in the respective studies. The adopted approach provided evidence for a shift to glucose-based metabolism and high proliferation in adenocarcinoma tissues, and the identification of chromatin remodeling complexes involved in mouse T-cell activation. The results correlate with the original interpretation of the experiments and provide novel biological details about the protein complexes affected. ComplexBrowser is, to our knowledge, the first tool to automate quantitative protein complex analysis for high-throughput studies, providing insights into protein complex regulation within minutes of analysis.
Mol Cell Proteomics 2019 11
PMID:ComplexBrowser: A Tool for Identification and Quantification of Protein Complexes in Large-scale Proteomics Datasets. 3144 28

Cancer precision medicine aims to predict the drug likely to yield the best response for a patient. Genomic sequencing of tumors is currently being used to better inform treatment options; however, this approach has had a limited clinical impact due to the paucity of actionable mutations. An alternative to mutation status is the use of gene expression signatures to predict response. Using data from two large-scale studies, The Genomics of Drug Sensitivity of Cancer (GDSC) and The Cancer Therapeutics Response Portal (CTRP), we investigated the relationship between the sensitivity of hundreds of cell lines to hundreds of drugs, and the relative expression levels of the targets these drugs are directed against. For approximately one third of the drugs considered (73/222 in GDSC and 131/360 in CTRP), sensitivity was significantly correlated with the expression of at least one of the known targets. Surprisingly, for 8% of the annotated targets, there was a significant anticorrelation between target expression and sensitivity. For several cases, this corresponded to drugs targeting multiple genes in the same family, with the expression of one target significantly correlated with sensitivity and another significantly anticorrelated suggesting a possible role in resistance. Furthermore, we identified nontarget genes that are significantly correlated or anticorrelated with drug sensitivity, and find literature linking several to sensitization and resistance. Our analyses provide novel and important insights into both potential mechanisms of resistance and relative efficacy of drugs against the same target.
Mol Cancer Ther 2019 12
PMID:Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics. 3146 81

An olfactory bulbectomy (OBX) rodent is a widely-used model for depression (especially for agitated depression). The present study aims to investigate the hippocampus metabolic profile and autophagy-related pathways in OBX rats and to explore the modulatory roles of fluoxetine. OBX rats were given a 30-day fluoxetine treatment after post-surgery rehabilitation, and then behavioral changes were evaluated. Subsequently, the hippocampus was harvested for metabonomics analysis and Western blot detection. As a result, OBX rats exhibited a significantly increased hyperemotionality score and declined spatial memory ability. Fluoxetine reduced the hyperemotional response, but failed to restore the memory deficit in OBX rats. Sixteen metabolites were identified as potential biomarkers for the OBX model including six that were rectified by fluoxetine. Disturbed pathways were involved in amino acid metabolism, fatty acid metabolism, purine metabolism, and energy metabolism. In addition, autophagy was markedly inhibited in the hippocampus of OBX rats. Fluoxetine could promote autophagy by up-regulating the expression of LC3 II, beclin1, and p-AMPK/AMPK, and down-regulating the levels of p62, p-Akt/Akt, p-mTOR/mTOR, and p-ULK1/ULK1. Our findings indicated that OBX caused marked abnormalities in hippocampus metabolites and autophagy, and fluoxetine could partly redress the metabolic disturbance and enhance autophagy to reverse the depressive-like behavior, but not the memory deficits in OBX rats.
Int J Mol Sci 2019 Sep 01
PMID:Hippocampus Metabolic Disturbance and Autophagy Deficiency in Olfactory Bulbectomized Rats and the Modulatory Effect of Fluoxetine. 3148 May 39

Protein-protein interactions (PPIs) control all functions and physiological states of the cell. Identification and understanding of novel PPIs would facilitate the discovery of new biological models and therapeutic targets for clinical intervention. Numerous resources and PPI databases have been developed to define a global interactome through the PPI data mining, curation, and integration of different types of experimental evidence obtained with various methods in different model systems. On the other hand, the recent advances in cancer genomics and proteomics have revealed a critical role of genomic alterations in acquisition of cancer hallmarks through a dysregulated network of oncogenic PPIs. Deciphering of cancer-specific interactome would uncover new mechanisms of oncogenic signaling for therapeutic interrogation. Toward this goal our team has developed a high-throughput screening platform to detect PPIs between cancer-associated proteins in the context of cancer cells. The established network of oncogenic PPIs, termed the OncoPPi network, is available through the OncoPPi Portal, an interactive web resource that allows to access and interpret a high-quality cancer-focused network of PPIs experimentally detected in cancer cell lines integrated with the analysis of mutual exclusivity of genomic alterations, cellular co-localization of interacting proteins, domain-domain interactions, and therapeutic connectivity. This chapter presents a guide to explore the OncoPPi network using the OncoPPi Portal to facilitate cancer biology.
Methods Mol Biol 2020
PMID:Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. 3158 37

Two-pore domain potassium (K2P) channels maintain the cell's background conductance by stabilizing the resting membrane potential. They assemble as dimers possessing four transmembrane helices in each subunit. K2P channels were crystallized in "up" and "down" states. The movements of the pore-lining transmembrane TM4 helix produce the aperture or closure of side fenestrations that connect the lipid membrane with the central cavity. When the TM4 helix is in the up-state, the fenestrations are closed, while they are open in the down-state. It is thought that the fenestration states are related to the activity of K2P channels and the opening of the channels preferentially occurs from the up-state. TASK-2, a member of the TALK subfamily of K2P channels, is opened by intracellular alkalization leading the deprotonation of the K245 residue at the end of the TM4 helix. This charge neutralization of K245 could be sensitive or coupled to the fenestration state. Here, we describe the relationship between the states of the intramembrane fenestrations and K245 residue in TASK-2 channel. By using molecular modeling and simulations, we show that the protonated state of K245 (K245+) favors the open fenestration state and, symmetrically, that the open fenestration state favors the protonated state of the lysine residue. We show that the channel can be completely blocked by Prozac, which is known to induce fenestration opening in TREK-2. K245 protonation and fenestration aperture have an additive effect on the conductance of the channel. The opening of the fenestrations with K245+ increases the entrance of lipids into the selectivity filter, blocking the channel. At the same time, the protonation of K245 introduces electrostatic potential energy barriers to ion entrance. We computed the free energy profiles of ion penetration into the channel in different fenestration and K245 protonation states, to show that the effects of the two transformations are summed up, leading to maximum channel blocking. Estimated rates of ion transport are in qualitative agreement with experimental results and support the hypothesis that the most important barrier for ion transport under K245+ and open fenestration conditions is the entrance of the ions into the channel.
Int J Mol Sci 2020 Jan 14
PMID:Elucidating the Structural Basis of the Intracellular pH Sensing Mechanism of TASK-2 K2P Channels. 3194 79

Clozapine is thought to induce obsessive compulsive symptoms (OCS) in schizophrenic patients. However, because OCS are often comorbid with schizophrenia regardless of clozapine treatment, it remains unclear whether clozapine can generate OCS de novo. Thus, it has been difficult to establish a causal link between clozapine and OCS in human studies. To address this question, we asked whether chronic treatment with clozapine can induce obsessive compulsive disorder (OCD)-like behavior in mice. We injected mice with long-term continuous release pellets embedded with clozapine four times at 60-day intervals and then monitored the mice for signs of OCD-like behavior up to 40 wk. of age. We found clozapine increases grooming behavior as early as 30 wk. of age. We also investigated the effect clozapine on grooming behavior in Sapap3 knockout (KO) mice, which are a well-known animal model of OCD. In Sapap3 heterozygous KO mice, clozapine increases grooming behavior much earlier than in wild-type mice, suggesting a clozapine-OCD gene interaction. Fluoxetine, which is often used in the treatment of OCS and OCD, reduced the grooming behavior induced by clozapine. These data demonstrate that chronic clozapine treatment can generate OCD-like behavior in mice and support the hypothesis that clozapine produces de novo OCS regardless of schizophrenia status.
Mol Brain 2020 05 29
PMID:Clozapine generates obsessive compulsive disorder-like behavior in mice. 3247 17

Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in FASTQ format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus.edu.sg/csingsportal.
Int J Mol Sci 2020 May 28
PMID:CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. 3248 89

Carcinoma of unknown primary (CUP), defined as metastatic cancers with unknown cancer origin, occurs in 3-5 per 100 cancer patients in the United States. Heterogeneity and metastasis of cancer brings great difficulties to the follow-up diagnosis and treatment for CUP. To find the tissue-of-origin (TOO) of the CUP, multiple methods have been raised. However, the accuracies for computed tomography (CT) and positron emission tomography (PET) to identify TOO were 20%-27% and 24%-40% respectively, which were not enough for determining targeted therapies. In this study, we provide a machine learning framework to trace tumor tissue origin by using gene length-normalized somatic mutation sequencing data. Somatic mutation data was downloaded from the Data Portal (Release 28) of the International Cancer Genome Consortium (ICGC), and 4909 samples for 13 cancers was used to identify primary site of cancers. Optimal results were obtained based on a 600-gene set by using the random forest algorithm with 10-fold cross-validation, and the average accuracy and F1-score were 0.8822 and 0.8886 respectively across 13 types of cancer. In conclusion, we provide an effective computational framework to infer cancer tissue-of-origin by combining DNA sequencing and machine learning techniques, which is promising in assisting clinical diagnosis of cancers.
Biochim Biophys Acta Mol Basis Dis 2020 11 01
PMID:A machine learning framework to trace tumor tissue-of-origin of 13 types of cancer based on DNA somatic mutation. 3277 16

Kv3.1 channel is abundantly expressed in neurons and its dysfunction causes sleep loss, neurodegenerative diseases and depression. Fluoxetine, a serotonin selective reuptake inhibitor commonly used to treat depression, acts also on Kv3.1. To define the relationship between Kv3.1 and serotonin receptors (SR) pharmacological modulation, we showed that 1C11, a serotonergic cell line, expresses different voltage gated potassium (VGK) channels subtypes in the presence (differentiated cells (1C11D)) or absence (not differentiated cells (1C11ND)) of induction. Only Kv1.2 and Kv3.1 transcripts increase even if the level of Kv3.1b transcripts is highest in 1C11D and, after fluoxetine, in 1C11ND but decreases in 1C11D. The Kv3.1 channel protein is expressed in 1C11ND and 1C11D but is enhanced by fluoxetine only in 1C11D. Whole cell measurements confirm that 1C11 cells express (VGK) currents, increasing sequentially as a function of cell development. Moreover, SR 5HT1b is highly expressed in 1C11D but fluoxetine increases the level of transcript in 1C11ND and significantly decreases it in 1C11D. Serotonin dosage shows that fluoxetine at 10 nM blocks serotonin reuptake in 1C11ND but slows down its release when cells are differentiated through a decrease of 5HT1b receptors density. We provide the first experimental evidence that 1C11 expresses Kv3.1b, which confirms its major role during differentiation. Cells respond to the fluoxetine effect by upregulating Kv3.1b expression. On the other hand, the possible relationship between the fluoxetine effect on the kinetics of 5HT1b differentiation and Kv3.1bexpression, would suggest the Kv3.1b channel as a target of an antidepressant drug as well as it was suggested for 5HT1b.
Int J Mol Sci 2020 Sep 29
PMID:First Evidence of Kv3.1b Potassium Channel Subtype Expression during Neuronal Serotonergic 1C11 Cell Line Development. 3300 79

Managing liver cirrhosis in clinical practice is still a challenging problem as its progression is associated with serious complications, such as variceal bleeding that may increase mortality. Portal hypertension (PH) is the main key for the development of liver cirrhosis complications. Portal pressure above 10 mmHg, termed as clinically significant portal hypertension, is associated with formation of varices; meanwhile, portal pressure above 12 mmHg is associated with variceal bleeding. Hepatic vein pressure gradient measurement and esophagogastroduodenoscopy remain the gold standard for assessing portal pressure and detecting varices. Recently, non-invasive methods have been studied for evaluation of portal pressure and varices detection in liver cirrhotic patients. Various guidelines have been published for clinicians' guidance in the management of esophagogastric varices which aims to prevent development of varices, acute variceal bleeding, and variceal rebleeding. This writing provides a comprehensive review on development of PH and varices in liver cirrhosis patients and its management based on current international guidelines and real experience in Indonesia.
Clin Mol Hepatol 2020 10
PMID:Managing liver cirrhotic complications: Overview of esophageal and gastric varices. 3305 28


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