Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways

BACKGROUND: SCA28 is an autosomal dominant ataxia associated with AFG3L2 gene mutations. We performed a whole genome expression profiling using lymphoblastoid cell lines (LCLs) from four SCA28 patients and six unrelated healthy controls matched for sex and age. METHODS: Gene expression was evaluated with the Affymetrix GeneChip Human Genome U133A 2.0 Arrays and data were validated by real-time PCR. RESULTS: We found 66 genes whose expression was statistically different in SCA28 LCLs, 35 of which were up-regulated and 31 down-regulated. The differentially expressed genes were clustered in five functional categories: (1) regulation of cell proliferation; (2) regulation of programmed cell death; (3) response to oxidative stress; (4) cell adhesion, and (5) chemical homeostasis. To validate these data, we performed functional experiments that proved an impaired SCA28 LCLs growth compared to controls (p\u2009<\u20090.005), an increased number of cells in the G0/G1 phase (p\u2009<\u20090.001), and an increased mortality because of apoptosis (p\u2009<\u20090.05). We also showed that respiratory chain activity and reactive oxygen species levels was not altered, although lipid peroxidation in SCA28 LCLs was increased in basal conditions (p\u2009<\u20090.05). We did not detect mitochondrial DNA large deletions. An increase of TFAM, a crucial protein for mtDNA maintenance, and of DRP1, a key regulator of mitochondrial dynamic mechanism, suggested an alteration of fission/fusion pathways. CONCLUSIONS: Whole genome expression profiling, performed on SCA28 LCLs, allowed us to identify five altered functional categories that characterize the SCA28 LCLs phenotype, the first reported in human cells to our knowledge. \ua9 2013 Mancini et al.; licensee BioMed Central Ltd

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

The Human Mitochondrial Genome: From Basic Biology to Disease

The Human Mitochondrial Genome: From Basic Biology to Disease offers a comprehensive, up-to-date examination of human mitochondrial genomics, connecting basic research to translational medicine across a range of disease types. Here, international experts discuss the essential biology of human mitochondrial DNA (mtDNA), including its maintenance, repair, segregation, and heredity. Furthermore, mtDNA evolution and exploitation, mutations, methods, and models for functional studies of mtDNA are dealt with. Disease discussion is accompanied by approaches for treatment strategies, with disease areas discussed including cancer, neurodegenerative, age-related, mtDNA depletion, deletion, and point mutation diseases. Nucleosides supplementation, mitoTALENs, and mitoZNF nucleases are among the therapeutic approaches examined in-depth. With increasing funding for mtDNA studies, many clinicians and clinician scientists are turning their attention to mtDNA disease association. This book provides the tools and background knowledge required to perform new, impactful research in this exciting space, from distinguishing a haplogroup-defining variant or disease-related mutation to exploring emerging therapeutic pathways

The proliferative response of HT-29 human colon adenocarcinoma cells to bombesin-like peptides

Bombesin-like peptides (BLP) and their receptors are widely distributed throughout the intestine and are potential mitogens for gastrointestinal cancers. In this study we characterized the proliferation induced by BLP in the human adenocarcinoma cell line HT-29. The number of HT-29 cells, partially serum deprived (1% fetal bovine serum) for 48 h, was increased after 24 h of stimulation with bombesin, GRP, neuromedin B (NMB) and neuromedin C (NMC) ranging from 0.1 nM up to 1 muM. Reverse transcription polymerase chain reaction studies, revealed the presence of mRNA for NMB and for the GRP preferring receptor (GRP-R). mRNA for GRP, NMB preferring receptor (NMB-R) and bombesin receptor subtype 3 (BRS-3) were not detected. [D-Phe(6)]bombesin-(6-13)methyl ester (Al) and BIM-23127 (A2), are considered as inhibitors of binding to GRP-R and NMB-R, respectively. Surprisingly, A I and A2 stimulated the proliferation of HT-29 cells. Moreover, in the simultaneous presence of 1 muM Al and 0.1 muM GRP or 0.1 nM or 0.1 muM bombesin, inhibition of the proliferation was observed. Our data demonstrate that the proliferation induced by BLP in HT-29 cells is due to interaction with the GR-P-R. (C) 2001 Elsevier Science Ireland Ltd. All rights reserved

Lack of effect by prostaglandin F2alpha on the proliferation of the HCT-8 and HT-29 human adenocarcinoma cell lines

A variety of studies have supported the finding that regular intake of aspirin or non-steroidal anti-inflammatory drugs can affect colorectal cancer carcinogenesis by decreasing the synthesis of prostaglandins (PGs). We report that PG F2alpha, in the presence of indomethacin, did not stimulate the proliferation in HCT-8 and HT-29 human colon adenocarcinoma cells. Moreover, in both cell lines fluprostenol, a specific agonist of FP receptors, did not increase intracellular Ca2+ concentration, monitored with the fluorescent dye fura-2. These results indicate that in HCT-8 and HT-29 cells: i) proliferation is not sensitive to PG F2alpha; ii) functional FP receptors are absent. Therefore, either PG F2alpha is not necessarily involved in the proliferation of colorectal mucosa or cell lines other than HCT-8 and HT-29 should be used to assess the role played by PG F2alpha in promoting cell proliferation in colon cancer

The effects of new sigma (σ) receptor ligands, PB190 and PB212, in the models predictive of antidepressant activity.

Background A number of σ receptor ligands have been demonstrated to possess antidepressant-like effect in some experimental paradigms (e.g. forced swim test, tail suspension test, olfactory bulbectomy model, conditioned fear stress). The objective of the present study was to find out whether PB190 and PB212, new σ1 receptor ligands, show the effects in some models predictive of antidepressant activity. Methods The impact of PB190 and PB212 on the immobility time in the forced swim test (FST) and tail suspension test (TST) was assessed in C57BL/6J male mice. Extracellular bradykinin triggers a transient increase in intracellular calcium concentration by activating the phospholipase C/IP3 pathway. The intracellular calcium concentration was estimated with the dual wavelength ratiometric probe Fura-2. Results In the FST model, PB190 showed a moderate antidepressant-like effect (only in the dose of 3 mg/kg) which was enhanced by joint treatment with amantadine (AMA), 10 mg/kg (inactive per se). The decrease in the immobility time induced by the combined treatment with PB190 and AMA was counteracted by PB212 and by BD1047, a σ1-receptor antagonist. The in vitro studies indicated that Ca2+-response was increased by 1 μM PB190, like by the σ1-agonist (+)-pentazocine, while 1 μM PB212 behaved line σ1-antagonist, BD1063. On the other hand, 100 μM PB190 negatively affected the Ca2+-response after bradykinin. Conclusions The obtained results: 1/indicated that in the in vivo conditions PB190 behaved as a σ1-receptor agonist while PB212 counteracted its effect, confirming the in vitro data; 2/gave support to the hypothesis that σ1-receptors might be one of possible mechanisms by which drugs induce antidepressant-like activity; 3/revealed that this effect may be potentiated by NMDA receptor antagonists, e.g. AMA