ALK kinase domain mutations in primary anaplastic large cell lymphoma: consequences on NPM-ALK activity and sensitivity to tyrosine kinase inhibitors.

ALK inhibitor crizotinib has shown potent antitumor activity in children with refractory Anaplastic Large Cell Lymphoma (ALCL) and the opportunity to include ALK inhibitors in first-line therapies is oncoming. However, recent studies suggest that crizotinib-resistance mutations may emerge in ALCL patients. In the present study, we analyzed ALK kinase domain mutational status of 36 paediatric ALCL patients at diagnosis to identify point mutations and gene aberrations that could impact on NPM-ALK gene expression, activity and sensitivity to small-molecule inhibitors. Amplicon ultra-deep sequencing of ALK kinase domain detected 2 single point mutations, R335Q and R291Q, in 2 cases, 2 common deletions of exon 23 and 25 in all the patients, and 7 splicing-related INDELs in a variable number of them. The functional impact of missense mutations and INDELs was evaluated. Point mutations were shown to affect protein kinase activity, signalling output and drug sensitivity. INDELs, instead, generated kinase-dead variants with dominant negative effect on NPM-ALK kinase, in virtue of their capacity of forming non-functional heterocomplexes. Consistently, when co-expressed, INDELs increased crizotinib inhibitory activity on NPM-ALK signal processing, as demonstrated by the significant reduction of STAT3 phosphorylation. Functional changes in ALK kinase activity induced by both point mutations and structural rearrangements were resolved by molecular modelling and dynamic simulation analysis, providing novel insights into ALK kinase domain folding and regulation. Therefore, these data suggest that NPM-ALK pre-therapeutic mutations may be found at low frequency in ALCL patients. These mutations occur randomly within the ALK kinase domain and affect protein activity, while preserving responsiveness to crizotinib.

The Antarctic krill Euphausia superba shows diurnal cycles of transcription under natural conditions.

BACKGROUND: Polar environments are characterized by extreme seasonal changes in day length, light intensity and spectrum, the extent of sea ice during the winter, and food availability. A key species of the Southern Ocean ecosystem, the Antarctic krill (Euphausia superba) has evolved rhythmic physiological and behavioral mechanisms to adapt to daily and seasonal changes. The molecular organization of the clockwork underlying these biological rhythms is, nevertheless, still only partially understood. METHODOLOGY/PRINCIPAL FINDINGS: The genome sequence of the Antarctic krill is not yet available. A normalized cDNA library was produced and pyrosequenced in the attempt to identify large numbers of transcripts. All available E. superba sequences were then assembled to create the most complete existing oligonucleotide microarray platform with a total of 32,217 probes. Gene expression signatures of specimens collected in the Ross Sea at five different time points over a 24-hour cycle were defined, and 1,308 genes differentially expressed were identified. Of the corresponding transcripts, 609 showed a significant sinusoidal expression pattern; about 40% of these exibithed a 24-hour periodicity while the other 60% was characterized by a shorter (about 12-hour) rhythm. We assigned the differentially expressed genes to functional categories and noticed that those concerning translation, proteolysis, energy and metabolic process, redox regulation, visual transduction and stress response, which are most likely related to daily environmental changes, were significantly enriched. Two transcripts of peroxiredoxin, thought to represent the ancestral timekeeping system that evolved about 2.5 billion years ago, were also identified as were two isoforms of the EsRh1 opsin and two novel arrestin1 sequences involved in the visual transduction cascade. CONCLUSIONS: Our work represents the first characterization of the krill diurnal transcriptome under natural conditions and provides a first insight into the genetic regulation of physiological changes, which occur around the clock during an Antarctic summer day.

RNA sequencing of the exercise transcriptome in equine athletes.

The horse is an optimal model organism for studying the genomic response to exercise-induced stress, due to its natural aptitude for athletic performance and the relative homogeneity of its genetic and environmental backgrounds. Here, we applied RNA-sequencing analysis through the use of SOLiD technology in an experimental framework centered on exercise-induced stress during endurance races in equine athletes. We monitored the transcriptional landscape by comparing gene expression levels between animals at rest and after competition. Overall, we observed a shift from coding to non-coding regions, suggesting that the stress response involves the differential expression of not annotated regions. Notably, we observed significant post-race increases of reads that correspond to repeats, especially the intergenic and intronic L1 and L2 transposable elements. We also observed increased expression of the antisense strands compared to the sense strands in intronic and regulatory regions (1 kb up- and downstream) of the genes, suggesting that antisense transcription could be one of the main mechanisms for transposon regulation in the horse under stress conditions. We identified a large number of transcripts corresponding to intergenic and intronic regions putatively associated with new transcriptional elements. Gene expression and pathway analysis allowed us to identify several biological processes and molecular functions that may be involved with exercise-induced stress. Ontology clustering reflected mechanisms that are already known to be stress activated (e.g., chemokine-type cytokines, Toll-like receptors, and kinases), as well as "nucleic acid binding" and "signal transduction activity" functions. There was also a general and transient decrease in the global rates of protein synthesis, which would be expected after strenuous global stress. In sum, our network analysis points toward the involvement of specific gene clusters in equine exercise-induced stress, including those involved in inflammation, cell signaling, and immune interactions.

Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA.

mRNA chimeras from chromosomal translocations often play a role as transforming oncogenes. However, cancer transcriptomes also contain mRNA chimeras that may play a role in tumor development, which arise as transcriptional or post-transcriptional events. To identify such chimeras, we developed a deterministic screening strategy for long-range sequence analysis. High-throughput, long-read sequencing was then performed on cDNA libraries from major tumor histotypes and corresponding normal tissues. These analyses led to the identification of 378 chimeras, with an unexpectedly high frequency of expression (≈2 x 10(-5) of all mRNA). Functional assays in breast and ovarian cancer cell lines showed that a large fraction of mRNA chimeras regulates cell replication. Strikingly, chimeras were shown to include both positive and negative regulators of cell growth, which functioned as such in a cell-type-specific manner. Replication-controlling chimeras were found to be expressed by most cancers from breast, ovary, colon, uterus, kidney, lung, and stomach, suggesting a widespread role in tumor development.

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.

Next-generation sequencing technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. In this context, an important issue is the need of a careful assessment of the accuracy of the assembly process. Here, we review the efficiency of a panel of assemblers, specifically designed to handle data from GS FLX 454 platform, on three bacterial data sets with different characteristics in terms of reads coverage and repeats content. Our aim is to investigate their strengths and weaknesses in the reconstruction of the reference genomes. In our benchmarking, we assess assemblers' performance, quantifying and characterizing assembly gaps and errors, and evaluating their ability to solve complex genomic regions containing repeats. The final goal of this analysis is to highlight pros and cons of each method, in order to provide the final user with general criteria for the right choice of the appropriate assembly strategy, depending on the specific needs. A further aspect we have explored is the relationship between coverage of a sequencing project and quality of the obtained results. The final outcome suggests that, for a good tradeoff between costs and results, the planned genome coverage of an experiment should not exceed 20-30 ×.

First survey of the wheat chromosome 5A composition through a next generation sequencing approach.

Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome.

Evaluation of metalloproteinases 2 and 9 and their inhibitors in physiologic and pre-eclamptic pregnancy.

Matrix metalloproteinases (MMPs) are a family of zinc and calcium-dependent endopeptidases involved in remodeling and physiological homeostasis of extracellular matrix (ECM). The metalloproteinases activity is predominantly modulated by specific tissue inhibitors of matrix metalloproteinases (TIMPs). The balance between MMPs and TIMPs is likely to play an important role in remodeling uterine arteries in pregnancy, and it may represent means by which vasodilatation is maintained in later pregnancy. Moreover, increased levels of MMPs and in particular MMP-2 play a role in the vascular alterations induced by hypertension. The aim of this study was the evaluation of MMP-2 and -9, along with their inhibitors TIMP-1 and -2, in pre-eclamptic women compared with normotensive pregnancy and non-pregnant women. Fourteen pre-eclamptic women were compared with 37 normotensive women in different gestational age and 21 non-pregnant women. Multiplexed sandwich enzyme-linked immunosorbent assay was used to measure MMPs and TIMPs simultaneously. MMP-2 levels were significantly higher in pre-eclamptic women vs. both non-pregnant and physiologic pregnant women. MMP-9 concentrations were significantly higher in physiologic pregnant vs. non-pregnant women. The serum levels of TIMP-1 were significantly higher in pre-eclamptic vs. both non-pregnant and physiologic pregnant women. TIMP-2 values were higher in physiologic pregnant women and pre-eclamptic women vs. non-pregnant women. A positive correlation between MMP-9 values and gestational age was observed in normal pregnant women. Results of the present investigation confirm that MMP-2 and TIMP-1 values are significantly higher in preeclampsia. We confirm that the modification of the fine balance between MMPs and their inhibitors plays a greater role in the structural and functional vascular changes of women with complicated pregnancies.

PASS: a program to align short sequences.

SUMMARY: Standard DNA alignment programs are inadequate to manage the data produced by new generation DNA sequencers. To answer this problem, we developed PASS with the objective of improving execution time and sensitivity when compared with other available programs. PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of 'seed' words (typically 11 and 12 bases) as well as an index of the precomputed scores of short words (typically seven and eight bases) aligned against each other. After building the genomic index, the program scans every query sequence performing three steps: (1) it finds matching seed words in the genome; (2) for every match checks the precomputed alignment of the short flanking regions; (3) if passes step 2, then it performs an exact dynamic alignment of a narrow region around the match. The performance of the program is very striking both for sensitivity and speed. For instance, gap alignment is achieved hundreds of times faster than BLAST and several times faster than SOAP, especially when gaps are allowed. Furthermore, PASS has a higher sensitivity when compared with the other available programs. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at http://pass.cribi.unipd.it, implemented in C++and supported on Linux and Windows.

Serum pro-inflammatory cytokines in physiological and pre-eclamptic pregnancies.

BACKGROUND: Pre-eclampsia is a heterogeneous syndrome ranging from mild hypertension and proteinuria to severe pre-eclampsia with complications, which can also be associated with an enhanced maternal inflammatory response. METHODS: Tumor necrosis factor-alpha (TNF-alpha), interleukin-1 (IL-1), interleukin-6 (IL-6) and interferon-gamma (IFN-gamma) were evaluated by multiplexed sandwich enzyme-linked immunosorbent assay in 14 pre-eclamptic women, 57 normotensive pregnant women (20 in the first, 20 in the second and 17 in the third trimester) and 21 non-pregnant women. RESULTS: The concentration of serum TNF-alpha was lower than the sensitivity limit of the assay in all groups. The prevalence of measurable IL-1 and IL-6 values, but not that of IFN-gamma, increased significantly in the second and third trimesters of pregnancy. However, the percentage of subjects with higher or detectable values of pro-inflammatory cytokines was statistically different between pre-eclamptic women and those in the second and third trimester of physiological pregnancy. CONCLUSIONS: Results of this study do not support standard screening for pro-inflammatory cytokines (TNF-alpha, IL-1, IL-6 and IFN-gamma) in pre-eclampsia.

Lipid and lipoprotein profile in physiological pregnancy.

Physiologic pregnancy is associated with a broad series of metabolic adaptations which may also influence the metabolism of lipids and lipoproteins. Although the modification of serum lipids and lipoproteins has been exhaustively investigated during and after pregnancy, the relative changes recorded vary widely among the different studies. A comprehensive lipid and lipoprotein profile was evaluated in 57 women with uncomplicated pregnancies at different gestational ages (20 in the first, 20 in the second, and 17 in the third trimester of pregnancy) and compared to that of 21 non-pregnant women. Conventional lipid parameters, including total cholesterol, high-density lipoprotein cholesterol and triglycerides, were evaluated on the Modular System P. Low-density lipoprotein cholesterol was quantified by the formula of Friedewald, the atherogenic index of plasma was quantified by the formula log (triglycerides/high-density lipoprotein cholesterol), whereas lipoprotein(a) was assayed on the BN II nephelometric analyzer. We observed that all the lipid parameters tested were significantly modified by the gestational age; in particular, women in the second and third trimester displayed significantly increased total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, total to high-density lipoprotein cholesterol ratio, lipoprotein(a) and atherogenic index of plasma (third trimester only) when compared to either the control population or the subgroup of women in the first trimester of pregnancy. The value distributions and the relative percentage of women with undesirable or abnormal values according to the current NCEP or AHA/ACC goals were comparable between controls and women in the first trimester. However, when compared with either controls or women in the first trimester, advanced pregnancy was associated with an increased prevalence of undesirable or abnormal values for total cholesterol, low-density lipoprotein cholesterol and triglycerides in the second trimester, and total cholesterol, low-density lipoprotein cholesterol, triglycerides, total to high-density lipoprotein cholesterol ratio and lipoprotein(a) (only from non-pregnant women) in the third trimester. The results of this case-control study demonstrate that physiological pregnancy is associated with a substantial modification of the lipid and lipoprotein metabolism from the second trimester, providing reference ranges for traditional and emerging cardiovascular risk predictors throughout the gestational period.

Fine-grained statistical torsion angle potentials are effective in discriminating native protein structures.

Modelling of drug targets requires the reliable selection of an accurate and representative structure from large ensembles of alternate models. Statistical potentials developed to discriminate native protein structures generally represent pairwise interactions between atoms, which are less sensitive to local conformational details. The discrimination of local distortions is therefore particularly difficult. Local interaction preferences, expressed through torsion angles, are rarely used, as some controversy exists in the literature regarding their discrimination power. The present study aims to benchmark the efficiency of different implementations of torsion angle propensities for selecting the native structure from ensembles of well-constructed decoys. Several statistical potentials derived from fine-grained discretisations of torsion angle space are constructed and evaluated. Results from a comparison with nine widely used statistical scoring functions show the torsion angle potentials to be more effective in recognising native structures and to improve with the number of torsion angles considered. These data suggest local structural propensities to be important for estimating the overall quality of native-like models.

Align: a C++ class library and web server for rapid sequence alignment prototyping.

Sequence alignment remains a fundamental tool in most tasks related to the prediction of protein sequence and structure. A C++ class library was developed to facilitate the rapid implementation of a variety of state-of-the-art pairwise sequence alignment techniques. These range from simple sequence to sequence to the advanced profile to profile alignments with optional secondary structure information. Suboptimal alignments, frequently used to estimate regions of confidence, can also be generated. The object oriented design facilitates rapid implementation, testing and extension of existing functionality. A simple web interface, which can also be useful in bioinformatics education, is also provided. Source code, online documentation and a prototypical web interface are freely accessible to academic users from the URL: http://protein.cribi.unipd.it/align/. A sample case study in the modelling of human Cytochrome P450 is discussed.