Targeted co-expression networks for the study of traits.

Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used approach for the generation of gene co-expression networks. However, networks generated with this tool usually create large modules with a large set of functional annotations hard to decipher. We have developed TGCN, a new method to create Targeted Gene Co-expression Networks. This method identifies the transcripts that best predict the trait of interest based on gene expression using a refinement of the LASSO regression. Then, it builds the co-expression modules around those transcripts. Algorithm properties were characterized using the expression of 13 brain regions from the Genotype-Tissue Expression project. When comparing our method with WGCNA, TGCN networks lead to more precise modules that have more specific and yet rich biological meaning. Then, we illustrate its applicability by creating an APP-TGCN on The Religious Orders Study and Memory and Aging Project dataset, aiming to identify the molecular pathways specifically associated with APP role in Alzheimer's disease. Main biological findings were further validated in two independent cohorts. In conclusion, we provide a new framework that serves to create targeted networks that are smaller, biologically relevant and useful in high throughput hypothesis driven research. The TGCN R package is available on Github: https://github.com/aliciagp/TGCN .

Splicing accuracy varies across human introns, tissues and age.

Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation. We show that mis-splicing occurs at different rates across introns and tissues and that these splicing inaccuracies are primarily affected by the abundance of core components of the spliceosome assembly and its regulators. Using publicly available data on short-hairpin RNA-knockdowns of numerous spliceosomal components and related regulators, we found support for the importance of RNA-binding proteins in mis-splicing. We also demonstrated that age is positively correlated with mis-splicing, and it affects genes implicated in neurodegenerative diseases. This in-depth characterisation of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.

Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease.

Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson's Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson's disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal-lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.

Changes in the levels of polymethoxyflavones and flavanones as part of the defense mechanism of Citrus sinensis (cv. Valencia Late) fruits against Phytophthora citrophthora.

Phytophthora citrophthora causes serious losses in Citrus fruits through brown rot lesion. The effect of infection with P. citrophthora on Citrus sinensis (cv. Valencia Late) fruits was studied, with particular reference to the levels of the flavanones hesperidin and isonaringin and the polymethoxyflavones sinensetin, nobiletin, tangeretin, and heptamethoxyflavone, because flavonoids are most probably involved as natural defense or resistance mechanisms in this genus. Changes in the levels of these flavonoids were detected after infection. The hesperidin and isonaringin contents fell by 13 and 67%, respectively, whereas the contents of their corresponding aglycons, hesperetin and naringenin, increased, suggesting the hydrolyzing effect of this fungus on the glycosylated flavanones. The heptamethoxyflavone, nobiletin, sinensetin, and tangeretin levels increased by 48, 28, 26, and 24%, respectively. The in vitro study revealed that these compounds acted as antifungal agents, the most active being the aglycons (naringenin and hesperetin), followed by the polymethoxyflavones and flavanone glycosides. The participation of these flavonoids in the defense mechanism of this Citrus species is discussed.

Increasing resistance against Phytophthora citrophthora in tangelo Nova fruits by modulating polymethoxyflavones levels.

The effect of 6-benzylaminopurine on polymethoxyflavone levels in tangelo Nova fruits and the possible participation of these secondary metabolites in defense mechanisms against Phytophthora citrophthora are studied. The in vitro study of the inhibitory effect of these compounds on fungal growth reveals that nobiletin is the most active agent followed by sinensetin, heptamethoxyflavone, and tangeretin. Treatment with 100 ppm of 6-benzylaminopurine increased the levels of these polymethoxyflavones in this Citrus hybrid and also enhanced the in vivo resistance of the fruit to the fungus by approximately 60%.

Modulation of the biosynthesis of some phenolic compounds in Olea europaea L. fruits: their influence on olive oil quality.

The phenolic composition of olive fruits (Olea europaea L.) (cv. Picual, Villalonga, Alfafarenca, and Cornicabra) grown in different areas of Spain was studied by high performance liquid chromatography-mass spectrometry. Different levels of tyrosol, catechin, p-coumaric acid, rutin, luteolin, and oleuropein were observed in the different varieties analyzed. Treating the fruit with 0.3% Brotomax 50 days after anthesis had a beneficial effect on fruit size, oil content, levels of polyphenolic compounds, and Trolox-equivalent antioxidant activity (TEAC) in all the varieties analyzed.

The decrease in auxin polar transport down the lupin hypocotyl could produce the indole-3-acetic Acid distribution responsible for the elongation growth pattern.

The variation of indole-3-acetic acid (IAA) transport along Lupinus albus L. hypocotyls was studied using decapitated seedlings and excised sections. To confirm that the mobile species was IAA and not IAA metabolites, dual isotope-labeled IAAs, [5-(3)H]IAA + [1-(14)C]IAA, were used. After apical application to decapitated seedlings, the longitudinal distribution of both isotopes at different transport periods showed that the velocity of IAA transport was higher in the apical, elongating region than in the basal, non-growing region. This variation in velocity was not a traumatic consequence of decapitation because after application of IAA to the basal region of decapitated seedlings, both the velocity and intensity of IAA transport were lower than in the apical treatment. The variation in IAA transport down the hypocotyl was confirmed when it was measured in excised sections located at different positions along the hypocotyl. The velocity and, to a greater extent, the intensity of IAA transport decreased from the apical to the basal sections. Consequently, if the amount of IAA reaching the apical zones of lupin hypocotyl were higher than the IAA transport capacity in the basal zones, accumulation of mobile IAA might be expected in zones located above the basal region. In fact, an IAA accumulation occurred in the elongating region during the first 4-h period of transport after apical treatment with IAA. It is proposed that the fall in IAA transport along the hypocotyl might be responsible for the IAA distribution and, consequently, for the growth distribution reported in this organ. An indirect proof of this was obtained from experiments that showed that the excision of the slowly transporting basal zones strongly reduced the growth in the remaining part of the organ, whereas excision of the root caused no significant modification in growth during a 20-h period.

Lateral diffusion of polarly transported indoleacetic acid and its role in the growth of Lupinus albus L. hypocotyls.

The transport and metabolism of indole-3-acetic acid (IAA) was studied in etiolated lupin (Lupinus albus L, cv. Multolupa) hypocotyls, following application of dual-isotope-labelled indole-3-acetic acid, [5-(3)H]IAA plus [1-(14)C]IAA, to decapitated plants. To study the radial distribution of the transported and metabolized IAA, experiments were carried out with plants in which the stele was separated from the cortex by a glass capillary. After local application of labelled IAA to the cortex, radioactivity remained immobilized in the cortex, near the application point, showing that polar transport cannot occur in the outer tissues. However, following application of IAA to the stele, radioactivity appeared in the cortex in those hypocotyl sections below the first 1 cm (in which the capillary was inserted), and the basipetal IAA movement was similar to that observed after application of IAA to the complete cut surface. In both assays, longitudinal distribution of (14)C and (3)H in the stele outside the first 1 cm was positively correlated with that of cortex, indicating that there was a lateral migration of IAA from the transport pathway (in the stele) to the outer tissues and that this migration depended on the amount of IAA in the stele. Both tissues (stele and cortex) exhibited intensive IAA metabolism, decarboxylation being higher in the stele than in the cortex while IAA conjugation was the opposite. Decapitation of the seedlings caused a drastic reduction of hypocotyl growth in the 24 h following decapitation, unless the hypocotyls were treated apically with IAA. Thus, exogenous IAA, polarly transported, was able to substitute the endogenous source of auxin (cotyledons plus meristem) to permit hypocotyl growth. It is proposed that IAA escapes from the transporting cells (in the stele) to the outer tissues in order to reach the growth-responsive cells. The IAA metabolism in the outer tissues could generate the IAA gradient necessary for the maintenance of its lateral flow, and consequently the auxin-induced cell elongation.