Transcriptional Co-expression Research Articles

Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng.

Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involved in ginsenoside biosynthesis have been cloned through orthologue analysis. Here, we report the identification of 21 genes controlling Rb1 biosynthesis by stepwise ginseng transcriptome and Rb1 content integrated analysis. We first identified the candidate genes for Rb1 biosynthesis by integrated analysis of genes with the trait from four aspects, including gene transcript differential expression between highest- and lowest-Rb1 content cultivars, gene transcript expression-Rb1 content correlation, and biological impacts of gene mutations on Rb1 content, followed by the gene transcript co-expression network. Twenty-two candidate genes were identified, of which 21 were functionally validated for Rb1 biosynthesis by gene regulation, genetic transformation, and mutation analysis. These genes were strongly correlated in expression with the previously cloned genes encoding key enzymes for Rb1 biosynthesis. Based on the correlations, a pathway for Rb1 biosynthesis was deduced to indicate the roles of the genes in Rb1 biosynthesis. Moreover, the genes formed a strong co-expression network with the previously cloned Rb1 biosynthesis genes, and the variation in the network was associated with the variation in the Rb1 content. These results indicate that Rb1 biosynthesis is a process of correlative interactions among Rb1 biosynthesis genes. Therefore, this study provides new knowledge, 21 new genes, and 96 biomarkers for Rb1 biosynthesis useful for enhanced research and breeding in ginseng.

Rational Approach to Finding Genes Encoding Molecular Biomarkers: Focus on Breast Cancer.

Early detection of cancer facilitates treatment and improves patient survival. We hypothesized that molecular biomarkers of cancer could be rationally predicted based on even partial knowledge of transcriptional regulation, functional pathways and gene co-expression networks. To test our data mining approach, we focused on breast cancer, as one of the best-studied models of this disease. We were particularly interested to check whether such a ‘guilt by association’ approach would lead to pan-cancer markers generally known in the field or whether molecular subtype-specific ‘seed’ markers will yield subtype-specific extended sets of breast cancer markers. The key challenge of this investigation was to utilize a small number of well-characterized, largely intracellular, breast cancer-related proteins to uncover similarly regulated and functionally related genes and proteins with the view to predicting a much-expanded range of disease markers, especially that of extracellular molecular markers, potentially suitable for the early non-invasive detection of the disease. We selected 23 previously characterized proteins specific to three major molecular subtypes of breast cancer and analyzed their established transcription factor networks, their known metabolic and functional pathways and the existing experimentally derived protein co-expression data. Having started with largely intracellular and transmembrane marker ‘seeds’ we predicted the existence of as many as 150 novel biomarker genes to be associated with the selected three major molecular sub-types of breast cancer all coding for extracellularly targeted or secreted proteins and therefore being potentially most suitable for molecular diagnosis of the disease. Of the 150 such predicted protein markers, 114 were predicted to be linked through the combination of regulatory networks to basal breast cancer, 48 to luminal and 7 to Her2-positive breast cancer. The reported approach to mining molecular markers is not limited to breast cancer and therefore offers a widely applicable strategy of biomarker mining.

A pro-inflammatory and fibrous cap thinning transcriptome profile accompanies carotid plaque rupture leading to stroke

Atherosclerotic plaque rupture is the etiology of ischemic stroke and myocardial infarction. The molecular mechanisms responsible for rupture remain unclear, in part, due to the lack of data from plaques at the time of rupture. Ribosome-depleted total RNA was sequenced from carotid plaques obtained from patients undergoing carotid endarterectomy with high-grade stenosis and either (1) a carotid-related ischemic cerebrovascular event within the previous 5 days ('recently ruptured,' n = 6) or (2) an absence of a cerebrovascular event ('asymptomatic,' n = 5). Principal component analysis confirmed plaque rupture was responsible for the greatest percentage of the variability between samples (23.2%), and recently ruptured plaques were enriched for transcripts associated with inflammation and extracellular matrix degradation. Hierarchical clustering achieved differentiation of the asymptomatic from the recently ruptured plaques. This analysis also found co-expression of transcripts for immunoglobulins and B lymphocyte function, matrix metalloproteinases, and interferon response genes. Examination of the differentially expressed genes supported the importance of inflammation and inhibition of proliferation and migration coupled with an increase in apoptosis. Thus, the transcriptome of recently ruptured plaques is enriched with transcripts associated with inflammation and fibrous cap thinning and support further examination of the role of B lymphocytes and interferons in atherosclerotic plaque rupture.

The Breast Cancer Protein Co-Expression Landscape.

Simple SummaryProteins are among the most fundamental building blocks and molecular players behind the functions of cells and tissues. Their abundance and interaction patterns shape, to a large extent, what happens at the cellular and organ levels. This is also true regarding tumor tissues. In this work, we explored the patterns of abundance and co-occurrence of a large number of proteins in breast cancer cells and their healthy counterparts. We discovered the main differences and tried to see whether those differences may be associated with relevant aspects of the biology of these tumors. Our final goal is to provide information to empower cancer clinicians and pharmacologists to develop better diagnostic, prognostic, and therapeutic tools.Breast cancer is a complex phenotype (or better yet, several complex phenotypes) characterized by the interplay of a large number of cellular and biomolecular entities. Biological networks have been successfully used to capture some of the heterogeneity of intricate pathophenotypes, including cancer. Gene coexpression networks, in particular, have been used to study large-scale regulatory patterns. Ultimately, biological processes are carried out by proteins and their complexes. However, to date, most of the tumor profiling research has focused on the genomic and transcriptomic information. Here, we tried to expand this profiling through the analysis of open proteomic data via mutual information co-expression networks’ analysis. We could observe that there are distinctive biological processes associated with communities of these networks and how some transcriptional co-expression phenomena are lost at the protein level. These kinds of data and network analyses are a broad resource to explore cellular behavior and cancer research.

Thiamine functions as a key activator for modulating plant health and broad-spectrum tolerance in cotton.

Global climate changes cause an increase of abiotic and biotic stresses that tremendously threaten the world's crop security. However, studies on broad-spectrum response pathways involved in biotic and abiotic stresses are relatively rare. Here, by comparing the time-dependent transcriptional changes and co-expression analysis of cotton (Gossypium hirsutum) root tissues under abiotic and biotic stress conditions, we discovered the common stress-responsive genes and stress metabolism pathways under different stresses, which included the circadian rhythm, thiamine and galactose metabolism, carotenoid, phenylpropanoid, flavonoid, and zeatin biosynthesis, and the mitogen-activated protein kinase signaling pathway. We found that thiamine metabolism was an important intersection between abiotic and biotic stresses; the key thiamine synthesis genes, GhTHIC and GhTHI1, were highly induced at the early stage of stresses. We confirmed that thiamine was crucial and necessary for cotton growth and development, and its deficiency could be recovered by exogenous thiamine supplement. Furthermore, we revealed that exogenous thiamine enhanced stress tolerance in cotton via increasing calcium signal transduction and activating downstream stress-responsive genes. Overall, our studies demonstrated that thiamine played a crucial role in the tradeoff between plant health and stress resistance. The thiamine deficiency caused by stresses could transiently induce upregulation of thiamine biosynthetic genes in vivo, while it could be totally salvaged by exogenous thiamine application, which could significantly improve cotton broad-spectrum stress tolerance and enhance plant growth and development.

Chronic Myelogenous Leukemia with Double Philadelphia Chromosome and Coexpression of p210 and p190 Fusion Transcripts.

The Philadelphia (Ph+) chromosome, t(9;22)(q34;q11.2), originates from a chimeric gene called BCR-ABL and is present in more than 90% of CML patients. Most patients with CML express the protein p210 BCR-ABL and, with a frequency lower than 5%, express rare isoforms, the main one being p190. In the transition from the chronic phase to the blast phase (BP), additional chromosomal abnormalities, such as the presence of the double Ph+ chromosome, are revealed. Of the 1132 patients analyzed via molecular biology in this study, two patients (0.17%) showed the co-expression of the p210 and p190 isoforms for the BCR-ABL transcript, with the concomitant presence of a double Ph+ chromosome, which was observed via conventional cytogenetics and confirmed by fluorescent in situ hybridization. The BCR-ABL/ABL% p210 and p190 ratio increased in these two patients from diagnosis to progression to blast crisis. To our knowledge, this is the first report in the literature of patients who co-expressed the two main BCR-ABL transcript isoforms and concomitantly presented Ph+ chromosome duplication. The evolution from the chronic phase to BP often occurs within 5 to 7 years, and, in this study, the evolution to BP was earlier, since disease-free survival was on average 4.5 months and overall survival was on average 9.5 months. The presence of the p190 transcript and the double Ph+ chromosome in CML may be related to the vertiginous progression of the disease.

Enhanced Bioremediation Potential of Shewanella decolorationis RNA Polymerase Mutants and Evidence for Novel Azo Dye Biodegradation Pathways.

Bioremediation has been considered as a promising method for recovering chemical polluted environments. Here Shewanella decolorationis strain Ni1-3 showed versatile abilities in bioremediation. To improve the bioremediation activity, RNA polymerase (RNAP) mutations of strain Ni1-3 were screened. Eleven mutants were obtained, of which mutant #40 showed enhanced Amaranth (AMR) degradation capacity, while mutant #21 showed defected capacity in AMR degradation but greatly enhanced capacity in cathodic metal leaching which is three to four times faster than that of the wild-type (WT) strain Ni1-3, suggesting that different pathways were involved in these two processes. Transcriptional profiling and gene co-expression networks between the mutants (i.e., #40 and #22) and the WT strain disclosed that the non-CymA-Mtr but cytochrome b- and flavin-oxidoreductase-dominated azo dye degradation pathways existed in S. decolorationis, which involved key proteins TorC, TorA, YceJ, YceI, Sye4, etc. Furthermore, the involvement of TorA was verified by trimethylamine N-oxide reduction and molybdenum enzyme inhibitory experiments. This study clearly demonstrates that RNAP mutations are effective to screen active microbial candidates in bioremediation. Meanwhile, by clarifying the novel gene co-expression network of extracellular electron transfer pathways, this study provides new insights in azo dye degradation and broadens the application of Shewanella spp. in bioremediation as well.

Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel

Post transcriptional modifications of RNA are powerful mechanisms by which eukaryotes expand their genetic diversity. For instance, researchers estimate that most transcripts in humans undergo alternative splicing and alternative polyadenylation. These splicing events produce distinct RNA molecules, which in turn yield distinct protein isoforms and/or influence RNA stability, translation, nuclear export, and RNA/protein cellular localization. Due to their pervasiveness and impact, we hypothesized that alternative splicing and alternative polyadenylation in brain can contribute to a predisposition for voluntary alcohol consumption. Using the HXB/BXH recombinant inbred rat panel (a subset of the Hybrid Rat Diversity Panel), we generated over one terabyte of brain RNA sequencing data (total RNA) and identified novel splice variants (via StringTie) and alternative polyadenylation sites (via aptardi) to determine the transcriptional landscape in the brains of these animals. After establishing an analysis pipeline to ascertain high quality transcripts, we quantitated transcripts and integrated genotype data to identify candidate transcript coexpression networks and individual candidate transcripts associated with predisposition to voluntary alcohol consumption in the two-bottle choice paradigm. For genes that were previously associated with this trait (e.g., Lrap, Ift81, and P2rx4) (Saba et al., Febs. J., 282, 3556–3578, Saba et al., Genes. Brain. Behav., 20, e12698), we were able to distinguish between transcript variants to provide further information about the specific isoforms related to the trait. We also identified additional candidate transcripts associated with the trait of voluntary alcohol consumption (i.e., isoforms of Mapkapk5, Aldh1a7, and Map3k7). Consistent with our previous work, our results indicate that transcripts and networks related to inflammation and the immune system in brain can be linked to voluntary alcohol consumption. Overall, we have established a pipeline for including the quantitation of alternative splicing and alternative polyadenylation variants in the transcriptome in the analysis of the relationship between the transcriptome and complex traits.

Chapter 2 - Central respiratory chemoreception

Brain PCO2 is sensed primarily via changes in [H+]. Small pH changes are detected in the medulla oblongata and trigger breathing adjustments that help maintain arterial PCO2 constant. Larger perturbations of brain CO2/H+, possibly also sensed elsewhere in the CNS, elicit arousal, dyspnea, and stress, and cause additional breathing modifications. The retrotrapezoid nucleus (RTN), a rostral medullary cluster of glutamatergic neurons identified by coexpression of Phoxb and Nmb transcripts, is the lynchpin of the central respiratory chemoreflex. RTN regulates breathing frequency, inspiratory amplitude, and active expiration. It is exquisitely responsive to acidosis in vivo and maintains breathing autorhythmicity during quiet waking, slow-wave sleep, and anesthesia. The RTN response to [H+] is partly an intrinsic neuronal property mediated by proton sensors TASK-2 and GPR4 and partly a paracrine effect mediated by astrocytes and the vasculature. The RTN also receives myriad excitatory or inhibitory synaptic inputs including from [H+]-responsive neurons (e.g., serotonergic). RTN is silenced by moderate hypoxia. RTN inactivity (periodic or sustained) contributes to periodic breathing and, likely, to central sleep apnea. RTN development relies on transcription factors Egr2, Phox2b, Lbx1, and Atoh1. PHOX2B mutations cause congenital central hypoventilation syndrome; they impair RTN development and consequently the central respiratory chemoreflex.

Coexpression of Gene Transcripts with Monoamine Oxidase A Quantified by Human In Vivo Positron Emission Tomography.

The monoamine oxidase A (MAO-A) is integral to monoamine metabolism and is thus relevant to the pathophysiology of various neuropsychiatric disorders; however, associated gene-enzyme relations are not well understood. This study aimed to unveil genes coexpressed with MAO-A. Therefore, 18 179 mRNA expression maps (based on the Allen Human Brain Atlas) were correlated with the cerebral distribution volume (VT) of MAO-A assessed in 36 healthy subjects (mean age ± standard deviation: 32.9 ± 8.8 years, 18 female) using [11C]harmine positron emission tomography scans. Coexpression analysis was based on Spearman's ρ, over-representation tests on Fisher's exact test with false discovery rate (FDR) correction. The analysis revealed 35 genes in cortex (including B-cell translocation gene family, member 3, implicated in neuroinflammation) and 247 genes in subcortex (including kallikrein-related peptidase 10, implicated in Alzheimer's disease). Significantly over-represented Gene Ontology terms included "neuron development", "neuron differentiation", and "cell-cell signaling" as well as "axon" and "neuron projection". In vivo MAO-A enzyme distribution and MAOA expression did not correlate in cortical areas (ρ = 0.08) while correlation was found in subcortical areas (ρ = 0.52), suggesting influences of region-specific post-transcriptional and -translational modifications. The herein reported information could contribute to guide future genetic studies, deepen the understanding of associated pathomechanisms and assist in the pursuit of novel therapeutic targets.

Genome-wide identification and co-expression analysis of GDSL genes related to suberin formation during fruit russeting in pear

Glycine-aspartic acid‑serine-leucine (GDSL) type lipases/esterases genes play critical roles in plant development and are related to the responses to abiotic and biotic stress. However, little is known about the GDSL family in pear (Pyrus spp.). Studies have shown GDSL-domain proteins play key roles in suberin deposition. Suberin deposition in the fruit epidermis, also called russeting, is an important defect that negatively affects consumer's appeal in some fruit species, such as pear, apple and grapevine. Fruit russeting is mainly associated with cuticle microcracking and suberin accumulation in the inner part of the epidermal cell walls. To gain insight into the role of the GDSL gene family in suberin deposition and russet development in pear, we performed a genome-wide characterization of the GDSL family, including their identification, chromosomal localization, phylogenetic relationships, and expression patterns, in different tissues/organs in pear. One hundred and thirteen GDSL-type lipases/esterases genes were identified in the pear genome, and a phylogenetic analysis revealed that GDSL family can be classified into four distinct groups. Thirty GDSL genes were co-expressed with five homolog pear genes of three well-known suberin biosynthesis Arabidopsis genes (AtGPAT5, AtASFT, and AtCYP86B1) in the transcriptional co-expression network during pear fruit development. Among the 30 co-expressed GDSL genes, twelve genes were further analyzed by quantitative Real-time PCR, and the results showed the expression levels of the 12 genes were different between the russet exocarp and green exocarp of sand pear at different fruit development stages. Our study provides a detailed overview of the GDSL gene family and lays the foundation for future functional characterization of GDSL genes in P. bretschneideri.

EPCO-26. INTEGRATIVE MULTI-OMICS IDENTIFIES CONVERGING DEVELOPMENTAL ORIGINS OF DISTINCT MEDULLOBLASTOMA SUBGROUPS

Abstract Understanding the interplay between normal development and tumorigenesis, including the identification and characterization of lineage-specific origins of MB, is a fundamental challenge in the field. Recent studies have highlighted novel associations between biologically distinct MB subgroups and diverse murine cerebellar lineages via cross-species single-cell transcriptomics. Specifically, Group 4-MB correlated with the unipolar brush cell lineage and Group 3-MB resembled Nestin+ stem cells of the early cerebellum. However, these analyses were hampered by low resolution due to the sparsity of pertinent cerebellar cell types and the cross-species nature of the approach. Herein, we profoundly expand the depth of these rare developmental populations in the murine cerebellum using a combination of lineage tracing and integrative multi-omics. Isolation and enrichment of spatially and temporally unique developmental trajectories of key rhombic lip-derived glutamatergic lineages provided an enhanced reference for mapping MB subgroups based on molecular overlap, especially for poorly defined Group 3- and Group 4-MB. Further comparisons to a novel single-cell atlas of the human fetal cerebellum, companioned with laser-capture microdissected transcriptional and epigenetic datasets, reinforced developmental insights extracted from the mouse. Characterization of compartment-specific transcriptional programs and co-expression networks identified in the human upper rhombic lip implicated convergent cellular correlates of Group 3- and Group 4-MB, suggestive of a common developmental link. Together, our results strongly implicate developmental lineages of the upper rhombic lip as the probable origins of poorly defined Group 3- and Group 4-MB. These important findings will shape future efforts to accurately model the biological heterogeneity underlying these subgroups and provide unprecedented opportunities to explore their cellular and mechanistic basis.

Incomplete genome doubling enables to consistently enhance plant growth for maximum biomass production by altering multiple transcript co-expression networks in potato.

Cytochimera potato plants, which mixed with diploid and tetraploid cells, could cause the highest and significantly increased biomass yield than the polyploid and diploid potato plants. Polyploidization is an important approach in crop breeding for agronomic trait improvement, especially for biomass production. Cytochimera contains two or more mixed cells with different levels of ploidy, which is considered a failure in whole genome duplication. Using colchicine treatment with diploid (Dip) potato (Solanum chacoense) plantlets, this study generated tetraploid (Tet) and cytochimera (Cyt) lines, which, respectively, contained complete and partial cells with genome duplication. Compared to the Dip potato, we observed remarkably enhanced plant growth and biomass yields in Tet and Cyt lines. Notably, the Cyt potato straw, which was generated from incomplete genome doubling, was of significantly higher biomass yield than that of the Tet with a distinctively altered cell wall composition. Meanwhile, we observed that one layer of the tetraploid cells (about 30%) in Cyt plants was sufficient to trigger a gene expression pattern similar to that of Tet, suggesting that the biomass dominance of Cyt may be related to the proportion of different ploidy cells. Further genome-wide analyses of co-expression networks indicated that down-regulation (against Dip) of spliceosomal-related transcripts might lead to differential alternative splicing for specifically improved agronomic traits such as plant growth, biomass yield, and lignocellulose composition in Tet and Cyt plants. In addition, this work examined that the genome of Cyt line was relatively stable after years of asexual reproduction. Hence, this study has demonstrated that incomplete genome doubling is a promising strategy to maximize biomass production in potatoes and beyond.

Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis 'Old Blush' After Exposure to a Gradual Drought Stress Followed by Recovery.

Rose is one of the most fundamental ornamental crops, but its yield and quality are highly limited by drought. The key transcription factors (TFs) and co-expression networks during rose’s response to drought stress and recovery after drought stress are still limited. In this study, the transcriptomes of leaves of 2-year-old cutting seedlings of Rosa chinensis ‘Old Blush’ from three continuous droughted stages (30, 60, 90 days after full watering) and rewatering were analyzed using RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network, which was associated with the physiological traits of drought response to discovering the hub TFs involved in drought response. More than 45 million high-quality clean reads were generated from the sample and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that drought stress caused significant changes in signal transduction, plant hormones including ABA, auxin, brassinosteroid (BR), cytokinin, ethylene (ET), jasmonic acid (JA) and salicylic acid (SA), primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules showed a high degree of correlation with physiological traits. In addition, 42 TFs including members of NACs, WRKYs, MYBs, AP2/ERFs, ARFs, and bHLHs with high connectivity in navajowhite1 and blue modules were screened. This study provides the transcriptome sequencing report of R. chinensis ‘Old Blush’ during drought stress and rewatering process. The study also identifies the response of candidate TFs to drought stress, providing guidelines for improving the drought tolerance of the rose through molecular breeding in the future.

LC-MS/MS targeting analysis of terpenoid metabolism in Carya cathayensis at different developmental stages

Terpenoid metabolism at different developmental stages of Carya cathayensis was elucidated based on LC-MS/MS analysis and multi-omics. Terpenoid metabolites 2-hydroxy-1,4-naphoquinone and 3-hydroxybenzoic acid reached the maximum at 105 days after pollination (DAP) (P2 stage). To reveal the complex mechanism of C. cathayensis embryogenesis in relation to terpenoid metabolites (90–165 DAP), a metabolomic and transcriptional co-expression analysis was conducted. Based on RNA-Seq analysis, 679 genes of 1144 terpenoid biosynthesis were differentially expressed. Six terpenoid metabolites and 86 differentially expressed genes related to terpenoquinone metabolism were identified. Comprehensive analysis of metabolome and transcriptional data revealed that terpenoquinone accumulated in the early phase was active in the later phase. Overall, we profiled the transcriptome and metabolome changes in C. cathayensis during the developmental phase to investigate the metabolic pathways and candidate genes underlying the changes at different growth stages.

Estrogen Regulation of the Molecular Phenotype and Active Translatome of AVPV Kisspeptin Neurons.

In females, ovarian estradiol (E2) exerts both negative and positive feedback regulation on the neural circuits governing reproductive hormone secretion, but the cellular and molecular mechanisms underlying this remain poorly understood. In rodents, estrogen receptor α-expressing kisspeptin neurons in the hypothalamic anteroventral periventricular region (AVPV) are prime candidates to mediate E2 positive feedback induction of preovulatory gonadotropin-releasing hormone and luteinizing hormone (LH) surges. E2 stimulates AVPV Kiss1 expression, but the full extent of estrogen effects in these neurons is unknown; whether E2 stimulates or inhibits other genes in AVPV Kiss1 cells has not been determined. Indeed, understanding of the function(s) of AVPV kisspeptin cells is limited, in part, by minimal knowledge of their overall molecular phenotype, as only a few genes are currently known to be co-expressed in AVPV Kiss1 cells. To provide a more detailed profiling of co-expressed genes in AVPV Kiss1 cells, including receptors and other signaling factors, and test how these genes respond to E2, we selectively isolated actively translated mRNAs from AVPV Kiss1 cells of female mice and performed RNA sequencing (RNA-seq). This identified >13 000 mRNAs co-expressed in AVPV Kiss1 cells, including multiple receptor and ligand transcripts positively or negatively regulated by E2. We also performed RNAscope to validate co-expression of several transcripts identified by RNA-seq, including Pdyn (prodynorphin), Penk (proenkephalin), Vgf (VGF), and Cartpt (CART), in female AVPV Kiss1 cells. Given the important role of AVPV kisspeptin cells in positive feedback, E2 effects on identified genes may relate to the LH surge mechanism and/or other physiological processes involving these cells.

Polee: RNA-Seq analysis using approximate likelihood.

The analysis of mRNA transcript abundance with RNA-Seq is a central tool in molecular biology research, but often analyses fail to account for the uncertainty in these estimates, which can be significant, especially when trying to disentangle isoforms or duplicated genes. Preserving uncertainty necessitates a full probabilistic model of the all the sequencing reads, which quickly becomes intractable, as experiments can consist of billions of reads. To overcome these limitations, we propose a new method of approximating the likelihood function of a sparse mixture model, using a technique we call the Pólya tree transformation. We demonstrate that substituting this approximation for the real thing achieves most of the benefits with a fraction of the computational costs, leading to more accurate detection of differential transcript expression and transcript coexpression.

A Review of Small-Molecule Inhibitors of One-Carbon Enzymes: SHMT2 and MTHFD2 in the Spotlight.

Metabolic reprogramming is a key hallmark of cancer and shifts cellular metabolism to meet the demands of biomass production necessary for abnormal cell reproduction. One-carbon metabolism (1CM) contributes to many biosynthetic pathways that fuel growth and is comprised of a complex network of enzymes. Methotrexate and 5-fluorouracil were pioneering drugs in this field and are still widely used today as anticancer agents as well as for other diseases such as arthritis. Besides dihydrofolate reductase and thymidylate synthase, two other enzymes of the folate cycle arm of 1CM have not been targeted clinically: serine hydroxymethyltransferase (SHMT) and methylenetetrahydrofolate dehydrogenase (MTHFD). An increasing body of literature suggests that the mitochondrial isoforms of these enzymes (SHMT2 and MTHFD2) are clinically relevant in the context of cancer. In this review, we focused on the 1CM pathway as a target for cancer therapy and, in particular, SHMT2 and MTHFD2. The function, regulation, and clinical relevance of SHMT2 and MTHFD2 are all discussed. We expand on previous clinical studies and evaluate the prognostic significance of these critical enzymes by performing a pan-cancer analysis of patient data from the The Cancer Genome Atlas and a transcriptional coexpression network enrichment analysis. We also provide an overview of preclinical and clinical inhibitors targeting the folate pathway, the methionine cycle, and folate-dependent purine biosynthesis enzymes.

PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington’s disease

DNA damage repair genes are modifiers of disease onset in Huntington's disease (HD), but how this process intersects with associated disease pathways remains unclear. Here we evaluated the mechanistic contributions of protein inhibitor of activated STAT-1 (PIAS1) in HD mice and HD patient-derived induced pluripotent stem cells (iPSCs) and find a link between PIAS1 and DNA damage repair pathways. We show that PIAS1 is a component of the transcription-coupled repair complex, that includes the DNA damage end processing enzyme polynucleotide kinase-phosphatase (PNKP), and that PIAS1 is a SUMO E3 ligase for PNKP. Pias1 knockdown (KD) in HD mice had a normalizing effect on HD transcriptional dysregulation associated with synaptic function and disease-associated transcriptional coexpression modules enriched for DNA damage repair mechanisms as did reduction of PIAS1 in HD iPSC-derived neurons. KD also restored mutant HTT-perturbed enzymatic activity of PNKP and modulated genomic integrity of several transcriptionally normalized genes. The findings here now link SUMO modifying machinery to DNA damage repair responses and transcriptional modulation in neurodegenerative disease.

Pan-Cancer Analysis of Head-to-Head Gene Pairs in Terms of Transcriptional Activity, Co-expression and Regulation.

BackgroundHead-to-Head (H2H) gene pairs are regulated by bidirectional promoters and divergently transcribed from opposite DNA strands with transcription start sites (TSSs) separated within 1 kb. H2H organization is ancient and conserved, and H2H pairs tend to exhibit similar expression patterns. Although some H2H genes have been reported to be associated with disease and cancer, there is a lack of systematic studies on H2H organization in the scenario of cancer development.MethodsHuman H2H gene pairs were identified based on GENCODE hg19 and the functional relevance of H2H pairs was explored through function enrichment and semantic similarity analysis. To investigate the association between H2H organization and carcinogenesis, pan-cancer differential analysis of H2H genes about transcriptional activity, co-expression and transcriptional regulation by transcription factors and enhancers were performed based on data from The Cancer Genome Atlas. Cox proportional hazards regression model and log-rank test were used to determine the prognostic powers of H2H pairs.ResultsIn the present study, we first updated H2H genes from 1,447 to 3,150 pairs, from which the peak group with TSS distance of 1–100 was observed as expected in our previous work. It was found that housekeeping genes, mitochondrial-functional associated genes and cancer genes tend to be organized in H2H arrangement. Pan-cancer analysis indicates that H2H genes are transcriptionally active than random genes in both normal and cancer tissues, but H2H pairs display higher correlation in cancer than in normal. Particularly, housekeeping H2H pairs are differentially correlated much more significantly than non-housekeeping H2H pairs are. Some of differentially correlated H2H pairs were found to be associated with prognosis. The alteration of TF similarity seems to contribute to differential co-expression of H2H pairs during carcinogenesis; meanwhile remote enhancers also at least partly explain the differential co-expression and co-regulation of H2H pairs.ConclusionH2H pairs tend to show much stronger positive expression correlation in cancer than in normal due to differential regulation of bidirectional promoters. The study provides insights into the significance of H2H organization in carcinogenesis and the underlying dysfunctional regulation mechanisms. Those differentially correlated H2H pairs associated with survival have the potential to be prognostic biomarkers and therapeutic targets for cancer.