Differential Isoform Research Articles

Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper

Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.

Alternative CDC20 translational isoforms tune mitotic arrest duration.

Mitotic defects activate the spindle-assembly checkpoint, which inhibits the anaphase-promoting complex co-activator CDC20 to induce a prolonged cell cycle arrest1,2. Once errors are corrected, the spindle-assembly checkpoint is silenced, allowing anaphase onset to occur. However, in the presence of persistent unresolvable errors, cells can undergo 'mitotic slippage', exiting mitosis into a tetraploid G1 state and escaping the cell death that results from a prolonged arrest. The molecular logic that enables cells to balance these duelling mitotic arrest and slippage behaviours remains unclear. Here we demonstrate that human cells modulate the duration of their mitotic arrest through the presence of conserved, alternative CDC20 translational isoforms. Downstream translation initiation results in a truncated CDC20 isoform that is resistant to spindle-assembly-checkpoint-mediated inhibition and promotes mitotic exit even in the presence of mitotic perturbations. Our study supports a model in which the relative levels of CDC20 translational isoforms control the duration of mitotic arrest. During a prolonged mitotic arrest, new protein synthesis and differential CDC20 isoform turnover create a timer, with mitotic exit occurring once the truncated Met43 isoform achieves sufficient levels. Targeted molecular changes or naturally occurring cancer mutations that alter CDC20 isoform ratios or its translational control modulate mitotic arrest duration and anti-mitotic drug sensitivity, with potential implications for the diagnosis and treatment of human cancers.

Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion.

A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycobacterium tuberculosis (Mtb) infection defined as persistently negative tuberculin skin test (TST) and interferon gamma release assay (IGRA) reactivity among highly exposed contacts (RSTR phenotype). Using transcript isoform analyses, we aimed to identify novel RSTR-associated genes hypothesizing that previous gene-level differential expression analysis obscures isoform-specific differences that contribute to phenotype. Monocytes from 49 RSTR versus 52 subjects with latent Mtb infection (LTBI) were infected with M. tuberculosis (H37Rv) or left unstimulated (media) prior to RNA isolation and sequencing. RSTR-associated gene expression was then identified using differential transcript isoform analysis. We identified 81 differentially expressed transcripts (DETs) in 70 genes (FDR <0.05) comparing RSTR and LTBI phenotypes with the majority (n = 79 DETs) identified under Mtb-stimulated conditions. Seventeen of these genes were previously identified with gene-level bulk RNAseq analyses including genes in the IFNγ response that had increased expression among LTBI subjects, findings consistent with a clinical phenotype based on IGRA reactivity. Among the subset of 23 genes with positive differential expression among Mtb-infected RSTR monocytes, 13 were not previously identified. These novel DET genes included PDE4A and ZEB2, which each had multiple DETs with higher expression among RSTR subjects, and ACSL4 and GAPDH that each had a single transcript isoform associated with RSTR. Transcript isoform-specific analyses identify transcriptional associations, such as those associated with resistance to TST/IGRA conversion, that are obscured when using gene-level approaches. These findings should be validated with additional RSTR cohorts and whether the newly identified candidate resistance genes directly influence the monocyte Mtb response requires functional study.

Limits of the thermal tolerance of two lentic crustaceans: The role of lactate dehydrogenase.

Limits of thermal tolerance in animal life is dependent on energy supply. Accordingly, the lowered ATP production capacity in ectotherms at high temperatures, which arises from a mismatch between oxygen supply and demand and the consequent switch from aerobic to anaerobic metabolism, affects the thermal resistance of these animals. The anaerobic ATP production capacity depends on the functional properties of the enzymes that reduce pyruvate. Thus, the present study focused on the role of the lactate dehydrogenase (LDH) of two daphnid species for anaerobic energy production at warm temperatures and the implications for their specific heat tolerances. Daphnia magna showed a higher thermal limit (indicated by immobilization time at 37°C) than Daphnia pulex, and in both species, this limit increased with rising acclimation temperature. In contrast to D. pulex, D. magna accumulated significant amounts of lactate at higher ambient temperatures. The intensity of anaerobic metabolism was also affected by acclimation temperature. Studying the functional enzyme properties revealed altered maximal reaction rates and substrate inhibitions of the LDH suites of the two daphnid species. D. magna LDH showed a significantly lower substrate inhibition than D. pulex LDH. The LDH isoform composition and the temperature-induced changes differed between both species. The detected qualitative modulations of the LDH suites may have resulted from differential isoform expression and different maturation processes. The species-specific LDH characteristics imply a higher anaerobic energy production at warm temperatures in D. magna, which likely contributes to the higher heat tolerance of this species.

A neutrophil mimicking metal-porphyrin-based nanodevice loaded with porcine pancreatic elastase for cancer therapy

Precise discrimination and eradication of cancer cells by immune cells independent of antigen recognition is promising for solid tumor therapeutics, yet remains a tremendous challenge. Inspired by neutrophils, here we design and construct a tumor discrimination nanodevice based on the differential histone H1 isoform expression. In this nanodevice, neutrophil membrane camouflage and glutathione (GSH)-unlocking effect on Fe-porphyrin metal−organic framework structure ensures selectivity to cancer cells. The released porcine pancreatic elastase (PPE) simulates neutrophils’ action to induce histone H1 release-dependent selective cancer cell killing. Meanwhile, nuclear localization signal (NLS) peptide-tagged porphyrin (porphyrin-NLS) acts as in-situ singlet oxygen (1O2) generator to amplify histone H1 nucleo-cytoplasmic translocation by inducing DNA double-strand breaks (DSBs) under laser irradiation, further promoting elimination of cancer cells. The overexpressed histone H1 isoform in cancer cells improves selectivity of our nanodevice to cancer cells. In vivo studies demonstrate that our design can not only inhibit primary tumor growth, but also induce adaptive T-cell response-mediated abscopal effect to against distal tumors.

Abstract 342: Differential CD45 isoform expression and function in AML versus healthy leukocytes

Abstract CD45 (the leukocyte common antigen) is a phosphatase present on all malignant and non-malignant leukocytes and hematopoietic progenitors and is the most abundant glycoprotein displayed by these cells. The human CD45 gene is alternatively spliced by reassortment of just three exons, exon 4 (“A”), exon 5 (“B”), and exon 6 (“C"), to create five distinct “R” isoforms (RO (no splice exons), RABC, RAB, RBC, and RB), with inclusion of A, B, or C exons enriching for expression of glycans (carbohydrates). Despite decades of investigation, the expression and phosphatase function of these isoforms on human AML cells remains unknown. To address this question, flow cytometry and western blot analysis was performed on AML primary cells (n=3) and KG1a and U937 cell lines versus healthy monocytes (n=3) utilizing exon-specific CD45-targetting mAbs. We then compared the contribution of CD45 phosphatase activity in KG1a and U937 cells versus healthy monocytes by employing a highly specific CD45 phosphatase inhibitor in cell culture for 24hrs, assessing induction of cell death after exposure to the inhibitor (n=3). Our results confirm reports of others indicating that "CD45RA- positivity" is a characteristic phenotype of AML cells, yet, distinctly, our data indicate that the most prevalent isoform identified on AML cells as "CD45RA-positive" is, actually, CD45RABC, the largest and most glycosylated isoform of CD45. This finding is in striking contrast to healthy monocytes, which do not express CD45RABC. Additionally, culturing of human AML cells with a CD45 phosphatase inhibitor induces rapid cell death within 24 hours but does not affect healthy monocytes. Thus, the conspicuous expression of the CD45 isoform CD45RABC among AML cells is associated with a survival advantage. Current studies in AML are directed to elaborating the prevalence of CD45RABC expression and uncovering the downstream effectors of its enzymatic activity to elucidate how such pathways sustain AML growth/survival. Citation Format: Evan Ales, Robert Sackstein. Differential CD45 isoform expression and function in AML versus healthy leukocytes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 342.

MERISTEM-DEFECTIVE / DEFECTIVELY ORGANIZED TRIBUTARIES2 regulates the balance between stemness and differentiation in the root meristem through RNA splicing control.

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of gene regulation is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES (DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human hSART1 and yeast Snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and repress stress response, cell differentiation and cell death pathways.

464 Alternative RNA Splicing Changes Underlie Meningioma DNA Methylation Groups

INTRODUCTION: Meningiomas are the most common primary intracranial tumor. They are associated with genetic mutations found across broad epigenetic or transcriptomic groups. Alternative RNA splicing (AS) is a critical step in gene expression that involves the differential inclusion of sequences into the mature mRNA. Dysregulation of AS is a hallmark of human tumors, but its contributions to meningioma tumorigenesis are incompletely understood. In particular, whether meningioma DNA-methylation groups are associated with specific downstream changes in AS is unknown. METHODS: AS events from 184 meningiomas were characterized using rMATS, a computational tool that quantifies percent splicing event inclusion (PSI) from short-read RNA-sequencing. Differential gene expression was quantified using DESeq2. RESULTS: Our analysis revealed 135 differentially spliced events in Immune-enriched vs. Hypermitotic meningiomas, 126 events in Immune-enriched vs. Merlin-intact meningiomas, and 185 events in Merlin-intact vs. Hypermitotic meningiomas. Hierarchical clustering of samples based on differential splicing events separated Hypermitotic from Merlin-intact and Immune-enriched meningiomas. The proto-oncogenes Misshapen-like Kinase 1 (MINK1) and Nuclear Auto-antigenic Sperm Protein (NASP) were differentially spliced across WHO grades, DNA methylation groups, and in primary vs. recurrent meningiomas and correlated with recurrence free survival. Differential gene expression analysis revealed alterations in the expression of several splicing factors across methylation groups, including those involved in tumorigenesis (MEX3A, SNRPE, SRSF5). CONCLUSIONS: AS promotes differential isoform expression across clinically important DNA-methylation groups of meningiomas. Our analyses capture a splicing signature that correlates with meningioma aggressiveness, identifies prognostic splicing events in known human proto-oncogenes (MINK1, NASP), and uncovers their potential upstream regulators. Validation of how these events impact meningioma tumorigenesis may allow for the development of novel diagnostic tests and therapies targeting AS.

The spatial landscape of gene expression isoforms in tissue sections.

In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.

Aggressive alternative splicing events discovered in cecum ligation and puncture induced lung injury

AimsAcute lung injury (ALI) induced by sepsis and its complications have high morbidity and mortality rates globally. The objective of this study was to enhance our understanding of the underlying mechanism of ALI by identifying potential splicing events that are regulated in this condition. Materials and methodsThe CLP mouse model was utilized for mRNA sequencing, and the expression and splicing data were analyzed. Verification of the changes in expression and splicing induced by CLP was conducted using qPCR and RT-PCR. ResultsOur results showed that splicing-related genes were regulated, suggesting that splicing regulation may be a key mechanism in ALI. We also found that more than 2900 genes displayed alternative splicing in the lungs of mice with sepsis. Using RT-PCR, we verified that TLR4 and other genes had differential splicing isoforms in the lungs of mice with sepsis. We confirmed the presence of TLR4-s in the lungs of mice with sepsis using RNA-fluorescence in situ hybridization. ConclusionOur results suggest that sepsis-induced ALI can significantly alter splicing in the lungs of mice. The list of DASGs and splicing factors is valuable for further study in the search for new treatment approaches for sepsis-induced ALI.

Alternative Splicing Changes in Human Aging Brain Samples

Alternative splicing affects differential isoform generation from genes and may also affect the protein products cellular function. Targeted splicing analysis of exon array analysis of young compared to middle and old post mortem brain samples from 1,234 samples (a total of 10 brain regions) aged from 16 to over 100 allowed me to detect significant alternative splicing changes upon human aging. This kind of data may allow us to better understand the underlying molecular mechanisms.

Acetylation of fission yeast tropomyosin does not promote differential association with cognate formins.

It was proposed from cellular studies that S. pombe tropomyosin Cdc8 (Tpm) segregates into two populations due to the presence or absence of an amino-terminal acetylation that specifies which formin-mediated F-actin networks it binds, but with no supporting biochemistry. To address this mechanism in vitro, we developed methods for S. pombe actin expression in Sf9 cells. We then employed 3-color TIRF microscopy using all recombinant S. pombe proteins to probe in vitro multicomponent mechanisms involving actin, acetylated and unacetylated Tpm, formins, and myosins. Acetyl-Tpm exhibits tight binding to actin in contrast to weaker binding by unacetylated Tpm. In disagreement with the differential recruitment model, Tpm showed no preferential binding to filaments assembled by the FH1-FH2-domains of two S. pombe formins, nor did Tpm binding have any bias towards the growing formin-bound actin filament barbed end. Although our in vitro findings do not support a direct formin-tropomyosin interaction, it is possible that formins bias differential tropomyosin isoform recruitment through undiscovered mechanisms. Importantly, despite a 12% sequence divergence between skeletal and S. pombe actin, S. pombe myosins Myo2 and Myo51 exhibited similar motile behavior with these two actins, validating key prior findings with these myosins that used skeletal actin.

DELongSeq for efficient detection of differential isoform expression from long-read RNA-seq data.

Conventional gene expression quantification approaches, such as microarrays or quantitative PCR, have similar variations of estimates for all genes. However, next-generation short-read or long-read sequencing use read counts to estimate expression levels with much wider dynamic ranges. In addition to the accuracy of estimated isoform expression, efficiency, which measures the degree of estimation uncertainty, is also an important factor for downstream analysis. Instead of read count, we present DELongSeq, which employs information matrix of EM algorithm to quantify uncertainty of isoform expression estimates to improve estimation efficiency. DELongSeq uses random-effect regression model for the analysis of DE isoform, in that within-study variation represents variable precision in isoform expression estimation and between-study variation represents variation in isoform expression levels across samples. More importantly, DELongSeq allows 1 case versus 1 control comparison of differential expression, which has specific application scenarios in precision medicine (such as before versus after treatment, or tumor versus stromal tissues). Through extensive simulations and analysis of several RNA-Seq datasets, we show that the uncertainty quantification approach is computationally reliable, and can improve the power of differential expression (DE) analysis of isoforms or genes. In summary, DELongSeq allows for efficient detection of differential isoform/gene expression from long-read RNA-Seq data.

Differential roles of ApoE isoforms in regulation of inflammatory cytokine expression

AbstractBackgroundApoE Ɛ4 has long been known as a top genetic risk factor in the development of late‐onset Alzheimer’s disease (LOAD). More recently the genetic variants of the innate immune receptor TREM2 such as R47H, which confers a similar risk as ApoE4 in LOAD, have been identified as genetic risk factors in the development of many neurodegenerative diseases with dysregulated neuroinflammation. TREM2 is expressed highly on microglia and macrophages and plays key roles in inflammation regulation. Our previous study (Dorey et al. 2017) has shown that ApoE isoforms play differential roles in Aβ‐induced inflammatory response. Atagi et al (2015) identified that ApoE is a ligand for TREM2. Given the physiological relationship between ApoE and TREM2 while also considering the three isoforms of ApoE, it is crucial to investigate and understand the mechanisms underlying the possibility differential ApoE isoform signaling through TREM2 surface receptor.MethodTHP‐1 (human monocytic leukemia cell line) cells were differentiated into macrophages (M0) using PMA and subsequently polarized to M1 and M2 using IFN‐γ/LPS and IL‐4/IL‐13, respectively. Following differentiation, 3uM of ApoE2, E3, or E4 was added to polarization media. RNA was extracted following 2 day polarization and used for RT‐qPCR in relative gene expression quantification.ResultApoE2 strongly stimulated the expression of anti‐inflammatory cytokines IL‐10 and TARC/CCL17 in M1 and M2 macrophages as compared to control, ApoE3 and ApoE4. While ApoE4 showed a massive reduction in these same transcripts in M0 and M2 macrophages. In contrast, ApoE4 strongly promoted the expression of pro‐inflammatory cytokines IL‐1β and TNF‐α in M0, M1, and M2 macrophages as compared to control, ApoE3 and ApoE2.ConclusionThe ability for ApoE2 to promote the expression of anti‐inflammatory cytokines in macrophages, suggests that ApoE2 may play a neuroprotective role; while ApoE4’s ability to promote inflammatory cytokine expression indicates its pro‐inflammatory role. Both ApoE2 and ApoE4 may play their roles via interacting with TREM2.

Differential isoform expression of Allergin-1 during acute and chronic inflammation.

Neutrophils are crucial to antimicrobial defense, but excessive neutrophilic inflammation elicits immune pathology. Currently, no effective treatment exists to curb neutrophil activation. However, neutrophils express a variety of inhibitory receptors which may represent potential therapeutic targets to limit neutrophilic inflammation. Indeed, we previously showed that the inhibitory collagen receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR-1) regulates neutrophilic airway inflammation and inhibits neutrophil extracellular trap formation. The inhibitory receptor Allergin-1 is expressed by myeloid cells and B cells. Allergin-1 suppresses mast cell and basophil activation, but a potential regulatory role on neutrophils remains unexplored. We aimed to demonstrate the regulation of neutrophils by Allergin-1. We examine Allergin-1 isoform expression on human neutrophils during homeostatic (healthy donors) and chronic inflammatory (systemic lupus erythematosus patients) conditions in comparison to other circulating leukocytes by flow cytometry. To reveal a potential role for Allergin-1 in regulating neutrophilic inflammation, we experimentally infect wild-type (WT) and Allergin-1-deficient mice with a respiratory syncytial virus (RSV) and monitor disease severity and examine cellular airway infiltrate. Flow cytometry was used to confirm Allergin-1 expression by airway-infiltrated neutrophils in RSV infection-induced bronchiolitis patients. Only the short 1 (S1) isoform, but not the long (L) or S2 isoform could be detected on blood leukocytes, with the exception of nonclassical monocytes, which exclusively express the S2 isoform. Allergin-1 expression levels did not vary significantly between healthy individuals and patients with the systemic inflammatory disease on any interrogated cell type. Airway-infiltrated neutrophils of pediatric RSV bronchiolitis patients were found to express Allergin-1S1. However, Allergin-1-deficient mice experimentally infected with RSV did not show exacerbated disease or increased neutrophil airway infiltration compared to WT littermates. Allergin-1 isoform expression is unaffected by chronic inflammatory conditions. In stark contrast to fellow inhibitory receptor LAIR-1, Allergin-1 does not regulate neutrophilic inflammation in a mouse model of RSV bronchiolitis.

Differential Expression of RSK4 Transcript Isoforms in Cancer and Its Clinical Relevance

While we previously revealed RSK4 as a therapeutic target in lung and bladder cancers, the wider role of this kinase in other cancers remains controversial. Indeed, other reports instead proposed RSK4 as a tumour suppressor in colorectal and gastric cancers and are contradictory in breast malignancies. One explanation for these discrepancies may be the expression of different RSK4 isoforms across cancers. Four RNAs are produced from the RSK4 gene, with two being protein-coding. Here, we analysed the expression of the latter across 30 normal and 33 cancer tissue types from the combined GTEx/TCGA dataset and correlated it with clinical features. This revealed the expression of RSK4 isoforms 1 and 2 to be independent prognostic factors for patient survival, pathological stage, cancer metastasis, recurrence, and immune infiltration in brain, stomach, cervical, and kidney cancers. However, we found that upregulation of either isoform can equally be associated with good or bad prognosis depending on the cancer type, and changes in the expression ratio of isoforms fail to predict clinical outcome. Hence, differential isoform expression alone cannot explain the contradictory roles of RSK4 in cancers, and further research is needed to highlight the underlying mechanisms for the context-dependent function of this kinase.

Mechano-growth factor E-domain modulates cardiac contractile function through 14-3-3 protein interactomes.

In the heart, alternative splicing of the igf-I gene produces two isoforms: IGF-IEa and IGF-IEc, (Mechano-growth factor, MGF). The sequence divergence between their E-domain regions suggests differential isoform function. To define the biological actions of MGF's E-domain, we performed in silico analysis of the unique C-terminal sequence and identified a phosphorylation consensus site residing within a putative 14-3-3 binding motif. To test the functional significance of Ser 18 phosphorylation, phospho-mimetic (S/E18) and phospho-null (S/A18) peptides were delivered to mice at different doses for 2 weeks. Cardiovascular function was measured using echocardiography and a pressure-volume catheter. At the lowest (2.25mg/kg/day) and highest (9mg/kg/day) doses, the peptides produced a depression in systolic and diastolic parameters. However, at 4.5mg/kg/day the peptides produced opposing effects on cardiac function. Fractional shortening analysis also showed a similar trend, but with no significant change in cardiac geometry. Microarray analysis discovered 21 genes (FDR p < 0.01), that were expressed accordant with the opposing effects on contractile function at 4.5mg/kg/day, with the nuclear receptor subfamily 4 group A member 2 (Nr4a2) identified as a potential target of peptide regulation. Testing the regulation of the Nr4a family, showed the E-domain peptides modulate Nr4a gene expression following membrane depolarization with KCl in vitro. To determine the potential role of 14-3-3 proteins, we examined 14-3-3 isoform expression and distribution. 14-3-3γ localized to the myofilaments in neonatal cardiac myocytes, the cardiac myocytes and myofilament extracts from the adult heart. Thermal shift analysis of recombinant 14-3-3γ protein showed the S/A18 peptide destabilized 14-3-3γ folding. Also, the S/A18 peptide significantly inhibited 14-3-3γ's ability to interact with myosin binding protein C (MYPC3) and phospholamban (PLN) in heart lysates from dobutamine injected mice. Conversely, the S/E18 peptide showed no effect on 14-3-3γ stability, did not inhibit 14-3-3γ's interaction with PLN but did inhibit the interaction with MYPC3. Replacing the glutamic acid with a phosphate group on Ser 18 (pSer18), significantly increased 14-3-3γ protein stability. We conclude that the state of Ser 18 phosphorylation within the 14-3-3 binding motif of MGF's E-domain, modulates protein-protein interactions within the 14-3-3γ interactome, which includes proteins involved in the regulation of contractile function.

Magnetique: an interactive web application to explore transcriptome signatures of heart failure

BackgroundDespite a recent increase in the number of RNA-seq datasets investigating heart failure (HF), accessibility and usability remain critical issues for medical researchers. We address the need for an intuitive and interactive web application to explore the transcriptional signatures of heart failure with this work.MethodsWe reanalysed the Myocardial Applied Genomics Network RNA-seq dataset, one of the largest publicly available datasets of left ventricular RNA-seq samples from patients with dilated (DCM) or hypertrophic (HCM) cardiomyopathy, as well as unmatched non-failing hearts (NFD) from organ donors and patient characteristics that allowed us to model confounding factors. We analyse differential gene expression, associated pathway signatures and reconstruct signaling networks based on inferred transcription factor activities through integer linear programming. We additionally focus, for the first time, on differential RNA transcript isoform usage (DTU) changes and predict RNA-binding protein (RBP) to target transcript interactions using a Global test approach. We report results for all pairwise comparisons (DCM, HCM, NFD).ResultsFocusing on the DCM versus HCM contrast (DCMvsHCM), we identified 201 differentially expressed genes, some of which can be clearly associated with changes in ERK1 and ERK2 signaling. Interestingly, the signs of the predicted activity for these two kinases have been inferred to be opposite to each other: In the DCMvsHCM contrast, we predict ERK1 to be consistently less activated in DCM while ERK2 was more activated in DCM. In the DCMvsHCM contrast, we identified 149 differently used transcripts. One of the top candidates is the O-linked N-acetylglucosamine (GlcNAc) transferase (OGT), which catalyzes a common post-translational modification known for its role in heart arrhythmias and heart hypertrophy. Moreover, we reconstruct RBP – target interaction networks and showcase the examples of CPEB1, which is differentially expressed in the DCMvsHCM contrast.ConclusionMagnetique (https://shiny.dieterichlab.org/app/magnetique) is the first online application to provide an interactive view of the HF transcriptome at the RNA isoform level and to include transcription factor signaling and RBP:RNA interaction networks. The source code for both the analyses (https://github.com/dieterich-lab/magnetiqueCode2022) and the web application (https://github.com/AnnekathrinSilvia/magnetique) is available to the public. We hope that our application will help users to uncover the molecular basis of heart failure.

Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses.

Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.

P372 Deciphering transcript isoform switching and utilization in mature biofilm of Candida glabrata through a global transcriptomic approach

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM ObjectiveEukaryotic cellular systems utilize alternative transcript isoforms generated via an isoform switching mechanism to thwart various stress conditions. To the best of our knowledge, transcript isoform switching and differential transcript isoform usage (DTU) in Candida glabrata have not been studied. Therefore, the present study was designed to delineate differential transcript isoform expression (DTE) and transcript isoform switching followed by DTU and the functional impact of transcripts in a mature biofilm of C. glabrata (clinical isolate; NCCPF 100037) through an RNA sequencing approach.ResultsDTE analysis generated 7837 transcript isoforms from the C. glabrata genome (5293 genes in total), and DTU investigations revealed that transcript isoforms of 292 genes were specifically utilized in the formation of mature biofilms via the isoform switching process. Gene Ontology/pathway analysis and protein-protein interactions further substantiated the functional attributes of switched transcript isoforms selectively used by C. glabrata in biofilm formation and survival.ConclusionThe present study elucidates that specific transcript isoforms utilized in mature biofilms of C. glabrata could be used as potential targets for the development of novel antifungal therapeutics.