Apolipoprotein E (APOE) is one of the most important genetic risk factors for late-onset sporadic Alzheimer’s disease (LOAD). APOE is a 35 kDa glycoprotein and ligand known to bind to members of the low-density lipoprotein receptor (LDLR) family, including APOE receptor 2 (apoER2; official gene name LRP8). ApoER2 is a type I transmembrane protein with a large extracellular domain (ECD) and a short cytoplasmic tail that can be proteolytic cleaved. In addition, apoER2 is enriched in the brain and plays an important role in synaptic function and plasticity. Interestingly, the ECD of apoER2 contains several ligand binding repeats that are organized into exons with aligning phase junctions, which allows exon skipping during alternative splicing to retain protein fidelity. The amount of alternative spliced isoforms distinguishes apoER2 from the rest of the LDLR family members. In fact, mouse Apoer2 has been identified as one of the top ten neuronal genes related to cell-type exon skipping events. Regarding human APOER2, we have identified over 40 different APOER2 isoforms from human brain using gene-specific primers and amplifying the N- and C-terminal open reading frame of APOER2. The majority of APOER2 variants consist of a diverse array of exon skipping events within the ligand binding domain (LBD). We therefore, hypothesized that human APOER2 splice variants act as functionally divergent isoforms that can influence ligand binding properties, receptor proteolysis and changes to synaptic function. ApoER2 undergoes sequential proteolytic cleavage in response to ligand binding, resulting in the release of C-terminal fragments (CTFs) and transcriptionally active intracellular domain (ICD). We therefore, systematically tested whether the diversity of human N-terminal APOER2 splice variants lacking various LBDs affects APOER2 cleavage and signaling events. We found that alternative splicing of certain APOER2 exons generated different amounts of CTFs compared to full-length APOER2 (APOER2-FL). The pattern was not simply based on the number of ligand binding domains suggesting that excision of certain exons may alter the tertiary structure of the receptor sufficiently to make the receptor more or less accessible to cleavage and generation of CTFs. To further characterize APOER2 splice variants, we specifically examined APOER2 splice variants that generated the highest and lowest amounts of CTF generation compared to APOER2-FL and focused on APOER2 splice variant lacking exons 5-8 (Δ5-8) and lacking exons 4-6 (Δ4-6), respectively. The differential CTF generation of APOER2 Δ5-8 and Δ4-6 reflects the proteolytic release of the APOER2-ICD. This APOER2-ICD mediates transcriptional activation, facilitated by the Mint1 adaptor protein. To investigate whether human N-terminal APOER2 splice variants influence APOE binding and receptor cleavage properties, we used microscale thermophoresis and tested the well-validated human APOE mimetic peptide. We found that specific exons or ligand-binding cassettes differentially affect APOE peptide binding to APOER2 splice variants. In addition, APOE peptide induces generation of APOER2-CTF acutely within one hour. Functionally, we demonstrated that APOER2 is required for spontaneous neurotransmitter release in mature neurons. Loss of mouse Apoer2 robustly decreased miniature event frequency in excitatory synapses compared to heterozygous Apoer2 neurons. We found APOER2-FL fully restored the miniature event frequency in excitatory synapses but not APOER2 Δ5-8. APOER2 Δ4-6 restored the miniature event frequency similar to heterozygous Apoer2 neurons. These results suggest that different human N-terminal APOER2 splice variants have distinct and differential synaptic properties signifying a role of APOER2 splice variants as regulators of synaptic function.

Indiana University-Purdue University Indianapolis (IUPUI) / The protein kinase General control non-derepressible-2 (GCN2) is a key regulator of the Integrated stress response that responds to various stress signals, including nutritional deprivation. As a result of high levels of uncharged tRNAs during amino acid depletion, GCN2 phosphorylates serine-51 of the α subunit of eukaryotic initiation factor-2 (eIF2), a translation factor that delivers initiator tRNA to ribosomes. Phosphorylation of eIF2α inhibits general translation, which conserves energy and nutrients and facilitates reprogramming of gene expression for remediation of stress damage. Phosphorylation of eIF2α also directs preferential translation of specific transcription factors, such as ATF4. ATF4 reprograms gene expression to alleviate stress damage; however, under chronic stress, ATF4 directs the transcriptional expression of CHOP, which can trigger apoptosis. Because multiple stresses can induce eIF2α phosphorylation and translational control in mammals, this pathway is referred to as the Integrated stress response. GCN2 and CHOP are subject to alternative splicing that results in multiple transcripts that differ in the 5'-end of the gene transcripts. However, the effect of the different GCN2 and CHOP isoforms on their function and regulation have not been investigated. Our data suggests that GCN2 is alternatively spliced into five different transcripts and the beta isoform of GCN2 is most abundant. Also alternative splicing of CHOP creates two CHOP transcripts with different 5'-leaders encoding inhibitory upstream open reading frames that are critical for translational control of CHOP during stress. This study suggests that alternative splicing can play an integral role in the implementation and regulation of key factors in the Integrated stress response.

DNA-basierte Systeme beschreiben formal ein alternatives Berechnungskonzept, beruhend auf der Anwendung molekularbiologischer Operationen. Der Grundgedanke ist dabei die Entwicklung alternativer und universeller Rechnerarchitekturen. Infolge der zugrunde liegenden maximalen Parallelität sowie der hohen Komplexität entsprechender Systeme ist die Korrektheit jedoch schwer zu beweisen. Um dies zu ermöglichen werden in der Arbeit zunächst für drei verschiedene Systemklassen mit unterschiedlichen Berechnungsparadigmen strukturelle operationelle Semantiken definiert und bekannte Formalismen der Prozesstheorie adaptiert. Nachfolgend werden Tableaubeweissysteme beschrieben, mithilfe derer einerseits Invarianten und andererseits die jeweilige Korrektheit von DNA-basierten Systemen mit universeller Berechnungsstärke bewiesen werden können. Durch Anwendung dieser Konzepte konnte für drei universelle Systeme die Korrektheit gezeigt und für ein System widerlegt werden.

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Indiana University-Purdue University Indianapolis (IUPUI) / Alternative RNA splicing is an important means of genetic control and transcriptome diversity. Alternative splicing events are frequently studied independently, and coordinated splicing controlled by common factors is often overlooked: The molecular mechanisms by which splicing regulators promote or repress specific pre-mRNA processing are still not yet well understood. It is well known that splicing factors can regulate splicing in a context-dependent manner, and the search for modulation of splicing factor activity via direct or indirect mechanisms is a worthwhile pursuit towards explaining context-dependent activity. We hypothesized that the combined analysis of hundreds of consortium RNA-seq datasets could identify trans-acting “modulators” whose expression is correlated with differential effects of a splicing factor on its target splice events in mRNAs. We first tested a genome-wide approach to identify relationships between RNA-binding proteins and their inferred modulators in kidney cancer. We then applied a more targeted approach to identify novel modulators of splicing factor SRSF1 function over dozens of its intron retention splicing targets in a neurological context using hundreds of dorsolateral prefrontal cortex samples. Our hypothesized model was further strengthened with the incorporation of genetic variants to impute gene expression in a Mendelian randomization-based approach. The modulators of intron retention splicing we identified may be associated with risk variants linked to Alzheimer’s Disease, among other neurological disorders, to explain disease-causing splicing mechanisms. Our strategy can be widely used to identify modulators of RNA-binding proteins involved in tissue-specific alternative splicing.

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