Alternative mRNA Splicing Research Articles

Phytophthora Effectors Modulate Genome-wide Alternative Splicing of Host mRNAs to Reprogram Plant Immunity

Alternative splicing (AS) of pre-mRNAs increases transcriptome and proteome diversity, regulates gene expression through multiple mechanisms, and plays important roles in plant development and stress responses. However, the prevalence of genome-wide plant AS changes during infection and the mechanisms by which pathogens modulate AS remain poorly understood. Here, we examined the global AS changes in tomato leaves infected with Phytophthora infestans, the infamous Irish famine pathogen. We show that more than 2000 genes exhibiting significant changes in AS are not differentially expressed, indicating that AS is a distinct layer of transcriptome reprogramming during plant–pathogen interactions. Furthermore, our results show that P. infestans subverts host immunity by repressing the AS of positive regulators of plant immunity and promoting the AS of susceptibility factors. To study the underlying mechanism, we established a luminescence-based AS reporter system in Nicotiana benthamiana to screen pathogen effectors modulating plant AS. We identified nine splicing regulatory effectors (SREs) from 87 P. infestans effectors. Further studies revealed that SRE3 physically binds U1-70K to manipulate the plant AS machinery and subsequently modulates AS-mediated plant immunity. Our study not only unveils genome-wide plant AS reprogramming during infection but also establishes a novel AS screening tool to identify SREs from a wide range of plant pathogens, providing opportunities to understand the splicing regulatory mechanisms through which pathogens subvert plant immunity.

Genome-wide analyses of the prognosis-related mRNA alternative splicing landscape and novel splicing factors based on large-scale low grade glioma cohort.

Alternative splicing (AS) changes are considered to be critical in predicting treatment response. Our study aimed to investigate differential splicing patterns and to elucidate the role of splicing factor (SF) as prognostic markers of low-grade glioma (LGG). We downloaded RNA-seq data from a cohort of 516 LGG tumors in The Cancer Genome Atlas and analyzed independent prognostic factors using LASSO regression and Cox proportional regression to build a network based on the correlation between SF-related survival AS events. We collected 100 patients from our center for immunohistochemistry and analyzed survival using χ2 test and Cox and Kaplan-Meier analyses. A total of 9,616 AS events related to LGG were screened and identified as well as established related models. Through analyzing specific splicing patterns in LGG, we screened 16 genes to construct a prognostic model to stratify the risk of LGG patients. Validation revealed that the expression level of the prognostic model in LGG tissue was increased, and patients with high expression showed worse prognosis. In summary, we demonstrated the role of SFs and AS events in the progression of LGG, which may provide insights into the clinical significance and aid the future exploration of LGG-associated AS.

Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development.

During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology for measuring gene expression from thousands of individual cells identified the different cell types in the developing kidney. However, that analysis did not include the additional layer of heterogeneity that alternative mRNA splicing creates. Full transcript length single-cell RNA sequencing characterized the transcriptomes of 544 individual cells from mouse embryonic kidneys. Gene expression levels measured with full transcript length single-cell RNA sequencing identified each cell type. Further analysis comprehensively characterized splice isoform switching during the transition between mesenchymal and epithelial cellular states, which is a key transitional process in kidney development. The study also identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2. Discovery of the sets of genes that are alternatively spliced as the fetal kidney mesenchyme differentiates into tubular epithelium will improve our understanding of the molecular mechanisms that drive kidney development.

Prognostic Value and Potential Role of Alternative mRNA Splicing Events in Cervical Cancer.

BackgroundIncreasing evidence suggests that aberrant alternative splicing (AS) events are associated with progression of cancer. This study evaluated the prognostic value and clarify the role of AS events in cervical cancer (CC).MethodsBased on RNA-seq AS event data and clinical information of CC patients in The Cancer Genome Atlas (TCGA) database, we sought to identify prognosis-related AS events in this setting. We selected several survival-associated AS events to construct a prognostic predictor for CC through the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression. Moreover, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses were performed on genes with prognosis-related AS events and constructed an AS-splicing factors (SFs) regulatory network.Results2770 AS events were significantly correlated with overall survival (OS). The area under the curve (AUC) values of receiver-operator characteristic curve (ROC) for the final prognostic predictor were 0.926, 0.946 and 0.902 at 3, 5, and 10 years, respectively. These values indicated efficiency in prognostic risk stratification for patients with CC. The final prognostic predictor was an independent predictor of OS (HR: 1.24; 95% CI: 1.020–1.504; P < 0.05). The AS-SFs correlation network may reveal an underlying regulatory mechanism of AS events.ConclusionAS events are essential participants in the prognosis of CC and hold great potentials for the prognostic stratification and development of treatment strategy.

Prognostic alternative mRNA splicing signatures and associated splicing factors in acute myeloid leukemia

The dysregulation of alternative splicing (AS) has emerged as a mechanism of acute myeloid leukemia (AML). However, the prognostic impact of AS events remains under-explored in AML. Here we report the prognostic value of AS events and associated splicing factors based on three datasets of AML patients. We defined the landscape of AS events in AML and identified 7033 AS events associated with the survival of AML patients. Based on these events, we further developed a composite 15 AS event-based prognostic signature, which was independent of the cytogenetic risk stratification and patient age, and showed a better performance than known gene expression signatures. More importantly, our new signature markedly improved the European LeukemiaNet (ELN) risk classification, indicating a broad applicability in the clinical management of AML. Furthermore, the splicing-regulatory network established the correlations between prognostic AS events and associated splicing factors. The finding was validated by CRISPR-based data, which indicated that the increased expression of RBM39 contributed to the higher exon inclusion of SETD5 and conferred a poor outcome. Together, AS events may serve as a novel assortment of prognosticators for AML and could refine the ELN risk stratification. The splicing regulatory network provides clues regarding the splicing factor-mediated mechanisms of AML.

Analysis of relapse-associated alternative mRNA splicing and construction of a prognostic signature predicting relapse in I–III colon cancer

The literature comprehensively analyzed alternative splicing (AS) events in colon cancer is little and corresponding prognostic signature is still a lack. Based on data of TCGA, the relapse-associated ASs were comprehensively analyzed and a signature was further constructed to predict the relapse in I–III colon cancer. In total 1912 ASs of 1384 mRNA were identified as relapse-associated ASs, protein-protein interactions (PPI) and ASs-splicing factors (SF) interactions network were identified. We finally built a robust signature to predict the relapse of I–III colon cancer with a considerable AUC value in both the training group and the test group. The AUC in the entire set at 1, 3 and 5 year was 0.85, 0.83 and 0.836. Our study provided a profile of relapse-associated ASs in I–III colon cancer and built a robust signature to predict the relapse of I–III colon cancer.

Targeting cellular senescence in cancer and aging: roles of p53 and its isoforms.

Cellular senescence and the associated secretory phenotype (SASP) promote disease in the aged population. Targeting senescent cells by means of removal, modulation of SASP or through cellular reprogramming represents a novel therapeutic avenue for treating cancer- and age-related diseases such as neurodegeneration, pulmonary fibrosis and renal disease. Cellular senescence is partly regulated by the TP53 gene, a critical tumor suppressor gene which encodes 12 or more p53 protein isoforms. This review marks a significant milestone of 40 years of Carcinogenesis publication history and p53 research and 15 years of p53 isoform research. The p53 isoforms are produced through initiation at alternative transcriptional and translational start sites and alternative mRNA splicing. These truncated p53 isoform proteins are endogenously expressed in normal human cells and maintain important functional roles, including modulation of full-length p53-mediated cellular senescence, apoptosis and DNA repair. In this review, we discuss the mechanisms and functions of cellular senescence and SASP in health and disease, the regulation of cellular senescence by p53 isoforms, and the therapeutic potential of targeting cellular senescence to treat cancer- and age-associated diseases.

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala \xd7 Culter alburnus

BackgroundMaternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animals.ResultsTwo reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. By comparing the expression of BSB- and TC- homoeologous genes between the two reciprocal cross hybrids, we identified 49–348 differentially expressed BSB-homoeologous genes and 54–354 differentially expressed TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonad, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TBF3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BTF3. These results further improve AS prediction at the homoeolog level. The various AS patterns in bmpr2a belonging to the bone morphogenetic protein family were selected as AS models to investigate the expression diversity and its potential effects to body shape traits.ConclusionsThe distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects were the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.

Evolution of neuronal and glial tau isoforms in chronic traumatic encephalopathy.

Chronic traumatic encephalopathy (CTE) is a neurodegenerative tauopathy characterized by accumulation of hyperphosphorylated tau (p-tau) in perivascular aggregates in neurons and glia at the depths of neocortical sulci and progresses to diffuse neocortical, allocortical and brainstem structures. The strongest risk factor is exposure to repetitive head impacts acquired most commonly through contact sports and military service. Given that CTE can only be definitively diagnosed after death, a better understanding of the cellular and molecular changes in CTE brains may lead to identification of mechanisms that could be used for novel biomarkers, monitoring progression or therapeutic development. Disruption of alternative pre-mRNA splicing of tau mRNA plays a pathogenic role in tauopathy, with multiple characteristic patterns of isoform accumulation varying among tauopathies. Limited data are available on CTE, particularly at early stages. Using biochemical and histological approaches, we performed a detailed characterization of tau isoform signatures in post-mortem human brain tissue from individuals with a range of CTE stages (n=99). In immunoblot analyses, severity was associated with decreased total monomeric tau and increased total oligomeric tau. Immunoblot with isoform-specific antisera revealed that oligomeric tau with three and four microtubule binding domain repeats (3R and 4R) also increased with CTE severity. Similarly, immunohistochemical studies revealed p-tau accumulation consisting of both 3R and 4R in perivascular lesions. When the ratio of 4R:3R was analyzed, there was mixed expression throughout CTE stages, although 4R predominated in early CTE stages (I-II), a 3R shift was observed in later stages (III-IV). While neurons were found to contain both 3R and 4R, astrocytes only contained 4R. These 4R-positive cells were exclusively neuronal at early stages. Overall, these findings demonstrate that CTE is a mixed 4R/3R tauopathy. Furthermore, histologic analysis reveals a progressive shift in tau isoforms that correlates with CTE stage and extent of neuronal pathology.

Adult-Onset Myopathy with Constitutive Activation of Akt following the Loss of hnRNP-U.

SummarySkeletal muscle has the remarkable ability to modulate its mass in response to changes in nutritional input, functional utilization, systemic disease, and age. This is achieved by the coordination of transcriptional and post-transcriptional networks and the signaling cascades balancing anabolic and catabolic processes with energy and nutrient availability. The extent to which alternative splicing regulates these signaling networks is uncertain. Here we investigate the role of the RNA-binding protein hnRNP-U on the expression and splicing of genes and the signaling processes regulating skeletal muscle hypertrophic growth. Muscle-specific Hnrnpu knockout (mKO) mice develop an adult-onset myopathy characterized by the selective atrophy of glycolytic muscle, the constitutive activation of Akt, increases in cellular and metabolic stress gene expression, and changes in the expression and splicing of metabolic and signal transduction genes. These findings link Hnrnpu with the balance between anabolic signaling, cellular and metabolic stress, and physiological growth.

AMP-activated protein kinase regulates alternative pre-mRNA splicing by phosphorylation of SRSF1.

AMP-activated protein kinase (AMPK) regulates cellular energy homeostasis by inhibiting anabolic processes and activating catabolic processes. Recent studies have demonstrated that metformin, which is an AMPK activator, modifies alternative precursor mRNA (pre-mRNA) splicing. However, no direct substrate of AMPK for alternative pre-mRNA splicing has been reported. In the present study, we identified the splicing factor serine/arginine-rich splicing factor 1 (SRSF1) as a novel AMPK substrate. AMPK directly phosphorylated SRSF1 at Ser133 in an RNA recognition motif. Ser133 phosphorylation suppressed the interaction between SRSF1 and specific RNA sequences without altering the subcellular localization of SRSF1. Moreover, AMPK regulated the SRSF1-mediated alternative pre-mRNA splicing of Ron, which is a macrophage-stimulating protein receptor, by suppressing its interaction with exon 12 of Ron pre-mRNA. The findings of this study revealed that the AMPK-dependent phosphorylation of SRSF1 at Ser133 inhibited the ability of SRSF1 to bind RNA and regulated alternative pre-mRNA splicing.

A signature predicting relapse based on integrated analysis on relapse-associated alternative mRNA splicing in I–III rectal cancer

Researches focusing on the effects of alternative splicing (AS) on relapse of rectal cancer is little and signature based on the AS is blank. In this study, bioinformatic analysis was performed to identify and analyze the relapse-associated ASs, a signature was also constructed. In conclusion, 829 relapse-associated ASs of 676 mRNA were identified. 603 proteins with 2119 interactions were involved in the PPI (protein-protein interactions) network. 43 relapse-associated ASs and 64 SFs (splicing factors) with 160 interactions were indicated. Finally, we built a robust signature to predict the relapse of I–III rectal cancer with a high AUC (0.98) of ROC at 1 year. Based on the ASs involved in the signature, 4 molecular subgroups that could distinguish the relapse rate in diverse groups were identified. Our research provided an overview of relapse-associated ASs in I–III rectal cancer.

Abstract B070: Mitotic kinases differentially phosphorylate survivin in African American TNBC: Clues for racial disparity

Abstract Protein diversity arising from alternative mRNA splicing or post-translational modifications (PTM) such as phosphorylation, methylation etc. plays a vital role in the modulation of cellular functions. Mitotic kinases such as polo-like kinase 1 (PLK1) and aurora B (AURKB) are known to phosphorylate survivin, an inhibitor of apoptosis family member, to promote cell survival and proliferation. This triad is significantly overexpressed in triple negative breast cancer (TNBC), an aggressive breast cancer (BC) subtype, associated with high proliferative capacity, propensity for distant metastasis and chemotherapeutic resistance. TNBC disproportionately afflicts African-American (AA) women relative to European-American (EA) women. AAs demonstrate a much more aggressive disease course compared to EAs. Thus far, efforts to examine molecular underpinnings of racial disparity in TNBC have largely focused on differences in gene expression and epigenetic aspects. Herein, we demonstrate the role of survivin phosphorylation, an important PTM, in enhancing cell proliferation and reducing apoptosis in AA compared to EA TNBC cells. Using the TCGA breast cancer dataset, our in silico analysis of various mitotic kinases yielded a significantly higher gene expression of PLK1 (p=0.061) and AURKB (p=0.003) in AA (n=41) compared to EA TNBC (n=86) patients. Surprisingly, we found no race-related differences in survivin gene expression in this dataset (n=127, p=0.343). In addition, there was no statistical difference in protein levels of survivin in TNBC clinical samples (n=142, p=0.45) as measured immunohistochemically. These findings led us to rationalize that the differential activation of survivin in AA vs. EA TNBC cells is based on PTM, and not due to its differential gene/protein expression levels. We hypothesize that differential phosphorylation of survivin by mitotic kinases underlies enhanced proliferative and anti-apoptotic activity in AA relative to EA TNBC. Survivin phosphorylation at Ser-20 and Thr-117 is known to regulate the activity of the chromosome passenger complex facilitating mitosis and cell proliferation. Moreover, p-survivin Thr-117 inhibits X-linked inhibitor of apoptosis-Smac interaction, which in turn prevents caspase-9 activation, leading to anti-apoptosis. We observed an upregulation of phosphorylated substrates of PLK1 and AURKB viz. p-survivin Ser-20 &amp; p-survivin Thr-117, respectively, in AA compared to EA TNBC cells. Survivin ablation significantly attentuated cell proliferation, cell cycle progression, and increased cell apoptosis in AA compared to EA TNBC cells. These data strongly support our premise that higher survivin phosphorylation confers enhanced proliferative capacity and anti-apoptosis in AA compared to EA TNBC cells, suggesting that modulating survivin PTM may be a viable therapeutic strategy for AA TNBC patients. Further studies intended to tease out the role of survivin phosphorylation in TNBC racial disparity are currently underway in our lab. Citation Format: Shriya Joshi, Chakravarthy Garlapati, Luciane Cavalli, Uma Krishnamurti, Shobhna Kapoor, Ritu Aneja. Mitotic kinases differentially phosphorylate survivin in African American TNBC: Clues for racial disparity [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr B070.

Abstract B053: Expression of alternative mRNA splicing variant MBD2_v2 promotes triple-negative breast cancer tumor initiation and is associated with body mass index

Abstract According to epidemiologic research, obesity is a risk factor for triple-negative breast cancer (TNBC). The underlying molecular biology remains unknown. We reasoned that obesity-induced chronic inflammation, reactive oxygen species (ROS) being central, serves as the general link to TNBC. We are the first to report that expression of the epigenetic reader methyl-CpG-binding domain protein 2 mRNA variant MBD2_v2 in TNBC cell cultures depends on ROS and is necessary to maintain and promote expansion of cancer stem cell-like cells (CSCs). The relevance of CSCs is that they are a subpopulation of cancer cells recognized as the source of malignant tumor initiation, and they give rise to drug resistance and metastatic recurrence. We also previously reported evidence that MBD2_v2 expression underlies TNBC resistance to EGFR inhibitor drugs. Now, having used a diet-induced obesity (DIO) mouse model that mimics human obesity, we report that MBD2_v2 and serine/arginine-rich mRNA splicing factor 2 (SRSF2) levels were increased in tumors that formed more frequently in DIO mice relative to lean controls. To more directly test if increased MBD2_v2 drives increased tumor initiation capacity, we stably modified MBD2_v2 or SRSF2 expression in TNBC cells prior to inoculation. MBD2_v2 overexpression increased tumor initiation while SRSF2 knockdown, resulting in decreased MBD2_v2 expression, attenuated tumor formation. In addition, our analysis of TNBC patient tumors revealed a significant positive association for MBD2_v2 expression and body mass index (BMI). African American (AA) women are 1.7 times more often obese relative to European American women, and a TNBC driver mechanism fueled by obesity-coupled inflammation could underlie the higher incidence of TNBC among AA women. Citation Format: Emily A. Teslow, Cristina Mitrea, Bin Bao, Ramzi M. Mohammad, Lisa A. Polin, Greg Dyson, Kristen S. Purrington, Aliccia Bollig-Fischer. Expression of alternative mRNA splicing variant MBD2_v2 promotes triple-negative breast cancer tumor initiation and is associated with body mass index [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B053.

Dietary Flavonoids Targeting Triple Negative Breast Cancer

Abstract Objectives Breast cancer remains the leading cause of malignancy-related death in females and continues to increase in prevalence worldwide. The lack of therapies for triple-negative breast cancer (TNBC) continues to be a challenge, owing to its highly metastatic and aggressive nature. Dietary flavonoids, found in fruits and vegetables, are attracting great interest in the prevention and treatment of TNBC due to their anti-carcinogenic, anti-oxidative, and anti-inflammatory properties. The goal of our project was to evaluate the structure-activity relationship and the mechanism by which flavonoids affect TNBC tumor growth and metastasis. Methods We investigated the effects of structurally related flavonoids on the migratory nature of human MDA-MB 231 TNBC cells by using a wound healing migration assay. To model the effects of flavonoids in tumor heterogeneity in vivo, 3-dimensional culture organoids from TNBC derived xenograft tumors were established. Small interfering RNA (siRNA) transfection of apigenin target heterogeneous nuclear ribonucleoproteins A2 (hnRNPA2), an oncogene overexpressed in cancer cells that leads to abnormal mRNA splicing, were employed to investigate how hnRNPA2 effects alternative mRNA splicing activity. Results We observed that the natural flavonoids apigenin and kaempferol inhibited migration in a dose-response manner. Conversely, the presence of a glucoside and/or the lack of double bonds within the flavonoid structure as in the case of apigenin-7-glucoside and flavanones exhibited no significant anti-metastatic effects. Analysis of hnRNPA2 knockdown revealed key insights into the interaction of apigenin with hnRNPA2 to regulate migratory behaviors. Conclusions These novel insights showcase dietary flavonoids as practical functional foods that can benefit clinical applications in TNBC cancer prevention and treatment of tumor metastases and growth. Funding Sources Through grants from United States Department of Agriculture, National Science Foundation, and MSU awarded to Dr. Andrea I. Doseff, NIH-T32 Plant Biotechnology for Health and Sustainability Fellowship to Meenakshi Sudhakaran, and the REPID Program funded by National Institute of Health and directed by Dr. Elahé Crockett.

Transcript expression-aware annotation improves rare variant interpretation

The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the ‘proportion expressed across transcripts’, which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies.

CRISPR-Cas9 gene editing causes alternative splicing of the targeting mRNA

The technique of CRISPR-Cas9 gene editing has been widely used to specifically delete the selected target genes through generating double strand breaks (DSBs) and inducing insertion and/or deletion (indel) of the genomic DNAs in the cells. We recently applied this technique to disrupt mineral dust-induced gene (mdig), a potential oncogene as previously reported, by single guide RNA (sgRNA) targeting the third exon of mdig gene in several cell types, including human bronchial epithelial cell line BEAS-2B, lung cancer cell line A549, and human triple negative breast cancer cell line MDA-MB-231 cells. In addition to the successful knockout of mdig gene in these cells, we unexpectedly noted generation of several alternatively spliced mdig mRNAs. Amplification of the mdig mRNAs during the screening of knockout clones by reverse transcription-polymerase chain reaction (RT-PCR) and the subsequent sanger sequencing of DNA revealed deletion and alternative splicing of mdig mRNAs induced by CRISPR-Cas9 gene editing. The most common deletions include nine and twenty-four nucleotides deletion around the DSBs. In addition, interestingly, some mdig mRNAs showed skipping of the entire exon 3, or alternative splicing between exon 2 and exon 8 using the new donor and accept splicing sites, leading to deletion of exons 3, 4, 5, 6, and 7. Accordingly, cautions should be taken when using CRISPR-Cas9 strategy to edit human genes due to the unintended alterative splicing of the target mRNAs. It is very likely that new proteins, some of which may be highly oncogenic, may be generated from CRISPR-Cas9 gene editing.

Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing.

Alternative mRNA splicing increases protein diversity, and alternative splicing events (ASEs) drive oncogenesis in multiple tumor types. However, the driving alterations that underlie the broad dysregulation of ASEs are incompletely defined. Using head and neck squamous cell carcinoma (HNSCC) as a model, we hypothesized that the genomic alteration of genes associated with the spliceosome may broadly induce ASEs across a broad range of target genes, driving an oncogenic phenotype. We identified 319 spliceosome genes and employed a discovery pipeline to identify 13 candidate spliceosome genes altered in HNSCC using The Cancer Genome Atlas (TCGA) HNSCC data. Phenotypic screens identified amplified and overexpressed CPSF1 as a target gene alteration that was validated in proliferation, colony formation, and apoptosis assays in cell line and xenograft systems as well as in primary HNSCC. We employed knockdown and overexpression assays followed by identification of ASEs regulated by CPSF1 overexpression to identify changes in ASEs, and the expression of these ASEs was validated using RNA from cell line models. Alterations in expression of spliceosome genes, including CPSF1, may contribute to HNSCC by mediating aberrant ASE expression.

Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy.

In recent years, the genetic architecture of dilated cardiomyopathy (DCM) has been more thoroughly elucidated. However, there is still insufficient knowledge on the modifiers and regulatory principles that lead to the failure of myocardial function. The current study investigates the association of epigenome-wide DNA methylation and alternative splicing, both of which are important regulatory principles in DCM. We analyzed screening and replication cohorts of cases and controls and identified distinct transcriptomic patterns in the myocardium that differ significantly, and we identified a strong association of intronic DNA methylation and flanking exons usage (p < 2 × 10−16). By combining differential exon usage (DEU) and differential methylation regions (DMR), we found a significant change of regulation in important sarcomeric and other DCM-associated pathways. Interestingly, inverse regulation of Titin antisense non-coding RNA transcript splicing and DNA methylation of a locus reciprocal to TTN substantiate these findings and indicate an additional role for non-protein-coding transcripts. In summary, this study highlights for the first time the close interrelationship between genetic imprinting by DNA methylation and the transport of this epigenetic information towards the dynamic mRNA splicing landscape. This expands our knowledge of the genome–environment interaction in DCM besides simple gene expression regulation.

Expression of the Src-family kinase LynA tunes myeloid-cell signaling and function

Abstract The activity of Src-family kinases (SFKs), which phosphorylate immunoreceptor tyrosine-based activation motifs (ITAMs) upon receptor ligation, is a critical factor regulating myeloid cell activation. The SFK Lyn has roles in activating myeloid cells, by phosphorylating ITAMs, and also in inducing suppressive signaling via phosphatase activation. Alternative splicing of lyn mRNA produces two proteins, LynA and LynB, and emerging evidence from our lab and others suggests that LynA and LynB interact with different proteins and preferentially activate different signal cascades. In macrophages LynA is uniquely susceptible to rapid ubiquitin-mediated degradation and functions as a rheostat that regulates ITAM signal strength. Phosphorylation of tyrosine 32 in the unique region of LynA preferentially targets LynA for polyubiquitination by the E3 ligase c-Cbl. In contrast to macrophages, mast cells express little c-Cbl. Upon activation, LynA is not rapidly degraded in mast cells, and SFK-mediated signaling is amplified relative to macrophages. Previous studies of LynA have been hampered by knockout models that lack both LynA and LynB. To understand the role LynA plays in immune development and activation, we used CRISPR-Cas9 gene editing to generate novel mouse strains that express either LynA or LynB. Preliminary studies in these mice have demonstrated novel roles for LynA. Notably, LynA−/− mice have an enrichment in splenic dendritic cells and alveolar macrophages. Thus, LynA is not only an important regulator of myeloid cell activation, tuning cell-specific signaling thresholds, but also helps regulate the function of these cells. Further studies will investigate the impact of LynA deletion in myeloid inflammation sensing.