Biology subjects

Zhu, C.

Publications and source records attributed to Zhu, C..

232 records · Page 13Linked to original sources

bioRxiv2019

Slc7a11 modulated by POU2F1 is involved in pigmentation in rabbit

Solute carrier family 7 member 11 (Slc7a11) codes for a cystine/glutamate xCT transporter and can control production of pheomelanin pigment to change fur and skin colors of animals. Previous studies found that the skin expression levels of Slc7a11 varied significantly with the fur colors of the Rex Rabbit. However, it is not yet known the molecular regulation mechanism of Slc7a11 in pigmentation. Here rabbit melanocytes were first isolated and identified. The distribution and expression pattern of Slc7a11 was confirmed in rabbit skin with different fur colors. Slc7a11 could affect the expression of pigmentation related genes and thus affect melanogenesis. Meanwhile, Slc7a11 decreased melanocytes apoptosis, but inhibition of Slc7a11 enhanced apoptosis. Furthermore, it was found that POU2F1 protein bound to the -713 to -703 bp region of Slc7a11 promoter to inhibite its activity by dual-luciferase reporter and site-directed mutagenesis assay. This study uncover the function of the Slc7a11 in melanogenesis and provided in-depth analysis of the mechanism of fur pigmentation.

molecular biology↗

bioRxiv2019

Chemokine signaling links cell cycle progression and cilia formation for left-right symmetry breaking

Zebrafish dorsal forerunner cells (DFCs) undergo vigorous proliferation during epiboly and then exit cell cycle to generate Kupffers vesicle (KV), a ciliated organ necessary for establishing left-right (L-R) asymmetry. DFC proliferation defects are often accompanied by impaired cilia elongation in KV, but the functional and molecular interaction between cell-cycle progression and cilia formation remains unknown. Here we show that chemokine receptor Cxcr4a is required for L-R laterality by controlling DFC proliferation and KV ciliogenesis. Functional analysis revealed that Cxcr4a accelerates G1/S transition in DFCs and stabilizes Foxj1a, a master regulator of motile cilia, by stimulating Cyclin D1 expression through ERK1/2 signaling. Mechanistically, Cyclin D1-CDK4/6 drives G1/S transition during DFC proliferation and phosphorylates Foxj1a, thereby disrupting its association with Psmd4b, a 19S regulatory subunit. This prevents the ubiquitin-independent proteasomal degradation of Foxj1a. Our study uncovers a role for Cxcr4 signaling in L-R patterning and provides fundamental insights into the molecular linkage between cell-cycle progression and ciliogenesis.\n\nAuthor summaryDuring the organogenesis of zebrafish L-R organizer named KV, DFCs proliferate rapidly during epiboly and then exit the cell cycle to differentiate into ciliated epithelial KV cells. Cell cycle defects in DFCs are often accompanied by an alteration in KV cilia elongation. However, whether the cell cycle and cilia formation are mechanistically linked remains as an open question. In this study, we report that Cxcr4 signaling is required for DFC proliferation and KV ciliogenesis. We reveal that Cxcl12b/Cxcr4a signaling activates ERK1/2, which then promotes Cyclin D1 expression. Cyclin D1-CDK4/6 accelerates the G1/S transition in DFCs, while also facilitates cilia formation via stabilization of Foxj1a. Notably, Foxj1 undergoes proteasomal degradation via Ub-independent pathway during KV organogenesis. Our study further demonstrates that CDK4 phosphorylates and stabilizes Foxj1a by disrupting its association with Psmd4b, a 19S regulatory subunit. In summary, Cxcl12b/Cxcr4a chemokine signaling links cell cycle progression and cilia formation for L-R symmetry breaking via regulating Cyclin D1 expression.

developmental biology↗

bioRxiv2019

Effects of topical PaiTeLing in nude mice implanted with human condyloma acuminatum tissue infected with HPV 6, 31, and 81: comparison with imiquimod and interferon-α-2b

BACKGROUNDThe standard treatment for condyloma acuminatum is topical imiquimod. In the current study, we used a mouse model to compare the effects of an herbal medication PaiTeLing. METHODSLesion tissue was obtained from a woman with genital condyloma acuminatum. DNA genotyping revealed HPV6, 31, and 81. Tissue prism (0.5 cm3) was implanted to BALB/C nude mice, 22 days after the implantation, mice began to receive topical treatment with imiquimod, interferon--2b gel, or PaiTeLing over the site of implantation for 2 consecutive weeks. Mice receiving tissue implantation but no other intervention was included as a control. Skin tissue was collected for H&E staining and anti-CD207 immunohistochemistry. Blood was collected to determine a panel of cytokines. RESULTSH&E staining showed lower number of koilocytes and higher number of Langerhans cells in the treatment groups, particularly in mice receiving imiquimod or PaiTeLing. Blood levels of TNF, IL-2, INF-{gamma} and IL-12p70 were increased in the treatment groups, particularly in mice receiving imiquimod or PaiTeLing. CONCLUSIONImmune response in nude mice infected with HPV6, 31, and 81 is enhanced by treatment with imiquimod, interferon--2b and PaiTeLing. Effects of imiquimod and PaiTeLing seems to be stronger than interferon--2b.

immunology↗

bioRxiv2019

Reticulon and CLIMP-63 control nanodomain organization of peripheral ER tubules

The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle composed of smooth peripheral tubules and rough, ribosome-studded central ER sheets whose morphology is determined, in part, by the ER-shaping proteins, reticulon and CLIMP-63, respectively. Here, STimulated Emission Depletion (STED) super-resolution microscopy shows that reticulon and CLIMP-63 also control the organization and dynamics of peripheral ER tubule nanodomains. STED imaging shows that lumenal ERmoxGFP, membrane Sec61{beta}GFP, knock-in calreticulin-GFP and antibody-labeled ER resident proteins calnexin and derlin-1 are all localized to periodic puncta along the length of peripheral ER tubules that are not readily observable by diffraction limited confocal microscopy. Reticulon segregates away from and restricts lumenal blob length while CLIMP-63 associates with and increases lumenal blob length. Reticulon and CLIMP-63 also regulate the nanodomain distribution of ER resident proteins, being required for the preferential segregation of calnexin and derlin-1 puncta away from lumenal ERmoxGFP blobs. High-speed (40 ms/frame) live cell STED imaging shows that reticulon and CLIMP-63 control nanoscale compartmentalization of lumenal flow in peripheral ER tubules. Reticulon enhances and CLIMP-63 disrupts the local accumulation of lumenal ERmoxGFP at spatially defined sites along ER tubules. The ER shaping proteins reticulon and CLIMP-63 therefore control lumenal ER nanodomain dynamics, heterogeneity and interaction with ER resident proteins in peripheral ER tubules.

cell biology↗

bioRxiv2019

Functional Near-Infrared Spectroscopy (fNIRS) informed neurofeedback: regional-specific modulation of lateral orbitofrontal activation and cognitive flexibility

Cognitive flexibility and reward processing critically rely on the orbitofrontal cortex. Dysregulations in these domains and orbitofrontal activation have been reported in major psychiatric disorders. Haemodynamic brain imaging informed neurofeedback allows regional-specific control over brain activation and thus may represent an innovative intervention to regulate orbitofrontal dysfunctions. Against this background the present proof-of-concept study evaluated the feasibility and behavioral relevance of functional Near-Infrared Spectroscopy (fNIRS) assisted neurofeedback training of the lateral orbitofrontal cortex (lOFC). In a randomized sham-controlled between-subject design 60 healthy participants underwent four subsequent runs of training to enhance lOFC activation. Training-induced changes in the lOFC, attentional set shifting performance and reward experience served as primary outcomes. Feedback from the target channel significantly increased regional-specific lOFC activation over the four training runs in comparison with sham feedback. The experimental group demonstrated a trend for faster responses during set shifting relative to the sham group. Within the experimental group stronger training-induced lOFC increases were associated with higher reward experience. The present results demonstrate that fNIRS-informed neurofeedback allows regional-specific regulation of lOFC activation and may have the potential to modulate associated behavioral domains. As such fNIRS-informed neurofeedback may represent a promising strategy to regulate OFC dysfunctions in psychiatric disorders.

neuroscience↗

bioRxiv2018

SARM1 deficiency, which prevents Wallerian degeneration, upregulates XAF1 and accelerates prion disease

SARM1 (sterile and HEAT/armadillo motifs containing protein) is a member of the MyD88 (myeloid differentiation primary response gene 88) family which mediates innate immune responses. Because inactivation of SARM1 prevents various forms of axonal degeneration, we tested whether it might protect against prion-induced neurotoxicity. Instead, we found that SARM1 deficiency exacerbates the progression of prion pathogenesis. This deleterious effect was not due to SARM1-dependent modulation of prion-induced neuroinflammation, since microglial activation, astrogliosis and brain cytokine profiles were not altered by SARM1 deficiency. Whole-transcriptome analyses indicated that SARM1 deficiency led to strong, selective overexpression of the pro-apoptotic gene XAF1 (X-linked inhibitor of apoptosis-associated factor 1). Consequently, the activity of proapoptotic caspases and neuronal death were enhanced in prion-infected SARM1-/- mice. These results point to an unexpected function of SARM1 as a regulator of prion-induced neurodegeneration, and suggest that XAF1 might constitute a therapeutic target in prion disease.

neuroscience↗

bioRxiv2018

Nitric oxide synthase-mediated early nitric oxide-burst alleviates drought-induced oxidative damage in ammonium supplied-rice roots

Ammonium (NH4+) can enhance rice drought tolerance in comparison to nitrate (NO3-). The mechanism underpinning this relationship was investigated based on the time-dependent nitric oxide (NO) production and its protective role in oxidative stress of NH4+-/NO3--supplied rice under drought. An early burst of NO was induced by drought 3h after root NH4+ treatment but not after NO3- treatment. Root oxidative damage induced by drought was significantly higher in NO3- than in NH4+-treatment due to its reactive oxygen species accumulation. Inducing NO production by applying NO donor 3h after NO3- treatment alleviated the oxidative damage, while inhibiting the early NO burst increased root oxidative damage in NH4+ treatment. Application of nitric oxide synthase (NOS) inhibitor N(G)-nitro-L-arginine methyl ester (L-NAME) completely suppressed NO synthesis in roots 3h after NH4+ treatment and aggravated drought-induced oxidative damage, indicating the aggravation of oxidative damage might have resulted from changes in NOS-mediated early NO burst. Drought also increased root antioxidant enzymes activities, which were further induced by NO donor but repressed by NO scavenger and NOS inhibitor in NH4+-treated roots. Thus, the NOS-mediated early NO burst plays an important role in alleviating oxidative damage induced by drought by enhancing antioxidant defenses in NH4+-supplied rice roots.\n\nHighlightNOS-mediated early NO burst plays an important role in alleviating oxidative damage induced by water stress, by enhancing the antioxidant defenses in roots supplemented with NH4+

physiology↗

bioRxiv2018

De novo transcriptomic characterization of Betta splendens for identifying sex-biased genes potentially involved in aggressive behavior modulation and EST-SSR maker development

Betta splendens is not only a commercially important labyrinth fish but also a nice research model for understanding the biological underpinnings of aggressive behavior. However, the shortage of basic genetic resource severely inhibits investigations on the molecular mechanism in sexual dimorphism of aggressive behavior typicality, which are essential for further behavior-related studies. There is a lack of knowledge regarding the functional genes involved in aggression expression. The scarce marker resource also impedes research progress of population genetics and genomics. In order to enrich genetic data and sequence resources, transcriptomic analysis was conducted for mature B. splendens using a multiple-tissues mixing strategy. A total of 105,505,486 clean reads were obtained and by de novo assembly, 69,836 unigenes were generated. Of which, 35,751 unigenes were annotated in at least one of queried databases. The differential expression analysis resulted in 17,683 transcripts differentially expressed between males and females. Plentiful sex-biased genes involved in aggression exhibition were identified via a screening from Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways, such as htr, drd, gabr, cyp11a1, cyp17a1, hsd17b3, dax1, sf-1, hsd17b7, gsdf1 and fem1c. These putative genes would make good starting points for profound mechanical exploration on aggressive behavioral regulation. Moreover, 12,751 simple sequence repeats were detected from 9,617 unigenes for marker development. Nineteen of the 100 randomly selected primer pairs were demonstrated to be polymorphic. The large amount of transcript sequences will considerably increase available genomic information for gene mining and function analysis, and contribute valuable microsatellite marker resources to in-depth studies on molecular genetics and genomics in the future.

zoology↗

bioRxiv2018

Unaltered prion disease in mice lacking developmental endothelial locus-1 (Del 1)

Progression of prion diseases is driven by the accumulation of prions in the brain. Ablation of microglia or deletion of the eat-me-signal milk-fat globule EGF factor VIII (Mfge8) accelerate prion pathogenesis, suggesting that microglia defends the brain by phagocytosing prions. Like Mfge8, Developmental endothelial locus-1 (Del-1) is a secreted protein that acts as an opsonin bridging phagocytes and apoptotic cells to facilitate phagocytosis. We therefore asked whether Del-1 might play a role in controlling prion pathogenesis. We first determined the expression pattern of Del-1 in mice, and found that the brain expresses the highest level of Del-1. In mouse brains, Del-1 was mainly expressed by neurons. We then assessed the anti-inflammatory and phagocytosis-promoting functions of Del-1 in prion disease, and determined whether Del-1 complements Mfge8 in prion clearance in mice with a C57BL/6J genetic background. We found that Del-1 deficiency did not change prion disease progression and lesion patterns. Also, prion clearance and PrPSc deposition were unaltered in Del-1 deficient mice. Additionally, prioninduced neuroinflammation was not affected by Del-1 deficiency. We conclude that Del-1 is not a major determinant of prion pathogenesis in this context.

neuroscience↗

bioRxiv2018

Genetic determinants of resistance and virulence among carbapenemase-producing Klebsiella pneumoniae from Sri Lanka.

Whole genome sequencing of carbapenem-resistant Enterobacteriaceae from the intensive care units of a Sri Lankan teaching hospital revealed the presence of carbapenemase gene, blaOXA-181 among isolates of carbapenase-producing Klebsiella pneumoniae belonging to ST437 (2 strains) and ST147 (8 strains) in 2015. blaOXA-181 genes were carried in three variants of ColE-type plasmids. Elevated carbapemen resistance were observed in ompK36 mutant strains. ESBL genes, plasmid-mediated quinolone resistance (PMQR) determinants (qnr, aac(6)-Ib-cr, oqxAB) and mutations on chromosomal quinolone resistance-determining regions (QRDRs) with substitutions at ser83[->]I of gyrA and ser80[->]I of parC were observed. All strains possessed yersiniabactin on the mobile element ICEkp and other virulence determinants. Strict infection control and judicious use of antibiotics are warranted to prevent further spread of multidrug-resistant Klebsiella pneumoniae in the intensive care units.

microbiology↗

bioRxiv2018

NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells

NADHX and NADPHX are hydrated and redox inactive forms of the NADH and NADPH cofactors, known to inhibit several dehydrogenases in vitro. A metabolite repair system that is conserved in all domains of life and that comprises the two enzymes NAD(P)HX dehydratase and NAD(P)HX epimerase, allows reconversion of both the S- and R-epimers of NADHX and NADPHX to the normal cofactors. An inherited deficiency in this system has recently been shown to cause severe neurometabolic disease in children. Although evidence for the presence of NAD(P)HX has been obtained in plant and human cells, little is known about the mechanism of formation of these derivatives in vivo and their potential effects on cell metabolism. Here, we show that NAD(P)HX dehydratase deficiency in yeast leads to an important, temperature-dependent NADHX accumulation in quiescent cells with a concomitant depletion of intracellular NAD+ and serine pools. We demonstrate that NADHX potently inhibits the first step of the serine synthesis pathway in yeast. Human cells deficient in the NAD(P)HX dehydratase also accumulated NADHX and showed decreased viability. In addition, those cells consumed more glucose and produced more lactate, potentially indicating impaired mitochondrial function. Our results provide first insights into how NADHX accumulation affects cellular functions and pave the way for a better understanding of the mechanism(s) underlying the rapid and severe neurodegeneration leading to early death in NADHX repair deficient children.

biochemistry↗

bioRxiv2018

Metabolomics and proteomics analyses of grain yield reduction in rice under abrupt drought-flood alternation

HighlightAbrupt drought-flood alteration is a frequent meteorological disaster that occurs during summer in southern China and the Yangtze river basin, which often causes a large area reduction of rice yield. We previously reported abrupt drought-flood alteration effects on yield and its components, physiological characteristics, matter accumulation and translocation, rice quality of rice. However, the molecular mechanism of rice yield reduction caused by abrupt drought-flood alternation has not been reported.\n\nIn this study, four treatments were provided, no drought and no floods (control), drought without floods (duration of drought 10 d), no drought with floods (duration of floods 8 d), and abrupt drought-flood alteration (duration of drought 10 d and floods 8 d). The quantitative analysis of spike metabolites was proceeded by LC-MS (liquid chromatograph-mass spectrometry) firstly. Then the Heat-map, PCA, PLS-DA, OPLS-DA and response ranking test of OPLS-DA model methods were used to analysis the function of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alteration. In addition, relative quantitative analysis of spike total proteins under the treatment was conducted iTRAQ (isobaric tags for relative and absolute quantification) and LC-MS. In this study, 5708 proteins were identified and 4803 proteins were quantified. The identification and analysis of DEPs function suggested that abrupt drought-flood alteration treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process, etc, during panicle differentiation stage. In this study relative quantitative proteomics, metabolomics and physiology data (soluble protein content, superoxide dismutase activity, hydrogen peroxidase activity, peroxidase activity, malondialdehyde content, free proline content, soluble sugar content and net photosynthetic rate) analysis were applied to explicit the response mechanism of rice panicle differentiation stage under abrupt drought-flood alteration and provides a theoretical basis for the disaster prevention and mitigation.\n\nAbstractAbrupt drought-flood alternation is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, a quantitative analysis of spike metabolites was conducted via liquid chromatograph-mass spectrometry (LC-MS), and Heat-map, PCA, PLS-DA, OPLS-DA, and a response ranking test of OPLS-DA model methods were used to analyze functions of differential metabolites (DMs) during the rice panicle differentiation stage under abrupt drought-flood alternation. The results showed that 102 DMs were identified from the rice spike between T1 (abrupt drought-flood alternation) and CK0 (control) treatment, 104 DMs were identified between T1 and CK1 (drought) treatment and 116 DMs were identified between T1 and CK2 (flood) treatment. In addition, a relative quantitative analysis of spike total proteins was conducted using isobaric tags for relative and absolute quantification (iTRAQ) and LC-MS. The identification and analysis of DEPs functions indicates that abrupt drought-flood alternation treatment can promote carbohydrate metabolic, stress response, oxidation-reduction, defense response, and energy reserve metabolic process during the panicle differentiation stage. In this study, relative quantitative metabolomics and proteomics analyses were applied to explore the response mechanism of rice panicle differentiation in response to abrupt drought-flood alternation.\n\nAbbreviations

plant biology↗

bioRxiv2018

YAP1 Oncogene is a Context-specific Driver for Pancreatic Ductal Adenocarcinoma

AbstractTranscriptomic profiling classifies pancreatic ductal adenocarcinoma (PDAC) into several molecular subtypes with distinctive histological and clinical characteristics. However, little is known about the molecular mechanisms that define each subtype and their correlation with clinical outcome. Mutant KRAS is the most prominent driver in PDAC, present in over 90% of tumors, but the dependence of tumors on oncogenic KRAS signaling varies between subtypes. In particular, squamous subtype are relatively independent of oncogenic KRAS signaling and typically display much more aggressive clinical behavior versus progenitor subtype. Here, we identified that YAP1 activation is enriched in the squamous subtype and associated with poor prognosis. Activation of YAP1 in progenitor subtype cancer cells profoundly enhanced malignant phenotypes and transformed progenitor subtype cells into squamous subtype. Conversely, depletion of YAP1 specifically suppressed tumorigenicity of squamous subtype PDAC cells. Mechanistically, we uncovered a significant positive correlation between WNT5A expression and the YAP1 activity in human PDAC, and demonstrated that WNT5A overexpression led to YAP1 activation and recapitulated YAP1-dependent but Kras-independent phenotype of tumor progression and maintenance. Thus, our study identifies YAP1 oncogene as a major driver of squamous subtype PDAC and uncovers the role of WNT5A in driving PDAC malignancy through activation of the YAP pathway.

cancer biology↗

bioRxiv2017

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

RNA sequencing (RNA-seq) is a sensitive and accurate method for quantifying gene expression. Small samples or those whose RNA is degraded, such as formalin-fixed, paraffin-embedded (FFPE) tissue, remain challenging to study with nonspecialized RNA-seq protocols. Here we present a new method, Smart-3SEQ, that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. We also obtain distinct biological profiles from FFPE single cells, which have been impossible to study with previous RNA-seq protocols, and we use these data to identify possible new macrophage phenotypes associated with the tumor microenvironment. We propose Smart-3SEQ as a highly cost-effective method to enable large gene-expression profiling experiments unconstrained by sample size and tissue availability. In particular, Smart-3SEQs compatibility with FFPE tissue unlocks an enormous number of archived clinical samples, and combined with LCM it allows unprecedented studies of small cell populations and single cells isolated by their in situ context.

genomics↗

bioRxiv2017

Insm1a regulates motor neuron development in zebrafish

Insulinoma-associated1a (Insm1a) is a zinc-finger transcription factor playing a series of functions in cell formation and differentiation of vertebrate central and peripheral nervous systems and neuroendocrine system. However, its roles on the development of motor neuron have still remained uncovered. Here, we provided evidences that insmla was a vital regulator of motor neuron development and provide a mechanistic understanding of how it contributes to this process. Firstly, we showed the localization of insmla in spinal cord and primary motor neurons (PMNs) of zebrafish embryos by in situ hybridization and imaging analysis of transgenic reporter line Tg(insmla: mCherry) ntu805. Then we demonstrated that the deficiency of insmla in zebrafish larvae lead to the defects of PMNs development, including the reduction of caudal primary motor neurons (CaP) and middle primary motor neurons (MiP), the excessive branching of motor axons, and the disorganized distance between adjacent CaPs. Additionally, knockout of insm1 impaired motor neuron differentiation in the spinal cord. Locomotion analysis showed that insmla-null zebrafish significantly reduced the swimming activity. Furthermore, we proved that the insmla loss of function significantly decreased the transcripts levels of both olig2 and nkx6.1. Microinjection of olig2 and nkx6.1 mRNA rescued the motor neuron defects in insmla deficient embryos. Taken together, these data indicate that insmla regulates the motor neuron development, at least in part, through modulation of the expressions of olig2 and nkx6.1.

developmental biology↗

bioRxiv2017

Gene fusion between CDKN1A and RAB44 caused by exon skipping like mechanism due to disruption of a splice site

Splicing contributes to gene regulation and protein diversity, while abnormal splicing underlies both hereditary diseases and cancers. Various mutations that disrupt splicing factors, exonic or intronic splicing enhancers or silencers, as well as splice sites, could be responsible for abnormal splicing. Characterization of abnormal splicing events is not only helpful for understanding the molecular processes linking mutations to disease phenotypes, but also provides promising targets for targeted therapies. In addition, CRISPR/Cas9 editing could be benefited once more attention is given to potential abnormal splicing outcomes other than off-target effects at the DNA level. Although large-scale multiplexed genome editing has been demonstrated in yeast, and has also been attempted for particular exons or genes in other eukaryotic cells to achieve saturation, in practice it is much more difficult to measure splicing consequences with genome-wide saturation editing in human cells. Instead, massive somatic mutations accumulated in cancer cohorts provide invaluable opportunities to study somatic mutation-associated splicing events. Abnormal splicing is not necessarily limited to single genes. Transcript fusion is a special form of abnormal splicing that connects two or more genes due to splicing on a transcriptional level (rather than chromosomal translocations such as BCR-ABL in chronic myeloid leukemia). It could arise from conventional splicing on read-through transcripts when the two genes are next to each other and on the same strand, or from trans-splicing when two genes are on different chromosomes, strands or far away - a few cases had been reported. However, it was found that these fusions not only occurred in tumors but also in normal tissues; there was limited investigation regarding how the fusion could happen, whether it be due to mutations or not, and what the downstream perturbations were. Here, in an effort to characterize somatic mutation-associated abnormal splicing (especially in its simplest form, exon skipping events), we identified over one hundred such events in various tumors, including those in MET, PTEN and TP53. Surprisingly, we detected a recurrent, but previously undescribed, tumor-specific transcript fusion event between the cyclin-dependent kinase inhibitor CDKN1A and the RAS oncogene family gene RAB44. By creating genome-edited cell lines, we demonstrate a causal relationship between splice-site mutations in CDKN1A and the fusion to the RAB44 transcript. We further provide evidence that the fusion arises from a readthrough transcript that escapes exosome-mediated degradation when the splice-site mutation occurred, and we show that the presence of the fusion transcript correlates with TP53 inactivation and CDK activation. The strong tissue specificity of RAB44 and the relatively high prevalence of this transcript fusion in multiple types of cancers warrants further study which could inform subclassifications of these cancers and the development of targeted therapies.

genetics↗