Browsing by Author "Li, Chao"

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    circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs
    (Oxford University Press, 2020-01-15) Chen, Li; Wang, Feng; Bruggeman, Emily C.; Li, Chao; Yao, Bing; Medicine, School of Medicine
    Motivation: Circular RNAs (circRNAs), a class of non-coding RNAs generated from non-canonical back-splicing events, have emerged to play key roles in many biological processes. Though numerous tools have been developed to detect circRNAs from rRNA-depleted RNA-seq data based on back-splicing junction-spanning reads, computational tools to identify critical genomic features regulating circRNA biogenesis are still lacking. In addition, rigorous statistical methods to perform differential expression (DE) analysis of circRNAs remain under-developed. Results: We present circMeta, a unified computational framework for circRNA analyses. circMeta has three primary functional modules: (i) a pipeline for comprehensive genomic feature annotation related to circRNA biogenesis, including length of introns flanking circularized exons, repetitive elements such as Alu elements and SINEs, competition score for forming circulation and RNA editing in back-splicing flanking introns; (ii) a two-stage DE approach of circRNAs based on circular junction reads to quantitatively compare circRNA levels and (iii) a Bayesian hierarchical model for DE analysis of circRNAs based on the ratio of circular reads to linear reads in back-splicing sites to study spatial and temporal regulation of circRNA production. Both proposed DE methods without and with considering host genes outperform existing methods by obtaining better control of false discovery rate and comparable statistical power. Moreover, the identified DE circRNAs by the proposed two-stage DE approach display potential biological functions in Gene Ontology and circRNA-miRNA-mRNA networks that are not able to be detected using existing mRNA DE methods. Furthermore, top DE circRNAs have been further validated by RT-qPCR using divergent primers spanning back-splicing junctions.
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    Correction to: Real-World Treatment Patterns in Patients with Vitiligo in the United States
    (Springer, 2023) Rosmarin, David; Soliman, Ahmed M.; Li, Chao; Dermatology, School of Medicine
    Correction to: Dermatol Ther (Heidelb) (2023) 13:2079–2091 10.1007/s13555-023-00983-3 Authors would like to update the middle name of co-author as Ahmed M. Soliman. The original article has been corrected.
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    The development and maintenance of paclitaxel-induced neuropathic pain require activation of the sphingosine 1-phosphate receptor subtype 1
    (ASBMB, 2014-07-25) Janes, Kali; Little, Joshua W.; Li, Chao; Bryant, Leesa; Chen, Collin; Chen, Zhoumou; Kamocki, Krzysztof; Doyle, Timothy; Snider, Ashley; Esposito, Emanuela; Cuzzocrea, Salvatore; Bieberich, Erhard; Obedi, Lina; Petrache, Irina; Nicol, Grant; Neumann, William L.; Salvemini, Daniela; Department of Pharmacology and Toxicology, IU School of Medicine
    The ceramide-sphingosine 1-phosphate (S1P) rheostat is important in regulating cell fate. Several chemotherapeutic agents, including paclitaxel (Taxol), involve pro-apoptotic ceramide in their anticancer effects. The ceramide-to-S1P pathway is also implicated in the development of pain, raising the intriguing possibility that these sphingolipids may contribute to chemotherapy- induced painful peripheral neuropathy, which can be a critical dose-limiting side effect of many widely used chemotherapeutic agents.We demonstrate that the development of paclitaxel-induced neuropathic pain was associated with ceramide and S1P formation in the spinal dorsal horn that corresponded with the engagement of S1P receptor subtype 1 (S1PR(1))- dependent neuroinflammatory processes as follows: activation of redox-sensitive transcription factors (NFκB) and MAPKs (ERK and p38) as well as enhanced formation of pro-inflammatory and neuroexcitatory cytokines (TNF-α and IL-1β). Intrathecal delivery of the S1PR1 antagonist W146 reduced these neuroinflammatory processes but increased IL-10 and IL-4, potent anti-inflammatory/ neuroprotective cytokines. Additionally, spinal W146 reversed established neuropathic pain. Noteworthy, systemic administration of the S1PR1 modulator FTY720 (Food and Drug Administration- approved for multiple sclerosis) attenuated the activation of these neuroinflammatory processes and abrogated neuropathic pain without altering anticancer properties of paclitaxel and with beneficial effects extended to oxaliplatin. Similar effects were observed with other structurally and chemically unrelated S1PR1 modulators (ponesimod and CYM-5442) and S1PR1 antagonists (NIBR-14/15) but not S1PR1 agonists (SEW2871). Our findings identify for the first time the S1P/S1PR1 axis as a promising molecular and therapeutic target in chemotherapy-induced painful peripheral neuropathy, establish a mechanistic insight into the biomolecular signaling pathways, and provide the rationale for the clinical evaluation of FTY720 in chronic pain patients.
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    Real-World Treatment Patterns in Patients with Vitiligo in the United States
    (Springer, 2023) Rosmarin, David; Soliman, Ahmed M.; Li, Chao; Dermatology, School of Medicine
    Introduction: Vitiligo is an autoimmune disorder resulting in skin depigmentation, with limited approved treatment options. This study evaluated medication utilization and treatment patterns among patients in the first year following vitiligo diagnosis. Methods: This retrospective analysis of claims data from the Merative® MarketScan Research Databases included patients aged ≥ 12 years newly diagnosed with vitiligo. Patients were identified between October 1, 2016, and April 30, 2021, and had ≥ 12 months of continuous enrollment pre- and post-vitiligo diagnosis. Medication use, treatment line of therapy, time to and number of medication claims, and length of therapy were reported in the 12 months post-vitiligo diagnosis. Results are reported separately for treatment initiators post-vitiligo diagnosis, patients with moderate-to-severe vitiligo, and adolescents (aged 12-17 years). Results: A total of 19,335 patients were included in the analysis, with half (N = 9648, 49.9%) not receiving any treatment during the 12-month follow-up. Switching was minimal among treatment initiators (N = 5845) in the 12 months post-vitiligo diagnosis, with the most frequent first-line treatments being high-potency topical corticosteroids (25.4%), oral corticosteroids (23.1%), and topical calcineurin inhibitors (TCI, 14.7%). Adolescents initiating treatment (N = 486) most frequently received TCI (30.9%) as first-line therapy. Patients with moderate-to-severe vitiligo (N = 3462) were very likely to receive treatment during follow-up, with only 1.5% not receiving treatment. Among patients with no vitiligo treatment prior to diagnosis, time to first medication claim ranged from 51.9 days (standard deviation [SD], 84.0) for TCI to 178.6 days (SD 116.0) for systemic immunosuppressants; mean total days supplied ranged from 14.4 days (SD 27.1) for oral corticosteroids to 121.0 (SD 114.0) for immunosuppressants. Conclusion: In this real-world study, a high proportion of patients did not receive any treatment. Among those receiving treatment, most were unlikely to switch or use a combination of treatments within the first year of vitiligo diagnosis.
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    Sphingosine 1-phosphate enhances excitability of sensory neurons through sphingosine 1-phosphate receptors 1 and/or 3
    (2014) Li, Chao; Vasko, Michael R.; Cummins, Theodore R.; Hudmon, Andrew; Nicol, Grant D.; Quilliam, Lawrence A.
    Sphingosine 1-phosphate (S1P) is a bioactive sphingolipid that has proven to be an important signaling molecule both as an extracellular primary messenger and as an intracellular second messenger. Extracellular S1P acts through a family of five S1P receptors, S1PR1-5, all of which are G protein-coupled receptors associated with different G proteins. Previous work from our laboratory shows that externally applied S1P increases the excitability of small-diameter sensory neurons by enhancing the action potential firing. The increased neuronal excitability is mediated primarily, but not exclusively, through S1PR1. This raises the question as to which other S1PRs mediate the enhanced excitability in sensory neurons. To address this question, the expression of different S1PR subtypes in small-diameter sensory neurons was examined by single-cell quantitative PCR. The results show that sensory neurons express the mRNAs for all five S1PRs, with S1PR1 mRNA level significantly greater than the other subtypes. To investigate the functional contribution of other S1PRs in augmenting excitability, sensory neurons were treated with a pool of three individual siRNAs targeted to S1PR1, R2 and R3. This treatment prevented S1P from augmenting excitability, indicating that S1PR1, R2 and/or R3 are essential in mediating S1P-induced sensitization. To study the role of S1PR2 in S1P-induced sensitization, JTE-013, a selective antagonist at S1PR2, was used. Surprisingly, JTE-013 by itself enhanced neuronal excitability. Alternatively, sensory neurons were pretreated with FTY720, which is an agonist at S1PR1/R3/R4/R5 and presumably downregulates these receptors. FTY720 pretreatment prevented S1P from increasing neuronal excitability, suggesting that S1PR2 does not mediate the S1P-induced sensitization. To test the hypothesis that S1PR1 and R3 mediate S1P-induced sensitization, sensory neurons were pretreated with specific antagonists for S1PR1 and R3, or with siRNAs targeted to S1PR1 and R3. Both treatments blocked the capacity of S1P to enhance neuronal excitability. Therefore my results demonstrate that the enhanced excitability produced by S1P is mediated by S1PR1 and/or S1PR3. Additionally, my results indicate that S1P/S1PR1 elevates neuronal excitability through the activation of mitogen-activated protein kinase kinase. The data from antagonism at S1PR1 to regulate neuronal excitability provides insight into the importance of S1P/S1PR1 axis in modulating pain signal transduction.
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    Sphingosine 1-phosphate enhances the excitability of rat sensory neurons through activation of sphingosine 1-phosphate receptors 1 and/or 3
    (Springer (Biomed Central Ltd.), 2015) Li, Chao; Li, Jun-nan; Kays, Joanne; Guerrero, Miguel; Nicol, Grant D.; Department of Pharmacology and Toxicology, IU School of Medicine
    BACKGROUND: Sphingosine-1-phosphate (S1P) is a bioactive sphingolipid that acts through a family of five G-protein-coupled receptors (S1PR1-5) and plays a key role in regulating the inflammatory response. Our previous studies demonstrated that rat sensory neurons express the mRNAs for all five S1PRs and that S1P increases neuronal excitability primarily, but not exclusively, through S1PR1. This raises the question as to which other S1PRs mediate the enhanced excitability. METHODS: Isolated sensory neurons were treated with either short-interfering RNAs (siRNAs) or a variety of pharmacological agents targeted to S1PR1/R2/R3 to determine the role(s) of these receptors in regulating neuronal excitability. The excitability of isolated sensory neurons was assessed by using whole-cell patch-clamp recording to measure the capacity of these cells to fire action potentials (APs). RESULTS: After siRNA treatment, exposure to S1P failed to augment the excitability. Pooled siRNA targeted to S1PR1 and R3 also blocked the enhanced excitability produced by S1P. Consistent with the siRNA results, pretreatment with W146 and CAY10444, selective antagonists for S1PR1 and S1PR3, respectively, prevented the S1P-induced increase in neuronal excitability. Similarly, S1P failed to augment excitability after pretreatment with either VPC 23019, which is a S1PR1 and R3 antagonist, or VPC 44116, the phosphonate analog of VPC 23019. Acute exposure (10 to 15 min) to either of the well-established functional antagonists, FTY720 or CYM-5442, produced a significant increase in the excitability. Moreover, after a 1-h pretreatment with FTY720 (an agonist for S1PR1/R3/R4/R5), neither SEW2871 (S1PR1 selective agonist) nor S1P augmented the excitability. However, after pretreatment with CYM-5442 (selective for S1PR1), SEW2871 was ineffective, but S1P increased the excitability of some, but not all, sensory neurons. CONCLUSIONS: These results demonstrate that the enhanced excitability produced by S1P is mediated by activation of S1PR1 and/or S1PR3.