Selected Publications

• Hsu KW, Liu SH, Lai YL, Chen FH, Lin LJ, Peng PH, Li CY, Wang SC, Chen JL, Wu HH, Wu MZ, Sher YP, Cheng WC* . Using bioinformatics approaches to identify survival-related oncomiRs as potential miRNA-based treatments for lung adenocarcinoma. Computational and Structural Biotechnology Journal (under review)
• Chao YC, Chang HC, Jiang JK, Yang CY, Chen FH, Lai YL, Lin WJ, Li CY, Wang SC, Yang MH, Lin YF*, Cheng WC* . Using bioinformatics approaches to investigate driver genes and identify BCL7A as a prognostic gene in colorectal cancer. Computational and Structural Biotechnology Journal (revision)
• Lin WJ, Chen PC, Liu HC, Cho YC, Hsu MK, Lin IC, Chen FH, Yang JC, Ma WL, Cheng WC* . LipidSig: a web-based tool for lipidomic data analysis. Nucleic Acids Res . 2021 (accepted)
• Liu SH, Hsu KW, Lai YL, Lin YF, Chen FH, Peng PH, Lin LJ, Wu HH, Li Chia Yang, Wang SC, Wu MZ, Sher YP*, Cheng WC* . Systematic identification of clinically relevant miRNAs for potential miRNA-based therapy in lung adenocarcinoma. Molecular Therapy-Nucleic Acids . 2021 (accepted)
• Laio TS☨, Cheng WC , Yang CY, Chen YQ, Su SH, Yeh TY, Lan HY, Lee CC, Lin HH, Lin CC, Lu RH, Chiou ET, Jing JK, Hwang WL. The microRNA-210-Stathmin1 Axis Decreases Cell Stiffness to Facilitate the Invasiveness of Colorectal Cancer Stem Cells. Cancers 2021, 13(8), 1833
• Cheng WC , Chang CY, Lo CC, Hsieh CY, Kuo TT, Tseng GC, Wong SC, Chiang SF, Huang KC, Lai LC, Lu TP, Chao KSC, Sher YP. Identification of theranostic factors for patients developing metastasis after surgery for early-stage lung adenocarcinoma. Theranostics . 2021 Jan 26;11(8):3661-3675
• Liu SH, Shen PC, Chen CY, Hsu AN, Cho YC, Lai YL, Chen FH, Li CY, Wang SC, Chen M, Chung IF, Cheng WC* . DriverDBv3: a multi-omics database for cancer driver gene research. Nucleic Acids Res . 2020 Jan 8;48(D1):D863-D870.
• Cheng WC , Liao TT, Lin CC, Yuan LE, Lan HY, Lin HH, Teng HW, Chang HC, Lin CH, Yang CY, Huang SC, Jiang JK, Yang SH, Yang MH*, Hwang WL*. RAB27B-activated secretion of stem-like tumor exosomes delivers the biomarker microRNA-146a-5p, which promotes tumorigenesis and associates with an immunosuppressive tumor microenvironment in colorectal cancer. Int J Cancer . 2019 Oct; 145(8):2209-2224
• Gong L, Wong CH, Cheng WC , Tjong H, Menghi F, Ngan CY, Liu ET, Wei CL. Picky comprehensively detects high-resolution structural variants in nanopore long reads. Nat Methods 2018 Jun;15(6):455-460
• Wu MZ, Cheng WC , Chen SF, Nieh S, Connor CO, Liu CL, Tsai WW, Wu CJ, Martin L, Lin YS, Wu KJ, Lu LF, and Belmonte JC. miR25/93 mediates hypoxia-induced immunosuppression by repressing cGAS. Nat Cell Biol . 2017 Oct;19(10):1286-1296.
• Chung IF, Chang SH, Chen CY, Liu SH, Li CY, Chan CH, Shih CC, and Cheng WC* . YM500v3: a database for small RNA sequencing in human cancer research Nucleic Acids Res . 2017 Jan; 45(D1):D925-D931.
• Chung IF, Chen CY, Su SC, Li CY, Wu KJ, Wang HW*, Cheng WC* . DriverDBv2: a database for human cancer driver gene research. Nucleic Acids Res . 2016 Jan;44(D1):D975-9.
• Cheng WC , Chung IF, Tsai CF, Huang TS, Cheng CY, Wang SC, Chang TY, Sun HJ, Chao YC, Cheng CC, Wu CW and Wang HW. YM500v2: A small RNA sequencing (smRNA-seq) database for human cancer miRNome research. Nucleic Acids Res ., 2015 JAN:43(D1):D862-867 (SCI, IF: 11.561; 10/292 (3.4%) in BIOCHEMISTRY & MOLECULAR BIOLOGY)
• Cheng WC , Chung IF,Chen CY, Sun HJ, Fen JJ, Teng WC, Chang TY, Wong TT*, Wang HW*. DriverDB: A exome sequencing (exome-seq) database for cancer driver gene identification. Nucleic Acids Res , 2014, JAN:42(D1):D1048-1054
• Cheng WC , Chung IF, Huang TS, Chang ST, Sun HJ, Wong TT*, Wang HW*. YM500: A small RNA Sequencing (smRNA-Seq) database for miRNA research. Nucleic Acids Res , 2013, JAN:41(D1): D285-D294.

Other Publications

2021
1. Su CC, Wang SC, Chen IC, Chiu FY, Liu PL, Huang CH, Huang KH, Fang SH, Cheng WC , Huang SP, Yeh HC, Liu CC, Lee PY, Huang MY, Li CY. Zerumbone suppresses the LPS-induced inflammatory response and represses activation of the NLRP3 inflammasome in macrophages. Front. Pharmacol . 2021 May ;12, 1008.
2. Lin YA, Chu PY, Ma WL, Cheng WC , Chan ST, Yang JC, Wu YC. Enzyme-Digested Peptides Derived from Lates calcarifer Enhance Wound Healing after Surgical Incision in a Murine Model. Mar Drugs . 2021 Mar 16;19(3):154.
3. Liu WL, Li CY, Cheng WC , Chang CY, Chen YH, Lu CY, Wang SC, Liu YR, Cheng MH, Chong IW, Liu PL.High Mobility Group Box 1 Promotes Lung Cancer Cell Migration and Motility via Regulation of Dynamin-Related Protein 1. Int J Mol Sci . 2021 Mar 31;22(7):3628.
2020
4. Qi Y, Lai YL, Shen PC, Chen FH, Lin LJ, Wu HH, Peng PH, Hsu KW, Cheng WC *. Identification and validation of a miRNA-based prognostic signature for cervical cancer through an integrated bioinformatics approach. Sci Rep . 2020 Dec; 10(1):22270
5. Tsai LH, Hsu KW, Chiang CM, Yang HJ, Liu YH, Yang SF, Peng PH, Cheng WC , Wu HH. Cite Share Targeting interleukin-17 receptor B enhances gemcitabine sensitivity through downregulation of mucins in pancreatic cancer. Sci Rep . 2020 Oct 20;10(1):17817.
6. Lin CC, Huang YK, Cho CF, Lin YS, Lo CC, Kuo TT, Tseng GC, Cheng WC , Chang WC, Hsiao TH, Lai LC, Shih JY, Liu YH, Chao KSC, Hsu JL, Lee PC, Sun X, Hung MC, Sher YP. Targeting positive feedback between BASP1 and EGFR as a therapeutic strategy for lung cancer progression. Theranostics . 2020 Aug 29;10(24):10925-10939.
7. Chen L☨, Ma WL☨, Cheng WC☨ , Yang JC, Wang HC, Su YT, Ahmad A, Hung YC, Chang WC. Targeting lipid droplet lysophosphatidylcholine for cisplatin chemotherapy. J Cell Mol Med . 2020 Jun 16;24(13):7187-7200
8. Ke CC, Chen LC, Yu CC, Cheng WC , Huang CY, Lin VC, Lu TL, Huang SP, Bao BY. Genetic Analysis Reveals a Significant Contribution of CES1 to Prostate Cancer Progression in Taiwanese Men. Cancers (Basel) . 2020 May 25;12(5):1346.
9. Chang WC, Wang HC, Cheng WC , Yang JC, Chung WM, Ho YP, Chen L, Hung YC, Ma WL*. LDLR-mediated lipidome-transcriptome reprogramming in cisplatin insensitivity. Endocr Relat Cancer . 2020 Feb;27(2):81-95.
2019
10. Yang JC, Chang N, Wu DC, Cheng WC , Chung WM, Chang WC, Lei FJ, Liu CJ, Wu IC, Lai HC, Ma WL*. Preclinical evaluation of exemestane as a novel chemotherapy for gastric cancer. J Cell Mol Med . 2019 Nov;23(11):7417-7426.
11. Liu LC, Wang YL, Lin PL, Zhang X, Cheng WC , Liu SH, Chen CJ, Hung Y, Jan CI, Chang LC, Qi X, Hsieh-Wilson LC, Wang SC*. Long non-coding RNA HOTAIR promotes invasion of breast cancer cells through chondroitin sulfotransferase CHST15. Int J Cancer . 2019 Nov 1;145(9):2478-2487.
12. Yu CC, Chen LC, Lin VC, Huang CY, Cheng WC , Hsieh AR, Chang TY, Lu TL, Lee CH, Huang SP, Bao BY. Effect of genetic variants in cell adhesion pathways on the biochemical recurrence in prostate cancer patients with radical prostatectomy. Cancer Med . 2019 Jun;8(6):2777-2783.
13. Hung YL, Wang SC, Suzuki K, Fang SH, Chen CS, Cheng WC , Su CC, Yeh HC, Tu HP, Liu PL, Huang MY, Li CY. Bavachin attenuates LPS-induced inflammatory response and inhibits the activation of NLRP3 inflammasome in macrophages. Phytomedicine . 2019 Jun;59:152785.
14. Kao SH, Cheng WC , Wang YT, Wu HT, Yeh HY, Chen YJ, Tsai MH, Wu KJ*. Regulation of miRNA biogenesis and histone modification by K63-polyubiquitinated DDX17 controls cancer stem-like features. Cancer Res . 2019 May 15;79(10):2549-2563.
15. Han Y, Yang J, Qian X, Cheng WC , Liu SH, Hua X, Zhou L, Yang Y, Wu Q, Liu P, Lu Y*. DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies. Nucleic Acids Res . 2019 May 7;47(8):e45.
16. Su CC, Hsieh KL, Liu PL, Yeh HC, Huang SP, Fang SH, Cheng WC , Huang KH, Chiu FY, Lin IL, Huang MY, Li CY*. AICAR Induces Apoptosis and Inhibits Migration and Invasion in Prostate Cancer Cells Through an AMPK/mTOR-Dependent Pathway. Int J Mol Sci . 2019 Apr 3;20(7).
17. Hsu RH, Hwu WL, Chen M, Chung IF, Peng SS, Chen CY, Cheng WC , Chien YH, Lee NC*. Next-generation sequencing identifies TRPV4-related skeletal dysplasia in a boy with progressive bowlegs. Pediatr Neonatol . 2019 Feb;60(1):102-104.
18. Hwang WL, Lan HY, Cheng WC , Huang SC, Yang MH*. Tumor stem-like cell-derived exosomal RNAs prime neutrophils for facilitating tumorigenesis of colon cancer. J Hematol Oncol . 2019 Jan;12(1):10.
2018
19. Huang CY, Hsueh YM, Chen LC, Cheng WC , Yu CC, Chen WJ, Lu TL, Lan KJ, Lee CH, Huang SP, Bao BY*. Clinical significance of glutamate metabotropic receptors in renal cell carcinoma risk and survival. Cancer Med . 2018 Dec;7(12):6104-6111.
20. Hung YL, Wang SC, Suzuki K, Fang SH, Chen CS, Cheng WC , Su CC, Yeh HC, Tu HP, Liu PL, Huang MY, Li CY. Bavachin attenuates LPS-induced inflammatory response and inhibits the activation of NLRP3 inflammasome in macrophages. Phytomedicine . 2018 Dec 10;59:152785
21. Huang MY, Tu CE, Wang SC, Hung YL, Su CC, Fang SH, Chen CS, Liu PL, Cheng WC , Huang YW, Li CY*. Corylin inhibits LPS-induced inflammatory response and attenuates the activation of NLRP3 inflammasome in microglia. BMC Complement Altern Med . 2018 Aug;18(1):221.
22. Shih JC, Ma GC, Cheng WC , Chen CY, Wu WJ, Chen M. SMAD2 as a risk locus for human left atrial isomerism detected by mother-fetus-pair exome sequencing and image studies including fetal ultrasound. Ultrasound Obstet Gynecol . 2019 May;53(5):702-705
23. Kao TL, Kuan YP, Cheng WC , Chang WC, Jeng LB, Yeh S, Ma WL. Estrogen receptors orchestrate cell growth and differentiation to facilitate liver regeneration. Theranostics . 2018 Apr 9;8(10):2672-2682.
24. Chang WC, Cheng WC , Cheng BH, Chen L, Ju LJ, Ou YJ, Jeng LB, Yang MD, Hung YC, Ma WL. Mitochondrial Acetyl-CoA Synthetase 3 is Biosignature of Gastric Cancer Progression. Cancer Med . 2018 Mar ; 7(4):1240-1252
25. Lin KH, Huang MY, Cheng WC , Wang SC, Fang SH, Tu HP, Su CC, Hung YL, Liu PL, Chen CS, Wang YT, Li CY. RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment. Sci Rep . 2018 Feb 8;8(1):2672.
2017
26. Fan CC, Cheng WC , Huang YC, Sher YP, Liou NJ, Chien YC, Lin PS, Lin PS, Chen CH, Chang WC. EFHD2 promotes epithelial-to-mesenchymal transition and correlates with postsurgical recurrence of stage I lung adenocarcinoma. Sci Rep . 2017 Nov 6;7(1):14617.
27. Chen L, Bao BY, Chang WC, Ho JY, Cheng BH, Wang CL, Tang Q, Cheng WC , Chang HW, Hung YC, Ma WL. Short androgen receptor poly-glutamine-promoted endometrial cancer is associated with benzo[a]pyrene-mediated aryl hydrocarbon receptor activation. J Cell Mol Med . 2017 Aug; 22(1):46-56
28. Chiu KL, Lin YS, Kuo TT, Lo CC, Huang YK, Chang HF, Chuang EY, Lin CC, Cheng WC , Liu YN, Lai LC, and Sher YP. ADAM9 Enhances CDCP1 by Inhibiting miR-1 through EGFR Signaling Activation in Lung Cancer Metastasis. Oncotarget . 2017 May;8(29):47365-47378
29. Hung YL, Fang SH, Wang SC, Cheng WC , Su CC, Chen CS, Huang MY, Hua KF, Shen KH, Wang YT, Suzuki K*, and Li CY*. Corylin protects LPS-induced sepsis and attenuates LPS-induced inflammatory response. Sci Rep . 2017 Apr; 7:46299
2016
30. Wu HT, Kuo YC, Hung JJ, Huang CH, Chen WY, Chou TY, Chen Y, Chen YJ, Chen YJ, Cheng WC , Teng SC, Wu KJ. K63-polyubiquitinated HAUSP deubiquitinates HIF-1α and dictates H3K56 acetylation promoting hypoxia-induced tumour progression. Nat Commun . 2016 Dec; 7:13644.
31. Chang WC, Huang SF, Lee YM, Lai HC, Cheng BH, Cheng WC , Ho YP, Jeng LB, Ma WL*. Cholesterol import and steroidogenesis are biosignatures for gastric cancer patient survival. Oncotarget 2016 Nov; 9:692-704
32. Lai HC, Yeh CC, Jeng LB, Huang SF, Liao PY, Lei FJ, Cheng WC , Hsu CL, Cai X, Chang C*, Ma WL*. Androgen receptor mitigates postoperative disease progression of hepatocellular carcinoma by suppressing CD90+ populations and cell migration and by promoting anoikis in circulating tumor cells. Oncotarget 2016 Jun;
Before 2016
33. Wang HW, Sun HJ, Chang TY, Lo HH, Cheng WC , Tseng GC, Lin CT, Chang SJ, Pal N, and Chung IF. Discovering monotonic stemness marker genes from time-series stem cell microarray data. BMC Genomics , 2015 JAN:16 Suppl 2:S2
34. Tsai YP, Chen HF, Chen SY, Cheng WC , Wang HW, Shen ZJ, Song C, Teng SC, He C, Wu KJ. TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator. Genome Biol . 2014 DEC:15(12):513.
35. Huang HN, Chen SY, Hwang SM, Yu CC, Su MW, Mai W, Wang HW, Cheng WC , Schuyler SC, Ma N, Lu FL, Lu J. miR-200c and GATA binding protein 4 regulate human embryonic stem cell renewal and differentiation. Stem cell research . 2014 MAR:12(2):338-353
36. Chen KH, Wang KJ, Tsai ML, Wang KM, Adrian AM, Cheng WC , Yang TS, Teng NC, Tan KP, Chang KS. Gene selection for cancer identification: a decision tree model empowered by particle swarm optimization algorithm. BMC Bioinformatics . 2014, FEB:15(1):49.
37. Li CY, Chiang CS, Cheng WC , Chen CR, Shu WY, Tsai ML, Huang CL, Chang HZ, Hseu RS, Chang CW, Fang SH, Hsu IC. Gene expression profiling of dendritic cells in different physiological stages under Cordyceps sinensis treatment. PLoS One 2012, JUL:7(7): e40824.
38. Cheng WC , Shu WY, Li CY, Tsai ML, Chang CW, Chen CR, Wang TH, Hsu IC. Inter- and intra-individual variance of gene expression in clinical studies. PLoS One 2012, JUN:7(6):e38650.
39. Chen CR, Shu WY, Tsai ML, Cheng WC , Hsu IC. THEME: a web tool for loop-design microarray data analysis. Computers in Biology and Medicine , 2012, FEB:42(2): 228-234.
40. Chang CW, Cheng WC , Chen CR, Shu WY, Tsai ML, Huang CL, Hsu IC. Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis. PLoS One 2011, JUL:6(7): e22859.
41. Cheng WC , Chang CW, Chen CR, Tsai ML, Shu WY, Li CY, Hsu IC. Identification of Reference Genes across Physiological States for qRT-PCR through Microarray. PLoS One 2011, FEB:6(2): e17347.
42. Li CY, Chao LP, Wang SC, Tsai ML, Chang HZ, Fang SH, Liao PC, Ho CL, Chen ST, Cheng WC , Chiang CS, Hua KF, Hsu IC. Honokiol Inhibits LPS-induced Maturation and Inflammatory Response on Human Monocyte-derived Dendritic Cells. Journal of Cellular Physiology . 2010, SEP:226(9): 2338-2349.
43. Cheng WC , Tsai ML, Chang CW, Huang CL, Chen CR, Shu WY, Lee YS, Wang TH, Hong JH, Li CY, Hsu IC. Microarray Meta-analysis Database (M2DB): A Uniformly Pre-processed, Quality Controlled, and Manually Curated Human Clinical Microarray Database. BMC Bioinformatics . 2010, AUG:10;11(1):421.

YM500

The YM500 database contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. The YM500v3 database http://ngs.ym.edu.tw/ym500/ is the updated version of YM500, which not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). As the growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis, we incorporate >10,000 cancer-related RNA-seq and > 3,000 more smRNA-seq data sets into the YM500v3 database. The YM500v3 database contains two main new sections, 'Survival' and 'Cancer'. The 'Survival' section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The 'Cancer' section provides the results of differential expression analyses, miRNA-gene interactions, and cancer miRNA-related pathways. Furthermore, in the 'Expression' section, sncRNA expression profiles across cancer and sample types are newly provided since cancer-related sncRNAs hold the potential for both biotech applications and basic research.

Reference

1. Chung IF, Chang SH, Chen CY, Liu SH, Li CY, Chan CH, Shih CC, and Cheng WC* . YM500v3: a database for small RNA sequencing in human cancer research Nucleic Acids Res . 2017 Jan; 45(D1):D925-D931.
2. Cheng WC , Chung IF, Tsai CF, Huang TS, Cheng CY, Wang SC, Chang TY, Sun HJ, Chao YC, Cheng CC, Wu CW and Wang HW. YM500v2: A small RNA sequencing (smRNA-seq) database for human cancer miRNome research. Nucleic Acids Res ., 2015 JAN:43(D1):D862-867 (SCI, IF: 11.561; 10/292 (3.4%) in BIOCHEMISTRY & MOLECULAR BIOLOGY)
3. Cheng WC , Chung IF, Huang TS, Chang ST, Sun HJ, Wong TT*, Wang HW*. YM500: A small RNA Sequencing (smRNA-Seq) database for miRNA research. Nucleic Acids Res , JAN:41(D1): D285-D294.

LipidSig

With the continuous rising of lipidomic studies, it is crucial to have a useful and comprehensive tool for facilitating lipidomic data analysis. The most important feature that makes lipids different from general metabolites are the various characteristics, including lipid classes, double bonds, chain lengths, etc. Lipid species can be classified into different categories based on these characteristics, and more interestingly, they can exert specific biological functions in a group. To simplify lipidomic analysis workflows and enhance the exploration of lipid characteristics, we have developed a highly flexible and user-friendly webserver, LipidSig. It consists of five sections, namely, profiling, differential expression, correlation, network, and machine learning, to evaluate lipid effects on cellular or disease phenotypes. One of the specialties of LipidSig is the conversion between lipid species and characteristics according to a user-defined characteristics table. This function can mine data of both individual lipids and subgroups of characteristics efficiently. Furthermore, we provide analyses focusing on fatty acid properties and multiple characteristics to expand the practical utility of the server.

LipidSig is expected to help users identify significant lipid-related features and to advance the field of lipid biology. The LipidSig webserver is freely available at http://chenglab.cmu.edu.tw/lipidsig .

Reference

1. Lin WJ, Chen PC, Liu HC, Cho YC, Hsu MK, Lin IC, Chen FH, Yang JC, Ma WL, Cheng WC* . LipidSig: a web-based tool for lipidomic data analysis. Nucleic Acids Res . 2021 (accepted)

SurvOmics

Integrating multi-omics analysis is required while identifying prognostic biomarkers and the root causes of cancer; therefore, we have presented a new database, SurvOmics http://survomics.bioinfomics.org/ to fulfill the need for cancer research.

The main specialties of SurvomicsDB are as below. First, the prognostic values of multi-omics levels, including somatic mutation, RNA expression, DNA methylation, and copy number variation, are provided respectively from two points of view, ‘Gene’ and ‘Cancer’ sections. The comprehensive yet sophisticated information is interpreted by clear and concise visualization. Second, to enhance the value of biomarkers in clinical applications, the results of multivariate Cox regression with clinical variables on survival analysis are provided. Third, the synergistic effect of different molecular levels is provided to investigate whether co-alternation events of multiple-omics layers may ultimately lead to the worst survival outcomes, compared to single-target only. Fourth, besides traditional cox model analysis, two extra algorithms, cure model and machine learning, are used in this database. The cure model algorithm identifies the prognostic biomarkers for long-term survival while the machine learning algorithms identify biomarkers in the high-dimensional omics dataset.

Reference

1. Liu SH, Shen PC, Chen CY, Hsu AN, Cho YC, Lai YL, Chen FH, Li CY, Wang SC, Chen M, Chung IF, Cheng WC* . DriverDBv3: a multi-omics database for cancer driver gene research. Nucleic Acids Res . 2020 Jan 8;48(D1):D863-D870.
2. Chung IF, Chen CY, Su SC, Li CY, Wu KJ, Wang HW*, Cheng WC* . DriverDBv2: a database for human cancer driver gene research. Nucleic Acids Res . 2016 Jan;44(D1):D975-9.
3. Cheng WC , Chung IF,Chen CY, Sun HJ, Fen JJ, Teng WC, Chang TY, Wong TT*, Wang HW*. DriverDB: A exome sequencing (exome-seq) database for cancer driver gene identification. Nucleic Acids Res , 2014, JAN:42(D1):D1048-1054