[논문]A Systems Biology Approach to Identifying a Master Regulator That Can Transform the Fast Growing Cellular State to a Slowly Growing One in Early Colorectal Cancer Development Model

Choi, Jihye; Gong, Jeong-Ryeol; Hwang, Chae Young; Joung, Chang Young; Lee, Soobeom; Cho, Kwang-Hyun

doi:10.3389/fgene.2020.570546

[해외논문] A Systems Biology Approach to Identifying a Master Regulator That Can Transform the Fast Growing Cellular State to a Slowly Growing One in Early Colorectal Cancer Development Model 원문보기

Frontiers in genetics, v.11, 2020년, pp.570546 -

Choi, Jihye , Gong, Jeong-Ryeol , Hwang, Chae Young , Joung, Chang Young , Lee, Soobeom , Cho, Kwang-Hyun

Abstract ▼ AI-Helper

Colorectal cancer (CRC) has been most extensively studied for characterizing genetic mutations along its development. However, we still have a poor understanding of CRC initiation due to limited measures of its observation and analysis. If we can unveil CRC initiation events, we might identify novel prognostic markers and therapeutic targets for early cancer detection and prevention. To tackle this problem, we establish the early CRC development model and perform transcriptome analysis of its single cell RNA-sequencing data. Interestingly, we find two subtypes, fast growing vs. slowly growing populations of distinct growth rate and gene signatures, and identify CCDC85B as a master regulator that can transform the cellular state of fast growing subtype cells into that of slowly growing subtype cells. We further validate this by in vitro experiments and suggest CCDC85B as a novel potential therapeutic target that may prevent malignant CRC development by suppressing stemness and uncontrolled cell proliferation.

Keyword

참고문헌 (48)

Aibar S. Gonzalez-Blas C. B. Moerman T. Huynh-Thu V. A. Imrichova H. Hulselmans G. . ( 2017 ). SCENIC: single-cell regulatory network inference and clustering . Nat. Methods 14 , 1083 ？ 1086 . 10.1038/nmeth.4463 , PMID: 28991892

상세보기
Alvarez M. J. Shen Y. Giorgi F. M. Lachmann A. Ding B. B. Ye B. H. . ( 2016 ). Functional characterization of somatic mutations in cancer using network-based inference of protein activity . Nat. Genet. 48 , 838 ？ 847 . 10.1038/ng.3593 , PMID: 27322546

상세보기
Ashburner M. Ball C. A. Blake J. A. Botstein D. Butler H. Cherry J. M. . ( 2000 ). Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium . Nat. Genet. 25 , 25 ？ 29 . 10.1038/75556 , PMID: 10802651

상세보기
Butler A. Hoffman P. Smibert P. Papalexi E. Satija R. ( 2018 ). Integrating single-cell transcriptomic data across different conditions, technologies, and species . Nat. Biotechnol. 36 , 411 ？ 420 . 10.1038/nbt.4096 29608179

상세보기
Califano A. Alvarez M. J. ( 2017 ). The recurrent architecture of tumour initiation, progression and drug sensitivity . Nat. Rev. Cancer 17 , 116 ？ 130 . 10.1038/nrc.2016.124 , PMID: 27977008

상세보기
Campbell T. M. Castro M. A. Ponder B. A. Meyer K. B. ( 2016 ). Identification of post-transcriptional modulators of breast cancer transcription factor activity using MINDy . PLoS One 11 : e0168770 . 10.1371/journal.pone.0168770 , PMID: 27997592

상세보기
Castro M. A. de Santiago I. Campbell T. M. Vaughn C. Hickey T. E. Ross E. . ( 2016 ). Regulators of genetic risk of breast cancer identified by integrative network analysis . Nat. Genet. 48 , 12 ？ 21 . 10.1038/ng.3458 , PMID: 26618344

상세보기
Cole A. M. Ridgway R. A. Derkits S. E. Parry L. Barker N. Clevers H. . ( 2010 ). p21 loss blocks senescence following Apc loss and provokes tumourigenesis in the renal but not the intestinal epithelium . EMBO Mol. Med. 2 , 472 ？ 486 . 10.1002/emmm.201000101 , PMID: 20976827

상세보기
Ding H. Douglass E. F. Jr. Sonabend A. M. Mela A. Bose S. Gonzalez C. . ( 2018 ). Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm . Nat. Commun. 9 : 1471 . 10.1038/s41467-018-03843-3 , PMID: 29662057

상세보기
Edgar R. Domrachev M. Lash A. E. ( 2002 ). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository . Nucleic Acids Res. 30 , 207 ？ 210 . 10.1093/nar/30.1.207 , PMID: 11752295

상세보기
Eldar A. Elowitz M. B. ( 2010 ). Functional roles for noise in genetic circuits . Nature 467 , 167 ？ 173 . 10.1038/nature09326 , PMID: 20829787

상세보기
Eraslan G. Simon L. M. Mircea M. Mueller N. S. Theis F. J. ( 2019 ). Single-cell RNA-seq denoising using a deep count autoencoder . Nat. Commun. 10 : 390 . 10.1038/s41467-018-07931-2 , PMID: 30674886

상세보기
Fearon E. R. Vogelstein B. ( 1990 ). A genetic model for colorectal tumorigenesis . Cell 61 , 759 ？ 767 . 10.1016/0092-8674(90)90186-i , PMID: 2188735

상세보기
Feng Y. Gao Y. Yu J. Jiang G. Zhang X. Lin X. . ( 2019 ). CCDC85B promotes non-small cell lung cancer cell proliferation and invasion . Mol. Carcinog. 58 , 126 ？ 134 . 10.1002/mc.22914 , PMID: 30242906

상세보기
Fletcher M. N. Castro M. A. Wang X. de Santiago I. O’Reilly M. Chin S. F. . ( 2013 ). Master regulators of FGFR2 signalling and breast cancer risk . Nat. Commun. 4 : 2464 . 10.1038/ncomms3464 , PMID: 24043118

상세보기
Huang S. ( 2009 ). Non-genetic heterogeneity of cells in development: more than just noise . Development 136 , 3853 ？ 3862 . 10.1242/dev.035139 , PMID: 19906852

상세보기
Ilicic T. Kim J. K. Kolodziejczyk A. A. Bagger F. O. McCarthy D. J. Marioni J. C. . ( 2016 ). Classification of low quality cells from single-cell RNA-seq data . Genome Biol. 17 : 29 . 10.1186/s13059-016-0888-1 , PMID: 26887813

상세보기
Johnson W. E. Li C. Rabinovic A. ( 2007 ). Adjusting batch effects in microarray expression data using empirical Bayes methods . Biostatistics 8 , 118 ？ 127 . 10.1093/biostatistics/kxj037 , PMID: 16632515

상세보기
Jurkin J. Zupkovitz G. Lagger S. Grausenburger R. Hagelkruys A. Kenner L. . ( 2011 ). Distinct and redundant functions of histone deacetylases HDAC1 and HDAC2 in proliferation and tumorigenesis . Cell Cycle 10 , 406 ？ 412 . 10.4161/cc.10.3.14712 , PMID: 21270520

상세보기
Kaufman C. K. Mosimann C. Fan Z. P. Yang S. Thomas A. J. Ablain J. . ( 2016 ). A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation . Science 351 : aad2197 . 10.1126/science.aad2197 , PMID: 26823433

상세보기
Kim J. R. Cho K. H. ( 2006 ). The multi-step phosphorelay mechanism of unorthodox two-component systems in E. coli realizes ultrasensitivity to stimuli while maintaining robustness to noises . Comput. Biol. Chem. 30 , 438 ？ 444 . 10.1016/j.compbiolchem.2006.09.004 17112785

상세보기
Kim S. Kim J. Cho K. H. ( 2007 ). Inferring gene regulatory networks from temporal expression profiles under time-delay and noise . Comput. Biol. Chem. 31 , 239 ？ 245 . 10.1016/j.compbiolchem.2007.03.013 , PMID: 17631421

상세보기
Kim J. R. Kim J. Kwon Y. K. Lee H. Y. Heslop-Harrison P. Cho K. H. ( 2011 ). Reduction of complex signaling networks to a representative kernel . Sci. Signal. 4 : ra35 . 10.1126/scisignal.2001390 , PMID: 21632468

상세보기
Kowalczyk M. S. Tirosh I. Heckl D. Rao T. N. Dixit A. Haas B. J. . ( 2015 ). Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells . Genome Res. 25 , 1860 ？ 1872 . 10.1101/gr.192237.115 , PMID: 26430063

상세보기
Kwon Y. K. Cho K. H. ( 2007 ). Boolean dynamics of biological networks with multiple coupled feedback loops . Biophys. J. 92 , 2975 ？ 2981 . 10.1529/biophysj.106.097097 , PMID: 17259267

상세보기
Leek J. T. Johnson W. E. Parker H. S. Jaffe A. E. Storey J. D. ( 2012 ). The sva package for removing batch effects and other unwanted variation in high-throughput experiments . Bioinformatics 28 , 882 ？ 883 . 10.18129/B9.bioc.sva , PMID: 22257669

상세보기
Liang M. Chen X. Liu W. Li S. Li C. Jiang L. . ( 2011 ). Role of the pituitary tumor transforming gene 1 in the progression of hepatocellular carcinoma . Cancer Biol. Ther. 11 , 337 ？ 345 . 10.4161/cbt.11.3.14102 , PMID: 21099350

상세보기
Liberzon A. Birger C. Thorvaldsdottir H. Ghandi M. Mesirov J. P. Tamayo P. ( 2015 ). The Molecular Signatures Database (MSigDB) hallmark gene set collection . Cell Syst. 1 , 417 ？ 425 . 10.1016/j.cels.2015.12.004 , PMID: 26771021

상세보기
Liberzon A. Subramanian A. Pinchback R. Thorvaldsdottir H. Tamayo P. Mesirov J. P. ( 2011 ). Molecular signatures database (MSigDB) 3.0 . Bioinformatics 27 , 1739 ？ 1740 . 10.1093/bioinformatics/btr260 , PMID: 21546393

상세보기
Linderman G. C. Zhao J. Kluger Y. ( 2018 ). Zero-preserving imputation of scRNA-seq data using low-rank approximation. bioRxiv [Preprint]. 10.1101/397588
Maamar H. Raj A. Dubnau D. ( 2007 ). Noise in gene expression determines cell fate in Bacillus subtilis . Science 317 , 526 ？ 529 . 10.1126/science.1140818 17569828

상세보기
Malta T. M. Sokolov A. Gentles A. J. Burzykowski T. Poisson L. Weinstein J. N. . ( 2018 ). Machine learning identifies stemness features associated with oncogenic dedifferentiation . Cell 173 , 338.e315 ？ 354.e315 . 10.1016/j.cell.2018.03.034 , PMID: 29625051

상세보기
McInnes L. Healy J. Melville J. ( 2018 ). Umap: uniform manifold approximation and projection for dimension reduction. arXiv [Preprint]. Available at: https://arxiv.org/abs/1802.03426v2
Murray P. J. Kang J. W. Mirams G. R. Shin S. Y. Byrne H. M. Maini P. K. ( 2010 ). Modelling spatially regulated beta-catenin dynamics and invasion in intestinal crypts . Biophys. J. 99 , 716 ？ 725 . 10.1016/j.bpj.2010.05.016 20682248

상세보기
Park S. G. Lee T. Kang H. Y. Park K. Cho K. H. Jung G. ( 2006 ). The influence of the signal dynamics of activated form of IKK on NF-kappaB and anti-apoptotic gene expressions: a systems biology approach . FEBS Lett. 580 , 822 ？ 830 . 10.1016/j.febslet.2006.01.004 , PMID: 16413545

상세보기
Petropoulos S. Edsgard D. Reinius B. Deng Q. Panula S. P. Codeluppi S. . ( 2016 ). Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos . Cell 165 , 1012 ？ 1026 . 10.1016/j.cell.2016.03.023 , PMID: 27062923

상세보기
Powell S. M. Zilz N. Beazer-Barclay Y. Bryan T. M. Hamilton S. R. Thibodeau S. N. . ( 1992 ). APC mutations occur early during colorectal tumorigenesis . Nature 359 , 235 ？ 237 . 10.1038/359235a0 , PMID: 1528264

상세보기
Quereda V. Malumbres M. ( 2009 ). Cell cycle control of pituitary development and disease . J. Mol. Endocrinol. 42 , 75 ？ 86 . 10.1677/jme-08-0146 , PMID: 18987159

상세보기
Schmidt H. Cho K. H. Jacobsen E. W. ( 2005 ). Identification of small scale biochemical networks based on general type system perturbations . FEBS J. 272 , 2141 ？ 2151 . 10.1111/j.1742-4658.2005.04605.x , PMID: 15853799

상세보기
Shannon P. Markiel A. Ozier O. Baliga N. S. Wang J. T. Ramage D. . ( 2003 ). Cytoscape: a software environment for integrated models of biomolecular interaction networks . Genome Res. 13 , 2498 ？ 2504 . 10.1101/gr.1239303 , PMID: 14597658

상세보기
Stuart T. Butler A. Hoffman P. Hafemeister C. Papalexi E. Mauck W. M. 3rd . ( 2019 ). Comprehensive integration of single-cell data . Cell 177 , 1888.e1821 ？ 1902.e1821 . 10.1016/j.cell.2019.05.031 , PMID: 31178118

상세보기
Subramanian A. Tamayo P. Mootha V. K. Mukherjee S. Ebert B. L. Gillette M. A. . ( 2005 ). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles . Proc. Natl. Acad. Sci. U. S. A. 102 , 15545 ？ 15550 . 10.1073/pnas.0506580102 , PMID: 16199517

상세보기
Szklarczyk D. Gable A. L. Lyon D. Junge A. Wyder S. Huerta-Cepas J. . ( 2019 ). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets . Nucleic Acids Res. 47 , D607 ？ D613 . 10.1093/nar/gky1131 , PMID: 30476243

상세보기
The Gene Ontology Consortium ( 2019 ). The Gene Ontology resource: 20 years and still GOing strong . Nucleic Acids Res. 47 , D330 ？ D338 . 10.1093/nar/gky1055 , PMID: 30395331

상세보기
Tirosh I. Izar B. Prakadan S. M. Wadsworth M. H. 2nd Treacy D. Trombetta J. J. . ( 2016 ). Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq . Science 352 , 189 ？ 196 . 10.1126/science.aad0501 , PMID: 27124452

상세보기
Valenta T. Hausmann G. Basler K. ( 2012 ). The many faces and functions of β-catenin . EMBO J. 31 , 2714 ？ 2736 . 10.1038/emboj.2012.150 , PMID: 22617422

상세보기
Wang K. Saito M. Bisikirska B. C. Alvarez M. J. Lim W. K. Rajbhandari P. . ( 2009 ). Genome-wide identification of post-translational modulators of transcription factor activity in human B cells . Nat. Biotechnol. 27 , 829 ？ 839 . 10.1038/nbt.1563 , PMID: 19741643

상세보기
Zheng G. X. Terry J. M. Belgrader P. Ryvkin P. Bent Z. W. Wilson R. . ( 2017 ). Massively parallel digital transcriptional profiling of single cells . Nat. Commun. 8 : 14049 . 10.1038/ncomms14049 , PMID: 28091601

상세보기

LOADING...

활용도 분석정보

상세보기

다운로드

내보내기

활용도 Top5 논문

해당 논문의 주제분야에서 활용도가 높은 상위 5개 콘텐츠를 보여줍니다.
더보기 버튼을 클릭하시면 더 많은 관련자료를 살펴볼 수 있습니다.

표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

내보내기 구분	파일저장 인쇄 메일전송
구성항목	기본정보 상세정보 관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관 관리번호, 논문명, 대등논문명, 저자 , 저널/프로시딩명, 발행기관, 발행년, 발행언어, 권, 호, 시작페이지, 끝페이지, ISBN, ISSN, 주제분야, 키워드, 초록(한글), 초록(영문), 저자(소속기관)
저장형식	Text(ASCII format) Excel format RefWorks Direct Export RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley
메일정보	받는사람 (필수) @ 보내는사람 (선택) @ 제목 내용 KISTI 검색결과 이메일 서비스
안내	총 건의 자료가 검색되었습니다. 다운받으실 자료의 인덱스를 입력하세요. (1-10,000) 검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다. 데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요) 다운로드 파일은 UTF-8 형태로 저장됩니다. 파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오. ~ Text(ASCII format) Excel format

연합인증