MAGE-TAB Version 1.1 Investigation Title Tumor metastasis to lymph node requires YAP-dependent metabolic adaptation Experimental Design disease state design Experimental Design Term Source REF EFO Experimental Design Term Accession Number EFO:0001756 Experimental Factor Name sampling site Experimental Factor Type sampling site Experimental Factor Term Source REF EFO Experimental Factor Term Accession Number Person Last Name Lee Person First Name Choong-kun Person Mid Initials Person Email cklee512@gmail.com Person Phone Person Fax Person Affiliation Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST) Person Address Daejeon 34141, Republic of Korea Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Quality Control Type Quality Control Term Source REF Quality Control Term Accession Number Replicate Type Replicate Term Source REF Replicate Term Accession Number Normalization Type Normalization Term Source REF Normalization Term Accession Number Date of Experiment 2017-07-31 Public Release Date 2019-02-09 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Publication Status Term Accession Number Experiment Description In cancer patients, metastasis of tumors to sentinel lymph nodes (LN) predicts disease progression and often guides treatment decisions. The mechanisms underlying tumor LN metastasis are poorly understood. Using comparative transcriptomics and metabolomics analyses of primary and LN metastatic tumors in mice, we found that LN metastasis requires that tumor cells undergo a metabolic shift toward fatty acid oxidation (FAO). Transcriptional co-activator yes-associated protein (YAP) is selectively activated in LN metastatic tumors, leading to upregulation of genes in the FAO signaling pathway. Pharmacological inhibition of FAO or genetic ablation of YAP suppressed LN metastasis in mice. Several bioactive bile acids were highly accumulated in the LN metastatic tumor. Inhibition of FAO or YAP may merit exploration as therapeutic strategies for mitigating tumor LN metastasis. Protocol Name P-MTAB-82343 P-MTAB-82342 P-MTAB-82345 P-MTAB-82344 P-MTAB-82346 Protocol Type nucleic acid extraction protocol sample collection protocol nucleic acid sequencing protocol nucleic acid library construction protocol normalization data transformation protocol Protocol Term Source REF EFO EFO EFO EFO EFO Protocol Term Accession Number EFO_0002944 EFO_0005518 EFO_0004170 EFO_0004184 EFO_0003816 Protocol Description Tissues were removed, digested, depleted CD45+ cells using AutoMACS, and GFP+ tumor cells were sorted by FACS Aria II. RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries. 5 x 10^5 B16F10-GFP cells were implanted subcutaneously into the footpad region of hind limb of 8~9-week-old male C57BL/6 mice. B16F10-GFP+ tumor cells from primary site (footpad) and pLNs (isolated at 3 weeks after implantation for micro-metastatic tumor with metastatic foci diameter less than 2 mm and at 4 weeks after implantation for macro-metastatic tumor) were isolated. The library was amplified to add the complete adapter sequences required for cluster generation. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, Inc.). RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols. Read count extraction and nomalization were performed using edgeR. Protocol Parameters Protocol Hardware NextSeq 500 Protocol Software Protocol Contact Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ Term Source Version 2.38 SDRF File E-MTAB-7621.sdrf.txt Comment [Submitted Name] Tumor metastasis to lymph node requires YAP-dependent metabolic adaptation Comment [SecondaryAccession] ERP113457 Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR3090776-ERR3090787 Comment [AEExperimentType] RNA-seq of coding RNA Comment[ArrayExpressAccession] E-MTAB-7621