Additional file 1 of LINE-1 promotes tumorigenicity and exacerbates tumor progression via stimulating metabolism reprogramming in non-small cell lung cancer
Creators: name: Sun, Zeguo
name: Zhang, Rui
name: Zhang, Xiao
name: Sun, Yifei
name: Liu, Pengpeng
name: Francoeur, Nancy
name: Han, Lei
name: Lam, Wan Yee
name: Yi, Zhengzi
name: Sebra, Robert
name: Walsh, Martin
name: Yu, Jinpu
name: Zhang, Weijia
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Figure S1. Validation of LCT activity in TJMUCH cohort.(A) Number of LCT events overlapped between TJMUCH cohort and TCGA LUSC cohort.(B) Comparison of overall methylation level between LUSC and LUAD patients fromTCGA. (C) Distribution of LCT event number in each sample. (D) Expression (readper mission) between tumor and control samples. (E) Frequency of the top 20 LCTevents (named by their target genes). (F) Enriched GO terms of the recurrentLCT affected genes (more than 2 samples). (G) Differentially expressed LCTsbetween tumor and normal samples. Left panel showing the number of samplesdetected with each LCT event and the right panel showing the expression ofcorresponding LCT event across samples (red represents tumor samples while bluerepresents normal samples). Figure S2. Association of LCT with Metabolic, Immuneprocess, Genomic Instability and Clinical States. (A) Enriched GO terms ofgenes positively or negatively co-expressed with overall LCT expression in eachsample. (B) The GSEA enrichment plot for meta-markers of each immune cell type.Genes are ranked by the fold change of expression in LCT-high samples (left)versus LCT-low samples (right) (C) Correlation of methylation level and CNVlevel with overall LCT activity in each sample. (D) Comparison of LCTexpression in different cancer stages and TMB quartiles. (E) Differentiallyexpressed LCT events (named by targeted gene), which are highly expressed intumor than control. Left panel shows the number of samples containing the LCT eventwhile right panel shows the expression of LCT events among all the samples,grouped by tumor (red) and normal control (blue). (F) Survival curve ofpatients grouped as L1-high and L1-low by the total expression of survivalrelated LCTs. Figure S3. Validation of the association of overall LCTactivity and Immune function in TJMUCH cohort. (A) Enriched GO terms of thegenes positively co-expressed with overall LCT activity. (B) Enriched GO termsof the genes negatively co-expressed with LCT activity. (C) GSEA analysis ofthe immune markers enrichment in LCT-high versus LCT-low samples. Figure S4. LCT activity in tumor cells. (A) Frequencyof overlapped LCT between bulk and single cell data sets. Left panel shows thefrequency of each LCT event in each cancer type from TCGA bulk sequencing.Right panel shows the occurrence of each LCT event in each sample from singlecell data set. (B) Umap of cells colored by individual. (C) Markers for annotationof each cell type. (D) the proportion of each cell type in each sample. Figure S5. LCT related DEGs between cellpopulation. (A) Umap and trajectory of tumor cells fromPatient1, Patient2 and Patient5. Cells detected with LCT events were coloredred. (B) DEGs between LCT enriched tumor subtype versus other tumor cells. (C)DEGs between LCT positive tumor cells versus LCT negative tumor cells in LCTenriched tumor subtype. FigureS6. The mitochondrialmorphology and functions. (A) The TEM results of H520OV-CTRL, H520OV-L1-FGGY, and BEAS-2B. (B) The OCR and ECAR results ofH520OV-CTRLand H520OV-L1-FGGY. (C) The MMP results of H520OV-CTRLand H520OV-L1-FGGY.(D) The ATP productionof H520OV-CTRLand H520OV-L1-FGGY. Figure S7. The oncogenic roles of L1-FGGY/12-LOX/GPR31in SK-MES-1 cells. (A) The relative RNA expression of 12-LOX and 15-LOXdetected in SK-MES-1OV-CTRL and SK-MES-1OV-L1-FGGY, as well as in SK-MES-1OV-L1-FGGY treated with either ML355 or PD146176. (B) The secretionvalue of 12S-HETE and 15S-HETE detected in SK-MES-1OV-CTRL, SK-MES-1OV-L1-FGGY, and SK-MES-1OV-L1-FGGY treated with either ML355or PD146176. (C) The proliferation of SK-MES-1OV-CTRL, SK-MES-1OV-L1-FGGY, SK-MES-1OV-L1-FGGY+sh-GPR31, and SK-MES-1OV-L1-FGGY treated with either ML355 or PD146176 was detectedusing CCK8 method. (D) The statistical results of migration rates of SK-MES-1OV-CTRL,SK-MES-1OV-L1-FGGY,SK-MES-1OV-L1-FGGY+sh-GPR31, and SK-MES-1OV-L1-FGGY treated with either ML355or PD146176 in wound healing assays. (E) The statistical results of invasionnumber of SK-MES-1OV-CTRL, SK-MES-1OV-L1-FGGY, SK-MES-1OV-L1-FGGY+sh-GPR31, and SK-MES-1OV-L1-FGGY treated with either ML355or PD146176 in trans-well invasion assays. The data are shown as mean ± SD withplots. * and ** indicate p&lt;0.05 and p&lt;0.01, respectively between thegroups as indicated. Figure S8. The results of nCounter® PanCancer IO-360™Panel detected in L1-FGGY+tissues and L1-FGGY-tissues (n=12). (A) The pathway scores of different signaling pathwayswere compared between L1-FGGY+tissues and L1-FGGY-tissues. (B) The cell type scores of immunocytes were compared between L1-FGGY+ tissues and L1-FGGY- tissues. Figure S9. The model of L1-FGGYactivated 12-LOX/GPR31/Wnt signaling through competitive combination-inducedUSP24-mediated deubiquitination. Figure S10. NVR and ML355 triggered metabolism reprogramming andaltered the immune microenvironment invivo. (A) The qPCR results of genes involved inglucose and lipid metabolism were shown as relative expression values in KLN205OV-CTRLmouse group, KLN205OV-L1-FGGYmouse group, NVR-treated KLN205OV-L1-FGGYmice, ML355-treated KLN205OV-L1-FGGYmice and NVR+ML355-treated KLN205OV-L1-FGGYmouse group. (B) The proportions of various immunocytes in different mousegroups using flow cytometry. Figure S11. Potential effects of drug on LCT activity. (A) Distribution of LCT expression in samples treatedwith Metaformin and control samples in two public data sets. (GSE141052 andGSE146982) (B) Distribution of L1 expression in samples treated withSimvastatin and control samples in two pancreatic cancer cell line (PANC-1 andMiaPaCa-2 (GSE149566)). Table S1. Basic statistics of LCT events in all 3cohorts. Table S2. Overlapped LCT genes between TCGA LUSCand LUAD. Table S3. Overlapped LCTgenes between TCGA and TJMUCH LUSC samples. Table S4. Overlapped GO BPterms enriched with recurrent LCT genes between TCGA LUSC and LUAD. Table S5. Enriched GO BPterms with recurrent LCT genes in TJMUCH cohort. Table S6. GO BP termsenriched with genes positively co-expressed with overall LCT level in TCGA LUSCand LUAD samples. Table S7. GO BP termsenriched with genes negatively co-expressed with overall LCT level in TCGA LUSCand LUAD samples. Table S8. GO BP termsenriched with genes positively co-expressed with overall LCT level in TJMUCHLUSC samples. Table S9. GO BP termsenriched with genes negatively co-expressed with overall LCT level in TJMUCHLUSC samples. Table S10. Differentiallyexpressed LCTs between tumor and normal samples in TCGA LUSC. Table S11. Differentiallyexpressed LCTs between tumor and normal samples in TJMUCH LUSC. Table S12. Differentiallyexpressed LCTs between tumor and normal samples in TCGA LUAD. Table S13. Survival relatedLCTs in TCGA LUSC.Table S14. Survival relatedLCTs in TCGA LUAD. Table S15. Recurrent LCTsbetween bulk RNAseq from TCGA and 19 SC RNAseq samples. TableS16. Differentially expressed genes between LCT enriched tumor cell cluster andother tumor cell clusters in each patient. TableS17.GO BP enrichment of differentially expressed genes between LCT enrichedtumor cell cluster and other tumor cell clusters in each patient. Table S18. Differentiallyexpressed genes between tumor cells with LCT versus tumor cells without LCT inLCT enriched tumor cell cluster in each patient. TableS19. GO BP enrichment of differentially expressed genes between tumor cells withLCT versus tumor cells without LCT in LCT enriched tumor cell cluster in eachpatient. Table S20. The basic clinical pathologicalinformation of all TJMUCH patients. Table S21.Distributions of clinical-pathological parameters of patients with L1-FGGY+and L1-FGGY- of TJMUCH.TableS22. List of 47 LCT related genes selected for grouping of patients.TableS23.The sequences of primers in RT-qPCR analysis.