Additional file 1 of Meningiomas in patients with neurofibromatosis type 2 predominantly comprise ‘immunogenic subtype’ tumours characterised by macrophage infiltration
Creators: name: Teranishi, Yu
name: Miyawaki, Satoru
name: Nakatochi, Masahiro
name: Okano, Atsushi
name: Ohara, Kenta
name: Hongo, Hiroki
name: Ishigami, Daiichiro
name: Sakai, Yu
name: Shimada, Daisuke
name: Takayanagi, Shunsaku
name: Ikemura, Masako
name: Komura, Daisuke
name: Katoh, Hiroto
name: Mitsui, Jun
name: Morishita, Shinichi
name: Ushiku, Tetsuo
name: Ishikawa, Shumpei
name: Nakatomi, Hirofumi
name: Saito, Nobuhito
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Additional file 1. Figure S1. Flow Chart in this study; Figure S2.A: The MA plot based on the RNA sequencing in NF2 patients and sporadic NF2-altered meningiomas. B: The volcano plot based on the RNA sequencing in NF2 patients and sporadic NF2-altered meningiomas. C: The principal component analysis based on the RNA sequencing in NF2 patients and sporadic NF2-altered meningiomas. D: Gene set variation analysis (GSVA) based on c7 immunologic signature gene sets clearly distinguished 2 clusters; Figure S3. The MA plot based on the RNA sequencing in germline NF2 patients and mosaic NF2 patients; Figure S4. A: Each immunologic gene expression in NF2 patients and sporadic NF2-altered meningiomas.B: Each immunologic gene expression in ‘1p loss (-)’ and ‘1p loss (+)’. C: Each immunologic gene expression in ‘recurrence (-)’ and ‘recurrence (+)’; Figure S5. Deconvoluted score using CIBERSORT, xCell, and ESTIMATE. A: Each deconvoluted score in NF2 patients and sporadic NF2-altered meningiomas. B: Each deconvoluted score in ‘1p loss (-)’ and ‘1p loss (+)’. C: Each deconvoluted score in ‘recurrence (-)’ and ‘recurrence (+)’; Figure S6. Infiltrated cells based on deconvoluted data. A: Each infiltrated cell in NF2 patients and sporadic NF2-altered meningiomas. B: Each infiltrated cell in ‘1p loss (-)’ and ‘1p loss (+)’. C: Each infiltrated cell in ‘recurrence (-)’ and ‘recurrence (+)’; Figure S7. GSEA using single-cell data (C8): NF2 vs sporadic; Figure S8. GSEA using single-cell data (C8): non-recurrence vs recurrence; Figure S9. Quantification of immune cell infiltration by IHC. A: Quantification of immune cells in “1p loss (-)” and ”1p loss (+)”. B: Quantification of immune cells in ‘recurrence (-)’ and ‘recurrence (+)’; Figure S10. Quantification of immune cell infiltration by IHC in each case; Figure S11. A-C: The correlation analysis of each RNA-seq–derived immune metrics (CIBERSORT vs ESTIMLATE [A], xCell vs CIBERSORT [B], and ESTIMATE vs xCell [C]). D,E: The correlation analysis of IHC-derived and RNA-seq–derived measures of leukocyte infiltration (CD45 cells vs CIBERSORT absolute score [D], and ESTIMATE immune score [E]); Figure S12. Gene expression regarding ‘immunogenic subtype’ of meningiomas.