List of abbreviations
AUC: Area under the curve; B.C: Breast cancer; BBB: Blood-brain barrier;
BrM: Brain metastasis; C.C: Colorectal cancer; CCT:
Chaperonin-containing tailless complex polypeptide 1; CDH1: Cadherin 1;
CNS: Central nervous system; CT: Computed tomography; CV: Coefficient of
variation; DEP: Differentially expressed protein; ECM: Extracellular
matrix; eIF: Eukaryotic initiation factor; FCGBP: TFc fragment of IgG
binding protein; GBM: Glioblastoma; GLDC: Glycine decarboxylase; GSEA:
Gene set enrichment analysis; GSM: Gliosarcoma; H: HeLa; IDH: Isocitrate
dehydrogenase; IQR: Interquartile range; L.C: Lung cancer; L1CAM: L1
cell adhesion molecule; LC-MS/MS: Liquid chromatography tandem mass
spectrometry; LFQ : Label free quantification; MCCV: Monte-Carlo
cross-validation; MEK1: Mitogen-activated protein kinase; MRI: Magnetic
resonance imaging; MS: Mass spectrometry; Mut: Mutation; O.C: Ovarian
cancer; PCA: Principal component analysis; PDLIM2: PDZ and LIM domain
protein 2; PLS-DA: Partial least squares discriminant analysis; PSM:
Propensity score matching; QC: Quality control; ROC: Receiver operating
characteristic; RP: Ribosomal protein; SDPR: Serum deprivation response
protein; SYNE1: Nesprin-1; TACSTD2: Tumor-associated calcium signal
transducer 2; TIC: Total ion current; VEGF: Vascular endothelial growth
factor; WT: Wild type.
References
1. Lah TT, Novak M, Breznik B. Brain malignancies: Glioblastoma and
brain metastases. Semin Cancer Biol. 2020;60:262-73.
2. Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, Burger PC, Jouvet A,
Scheithauer BW, Kleihues P. The 2007 WHO classification of tumours of
the central nervous system. Acta Neuropathol. 2007;114(2):97-109.
3. Ostrom QT, Gittleman H, Stetson L, Virk SM, Barnholtz-Sloan JS.
Epidemiology of gliomas. Cancer Treat Res. 2015;163:1-14.
4. Louis DN, Perry A, Reifenberger G, von Deimling A, Figarella-Branger
D, Cavenee WK, Ohgaki H, Wiestler OD, Kleihues P, Ellison DW. The 2016
World Health Organization Classification of Tumors of the Central
Nervous System: a summary. Acta Neuropathol. 2016;131(6):803-20.
5. Tom MC, Cahill DP, Buckner JC, Dietrich J, Parsons MW, Yu JS.
Management for Different Glioma Subtypes: Are All Low-Grade Gliomas
Created Equal? Am Soc Clin Oncol Educ Book. 2019;39:133-45.
6. Aldape K, Brindle KM, Chesler L, Chopra R, Gajjar A, Gilbert MR,
Gottardo N, Gutmann DH, Hargrave D, Holland EC, Jones DTW, Joyce JA,
Kearns P, Kieran MW, Mellinghoff IK, Merchant M, Pfister SM, Pollard SM,
Ramaswamy V, Rich JN, Robinson GW, Rowitch DH, Sampson JH, Taylor MD,
Workman P, Gilbertson RJ. Challenges to curing primary brain tumours.
Nat Rev Clin Oncol. 2019;16(8):509-20.
7. Cagney DN, Martin AM, Catalano PJ, Redig AJ, Lin NU, Lee EQ, Wen PY,
Dunn IF, Bi WL, Weiss SE, Haas-Kogan DA, Alexander BM, Aizer AA.
Incidence and prognosis of patients with brain metastases at diagnosis
of systemic malignancy: a population-based study. Neuro Oncol.
2017;19(11):1511-21.
8. Lin X, DeAngelis LM. Treatment of Brain Metastases. J Clin Oncol.
2015;33(30):3475-84.
9. Fink JR, Muzi M, Peck M, Krohn KA. Multimodality Brain Tumor Imaging:
MR Imaging, PET, and PET/MR Imaging. J Nucl Med. 2015;56(10):1554-61.
10. Suh JH, Kotecha R, Chao ST, Ahluwalia MS, Sahgal A, Chang EL.
Current approaches to the management of brain metastases. Nat Rev Clin
Oncol. 2020;17(5):279-99.
11. Nejo T, Mende A, Okada H. The current state of immunotherapy for
primary and secondary brain tumors: similarities and differences. Jpn J
Clin Oncol. 2020;50(11):1231-45.
12. Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A,
Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K, Ligon KL,
Tabernero J, Seoane J, Martinez-Saez E, Curry WT, Dunn IF, Paek SH, Park
SH, McKenna A, Chevalier A, Rosenberg M, Barker FG, 2nd, Gill CM, Van
Hummelen P, Thorner AR, Johnson BE, Hoang MP, Choueiri TK, Signoretti S,
Sougnez C, Rabin MS, Lin NU, Winer EP, Stemmer-Rachamimov A, Meyerson M,
Garraway L, Gabriel S, Lander ES, Beroukhim R, Batchelor TT, Baselga J,
Louis DN, Getz G, Hahn WC. Genomic Characterization of Brain Metastases
Reveals Branched Evolution and Potential Therapeutic Targets. Cancer
Discov. 2015;5(11):1164-77.
13. Fukumura K, Malgulwar PB, Fischer GM, Hu X, Mao X, Song X, Hernandez
SD, Zhang XH, Zhang J, Parra ER, Yu D, Debeb BG, Davies MA, Huse JT.
Multi-omic molecular profiling reveals potentially targetable
abnormalities shared across multiple histologies of brain metastasis.
Acta Neuropathol. 2021;141(2):303-21.
14. Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS,
Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE,
Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML,
Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses
identify epigenetic regulators of cellular plasticity and environmental
stress response. Nat Genet. 2021;53(10):1456-68.
15. Schaffenrath J, Wyss T, He L, Rushing EJ, Delorenzi M, Vasella F,
Regli L, Neidert MC, Keller A. Blood-brain barrier alterations in human
brain tumors revealed by genome-wide transcriptomic profiling. Neuro
Oncol. 2021;23(12):2095-106.
16. Gonzalez H, Mei W, Robles I, Hagerling C, Allen BM, Hauge Okholm TL,
Nanjaraj A, Verbeek T, Kalavacherla S, van Gogh M, Georgiou S, Daras M,
Phillips JJ, Spitzer MH, Roose JP, Werb Z. Cellular architecture of
human brain metastases. Cell. 2022;185(4):729-45 e20.
17. Klemm F, Maas RR, Bowman RL, Kornete M, Soukup K, Nassiri S,
Brouland JP, Iacobuzio-Donahue CA, Brennan C, Tabar V, Gutin PH, Daniel
RT, Hegi ME, Joyce JA. Interrogation of the Microenvironmental Landscape
in Brain Tumors Reveals Disease-Specific Alterations of Immune Cells.
Cell. 2020;181(7):1643-60 e17.
18. Wang D, Eraslan B, Wieland T, Hallstrom B, Hopf T, Zolg DP, Zecha J,
Asplund A, Li LH, Meng C, Frejno M, Schmidt T, Schnatbaum K, Wilhelm M,
Ponten F, Uhlen M, Gagneur J, Hahne H, Kuster B. A deep proteome and
transcriptome abundance atlas of 29 healthy human tissues. Mol Syst
Biol. 2019;15(2):e8503.
19. Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D,
Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A,
Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG,
Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S,
Gumus ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L,
Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B,
Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon
J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM,
Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe
ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T,
Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A,
Wiznerowicz M, Schurer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI,
Fenyo D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB,
Rood BR, Wang P, Children’s Brain Tumor N, Clinical Proteomic Tumor
Analysis C. Integrated Proteogenomic Characterization across Major
Histological Types of Pediatric Brain Cancer. Cell. 2020;183(7):1962-85
e31.
20. Kulak NA, Pichler G, Paron I, Nagaraj N, Mann M. Minimal,
encapsulated proteomic-sample processing applied to copy-number
estimation in eukaryotic cells. Nat Methods. 2014;11(3):319-24.
21. Chong J, Soufan O, Li C, Caraus I, Li S, Bourque G, Wishart DS, Xia
J. MetaboAnalyst 4.0: towards more transparent and integrative
metabolomics analysis. Nucleic Acids Res. 2018;46(W1):W486-W94.
22. Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O,
Benner C, Chanda SK. Metascape provides a biologist-oriented resource
for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523.
23. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N,
Schwikowski B, Ideker T. Cytoscape: a software environment for
integrated models of biomolecular interaction networks. Genome Res.
2003;13(11):2498-504.
24. Welch DR, Hurst DR. Defining the Hallmarks of Metastasis. Cancer
Research. 2019;79(12):3011-27.
25. Kalinina J, Peng J, Ritchie JC, Van Meir EG. Proteomics of gliomas:
initial biomarker discovery and evolution of technology. Neuro Oncol.
2011;13(9):926-42.
26. Pienkowski T, Kowalczyk T, Kretowski A, Ciborowski M. A review of
gliomas-related proteins. Characteristics of potential biomarkers. Am J
Cancer Res. 2021;11(7):3425-44.
27. Aldape K, Zadeh G, Mansouri S, Reifenberger G, von Deimling A.
Glioblastoma: pathology, molecular mechanisms and markers. Acta
Neuropathol. 2015;129(6):829-48.
28. Chen R, Smith-Cohn M, Cohen AL, Colman H. Glioma Subclassifications
and Their Clinical Significance. Neurotherapeutics. 2017;14(2):284-97.
29. Liu H-j, Hu H-m, Li G-z, Zhang Y, Wu F, Liu X, Wang K-y, Zhang C-b,
Jiang T. Ferroptosis-Related Gene Signature Predicts Glioma Cell Death
and Glioma Patient Progression. Frontiers in Cell and Developmental
Biology. 2020;8.
30. Zhuo S, Chen Z, Yang Y, Zhang J, Tang J, Yang K. Clinical and
Biological Significances of a Ferroptosis-Related Gene Signature in
Glioma. Frontiers in Oncology. 2020;10.
31. Altevogt P, Doberstein K, Fogel M. L1CAM in human cancer. Int J
Cancer. 2016;138(7):1565-76.
32. Angiolini F, Cavallaro U. The Pleiotropic Role of L1CAM in Tumor
Vasculature. Int J Mol Sci. 2017;18(2).
33. Ricard-Blum S. The collagen family. Cold Spring Harb Perspect Biol.
2011;3(1):a004978.
34. Eble JA, Niland S. The extracellular matrix in tumor progression and
metastasis. Clin Exp Metastasis. 2019;36(3):171-98.
35. Teglasi V, Csury DT, Dezso K, Bugyik E, Szabo V, Szallasi Z, Paku S,
Reiniger L. Origin and Distribution of Connective Tissue and Pericytes
Impacting Vascularization in Brain Metastases With Different Growth
Patterns. J Neuropathol Exp Neurol. 2019;78(4):326-39.
36. Claesson-Welsh L, Welsh M. VEGFA and tumour angiogenesis. J Intern
Med. 2013;273(2):114-27.
37. Shen M, Jiang YZ, Wei Y, Ell B, Sheng X, Esposito M, Kang J, Hang X,
Zheng H, Rowicki M, Zhang L, Shih WJ, Celia-Terrassa T, Liu Y, Cristea
I, Shao ZM, Kang Y. Tinagl1 Suppresses Triple-Negative Breast Cancer
Progression and Metastasis by Simultaneously Inhibiting Integrin/FAK and
EGFR Signaling. Cancer Cell. 2019;35(1):64-80 e7.
38. Hao P, Yu J, Ward R, Liu Y, Hao Q, An S, Xu T. Eukaryotic
translation initiation factors as promising targets in cancer therapy.
Cell Commun Signal. 2020;18(1):175.
39. Vallin J, Grantham J. The role of the molecular chaperone CCT in
protein folding and mediation of cytoskeleton-associated processes:
implications for cancer cell biology. Cell Stress Chaperones.
2019;24(1):17-27.
40. Masica DL, Karchin R. Correlation of somatic mutation and expression
identifies genes important in human glioblastoma progression and
survival. Cancer Res. 2011;71(13):4550-61.
41. Serao NV, Delfino KR, Southey BR, Beever JE, Rodriguez-Zas SL. Cell
cycle and aging, morphogenesis, and response to stimuli genes are
individualized biomarkers of glioblastoma progression and survival. BMC
Med Genomics. 2011;4:49.
42. Xie ZC, Wu HY, Dang YW, Chen G. Role of alternative splicing
signatures in the prognosis of glioblastoma. Cancer Med.
2019;8(18):7623-36.
43. Kim D, Fiske BP, Birsoy K, Freinkman E, Kami K, Possemato RL,
Chudnovsky Y, Pacold ME, Chen WW, Cantor JR, Shelton LM, Gui DY, Kwon M,
Ramkissoon SH, Ligon KL, Kang SW, Snuderl M, Vander Heiden MG, Sabatini
DM. SHMT2 drives glioma cell survival in ischaemia but imposes a
dependence on glycine clearance. Nature. 2015;520(7547):363-7.
44. Tiwari V, Daoud EV, Hatanpaa KJ, Gao A, Zhang S, An Z, Ganji SK,
Raisanen JM, Lewis CM, Askari P, Baxter J, Levy M, Dimitrov I, Thomas
BP, Pinho MC, Madden CJ, Pan E, Patel TR, DeBerardinis RJ, Sherry AD,
Mickey BE, Malloy CR, Maher EA, Choi C. Glycine by MR spectroscopy is an
imaging biomarker of glioma aggressiveness. Neuro Oncol.
2020;22(7):1018-29.
45. Wang Y, Song Z, Leng P, Liu Y. A systematic analysis reveals gene
expression alteration of serum deprivation response (SDPR) gene is
significantly associated with the survival of patients with cancer.
Oncol Rep. 2019;42(3):1161-72.
46. Deininger MH, Meyermann R, Schluesener HJ. Expression and release of
CD14 in astrocytic brain tumors. Acta Neuropathol. 2003;106(3):271-7.
47. Takenaka MC, Gabriely G, Rothhammer V, Mascanfroni ID, Wheeler MA,
Chao CC, Gutierrez-Vazquez C, Kenison J, Tjon EC, Barroso A, Vandeventer
T, de Lima KA, Rothweiler S, Mayo L, Ghannam S, Zandee S, Healy L, Sherr
D, Farez MF, Prat A, Antel J, Reardon DA, Zhang H, Robson SC, Getz G,
Weiner HL, Quintana FJ. Control of tumor-associated macrophages and T
cells in glioblastoma via AHR and CD39. Nat Neurosci. 2019;22(5):729-40.
48. Yan T, Tian D, Chen J, Tan Y, Cheng Y, Ye L, Deng G, Liu B, Yuan F,
Zhang S, Cai L, Chen Q. FCGBP Is a Prognostic Biomarker and Associated
With Immune Infiltration in Glioma. Front Oncol. 2021;11:769033.
49. MacDonald TJ, Brown KM, LaFleur B, Peterson K, Lawlor C, Chen Y,
Packer RJ, Cogen P, Stephan DA. Expression profiling of medulloblastoma:
PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic
disease. Nat Genet. 2001;29(2):143-52.
50. Ryall S, Tabori U, Hawkins C. Pediatric low-grade glioma in the era
of molecular diagnostics. Acta Neuropathol Commun. 2020;8(1):30.
51. Guo ZS, Qu Z. PDLIM2: Signaling pathways and functions in cancer
suppression and host immunity. Biochim Biophys Acta Rev Cancer.
2021;1876(2):188630.
52. Karantza V. Keratins in health and cancer: more than mere epithelial
cell markers. Oncogene. 2011;30(2):127-38.
53. Lenart S, Lenart P, Smarda J, Remsik J, Soucek K, Benes P. Trop2:
Jack of All Trades, Master of None. Cancers (Basel). 2020;12(11).
54. Wong SHM, Fang CM, Chuah LH, Leong CO, Ngai SC. E-cadherin: Its
dysregulation in carcinogenesis and clinical implications. Crit Rev
Oncol Hematol. 2018;121:11-22.
55. Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He
F, Hermjakob H, Zhu Y. iProX: an integrated proteome resource. Nucleic
Acids Res. 2019;47(D1):D1211-D7.