Advances in proteomics in diffuse large B‑cell lymphoma (Review)
- Authors:
- Zihan Guo
- Chenchen Wang
- Xinyi Shi
- Zixuan Wang
- Jingyi Tao
- Jiaying Ma
- Lintao Bi
-
Affiliations: Department of Hematology and Oncology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China - Published online on: May 9, 2024 https://doi.org/10.3892/or.2024.8746
- Article Number: 87
This article is mentioned in:
Abstract
Thandra KC, Barsouk A, Saginala K, Padala SA, Barsouk A and Rawla P: Epidemiology of non-hodgkin's lymphoma. Med Sci (Basel). 9:52021.PubMed/NCBI | |
de Leval L and Jaffe ES: Lymphoma classification. Cancer. 26:176–185. 2020. View Article : Google Scholar : PubMed/NCBI | |
Harrington F, Greenslade M, Talaulikar D and Corboy G: Genomic characterisation of diffuse large B-cell lymphoma. Pathology. 53:367–376. 2021. View Article : Google Scholar : PubMed/NCBI | |
Opinto G, Vegliante MC, Negri A, Skrypets T, Loseto G, Pileri SA, Guarini A and Ciavarella S: The tumor microenvironment of DLBCL in the computational era. Front Oncol. 10:3512020. View Article : Google Scholar : PubMed/NCBI | |
McCarthy L, Bentley-DeSousa A, Denoncourt A, Tseng YC, Gabriel M and Downey M: Proteins required for vacuolar function are targets of lysine polyphosphorylation in yeast. FEBS Lett. 594:21–30. 2020. View Article : Google Scholar : PubMed/NCBI | |
Kanduc D: The role of proteomics in defining autoimmunity. Expert Rev Proteomics. 18:177–184. 2021. View Article : Google Scholar : PubMed/NCBI | |
Liang XJ, Song XY, Wu JL, Liu D, Lin BY, Zhou HS and Wang L: Advances in multi-omics study of prognostic biomarkers of diffuse large B-cell lymphoma. Int J Biol Sci. 18:1313–1327. 2022. View Article : Google Scholar : PubMed/NCBI | |
Stegemann M, Denker S and Schmitt CA: DLBCL 1L-what to expect beyond R-CHOP? Cancers (Basel). 14:14532022. View Article : Google Scholar : PubMed/NCBI | |
McArdle AJ and Menikou S: What is proteomics? Arch Dis Child Educ Pract Ed. 106:178–181. 2021. View Article : Google Scholar : PubMed/NCBI | |
Punetha A and Kotiya D: Advancements in oncoproteomics technologies: Treading toward translation into clinical practice. Proteomes. 11:22023. View Article : Google Scholar : PubMed/NCBI | |
Huang Z, Ma L, Huang C, Li Q and Nice EC: Proteomic profiling of human plasma for cancer biomarker discovery. Proteomics. 17:2017. View Article : Google Scholar | |
Kothalawala WJ, Barták BK, Nagy ZB, Zsigrai S, Szigeti KA, Valcz G, Takács I, Kalmár A and Molnár B: A detailed overview about the single-cell analyses of solid tumors focusing on colorectal cancer. Pathol Oncol Res. 28:16103422022. View Article : Google Scholar : PubMed/NCBI | |
Gao HX, Li SJ, Niu J, Ma ZP, Nuerlan A, Xue J, Wang MB, Cui WL, Abulajiang G, Sang W, et al: TCL1 as a hub protein associated with the PI3K/AKT signaling pathway in diffuse large B-cell lymphoma based on proteomics methods. Pathol Res Pract. 216:1527992020. View Article : Google Scholar : PubMed/NCBI | |
Bingham GC, Lee F, Naba A and Barker TH: Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology. Matrix Biol. 91-92:152–166. 2020. View Article : Google Scholar : PubMed/NCBI | |
Ednersson SB, Stern M, Fagman H, Nilsson-Ehle H, Hasselblom S, Thorsell A and Andersson PO: Proteomic analysis in diffuse large B-cell lymphoma identifies dysregulated tumor microenvironment proteins in non-GCB/ABC subtype patients. Leuk Lymphoma. 62:2360–2373. 2021. View Article : Google Scholar : PubMed/NCBI | |
Zhuang K, Zhang Y, Mo P, Deng L, Jiang Y, Yu L, Mei F, Huang S, Chen X, Yan Y, et al: Plasma proteomic analysis reveals altered protein abundances in HIV-infected patients with or without non-Hodgkin lymphoma. J Med Virol. 94:3876–3889. 2022. View Article : Google Scholar : PubMed/NCBI | |
Ysebaert L, Quillet-Mary A, Tosolini M, Pont F, Laurent C and Fournié JJ: Lymphoma heterogeneity unraveled by single-cell transcriptomics. Front Immunol. 12:5976512021. View Article : Google Scholar : PubMed/NCBI | |
Jiang M, Bennani NN and Feldman AL: Lymphoma classification update: T-cell lymphomas, Hodgkin lymphomas, and histiocytic/dendritic cell neoplasms. Expert Rev Hematol. 10:239–249. 2017. View Article : Google Scholar : PubMed/NCBI | |
Zhang J, Gu Y and Chen B: Drug-resistance mechanism and new targeted drugs and treatments of relapse and refractory DLBCL. Cancer Manag Res. 15:245–225. 2023. View Article : Google Scholar : PubMed/NCBI | |
Liu Y, Zeng L, Zhang S, Zeng S, Huang J, Tang Y and Zhong M: Identification of differentially expressed proteins in chemotherapy-sensitive and chemotherapy-resistant diffuse large B cell lymphoma by proteomic methods. Med Oncol. 30:5282013. View Article : Google Scholar : PubMed/NCBI | |
Xie M, Huang X, Ye X and Qian W: Prognostic and clinicopathological significance of PD-1/PD-L1 expression in the tumor microenvironment and neoplastic cells for lymphoma. Int Immunopharmacol. 77:1059992019. View Article : Google Scholar : PubMed/NCBI | |
Steen CB, Luca BA, Esfahani MS, Azizi A, Sworder BJ, Nabet BY, Kurtz DM, Liu CL, Khameneh F, Advani RH, et al: The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer Cell. 39:1422–37.e10. 2021. View Article : Google Scholar : PubMed/NCBI | |
Cioroianu AI, Stinga PI, Sticlaru L, Cioplea MD, Nichita L, Popp C and Staniceanu F: Tumor microenvironment in diffuse large B-cell lymphoma: role and prognosis. Anal Cell Pathol (Amst). 2019:85863542019.PubMed/NCBI | |
Ceccato J, Piazza M, Pizzi M, Manni S, Piazza F, Caputo I, Cinetto F, Pisoni L, Trojan D, Scarpa R, et al: A bone-based 3D scaffold as an in-vitro model of microenvironment-DLBCL lymphoma cell interaction. Front Oncol. 12:9478232022. View Article : Google Scholar : PubMed/NCBI | |
de Groot FA, de Groen RAL, van den Berg A, Jansen PM, Lam KH, Mutsaers PGNJ, van Noesel CJM, Chamuleau MED, Stevens WBC, Plaça JR, et al: Biological and clinical implications of gene-expression profiling in diffuse large B-cell lymphoma: A proposal for a targeted BLYM-777 consortium panel as part of a multilayered analytical approach. Cancers (Basel). 14:18572022. View Article : Google Scholar : PubMed/NCBI | |
Takahara T, Nakamura S, Tsuzuki T and Satou A: The immunology of DLBCL. Cancers (Basel). 15:8352023. View Article : Google Scholar : PubMed/NCBI | |
Ofori K, Bhagat G and Rai AJ: Exosomes and extracellular vesicles as liquid biopsy biomarkers in diffuse large B-cell lymphoma: Current state of the art and unmet clinical needs. Brit J Clin Pharmaco. 87:284–294. 2021. View Article : Google Scholar : PubMed/NCBI | |
Liu X, Zhao X, Yang J, Wang H, Piao Y and Wang L: High expression of AP2M1 correlates with worse prognosis by regulating immune microenvironment and drug resistance to R-CHOP in diffuse large B cell lymphoma. Eur J Haematol. 110:198–208. 2023. View Article : Google Scholar : PubMed/NCBI | |
Ejtehadifar M, Zahedi S, Gameiro P, Cabeçadas J, da Silva MG, Beck HC, Carvalho AS and Matthiesen R: Meta-analysis of MS-based proteomics studies indicates interferon regulatory factor 4 and nucleobindin1 as potential prognostic and drug resistance biomarkers in diffuse large B cell lymphoma. Cells. 12:1962023. View Article : Google Scholar : PubMed/NCBI | |
Ma J, Pang X, Li J, Zhang W and Cui W: The immune checkpoint expression in the tumor immune microenvironment of DLBCL: Clinicopathologic features and prognosis. Front Oncol. 12:10693782022. View Article : Google Scholar : PubMed/NCBI | |
Kotlov N, Bagaev A, Revuelta MV, Phillip JM, Cacciapuoti MT, Antysheva Z, Svekolkin V, Tikhonova E, Miheecheva N, Kuzkina N, et al: Clinical and biological subtypes of B-cell lymphoma revealed by microenvironmental signatures. Cancer Discov. 11:1468–1489. 2021. View Article : Google Scholar : PubMed/NCBI | |
Bouwstra R, He Y, de Boer J, Kooistra H, Cendrowicz E, Fehrmann RSN, Ammatuna E, Zu Eulenburg C, Nijland M, Huls G, et al: CD47 Expression defines efficacy of rituximab with CHOP in non-germinal center B-cell (non-GCB) diffuse large B-cell lymphoma patients (DLBCL), but not in GCB DLBCL. Cancer Immunol Res. 7:1663–1671. 2019. View Article : Google Scholar : PubMed/NCBI | |
Xu-Monette ZY, Wei L, Fang X, Au Q, Nunns H, Nagy M, Tzankov A, Zhu F, Visco C, Bhagat G, et al: Genetic subtyping and phenotypic characterization of the immune microenvironment and MYC/BCL2 double expression reveal heterogeneity in diffuse large B-cell lymphoma. Clin Cancer Res. 28:972–983. 2022. View Article : Google Scholar : PubMed/NCBI | |
Feng Y, Zhong M, Tang Y, Liu X, Liu Y, Wang L and Zhou H: The role and underlying mechanism of exosomal CA1 in chemotherapy resistance in diffuse large B cell lymphoma. Mol Ther Nucleic Acids. 21:452–463. 2020. View Article : Google Scholar : PubMed/NCBI | |
Klein C, Jamois C and Nielsen T: Anti-CD20 treatment for B-cell malignancies: Current status and future directions. Expert Opin Biol Ther. 21:161–181. 2021. View Article : Google Scholar : PubMed/NCBI | |
Poletto S, Novo M, Paruzzo L, Frascione PMM and Vitolo U: Treatment strategies for patients with diffuse large B-cell lymphoma. Cancer Treat Rev. 110:1024432022. View Article : Google Scholar : PubMed/NCBI | |
Susanibar-Adaniya S and Barta SK: 2021 Update on diffuse large B cell lymphoma: A review of current data and potential applications on risk stratification and management. Am J Hematol. 96:617–629. 2021. View Article : Google Scholar : PubMed/NCBI | |
Roider T, Seufert J, Uvarovskii A, Frauhammer F, Bordas M, Abedpour N, Stolarczyk M, Mallm JP, Herbst SA, Bruch PM, et al: Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels. Nat Cell Biol. 22:896–906. 2020. View Article : Google Scholar : PubMed/NCBI | |
Ferreri AJM, Doorduijn JK, Re A, Cabras MG, Smith J, Ilariucci F, Luppi M, Calimeri T, Cattaneo C, Khwaja J, et al: MATRix-RICE therapy and autologous haematopoietic stem-cell transplantation in diffuse large B-cell lymphoma with secondary CNS involvement (MARIETTA): An international, single-arm, phase 2 trial. Lancet Haematol. 8:e110–e121. 2021. View Article : Google Scholar : PubMed/NCBI | |
Yan J, Yuan W, Zhang J, Li L, Zhang L, Zhang X and Zhang M: Identification and validation of a prognostic prediction model in diffuse large B-cell lymphoma. Front Endocrinol (Lausanne). 13:8463572022. View Article : Google Scholar : PubMed/NCBI | |
Stanwood SR, Chong LC, Steidl C and Jefferies WA: Distinct gene expression patterns of calcium channels and related signaling pathways discovered in lymphomas. Front Pharmacol. 13:7951762022. View Article : Google Scholar : PubMed/NCBI | |
Frontzek F, Karsten I, Schmitz N and Lenz G: Current options and future perspectives in the treatment of patients with relapsed/refractory diffuse large B-cell lymphoma. Ther Adv Hematol. 13:204062072211033212022. View Article : Google Scholar : PubMed/NCBI | |
Li S, Young KH and Medeiros LJ: Diffuse large B-cell lymphoma. Pathology. 50:74–87. 2018. View Article : Google Scholar : PubMed/NCBI | |
Gao HX, Nuerlan A, Abulajiang G, Cui WL, Xue J, Sang W, Li SJ, Niu J, Ma ZP, Zhang W and Li XX: Quantitative proteomics analysis of differentially expressed proteins in activated B-cell-like diffuse large B-cell lymphoma using quantitative proteomics. Pathol Res Pract. 215:1525282019. View Article : Google Scholar : PubMed/NCBI | |
Robotti E, Calà E and Marengo E: Two-dimensional gel electrophoresis image analysis. Methods Mol Biol. 2361:3–13. 2021. View Article : Google Scholar : PubMed/NCBI | |
Rotello RJ and Veenstra TD: Mass spectrometry techniques: Principles and practices for quantitative proteomics. Curr Protein Pept Sci. 22:121–133. 2021. View Article : Google Scholar : PubMed/NCBI | |
Yang J, Li Y, Zhang Y, Fang X, Chen N, Zhou X and Wang X: Sirt6 promotes tumorigenesis and drug resistance of diffuse large B-cell lymphoma by mediating PI3K/Akt signaling. J Exp Clin Cancer Res. 39:1422020. View Article : Google Scholar : PubMed/NCBI | |
Zhang X, Duan YT, Wang Y, Zhao XD, Sun YM, Lin DZ, Chen Y, Wang YX, Zhou ZW, Liu YX, et al: SAF-248, a novel PI3Kδ-selective inhibitor, potently suppresses the growth of diffuse large B-cell lymphoma. Acta Pharmacol Sin. 43:209–219. 2022. View Article : Google Scholar : PubMed/NCBI | |
Chen CC, Hsu CC, Chen SL, Lin PH, Chen JP, Pan YR, Huang CE, Chen YJ, Chen YY, Wu YY and Yang MH: RAS mediates BET inhibitor-endued repression of lymphoma migration and prognosticates a novel proteomics-based subgroup of DLBCL through its negative regulator IQGAP3. Cancers (Basel). 13:50242021. View Article : Google Scholar : PubMed/NCBI | |
Wang N, Wu R, Tang D and Kang R: The BET family in immunity and disease. Signal Transduct Target Ther. 6:232021. View Article : Google Scholar : PubMed/NCBI | |
Sun F, Fang X and Wang X: Signal pathways and therapeutic prospects of diffuse large B cell lymphoma. Anticancer Agents Med Chem. 19:2047–2059. 2019. View Article : Google Scholar : PubMed/NCBI | |
Xu W, Berning P and Lenz G: Targeting B-cell receptor and PI3K signaling in diffuse large B-cell lymphoma. Blood. 138:1110–1119. 2021. View Article : Google Scholar : PubMed/NCBI | |
Dunleavy K, Erdmann T and Lenz G: Targeting the B-cell receptor pathway in diffuse large B-cell lymphoma. Cancer Treat Rev. 65:41–46. 2018. View Article : Google Scholar : PubMed/NCBI | |
Bisserier M and Wajapeyee N: Mechanisms of resistance to EZH2 inhibitors in diffuse large B-cell lymphomas. Blood. 131:2125–2137. 2018. View Article : Google Scholar : PubMed/NCBI | |
Coronado BNL, da Cunha FBS, de Toledo Nobrega O and Martins AMA: The impact of mass spectrometry application to screen new proteomics biomarkers in ophthalmology. Int Ophthalmol. 41:2619–2633. 2021. View Article : Google Scholar : PubMed/NCBI | |
Dallavalasa S, Beeraka NM, Basavaraju CG, Tulimilli SV, Sadhu SP, Rajesh K, Aliev G and Madhunapantula SV: The role of tumor associated macrophages (TAMs) in cancer progression, chemoresistance, angiogenesis and metastasis-current status. Curr Med Chem. 28:8203–8236. 2021. View Article : Google Scholar : PubMed/NCBI | |
Kelly RT: Single-cell proteomics: Progress and prospects. Mol Cell Proteomics. 19:1739–1748. 2020. View Article : Google Scholar : PubMed/NCBI | |
Hasin Y, Seldin M and Lusis A: Multi-omics approaches to disease. Genome Biol. 18:832017. View Article : Google Scholar : PubMed/NCBI | |
Wang L, Li LR and Young KH: New agents and regimens for diffuse large B cell lymphoma. J Hematol Oncol. 13:1752020. View Article : Google Scholar : PubMed/NCBI | |
Xiong J, Cui BW, Wang N, Dai YT, Zhang H, Wang CF, Zhong HJ, Cheng S, Ou-Yang BS, Hu Y, et al: Genomic and transcriptomic characterization of natural killer T cell lymphoma. Cancer Cell. 37:403–419.e6. 2020. View Article : Google Scholar : PubMed/NCBI | |
van der Meeren LE, Kluiver J, Rutgers B, Alsagoor Y, Kluin PM, van den Berg A and Visser L: A super-SILAC based proteomics analysis of diffuse large B-cell lymphoma-NOS patient samples to identify new proteins that discriminate GCB and non-GCB lymphomas. PLoS One. 14:e02232602019. View Article : Google Scholar : PubMed/NCBI | |
Zhang P and Zhang M: Epigenetic alterations and advancement of treatment in peripheral T-cell lymphoma. Clin Epigenetics. 12:1692020. View Article : Google Scholar : PubMed/NCBI | |
Jiang H, Li A, Ji Z, Tian M and Zhang H: Role of radiomics-based baseline PET/CT imaging in lymphoma: Diagnosis, prognosis, and response assessment. Mol Imaging Biol. 24:537–549. 2022. View Article : Google Scholar : PubMed/NCBI | |
Fornecker LM, Muller L, Bertrand F, Paul N, Pichot A, Herbrecht R, Chenard MP, Mauvieux L, Vallat L, Bahram S, et al: Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma. Sci Rep. 9:8952019. View Article : Google Scholar : PubMed/NCBI | |
Bresnick AR, Weber DJ and Zimmer DB: S100 proteins in cancer. Nat Rev Cancer. 15:96–109. 2015. View Article : Google Scholar : PubMed/NCBI | |
Ye X, Wang L, Nie M, Wang Y, Dong S, Ren W, Li G, Li ZM, Wu K and Pan-Hammarström Q: A single-cell atlas of diffuse large B cell lymphoma. Cell Rep. 39:1107132022. View Article : Google Scholar : PubMed/NCBI | |
Wang N, Li X, Wang R and Ding Z: Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment. Biotechnol J. 16:e21000412021. View Article : Google Scholar : PubMed/NCBI | |
Cumming IA, Degorce SL, Aagaard A, Braybrooke EL, Davies NL, Diène CR, Eatherton AJ, Felstead HR, Groombridge SD, Lenz EM, et al: Identification and optimisation of a pyrimidopyridone series of IRAK4 inhibitors. Bioorg Med Chem. 63:1167292022. View Article : Google Scholar : PubMed/NCBI | |
Yoon SB, Hong H, Lim HJ, Choi JH, Choi YP, Seo SW, Lee HW, Chae CH, Park WK, Kim HY, et al: A novel IRAK4/PIM1 inhibitor ameliorates rheumatoid arthritis and lymphoid malignancy by blocking the TLR/MYD88-mediated NF-κB pathway. Acta Pharm Sin B. 13:1093–1109. 2023. View Article : Google Scholar : PubMed/NCBI | |
Zhang J, Fu L, Shen B, Liu Y, Wang W, Cai X, Kong L, Yan Y, Meng R, Zhang Z, et al: Assessing IRAK4 functions in ABC DLBCL by IRAK4 kinase inhibition and protein degradation. Cell Chem Biol. 27:1500–1509.e13. 2020. View Article : Google Scholar : PubMed/NCBI | |
Boșoteanu M, Cristian M, Așchie M, Deacu M, Mitroi AF, Brînzan CS and Bălțătescu GI: Proteomics and genomics of a monomorphic epitheliotropic intestinal T-cell lymphoma: An extremely rare case report and short review of literature. Medicine (Baltimore). 101:e319512022. View Article : Google Scholar : PubMed/NCBI | |
Coradduzza D, Ghironi A, Azara E, Culeddu N, Cruciani S, Zinellu A, Maioli M, De Miglio MR, Medici S, Fozza C and Carru C: Role of polyamines as biomarkers in lymphoma patients: A pilot study. Diagnostics (Basel). 12:21512022. View Article : Google Scholar : PubMed/NCBI | |
Cheson BD, Nowakowski G and Salles G: Diffuse large B-cell lymphoma: New targets and novel therapies. Blood Cancer J. 11:682021. View Article : Google Scholar : PubMed/NCBI | |
Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Ng SY, Tsou CC, Brown NA, et al: Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas. Proc Natl Acad Sci USA. 114:6581–6586. 2017. View Article : Google Scholar : PubMed/NCBI | |
Huang L, Brunell D, Stephan C, Mancuso J, Yu X, He B, Zinner R, Kim J, Davies P and Wong STC: Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction. Bioinformatics. 35:3709–3717. 2019. View Article : Google Scholar : PubMed/NCBI | |
Chakraborty S, Hosen MI, Ahmed M and Shekhar HU: Onco-multi-OMICS approach: A new frontier in cancer research. Biomed Res Int. 2018:98362562018. View Article : Google Scholar : PubMed/NCBI | |
Gohil SH, Iorgulescu JB, Braun DA, Keskin DB and Livak KJ: Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Nat Rev Clin Oncol. 18:244–256. 2021. View Article : Google Scholar : PubMed/NCBI | |
Yang D, Wang J, Hu M, Li F, Yang F, Zhao Y, Xu Y and Zhang X, Tang L and Zhang X: Combined multiomics analysis reveals the mechanism of CENPF overexpression-mediated immune dysfunction in diffuse large B-cell lymphoma in vitro. Front Genet. 13:10726892022. View Article : Google Scholar : PubMed/NCBI | |
Landeira-Viñuela A, Diez P, Juanes-Velasco P, Lécrevisse Q, Orfao A, De Las Rivas J and Fuentes M: Deepening into intracellular signaling landscape through integrative spatial proteomics and transcriptomics in a lymphoma model. Biomolecules. 11:17762021. View Article : Google Scholar : PubMed/NCBI | |
Jamil MO and Mehta A: Diffuse large B-cell lymphoma: Prognostic markers and their impact on therapy. Expert Rev Hematol. 9:471–477. 2016. View Article : Google Scholar : PubMed/NCBI | |
Maurer MJ, Micallef INM, Cerhan JR, Katzmann JA, Link BK, Colgan JP, Habermann TM, Inwards DJ, Markovic SN, Ansell SM, et al: Elevated serum free light chains are associated with event-free and overall survival in two independent cohorts of patients with diffuse large B-cell lymphoma. J Clin Oncol. 29:1620–1626. 2011. View Article : Google Scholar : PubMed/NCBI | |
Witzig TE, Maurer MJ, Stenson MJ, Allmer C, Macon W, Link B, Katzmann JA and Gupta M: Elevated serum monoclonal and polyclonal free light chains and interferon inducible protein-10 predicts inferior prognosis in untreated diffuse large B-cell lymphoma. Am J Hematol. 89:417–422. 2014. View Article : Google Scholar : PubMed/NCBI | |
Grünwald BT, Devisme A, Andrieux G, Vyas F, Aliar K, McCloskey CW, Macklin A, Jang GH, Denroche R, Romero JM, et al: Spatially confined sub-tumor microenvironments in pancreatic cancer. Cell. 184:5577–5592.e18. 2021. View Article : Google Scholar : PubMed/NCBI | |
Akhtar M, Haider A, Rashid S and Al-Nabet ADMH: Paget's ‘seed and soil’ theory of cancer metastasis: An idea whose time has come. Adv Anat Pathol. 26:69–74. 2019. View Article : Google Scholar : PubMed/NCBI | |
Cords L, Tietscher S, Anzeneder T, Langwieder C, Rees M, de Souza N and Bodenmiller B: Cancer-associated fibroblast classification in single-cell and spatial proteomics data. Nat Commun. 14:42942023. View Article : Google Scholar : PubMed/NCBI | |
Franciosa G, Kverneland AH, Jensen AWP, Donia M and Olsen JV: Proteomics to study cancer immunity and improve treatment. Semin Immunopathol. 45:241–251. 2023. View Article : Google Scholar : PubMed/NCBI | |
Gatto L, Breckels LM and Lilley KS: Assessing sub-cellular resolution in spatial proteomics experiments. Curr Opin Chem Biol. 48:123–149. 2019. View Article : Google Scholar : PubMed/NCBI | |
Liu X, Salokas K, Tamene F, Jiu Y, Weldatsadik RG, Öhman T and Varjosalo M: An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat Commun. 9:11882018. View Article : Google Scholar : PubMed/NCBI | |
Pankow S, Martínez-Bartolomé S, Bamberger C and Yates JR: Understanding molecular mechanisms of disease through spatial proteomics. Curr Opin Chem Biol. 48:19–25. 2019. View Article : Google Scholar : PubMed/NCBI | |
Guilliams M, Bonnardel J, Haest B, Vanderborght B, Wagner C, Remmerie A, Bujko A, Martens L, Thoné T, Browaeys R, et al: Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 185:379–396.e38. 2022. View Article : Google Scholar : PubMed/NCBI | |
Lee PY, Saraygord-Afshari N and Low TY: The evolution of two-dimensional gel electrophoresis-from proteomics to emerging alternative applications. J Chromatogr A. 1615:4607632020. View Article : Google Scholar : PubMed/NCBI | |
Strohkamp S, Gemoll T and Habermann JK: Possibilities and limitations of 2DE-based analyses for identifying low-abundant tumor markers in human serum and plasma. Proteomics. 16:2519–2532. 2016. View Article : Google Scholar : PubMed/NCBI | |
Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ and Shi T: Mass spectrometry-based targeted proteomics for analysis of protein mutations. Mass Spectrom Rev. 42:796–821. 2023. View Article : Google Scholar : PubMed/NCBI | |
Noor Z, Ahn SB, Baker MS, Ranganathan S and Mohamedali A: Mass spectrometry-based protein identification in proteomics-a review. Brief Bioinform. 22:1620–1638. 2021. View Article : Google Scholar : PubMed/NCBI | |
Ren AH, Diamandis EP and Kulasingam V: Uncovering the depths of the human proteome: Antibody-based technologies for ultrasensitive multiplexed protein detection and quantification. Mol Cell Proteomics. 20:1001552021. View Article : Google Scholar : PubMed/NCBI | |
Syu GD, Dunn J and Zhu H: Developments and applications of functional protein microarrays. Mol Cell Proteomics. 19:916–927. 2020. View Article : Google Scholar : PubMed/NCBI |