Single‑cell multi‑omics advances in lymphoma research (Review)
- Authors:
- Chanjuan Jin
- Di Zhou
- Jun Li
- Lintao Bi
- Lisha Li
-
Affiliations: Department of Hematology and Oncology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Hematology and Oncology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China - Published online on: August 23, 2023 https://doi.org/10.3892/or.2023.8621
- Article Number: 184
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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 | |
|
Bocci F, Gearhart-Serna L, Boareto M, Ribeiro M, Ben-Jacob E, Devi GR, Levine H, Onuchic JN and Jolly MK: Toward understanding cancer stem cell heterogeneity in the tumor microenvironment. Proc Natl Acad Sci USA. 116:148–157. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Lei Y, Tang R, Xu J, Wang W, Zhang B, Liu J, Yu X and Shi S: Applications of single-cell sequencing in cancer research: Progress and perspectives. J Hematol Oncol. 14:912021. View Article : Google Scholar : PubMed/NCBI | |
|
Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, et al: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403:503–511. 2000. View Article : Google Scholar : PubMed/NCBI | |
|
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES and Mesirov JP: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 102:15545–15550. 2005. View Article : Google Scholar : PubMed/NCBI | |
|
Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M and Alizadeh AA: Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 12:453–457. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, Nair VS, Xu Y, Khuong A, Hoang CD, et al: The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat Med. 21:938–945. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
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 | |
|
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. | |
|
Borcherding N, Voigt AP, Liu V, Link BK, Zhang W and Jabbari A: Single-Cell profiling of cutaneous T-Cell lymphoma reveals underlying heterogeneity associated with disease progression. Clin Cancer Res. 25:2996–3005. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Gaydosik AM, Tabib T, Geskin LJ, Bayan CA, Conway JF, Lafyatis R and Fuschiotti P: Single-Cell lymphocyte heterogeneity in advanced cutaneous T-cell lymphoma skin tumors. Clin Cancer Res. 25:4443–4454. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Zhang W, Yang B, Weng L, Li J, Bai J, Wang T, Wang J, Ye J, Jing H, Jiao Y, et al: Single cell sequencing reveals cell populations that predict primary resistance to imatinib in chronic myeloid leukemia. Aging (Albany NY). 12:25337–25355. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Ren J, Qu R, Rahman NT, Lewis JM, King ALO, Liao X, Mirza FN, Carlson KR, Huang Y, Gigante S, et al: Integrated transcriptome and trajectory analysis of cutaneous T-cell lymphoma identifies putative precancer populations. Blood Adv. 7:445–457. 2023. View Article : Google Scholar : PubMed/NCBI | |
|
Yamagishi M, Kubokawa M, Kuze Y, Suzuki A, Yokomizo A, Kobayashi S, Nakashima M, Makiyama J, Iwanaga M, Fukuda T, et al: Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma. Nat Commun. 12:48212021. View Article : Google Scholar : PubMed/NCBI | |
|
Haebe S, Shree T, Sathe A, Day G, Czerwinski DK, Grimes SM, Lee H, Binkley MS, Long SR, Martin B, et al: Single-cell analysis can define distinct evolution of tumor sites in follicular lymphoma. Blood. 137:2869–2880. 2021. View Article : Google Scholar : PubMed/NCBI | |
|
Borcherding N, Severson KJ, Henderson N, Ortolan LS, Rosenthal AC, Bellizzi AM, Liu V, Link BK, Mangold AR and Jabbari A: Single-cell analysis of Sézary syndrome reveals novel markers and shifting gene profiles associated with treatment. Blood Adv. 7:321–335. 2023. View Article : Google Scholar : PubMed/NCBI | |
|
Valentin Hansen S, Høy Hansen M, Cédile O, Møller MB, Haaber J, Abildgaard N and Guldborg Nyvold C: Detailed characterization of the transcriptome of single B cells in mantle cell lymphoma suggesting a potential use for SOX4. Sci Rep. 11:190922021. View Article : Google Scholar : PubMed/NCBI | |
|
Pritchett JC, Yang ZZ, Kim HJ, Villasboas JC, Tang X, Jalali S, Cerhan JR, Feldman AL and Ansell SM: High-dimensional and single-cell transcriptome analysis of the tumor microenvironment in angioimmunoblastic T cell lymphoma (AITL). Leukemia. 36:165–176. 2022. View Article : Google Scholar : PubMed/NCBI | |
|
Wei B, Liu Z, Fan Y, Wang S, Dong C, Rao W, Yang F, Cheng G and Zhang J: Analysis of cellular heterogeneity in immune microenvironment of primary central nervous system lymphoma by single-cell sequencing. Front Oncol. 11:6830072021. View Article : Google Scholar : PubMed/NCBI | |
|
Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, et al: Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 161:1202–1214. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA and Kirschner MW: Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 161:1187–1201. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, et al: Massively parallel digital transcriptional profiling of single cells. Nat Commun. 8:140492017. View Article : Google Scholar : PubMed/NCBI | |
|
Gong H, Do D and Ramakrishnan R: Single-Cell mRNA-Seq using the fluidigm C1 system and integrated fluidics circuits. Methods Mol Biol. 1783:193–207. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC and Guo G: Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome Biol. 19:472018. View Article : Google Scholar : PubMed/NCBI | |
|
Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, Leonhardt H, Heyn H, Hellmann I and Enard W: Comparative analysis of single-cell RNA sequencing methods. Mol Cell. 65:631–643.e4. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Xin Y, Kim J, Ni M, Wei Y, Okamoto H, Lee J, Adler C, Cavino K, Murphy AJ, Yancopoulos GD, et al: Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. Proc Natl Acad Sci USA. 113:3293–3298. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Gierahn TM, Wadsworth MH II, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC and Shalek AK: Seq-Well: Portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods. 14:395–398. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Aicher TP, Carroll S, Raddi G, Gierahn T, Wadsworth MH II, Hughes TK, Love C and Shalek AK: Seq-Well: A sample-efficient, portable picowell platform for massively parallel single-cell RNA sequencing. Methods Mol Biol. 1979:111–132. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, et al: Mapping the mouse cell atlas by microwell-seq. Cell. 173:13072018. View Article : Google Scholar : PubMed/NCBI | |
|
Lai S, Huang W, Xu Y, Jiang M, Chen H, Cheng C, Lu Y, Huang H, Guo G and Han X: Comparative transcriptomic analysis of hematopoietic system between human and mouse by Microwell-seq. Cell Discov. 4:342018. View Article : Google Scholar : PubMed/NCBI | |
|
Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW and Klein AM: The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science. 360:eaar57802018. View Article : Google Scholar : PubMed/NCBI | |
|
Tosches MA, Yamawaki TM, Naumann RK, Jacobi AA, Tushev G and Laurent G: Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles. Science. 360:881–888. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, Cohen N, Jung S, Tanay A and Amit I: Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science. 343:776–779. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R and Smibert P: Simultaneous epitope and transcriptome measurement in single cells. Nat Methods. 14:865–868. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Mimitou EP, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, et al: Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nat Methods. 16:409–412. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Harris NL, Jaffe ES, Stein H, Banks PM, Chan JK, Cleary ML, Delsol G, De Wolf-Peeters C, Falini B, Gatter KC, et al: A revised European-American classification of lymphoid neoplasms: A proposal from the International Lymphoma Study Group. Blood. 84:1361–1392. 1994. View Article : Google Scholar : PubMed/NCBI | |
|
Barbui T, Thiele J, Gisslinger H, Kvasnicka HM, Vannucchi AM, Guglielmelli P, Orazi A and Tefferi A: The 2016 WHO classification and diagnostic criteria for myeloproliferative neoplasms: Document summary and in-depth discussion. Blood Cancer J. 8:152018. View Article : Google Scholar : PubMed/NCBI | |
|
Glaser SL and Jarrett RF: The epidemiology of Hodgkin's disease. Baillieres Clin Haematol. 9:401–416. 1996. View Article : Google Scholar : PubMed/NCBI | |
|
Marafioti T, Hummel M, Foss HD, Laumen H, Korbjuhn P, Anagnostopoulos I, Lammert H, Demel G, Theil J, Wirth T and Stein H: Hodgkin and reed-sternberg cells represent an expansion of a single clone originating from a germinal center B-cell with functional immunoglobulin gene rearrangements but defective immunoglobulin transcription. Blood. 95:1443–1450. 2000. View Article : Google Scholar : PubMed/NCBI | |
|
Kanzler H, Küppers R, Hansmann ML and Rajewsky K: Hodgkin and Reed-Sternberg cells in Hodgkin's disease represent the outgrowth of a dominant tumor clone derived from (crippled) germinal center B cells. J Exp Med. 184:1495–1505. 1996. View Article : Google Scholar : PubMed/NCBI | |
|
Grimm KE and O'Malley DP: Aggressive B cell lymphomas in the 2017 revised WHO classification of tumors of hematopoietic and lymphoid tissues. Ann Diagn Pathol. 38:6–10. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
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 J. 26:176–185. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
García-Sanz R and Jiménez C: Time to move to the single-cell level: Applications of single-cell multi-omics to hematological malignancies and Waldenström's Macroglobulinemia-A particularly heterogeneous lymphoma. Cancers (Basel). 13:15412021. View Article : Google Scholar : PubMed/NCBI | |
|
Glass DR, Tsai AG, Oliveria JP, Hartmann FJ, Kimmey SC, Calderon AA, Borges L, Glass MC, Wagar LE, Davis MM and Bendall SC: An Integrated Multi-omic Single-cell atlas of human B cell identity. Immunity. 53:217–232.e5. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Crinier A, Dumas PY, Escalière B, Piperoglou C, Gil L, Villacreces A, Vély F, Ivanovic Z, Milpied P, Narni-Mancinelli É and Vivier É: Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemia. Cell Mol Immunol. 18:1290–1304. 2021. View Article : Google Scholar : PubMed/NCBI | |
|
Aoki T, Chong LC, Takata K, Milne K, Hav M, Colombo A, Chavez EA, Nissen M, Wang X, Miyata-Takata T, et al: Single-Cell transcriptome analysis reveals disease-defining T-cell subsets in the tumor microenvironment of classic Hodgkin Lymphoma. Cancer Discov. 10:406–421. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Pizzolato G, Kaminski H, Tosolini M, Franchini DM, Pont F, Martins F, Valle C, Labourdette D, Cadot S, Quillet-Mary A, et al: Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes. Proc Natl Acad Sci USA. 116:11906–11915. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Singh M, Al-Eryani G, Carswell S, Ferguson JM, Blackburn J, Barton K, Roden D, Luciani F, Giang Phan T, Junankar S, et al: High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Nat Commun. 10:31202019. View Article : Google Scholar : PubMed/NCBI | |
|
Vitak SA, Torkenczy KA, Rosenkrantz JL, Fields AJ, Christiansen L, Wong MH, Carbone L, Steemers FJ and Adey A: Sequencing thousands of single-cell genomes with combinatorial indexing. Nat Methods. 14:302–328. 2017. 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 | |
|
Li P, Chai J, Chen Z, Liu Y, Wei J, Liu Y, Zhao D, Ma J, Wang K, Li X, et al: Genomic mutation profile of primary gastrointestinal diffuse large B-Cell Lymphoma. Front Oncol. 11:6226482021. View Article : Google Scholar : PubMed/NCBI | |
|
Radke J, Ishaque N, Koll R, Gu Z, Schumann E, Sieverling L, Uhrig S, Hübschmann D, Toprak UH, López C, et al: The genomic and transcriptional landscape of primary central nervous system lymphoma. Nat Commun. 13:25582022. View Article : Google Scholar : PubMed/NCBI | |
|
Yi S, Yan Y, Jin M, Bhattacharya S, Wang Y, Wu Y, Yang L, Gine E, Clot G, Chen L, et al: Genomic and transcriptomic profiling reveals distinct molecular subsets associated with outcomes in mantle cell lymphoma. J Clin Invest. 132:e1532832022. View Article : Google Scholar : PubMed/NCBI | |
|
Nadeu F, Martin-Garcia D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, et al: Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes. Blood. 136:1419–1432. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
De Bie J, Demeyer S, Alberti-Servera L, Geerdens E, Segers H, Broux M, De Keersmaecker K, Michaux L, Vandenberghe P, Voet T, et al: Single-cell sequencing reveals the origin and the order of mutation acquisition in T-cell acute lymphoblastic leukemia. Leukemia. 32:1358–1369. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, et al: Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nat Commun. 10:14592019. View Article : Google Scholar : PubMed/NCBI | |
|
Küçük C, Hu X, Gong Q, Jiang B, Cornish A, Gaulard P, McKeithan T and Chan WC: Diagnostic and biological significance of KIR EXPRESSION PROFILE DETErmined by RNA-Seq in Natural Killer/T-Cell Lymphoma. Am J Pathol. 186:1435–1441. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Andor N, Simonds EF, Czerwinski DK, Chen J, Grimes SM, Wood-Bouwens C, Zheng GXY, Kubit MA, Greer S, Weiss WA, et al: Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints. Blood. 133:1119–1129. 2019. 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((6))2017. | |
|
Kim MK, Song JY, Koh DI, Kim JY, Hatano M, Jeon BN, Kim MY, Cho SY, Kim KS and Hur MW: Reciprocal negative regulation between the tumor suppressor protein p53 and B cell CLL/lymphoma 6 (BCL6) via control of caspase-1 expression. J Biol Chem. 294:299–313. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Daniunaite K, Jarmalaite S and Kriukiene E: Epigenomic technologies for deciphering circulating tumor DNA. Curr Opin Biotechnol. 55:23–29. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Ng SB, Yan J, Huang G, Selvarajan V, Tay JL, Lin B, Bi C, Tan J, Kwong YL, Shimizu N, et al: Dysregulated microRNAs affect pathways and targets of biologic relevance in nasal-type natural killer/T-cell lymphoma. Blood. 118:4919–4929. 2011. View Article : Google Scholar : PubMed/NCBI | |
|
Zhang X, Ji W, Huang R, Li L, Wang X, Li L, Fu X, Sun Z, Li Z, Chen Q and Zhang M: MicroRNA-155 is a potential molecular marker of natural killer/T-cell lymphoma. Oncotarget. 7:53808–53819. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Yan J, Ng SB, Tay JL, Lin B, Koh TL, Tan J, Selvarajan V, Liu SC, Bi C, Wang S, et al: EZH2 overexpression in natural killer/T-cell lymphoma confers growth advantage independently of histone methyltransferase activity. Blood. 121:4512–4520. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Liang L, Nong L, Zhang S, Zhao J, Ti H, Dong Y, Zhang B and Li T: The downregulation of PRDM1/Blimp-1 is associated with aberrant expression of miR-223 in extranodal NK/T-cell lymphoma, nasal type. J Exp Clin Cancer Res. 33:72014. View Article : Google Scholar : PubMed/NCBI | |
|
Küçük C, Hu X, Jiang B, Klinkebiel D, Geng H, Gong Q, Bouska A, Iqbal J, Gaulard P, McKeithan TW and Chan WC: Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma. Clin Cancer Res. 21:1699–1711. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Chen YW, Guo T, Shen L, Wong KY, Tao Q, Choi WW, Au-Yeung RK, Chan YP, Wong ML, Tang JC, et al: Receptor-type tyrosine-protein phosphatase κ directly targets STAT3 activation for tumor suppression in nasal NK/T-cell lymphoma. Blood. 125:1589–1600. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB and Cvejic A: Integrative Single-Cell RNA-Seq and ATAC-seq analysis of human developmental hematopoiesis. Cell Stem Cell. 28:472–487.e7. 2021. View Article : Google Scholar : PubMed/NCBI | |
|
Yu J, Gemenetzis G, Kinny-Köster B, Habib JR, Groot VP, Teinor J, Yin L, Pu N, Hasanain A, van Oosten F, et al: Pancreatic circulating tumor cell detection by targeted single-cell next-generation sequencing. Cancer Lett. 493:245–253. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Zhang L, Dong X, Lee M, Maslov AY, Wang T and Vijg J: Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan. Proc Natl Acad Sci USA. 116:9014–9019. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Psatha K, Kollipara L, Voutyraki C, Divanach P, Sickmann A, Rassidakis GZ, Drakos E and Aivaliotis M: Deciphering lymphoma pathogenesis via state-of-the-art mass spectrometry-based quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 1047:2–14. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Bacher U, Haferlach T, Alpermann T, Kern W, Schnittger S and Haferlach C: Several lymphoma-specific genetic events in parallel can be found in mature B-cell neoplasms. Genes Chromosomes Cancer. 50:43–50. 2011. View Article : Google Scholar : PubMed/NCBI | |
|
Okosun J, Bödör C, Wang J, Araf S, Yang CY, Pan C, Boller S, Cittaro D, Bozek M, Iqbal S, et al: Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nat Genet. 46:176–181. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Sewastianik T, Prochorec-Sobieszek M, Chapuy B and Juszczyński P: MYC deregulation in lymphoid tumors: Molecular mechanisms, clinical consequences and therapeutic implications. Biochim Biophys Acta. 1846:457–467. 2014.PubMed/NCBI | |
|
Rosenthal A and Rimsza L: Genomics of aggressive B-cell lymphoma. Hematology Am Soc Hematol Educ Program. 2018:69–74. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Gawad C, Koh W and Quake SR: Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics. Proc Natl Acad Sci USA. 111:17947–17952. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Snuderl M, Kolman OK, Chen YB, Hsu JJ, Ackerman AM, Dal Cin P, Ferry JA, Harris NL, Hasserjian RP, Zukerberg LR, et al: B-cell lymphomas with concurrent IGH-BCL2 and MYC rearrangements are aggressive neoplasms with clinical and pathologic features distinct from Burkitt lymphoma and diffuse large B-cell lymphoma. Am J Surg Pathol. 34:327–340. 2010. View Article : Google Scholar : PubMed/NCBI | |
|
Huang W, Medeiros LJ, Lin P, Wang W, Tang G, Khoury J, Konoplev S, Yin CC, Xu J, Oki Y and Li S: MYC/BCL2/BCL6 triple hit lymphoma: A study of 40 patients with a comparison to MYC/BCL2 and MYC/BCL6 double hit lymphomas. Mod Pathol. 31:1470–1478. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Moore EM, Aggarwal N, Surti U and Swerdlow SH: Further exploration of the complexities of large B-Cell Lymphomas With MYC abnormalities and the importance of a blastoid morphology. Am J Surg Pathol. 41:1155–1166. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LH, Melnick AM, Tam W and Elemento O: Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas. Genome Biol. 15:4322014. View Article : Google Scholar : PubMed/NCBI | |
|
Ding S, Chen X and Shen K: Single-cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy. Cancer Commun (Lond). 40:329–344. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Kim E, Hurtz C, Koehrer S, Wang Z, Balasubramanian S, Chang BY, Müschen M, Davis RE and Burger JA: Ibrutinib inhibits pre-BCR(+) B-cell acute lymphoblastic leukemia progression by targeting BTK and BLK. Blood. 129:1155–1165. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Wang L, Mo S, Li X, He Y and Yang J: Single-cell RNA-seq reveals the immune escape and drug resistance mechanisms of mantle cell lymphoma. Cancer Biol Med. 17:726–739. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Marcus R, Imrie K, Solal-Celigny P, Catalano JV, Dmoszynska A, Raposo JC, Offner FC, Gomez-Codina J, Belch A, Cunningham D, et al: Phase III study of R-CVP compared with cyclophosphamide, vincristine, and prednisone alone in patients with previously untreated advanced follicular lymphoma. J Clin Oncol. 26:4579–4586. 2008. View Article : Google Scholar : PubMed/NCBI | |
|
Lim SH, Vaughan AT, Ashton-Key M, Williams EL, Dixon SV, Chan HT, Beers SA, French RR, Cox KL, Davies AJ, et al: Fc gamma receptor IIb on target B cells promotes rituximab internalization and reduces clinical efficacy. Blood. 118:2530–2540. 2011. View Article : Google Scholar : PubMed/NCBI | |
|
Zhang J, Dominguez-Sola D, Hussein S, Lee JE, Holmes AB, Bansal M, Vlasevska S, Mo T, Tang H, Basso K, et al: Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis. Nat Med. 21:1190–1198. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, Bloomfield CD, Cazzola M and Vardiman JW: The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 127:2391–2405. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Swerdlow SH and Cook JR: As the world turns, evolving lymphoma classifications-past, present and future. Hum Pathol. 95:55–77. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Takagi M: DNA damage response and hematological malignancy. Int J Hematol. 106:345–356. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, et al: Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med. 8:542016. View Article : Google Scholar : PubMed/NCBI | |
|
Chiche J, Reverso-Meinietti J, Mouchotte A, Rubio-Patiño C, Mhaidly R, Villa E, Bossowski JP, Proics E, Grima-Reyes M, Paquet A, et al: GAPDH expression predicts the response to R-CHOP, the tumor metabolic status, and the response of DLBCL patients to metabolic inhibitors. Cell Metab. 29:1243–1257.e10. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Klener P and Klanova M: Drug Resistance in Non-Hodgkin Lymphomas. Int J Mol Sci. 21:20812020. View Article : Google Scholar : PubMed/NCBI | |
|
Wang X, Li G, Zhang Y, Li L, Qiu L, Qian Z, Zhou S, Wang X, Li Q and Zhang H: Pan-Cancer analysis reveals genomic and clinical characteristics of TRPV Channel-related genes. Front Oncol. 12:8131002022. View Article : Google Scholar : PubMed/NCBI | |
|
Russo M, Crisafulli G, Sogari A, Reilly NM, Arena S, Lamba S, Bartolini A, Amodio V, Magrì A, Novara L, et al: Adaptive mutability of colorectal cancers in response to targeted therapies. Science. 366:1473–1480. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Kater L, Kater B, Jakupec MA, Keppler BK and Prokop A: KP772 overcomes multiple drug resistance in malignant lymphoma and leukemia cells in vitro by inducing Bcl-2-independent apoptosis and upregulation of Harakiri. J Biol Inorg Chem. 26:897–907. 2021. View Article : Google Scholar : PubMed/NCBI | |
|
Sciarrillo R, Wojtuszkiewicz A, Assaraf YG, Jansen G, Kaspers GJL, Giovannetti E and Cloos J: The role of alternative splicing in cancer: From oncogenesis to drug resistance. Drug Resist Updat. 53:1007282020. 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 | |
|
Wills QF, Livak KJ, Tipping AJ, Enver T, Goldson AJ, Sexton DW and Holmes C: Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nat Biotechnol. 31:748–752. 2013. 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 | |
|
Croci GA, Au-Yeung RKH, Reinke S, Staiger AM, Koch K, Oschlies I, Richter J, Poeschel V, Held G, Loeffler M, et al: SPARC-positive macrophages are the superior prognostic factor in the microenvironment of diffuse large B-cell lymphoma and independent of MYC rearrangement and double-/triple-hit status. Ann Oncol. 32:1400–1409. 2021. View Article : Google Scholar : PubMed/NCBI | |
|
Abe Y, Sakata-Yanagimoto M, Fujisawa M, Miyoshi H, Suehara Y, Hattori K, Kusakabe M, Sakamoto T, Nishikii H, Nguyen TB, et al: A single-cell atlas of non-haematopoietic cells in human lymph nodes and lymphoma reveals a landscape of stromal remodelling. Nat Cell Biol. 24:565–578. 2022. View Article : Google Scholar : PubMed/NCBI | |
|
Ferreri AJ, Cwynarski K, Pulczynski E, Ponzoni M, Deckert M, Politi LS, Torri V, Fox CP, Rosée PL, Schorb E, et al: Chemoimmunotherapy with methotrexate, cytarabine, thiotepa, and rituximab (MATRix regimen) in patients with primary CNS lymphoma: Results of the first randomisation of the International Extranodal Lymphoma Study Group-32 (IELSG32) phase 2 trial. Lancet Haematol. 3:e217–e227. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Bromberg JEC, Issa S, Bakunina K, Minnema MC, Seute T, Durian M, Cull G, Schouten HC, Stevens WBC, Zijlstra JM, et al: Rituximab in patients with primary CNS lymphoma (HOVON 105/ALLG NHL 24): A randomised, open-label, phase 3 intergroup study. Lancet Oncol. 20:216–228. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Ruggieri S, Tamma R, Resta N, Albano F, Coccaro N, Loconte D, Annese T, Errede M, Specchia G, Senetta R, et al: Stat3-positive tumor cells contribute to vessels neoformation in primary central nervous system lymphoma. Oncotarget. 8:31254–31269. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Zhou Y, Liu W, Xu Z, Zhu H, Xiao D, Su W, Zeng R, Feng Y, Duan Y, Zhou J and Zhong M: Analysis of genomic alteration in primary central nervous system lymphoma and the expression of some related genes. Neoplasia. 20:1059–1069. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Ribatti D, Nico B, Ranieri G, Specchia G and Vacca A: The role of angiogenesis in human non-Hodgkin lymphomas. Neoplasia. 15:231–238. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Clozel T, Yang S, Elstrom RL, Tam W, Martin P, Kormaksson M, Banerjee S, Vasanthakumar A, Culjkovic B, Scott DW, et al: Mechanism-based epigenetic chemosensitization therapy of diffuse large B-cell lymphoma. Cancer Discov. 3:1002–1019. 2013. View Article : Google Scholar : PubMed/NCBI | |
|
Hazar B, Paydas S, Zorludemir S, Sahin B and Tuncer I: Prognostic significance of microvessel density and vascular endothelial growth factor (VEGF) expression in non-Hodgkin's lymphoma. Leuk Lymphoma. 44:2089–2093. 2003. View Article : Google Scholar : PubMed/NCBI | |
|
Carlo-Stella C and Santoro A: Microenvironment-related biomarkers and novel targets in classical Hodgkin's lymphoma. Biomark Med. 9:807–817. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Holmes AB, Corinaldesi C, Shen Q, Kumar R, Compagno N, Wang Z, Nitzan M, Grunstein E, Pasqualucci L, Dalla-Favera R and Basso K: Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome. J Exp Med. 217:e202004832020. View Article : Google Scholar : PubMed/NCBI | |
|
Mintz MA and Cyster JG: T follicular helper cells in germinal center B cell selection and lymphomagenesis. Immunol Rev. 296:48–61. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Turqueti-Neves A, Otte M, Prazeres da Costa O, Höpken UE, Lipp M, Buch T and Voehringer D: B-cell-intrinsic STAT6 signaling controls germinal center formation. Eur J Immunol. 44:2130–2138. 2014. View Article : Google Scholar : PubMed/NCBI | |
|
Mintz MA, Felce JH, Chou MY, Mayya V, Xu Y, Shui JW, An J, Li Z, Marson A, Okada T, et al: The HVEM-BTLA Axis Restrains T cell help to germinal center B cells and functions as a cell-extrinsic suppressor in lymphomagenesis. Immunity. 51:310–323.e7. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Hashwah H, Schmid CA, Kasser S, Bertram K, Stelling A, Manz MG and Müller A: Inactivation of CREBBP expands the germinal center B cell compartment, down-regulates MHCII expression and promotes DLBCL growth. Proc Natl Acad Sci USA. 114:9701–9706. 2017. View Article : Google Scholar : PubMed/NCBI | |
|
Deng Q, Han G, Puebla-Osorio N, Ma MCJ, Strati P, Chasen B, Dai E, Dang M, Jain N, Yang H, et al: Characteristics of anti-CD19 CAR T cell infusion products associated with efficacy and toxicity in patients with large B cell lymphomas. Nat Med. 26:1878–1887. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Parker KR, Migliorini D, Perkey E, Yost KE, Bhaduri A, Bagga P, Haris M, Wilson NE, Liu F, Gabunia K, et al: Single-Cell analyses identify brain mural cells expressing CD19 as potential off-tumor targets for CAR-T immunotherapies. Cell. 183:126–142.e17. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Shi Y, Ding W, Gu W, Shen Y, Li H, Zheng Z, Zheng X, Liu Y and Ling Y: Single-cell phenotypic profiling to identify a set of immune cell protein biomarkers for relapsed and refractory diffuse large B cell lymphoma: A single-center study. J Leukoc Biol. 112:1633–1648. 2022. View Article : Google Scholar : PubMed/NCBI | |
|
Shin D, Lee W, Lee JH and Bang D: Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations. Sci Adv. 5:eaav22492019. View Article : Google Scholar : PubMed/NCBI | |
|
Krieg C, Nowicka M, Guglietta S, Schindler S, Hartmann FJ, Weber LM, Dummer R, Robinson MD, Levesque MP and Becher B: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nat Med. 24:144–153. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Yost KE, Satpathy AT, Wells DK, Qi Y, Wang C, Kageyama R, McNamara KL, Granja JM, Sarin KY, Brown RA, et al: Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat Med. 25:1251–1259. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Wu TD, Madireddi S, de Almeida PE, Banchereau R, Chen YJ, Chitre AS, Chiang EY, Iftikhar H, O'Gorman WE, Au-Yeung A, et al: Peripheral T cell expansion predicts tumour infiltration and clinical response. Nature. 579:274–278. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, Lönnerberg P, Furlan A, et al: RNA velocity of single cells. Nature. 560:494–498. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Simmons SK, Lithwick-Yanai G, Adiconis X, Oberstrass F, Iremadze N, Geiger-Schuller K, Thakore PI, Frangieh CJ, Barad O, Almogy G, et al: Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing. Nat Biotechnol. 41:204–211. 2023. View Article : Google Scholar : PubMed/NCBI | |
|
Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F and Huang Y: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 16:1482015. View Article : Google Scholar : PubMed/NCBI | |
|
Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, et al: G&T-seq: Parallel sequencing of single-cell genomes and transcriptomes. Nat Methods. 12:519–522. 2015. View Article : Google Scholar : PubMed/NCBI | |
|
Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, Wu X, Wen L, Tang F, Huang Y and Peng J: Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res. 26:304–319. 2016. View Article : Google Scholar : PubMed/NCBI | |
|
Katzenelenbogen Y, Sheban F, Yalin A, Yofe I, Svetlichnyy D, Jaitin DA, Bornstein C, Moshe A, Keren-Shaul H, Cohen M, et al: Coupled scRNA-Seq and intracellular protein activity reveal an immunosuppressive role of TREM2 in cancer. Cell. 182:872–885.e19. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Svensson V, Vento-Tormo R and Teichmann SA: Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc. 13:599–604. 2018. View Article : Google Scholar : PubMed/NCBI | |
|
Bai X, Li Y, Zeng X, Zhao Q and Zhang Z: Single-cell sequencing technology in tumor research. Clin Chim Acta. 518:101–109. 2021. View Article : Google Scholar : PubMed/NCBI | |
|
McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, et al: MULTI-seq: Sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods. 16:619–626. 2019. View Article : Google Scholar : PubMed/NCBI | |
|
Kashima Y, Sakamoto Y, Kaneko K, Seki M, Suzuki Y and Suzuki A: Single-cell sequencing techniques from individual to multiomics analyses. Exp Mol Med. 52:1419–1427. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Ando Y, Kwon AT and Shin JW: An era of single-cell genomics consortia. Exp Mol Med. 52:1409–1418. 2020. View Article : Google Scholar : PubMed/NCBI | |
|
Landeira-Viñuela A, Díez 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 | |
|
Du J, Qiu C, Li WS, Wang B, Han XL, Lin SW, Fu XH, Hou J and Huang ZF: Spatial transcriptomics analysis reveals that CCL17 and CCL22 are robust indicators of a suppressive immune environment in angioimmunoblastic T cell lymphoma (AITL). Front Biosci (Landmark Ed). 27:2702022. View Article : Google Scholar : PubMed/NCBI | |
|
Tripodo C, Zanardi F, Iannelli F, Mazzara S, Vegliante M, Morello G, Di Napoli A, Mangogna A, Facchetti F, Sangaletti S, et al: A spatially resolved dark-versus light-zone microenvironment signature subdivides germinal center-related aggressive B cell lymphomas. iScience. 23:1015622020. View Article : Google Scholar : PubMed/NCBI | |
|
Colombo AR, Hav M, Singh M, Xu A, Gamboa A, Lemos T, Gerdtsson E, Chen D, Houldsworth J, Shaknovich R, et al: Single-cell spatial analysis of tumor immune architecture in diffuse large B-cell lymphoma. Blood Adv. 6:4675–4690. 2022. View Article : Google Scholar : PubMed/NCBI | |
|
Efremova M, Vento-Tormo R, Park JE, Teichmann SA and James KR: Immunology in the Era of single-cell technologies. Annu Rev Immunol. 38:727–757. 2020. View Article : Google Scholar : PubMed/NCBI |
