Transcriptomic clustering of chronic lymphocytic leukemia: molecular subtypes based on Bruton’s tyrosine kinase expression levels

Kipps TJ, Stevenson FK, Wu CJ, Croce CM, Packham G, Wierda WG, et al. Chronic lymphocytic leukaemia. Nat Rev Dis Prim. 2017;3:16096.

Article  PubMed  Google Scholar 

Dohner H, Stilgenbauer S, Benner A, Leupolt E, Krober A, Bullinger L, et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med. 2000;343:1910–6.

Article  CAS  PubMed  Google Scholar 

Landau DA, Tausch E, Taylor-Weiner AN, Stewart C, Reiter JG, Bahlo J, et al. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526:525–30.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rassenti LZ, Huynh L, Toy TL, Chen L, Keating MJ, Gribben JG, et al. ZAP-70 compared with immunoglobulin heavy-chain gene mutation status as a predictor of disease progression in chronic lymphocytic leukemia. N Engl J Med. 2004;351:893–901.

Article  CAS  PubMed  Google Scholar 

Lavallee VP, Baccelli I, Krosl J, Wilhelm B, Barabe F, Gendron P, et al. The transcriptomic landscape and directed chemical interrogation of MLL-rearranged acute myeloid leukemias. Nat Genet. 2015;47:1030–7.

Article  CAS  PubMed  Google Scholar 

Li JF, Dai YT, Lilljebjorn H, Shen SH, Cui BW, Bai L, et al. Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases. Proc Natl Acad Sci USA. 2018;115:E11711–E20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shiba N, Yoshida K, Hara Y, Yamato G, Shiraishi Y, Matsuo H, et al. Transcriptome analysis offers a comprehensive illustration of the genetic background of pediatric acute myeloid leukemia. Blood Adv. 2019;3:3157–69.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, et al. Genetics and pathogenesis of diffuse large B-cell lymphoma. N Engl J Med. 2018;378:1396–407.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chuang HY, Rassenti L, Salcedo M, Licon K, Kohlmann A, Haferlach T, et al. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood. 2012;120:2639–49.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26:1572–3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ramsay AJ, Martinez-Trillos A, Jares P, Rodriguez D, Kwarciak A, Quesada V. Next-generation sequencing reveals the secrets of the chronic lymphocytic leukemia genome. Clin Transl Oncol. 2013;15:3–8.

Article  CAS  PubMed  Google Scholar 

Herold T, Jurinovic V, Metzeler KH, Boulesteix AL, Bergmann M, Seiler T, et al. An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia. Leukemia. 2011;25:1639–45.

Article  CAS  PubMed  Google Scholar 

Chen LS, Keating MJ, Gandhi V. Blood collection methods affect cellular protein integrity: implications for clinical trial biomarkers and ZAP-70 in CLL. Blood. 2014;124:1192–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Patel V, Chen LS, Wierda WG, Balakrishnan K, Gandhi V. Impact of bone marrow stromal cells on Bcl-2 family members in chronic lymphocytic leukemia. Leuk lymphoma. 2014;55:899–910.

Article  CAS  PubMed  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.

Article  CAS  PubMed  Google Scholar 

Anders S, Pyl PT, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.

Article  CAS  PubMed  Google Scholar 

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

Article  PubMed  PubMed Central  Google Scholar 

Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC. Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinforma. 2011;12:474.

Article  Google Scholar 

Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinforma. 2013;14:7.

Article  Google Scholar 

Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267–73.

Article  CAS  PubMed  Google Scholar 

Ju Z, Liu W, Roebuck PL, Siwak DR, Zhang N, Lu Y, et al. Development of a robust classifier for quality control of reverse-phase protein arrays. Bioinformatics. 2015;31:912–8.

Article  CAS  PubMed  Google Scholar 

Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289–300.

Article  Google Scholar 

Wagner A, Rouleau M, Villeneuve L, Le T, Peltier C, Allain EP. et al. A non-canonical role for theglycosyltransferase enzyme UGT2B17 as a novel constituent of the B cell receptor signalosome. Cells. 2023;12:1295.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sivina M, Hartmann E, Kipps TJ, Rassenti L, Krupnik D, Lerner S, et al. CCL3 (MIP-1alpha) plasma levels and the risk for disease progression in chronic lymphocytic leukemia. Blood. 2011;117:1662–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Byrd JC, Furman RR, Coutre SE, Flinn IW, Burger JA, Blum KA, et al. Targeting BTK with ibrutinib in relapsed chronic lymphocytic leukemia. N. Engl J Med. 2013;369:32–42.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Burger JA. Treatment of chronic lymphocytic leukemia. N Engl J Med. 2020;383:460–73.

Article  CAS  PubMed  Google Scholar 

Hallek M, Cheson BD, Catovsky D, Caligaris-Cappio F, Dighiero G, Dohner H, et al. iwCLL guidelines for diagnosis, indications for treatment, response assessment, and supportive management of CLL. Blood. 2018;131:2745–60.

Article  CAS  PubMed  Google Scholar 

Shadman M. Diagnosis and treatment of chronic lymphocytic leukemia: a review. JAMA. 2023;329:918–32.

Article  CAS  PubMed  Google Scholar 

Aslan B, Kismali G, Chen LS, Iles LR, Mahendra M, Peoples M, et al. Development and characterization of prototypes for in vitro and in vivo mouse models of ibrutinib-resistant CLL. Blood Adv. 2021;5:3134–46.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stevenson FK, Forconi F, Kipps TJ. Exploring the pathways to chronic lymphocytic leukemia. Blood. 2021;138:827–35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stevenson FK, Forconi F, Packham G. The meaning and

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