Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue.

B-Lymphocytes / metabolism Cell Lineage / genetics Chromatography, Liquid / methods Formaldehyde Gene Expression Profiling / methods Germinal Center / metabolism Humans Lymphoma, Large B-Cell, Diffuse / classification Mass Spectrometry / methods Nanotechnology / methods Paraffin Embedding / methods Proteins / genetics Proteome / genetics Proteomics / methods Tissue Fixation / methods

Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
12 05 2020
Historique:
received: 16 01 2019
accepted: 09 04 2020
entrez: 14 5 2020
pubmed: 14 5 2020
medline: 1 12 2020
Statut: epublish

Résumé

Diffuse large B-cell lymphoma (DLBCL) is commonly classified by gene expression profiling according to its cell of origin (COO) into activated B-cell (ABC)-like and germinal center B-cell (GCB)-like subgroups. Here we report the application of label-free nano-liquid chromatography - Sequential Window Acquisition of all THeoretical fragment-ion spectra - mass spectrometry (nanoLC-SWATH-MS) to the COO classification of DLBCL in formalin-fixed paraffin-embedded (FFPE) tissue. To generate a protein signature capable of predicting Affymetrix-based GCB scores, the summed log

Identifiants

DOI: 10.1038/s41598-020-64212-z PMID: 32398793 PMC: PMC7217957
pubmed: 32398793
doi: 10.1038/s41598-020-64212-z
pii: 10.1038/s41598-020-64212-z
pmc: PMC7217957
doi:

Substances chimiques

Proteins 0
Proteome 0
Formaldehyde 1HG84L3525

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

7876

Références

Rosenwald, A. et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346, 1937–1947 (2002).
pubmed: 12075054 doi: 10.1056/NEJMoa012914 pmcid: 12075054
Rutherford, S. C. & Leonard, J. P. DLBCL Cell of Origin: what role should it play in care today? Oncology 32, 445–449 (2018).
pubmed: 30248164 pmcid: 30248164
Meyer, P. N. et al. Immunohistochemical methods for predicting cell of origin and survival in patients with diffuse large B-cell lymphoma treated with rituximab. J. Clin. Oncol. 29, 200–207 (2011).
pubmed: 21135273 doi: 10.1200/JCO.2010.30.0368 pmcid: 21135273
Hans, C. P. et al. Confirmation of the molecular classification of diffuse large B-cell lymphoma by immunohistochemistry using a tissue microarray. Blood 103, 275–282 (2004).
pubmed: 14504078 doi: 10.1182/blood-2003-05-1545 pmcid: 14504078
Ott, G. et al. Immunoblastic morphology but not the immunohistochemical GCB/nonGCB classifier predicts outcome in diffuse large B-cell lymphoma in the RICOVER-60 trial of the DSHNHL. Blood 116, 4916–4925 (2010).
pubmed: 20736456 doi: 10.1182/blood-2010-03-276766 pmcid: 20736456
Rimsza, L. M. et al. Accurate classification of diffuse large B-cell lymphoma into germinal center and activated B-cell subtypes using a nuclease protection assay on formalin-fixed, paraffin-embedded tissues. Clin. Cancer Res. 17, 3727–3732 (2011).
pubmed: 21364035 pmcid: 3107869 doi: 10.1158/1078-0432.CCR-10-2573
Masqué-Soler, N., Szczepanowski, M., Kohler, C. W., Spang, R. & Klapper, W. Molecular classification of mature aggressive B-cell lymphoma using digital multiplexed gene expression on formalin-fixed paraffin-embedded biopsy specimens. Blood 122, 1985–1986 (2013).
pubmed: 24030260 doi: 10.1182/blood-2013-06-508937 pmcid: 24030260
Geiss, G. K. et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat. Biotechnol. 26, 317–325 (2008).
pubmed: 18278033 doi: 10.1038/nbt1385 pmcid: 18278033
Veldman-Jones, M. H. et al. Reproducible, quantitative, and flexible molecular subtyping of clinical DLBCL samples using the NanoString nCounter system. Clin. Cancer Res. 21, 2367–2378 (2014).
pubmed: 25301847 doi: 10.1158/1078-0432.CCR-14-0357 pmcid: 25301847
Scott, D. W. et al. Determining cell-of-origin subtypes of diffuse large B-cell lymphoma using gene expression in formalin-fixed paraffin-embedded tissue. Blood 123, 1214–1217 (2014).
pubmed: 24398326 pmcid: 3931191 doi: 10.1182/blood-2013-11-536433
Scott, D. W. et al. Prognostic significance of diffuse large B-cell lymphoma cell of origin determined by digital gene expression in formalin-fixed paraffin-embedded tissue biopsies. J. Clin. Oncol. 33, 2848–2856 (2015).
pubmed: 26240231 pmcid: 4554747 doi: 10.1200/JCO.2014.60.2383
Xue, X., Zeng, N., Gao, Z. & Du, M. Q. Diffuse large B-cell lymphoma: sub-classification by massive parallel quantitative RT-PCR. Lab. Invest. 95, 113–120 (2015).
pubmed: 25418578 doi: 10.1038/labinvest.2014.136 pmcid: 25418578
Deeb, S. J. et al. Machine learning-based classification of diffuse large B-cell lymphoma by their protein expression profiles. Mol. Cell. Proteomics 14, 2947–2960 (2015).
pubmed: 26311899 pmcid: 4638038 doi: 10.1074/mcp.M115.050245
Ennishi, D. et al. Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin-specific clinical impact. Blood 129, 2760–2770 (2017).
pubmed: 28351934 doi: 10.1182/blood-2016-11-747022 pmcid: 28351934
Lim, E. L. et al. Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients. Genome Biol. 16, 18 (2015).
pubmed: 25723320 pmcid: 4308918 doi: 10.1186/s13059-014-0568-y
Gillet, L. C. et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11, O111.016717 (2012).
pubmed: 22261725 pmcid: 3433915 doi: 10.1074/mcp.O111.016717
Schwarzfischer, P. et al. Comprehensive metaboproteomics of Burkitt’s and diffuse large B-cell lymphoma cell lines and primary tumor tissues reveals distinct differences in pyruvate content and metabolism. J. Proteome Res. 16, 1105–1120 (2017).
pubmed: 28161958 doi: 10.1021/acs.jproteome.6b00164 pmcid: 28161958
Altenbuchinger, M. et al. Reference point insensitive molecular data analysis. Bioinformatics 33, 219–226 (2017).
pubmed: 27634945 doi: 10.1093/bioinformatics/btw598 pmcid: 27634945
Altenbuchinger, M. et al. Molecular signatures that can be transferred across different omics platforms. Bioinformatics 33, i333–i340 (2017).
pubmed: 28881975 pmcid: 5870545 doi: 10.1093/bioinformatics/btx241
Klapper, W. et al. Patient age at diagnosis is associated with the molecular characteristics of diffuse large B-cell lymphoma. Blood 119, 1882–1887 (2012).
pubmed: 22238326 doi: 10.1182/blood-2011-10-388470 pmcid: 22238326
Szczepanowski, M. et al. Cell-of-origin classification by gene expression and MYC-rearrangements in diffuse large B-cell lymphomas of children and adolescents. Br. J. Haematol. 179, 116–119 (2017).
pubmed: 28643426 doi: 10.1111/bjh.14812 pmcid: 28643426
Ostasiewicz, P., Zielinska, D. F., Mann, M. & Wisniewski, J. R. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. J. Proteome Res. 9, 3688–3700 (2010).
pubmed: 20469934 doi: 10.1021/pr100234w pmcid: 20469934
Fischer, R. & Kessler, B. M. Gel-aided sample preparation (GASP) - a simplified method for gel-assisted proteomic sample generation from protein extracts and intact cells. Proteomics 15, 1224–1229 (2015).
pubmed: 25515006 pmcid: 4409837 doi: 10.1002/pmic.201400436
Zhang, Y. et al. The use of variable Q1 isolation windows improves selectivity in LC-SWATH-MS acquisition. J. Proteome Res. 14, 4359–4371 (2015).
pubmed: 26302369 doi: 10.1021/acs.jproteome.5b00543 pmcid: 26302369
Simbürger, J. M., Dettmer, K., Oefner, P. J. & Reinders, J. Optimizing the SWATH-MS-workflow for label-free proteomics. J. Proteomics 145, 137–140 (2016).
pubmed: 27107778 doi: 10.1016/j.jprot.2016.04.021 pmcid: 27107778
Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. https://doi.org/10.1093/nar/gky1106 (2018).
Tibshirani, R. Regression shrinkage and selection via the lasso. J. R. Stat. Soc. Series B Stat. Methodol. 58, 267–288 (1996).
Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33, 1–22 (2010).
pubmed: 20808728 pmcid: 2929880 doi: 10.18637/jss.v033.i01
Gutiérrez-García, G. et al. Gene-expression profiling and not immunophenotypic algorithms predicts prognosis in patients with diffuse large B-cell lymphoma treated with immunochemotherapy. Blood 117, 4836–4843 (2011).
pubmed: 21441466 doi: 10.1182/blood-2010-12-322362 pmcid: 21441466
Geiss, G. K. et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat. Biotechnol. 26, 317–325 (2008).
pubmed: 18278033 doi: 10.1038/nbt1385 pmcid: 18278033
Sequeiros, T. et al. Molecular markers for prostate cancer in formalin-fixed paraffin-embedded tissues. Biomed. Res. Int. 2013, 283635 (2013).
pubmed: 24371818 pmcid: 3859157 doi: 10.1155/2013/283635
Lou, J. J. et al. A review of room temperature storage of biospecimen tissue and nucleic acids for anatomic pathology laboratories and biorepositories. Clin. Biochem. 47, 267–73 (2014).
pubmed: 24362270 doi: 10.1016/j.clinbiochem.2013.12.011 pmcid: 24362270
Meyer, J. G. & Schilling, B. Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques. Expert Rev. Proteomics 14, 419–429 (2017).
pubmed: 28436239 pmcid: 5671767 doi: 10.1080/14789450.2017.1322904
Basak, T. et al. In-depth comparative proteomic analysis of yeast proteome using iTRAQ and SWATH based MS. Mol. Biosyst. 11, 2135–43 (2015).
pubmed: 26099114 doi: 10.1039/C5MB00234F pmcid: 26099114
Jylhä, A. et al. Comparison of iTRAQ and SWATH in a clinical study with multiple time points. Clin. Proteomics 15, 24 (2018).
pubmed: 30069167 pmcid: 6065059 doi: 10.1186/s12014-018-9201-5
Bourassa, S. et al. Evaluation of iTRAQ and SWATH-MS for the Quantification of Proteins Associated with Insulin Resistance in Human Duodenal Biopsy Samples. PLoS One 10, e0125934 (2015).
pubmed: 25950531 pmcid: 4423961 doi: 10.1371/journal.pone.0125934
Compagno, M. et al. Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature 459, 717–721 (2009).
pubmed: 19412164 pmcid: 2973325 doi: 10.1038/nature07968
Hinz, M. et al. Nuclear factor kappaB-dependent gene expression profiling of Hodgkin’s disease tumor cells, pathogenetic significance, and link to constitutive signal transducer and activator of transcription 5a activity. J. Exp. Med. 196, 605–617 (2002).
pubmed: 12208876 pmcid: 2194004 doi: 10.1084/jem.20020062
Tzankov, A. et al. Prognostic significance of CD44 expression in diffuse large B cell lymphoma of activated and germinal centre B cell-like types: a tissue microarray analysis of 90 cases. J. Clin. Pathol. 56, 747–752 (2003).
pubmed: 14514777 pmcid: 1770073 doi: 10.1136/jcp.56.10.747
Zabolotny, J. M. et al. Protein-tyrosine phosphatase 1B expression is induced by inflammation in vivo. J. Biol. Chem. 283, 14230–14241 (2008).
pubmed: 18281274 pmcid: 2386946 doi: 10.1074/jbc.M800061200
Lu, X. et al. PTP1B is a negative regulator of interleukin 4-induced STAT6 signaling. Blood 112, 4098–4108 (2008).
pubmed: 18716132 pmcid: 2582009 doi: 10.1182/blood-2008-03-148726
Lenz, G. et al. Stromal gene signatures in large-B-cell lymphomas. N. Engl. J. Med. 359, 2313–2323 (2008).
pubmed: 19038878 doi: 10.1056/NEJMoa0802885 pmcid: 19038878
Rydström, K. et al. Gene expression profiling indicates that immunohistochemical expression of CD40 is a marker of an inflammatory reaction in the tumor stroma of diffuse large B-cell lymphoma. Leuk. Lymphoma 53, 1764–1768 (2012).
pubmed: 22335531 doi: 10.3109/10428194.2012.666541 pmcid: 22335531
Ratajczak-Wielgomas, K. & Dziegiel, P. The role of periostin in neoplastic processes. Folia Histochem. Cytobiol. 53, 120–132 (2015).
pubmed: 26150285 doi: 10.5603/FHC.a2015.0014 pmcid: 26150285
Assaf, C. & Hwang, S. T. Mac attack: macrophages as key drivers of cutaneous T-cell lymphoma pathogenesis. Exp. Dermatol. 25, 105–106 (2016).
pubmed: 26566710 doi: 10.1111/exd.12894 pmcid: 26566710
Bellot, G. et al. TOM22, a core component of the mitochondria outer membrane protein translocation pore, is a mitochondrial receptor for the proapoptotic protein Bax. Cell Death Differ. 14, 785–794 (2007).
pubmed: 17096026 doi: 10.1038/sj.cdd.4402055 pmcid: 17096026
Sohn, S. K. et al. Prognostic significance of bcl-2, bax, and p53 expression in diffuse large B-cell lymphoma. Am. J. Hematol. 73, 101–107 (2003).
pubmed: 12749011 doi: 10.1002/ajh.10333 pmcid: 12749011
Brown, P. J. et al. FOXP1 suppresses immune response signatures and MHC II class expression in activated B-cell-like diffuse large B-cell lymphomas. Leukemia 30, 605–616 (2016).
pubmed: 26500140 doi: 10.1038/leu.2015.299 pmcid: 26500140
Blenk, S. et al. Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): analysis of molecular predictors, signatures, cell cycle state and patient survival. Cancer Inform. 3, 399–420 (2007).
pubmed: 19455257 pmcid: 2675856 doi: 10.1177/117693510700300004
Daftuar, L., Zhu, Y., Jacq, X. & Prives, C. Ribosomal proteins RPL37, RPS15 and RPS20 regulate the Mdm2-p53-MdmX network. PLoS One 8, e68667 (2013).
pubmed: 23874713 pmcid: 3713000 doi: 10.1371/journal.pone.0068667
Ljungström, V. et al. Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations. Blood 127, 1007–1016 (2016).
pubmed: 26675346 pmcid: 4768426 doi: 10.1182/blood-2015-10-674572
Xie, R. et al. Factors influencing the degradation of archival formalin-fixed paraffin-embedded tissue sections. J. Histochem. Cytochem. 59, 356–365 (2011).
pubmed: 21411807 pmcid: 3201147 doi: 10.1369/0022155411398488

Auteurs

Jörg Reinders (J)

Chair and Institute of Functional Genomics, University of Regensburg, 93053, Regensburg, Germany. reinders@ifado.de.
Analytical Chemistry Support Unit, Leibniz Research Centre for Working Environment and Human Factors, 44139, Dortmund, Germany. reinders@ifado.de.

Michael Altenbuchinger (M)

Chair of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, 93053, Regensburg, Germany.

Katharina Limm (K)

Chair and Institute of Functional Genomics, University of Regensburg, 93053, Regensburg, Germany.
ORCID: 0000-0001-9785-2338

Philipp Schwarzfischer (P)

Chair and Institute of Functional Genomics, University of Regensburg, 93053, Regensburg, Germany.

Tamara Scheidt (T)

Department of Biosciences, Bioanalytical Research Labs, and Cancer Cluster Salzburg, University of Salzburg, 5020, Salzburg, Austria.

Lisa Strasser (L)

Department of Biosciences, Bioanalytical Research Labs, and Cancer Cluster Salzburg, University of Salzburg, 5020, Salzburg, Austria.

Julia Richter (J)

Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, 24106, Kiel, Germany.
ORCID: 0000-0002-9543-4084

Monika Szczepanowski (M)

Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, 24106, Kiel, Germany.

Christian G Huber (CG)

Department of Biosciences, Bioanalytical Research Labs, and Cancer Cluster Salzburg, University of Salzburg, 5020, Salzburg, Austria.
ORCID: 0000-0001-8358-1880

Wolfram Klapper (W)

Department of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel/Christian-Albrecht University, 24106, Kiel, Germany.
ORCID: 0000-0001-7208-4117

Rainer Spang (R)

Chair of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, 93053, Regensburg, Germany.

Peter J Oefner (PJ)

Chair and Institute of Functional Genomics, University of Regensburg, 93053, Regensburg, Germany.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Effectiveness of Virtual Yoga for Chronic Low Back Pain: A Randomized Clinical Trial.

Hallie Tankha, Devyn Gaskins, Amanda Shallcross et al.
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH

questionsmedicales.fr › Systèmes sanguin et immunitaire › Système immunitaire › Leucocytes › Agranulocytes › Lymphocytes › Lymphocytes B › Platform independent protein-based...
questionsmedicales.fr › Phénomènes physiologiques des appareils urinaire et reproducteur › Phénomènes physiologiques de la reproduction › Reproduction › Développement embryonnaire et foetal › Développement embryonnaire › Lignage cellulaire › Platform independent protein-based...
questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Chromatographie › Chromatographie en phase liquide › Platform independent protein-based...
questionsmedicales.fr › Composés chimiques organiques › Aldéhydes › Formaldéhyde › Platform independent protein-based...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › Platform independent protein-based...
questionsmedicales.fr › Systèmes sanguin et immunitaire › Système immunitaire › Système lymphatique › Tissu lymphoïde › Noeuds lymphatiques › Centre germinatif › Platform independent protein-based...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Platform independent protein-based...
questionsmedicales.fr › Maladies du système immunitaire › Syndromes immunoprolifératifs › Syndromes lymphoprolifératifs › Lymphomes › Lymphome malin non hodgkinien › Lymphome B › Lymphome B diffus à grandes cellules › Platform independent protein-based...
questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Spectrométrie de masse › Platform independent protein-based...
questionsmedicales.fr › Technologie, industrie et agriculture › Technologie › Miniaturisation › Nanotechnologie › Platform independent protein-based...
questionsmedicales.fr › Techniques d'investigation › Techniques de laboratoire clinique › Techniques histologiques › Techniques de préparation histocytologique › Inclusion de tissu › Inclusion en paraffine › Platform independent protein-based...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Platform independent protein-based...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéome › Platform independent protein-based...
questionsmedicales.fr › Disciplines des sciences naturelles › Chimie › Biochimie › Protéomique › Platform independent protein-based...
questionsmedicales.fr › Techniques d'investigation › Techniques de laboratoire clinique › Techniques histologiques › Techniques de préparation histocytologique › Fixation tissulaire › Platform independent protein-based...