Whole exome sequencing of microdissected splenic marginal zone lymphoma: a study to discover novel tumor-specific mutations.
BACKGROUND
Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking.


METHODS
We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort.


RESULTS
Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15% of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations.


CONCLUSIONS
In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10 % of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation.
Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany. jan.peveling-oberhag@kgu.de.
Jan
J
Peveling-Oberhag
Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany. franziwolters@web.de.
Franziska
F
Wolters
Senckenbergisches Institut für Pathologie, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany. C.Doering@em.uni-frankfurt.de.
Claudia
C
Döring
Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany. Dirk.Walter@kgu.de.
Dirk
D
Walter
Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, Essen, Germany. LSellmann@gmx.net.
Ludger
L
Sellmann
Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, Essen, Germany. rene.scholtysik@uni-due.de.
René
R
Scholtysik
Department of Human Pathology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy. m.lucioni@smatteo.pv.it.
Marco
M
Lucioni
Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, Germany. maxschubach@web.de.
Max
M
Schubach
Department of Human Pathology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy. m.paulli@smatteo.pv.it.
Marco
M
Paulli
CeGaT GmbH, Paul-Ehrlich-Straße 23, Tübingen, Germany. saskia.biskup@cegat.de.
Saskia
S
Biskup
Medizinische Klinik 1, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany. Zeuzem@em.uni-frankfurt.de.
Stefan
S
Zeuzem
Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, Essen, Germany. ralf.kueppers@uk-essen.de.|German Cancer Consortium (DKTK), Heidelberg, Germany. ralf.kueppers@uk-essen.de.
Ralf
R
Küppers
Senckenbergisches Institut für Pathologie, Klinikum der Johann Wolfgang Goethe-Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany. martin.l.hansmann@em.uni-frankfurt.de.|German Cancer Consortium (DKTK), Heidelberg, Germany. martin.l.hansmann@em.uni-frankfurt.de.
Martin-Leo
ML
Hansmann
D014408:Biomarkers, Tumor / Q000235:genetics; D004252:DNA Mutational Analysis; D059472:Exome / Q000235:genetics*; D005260:Female; D006801:Humans; D018442:Lymphoma, B-Cell, Marginal Zone / Q000235:genetics*; D008297:Male; D046228:Microarray Analysis; D008875:Middle Aged; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D013160:Splenic Neoplasms / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D014157:Transcription Factors