A novel approach to detect resistance mechanisms reveals FGR as a factor mediating HDAC inhibitor SAHA resistance in B-cell lymphoma.
Histone deacetylase (HDAC) inhibitors such as suberoylanilide hydroxamic acid (SAHA) are not commonly used in clinical practice for treatment of B-cell lymphomas, although a subset of patients with refractory or relapsed B-cell lymphoma achieved partial or complete remissions. Therefore, the purpose of this study was to identify molecular features that predict the response of B-cell lymphomas to SAHA treatment. We designed an integrative approach combining drug efficacy testing with exome and captured target analysis (DETECT). In this study, we tested SAHA sensitivity in 26 B-cell lymphoma cell lines and determined SAHA-interacting proteins in SAHA resistant and sensitive cell lines employing a SAHA capture compound (CC) and mass spectrometry (CCMS). In addition, we performed exome mutation analysis. Candidate validation was done by expression analysis and knock-out experiments. An integrated network analysis revealed that the Src tyrosine kinase Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR) is associated with SAHA resistance. FGR was specifically captured by the SAHA-CC in resistant cells. In line with this observation, we found that FGR expression was significantly higher in SAHA resistant cell lines. As functional proof, CRISPR/Cas9 mediated FGR knock-out in resistant cells increased SAHA sensitivity. In silico analysis of B-cell lymphoma samples (n = 1200) showed a wide range of FGR expression indicating that FGR expression might help to stratify patients, which clinically benefit from SAHA therapy. In conclusion, our comprehensive analysis of SAHA-interacting proteins highlights FGR as a factor involved in SAHA resistance in B-cell lymphoma.
Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
Maria
M
Joosten
Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany; Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Grantham-Allee 20, 53757 Sankt Augustin, Germany.
Sebastian
S
Ginzel
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Christian
C
Blex
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Dmitri
D
Schmidt
Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany.
Michael
M
Gombert
Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany.
Cai
C
Chen
Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany.
René Martin
RM
Linka
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Olivia
O
Gräbner
Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany.
Anika
A
Hain
Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
Burkhard
B
Hirsch
Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
Anke
A
Sommerfeld
Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
Anke
A
Seegebarth
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Uschi
U
Gruber
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Corinna
C
Maneck
Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany; Department of Hematology, Union Hospital, Fujian Medical University, NO.29,Xinquan Road, Fuzhou City, Fujian Province, China.
Langhui
L
Zhang
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Katharina
K
Stenin
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Henrik
H
Dieks
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Michael
M
Sefkow
Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany.
Carsten
C
Münk
Department of Hematology and Oncology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
Claudia D
CD
Baldus
Department of Computer Science, Bonn-Rhine-Sieg University of Applied Sciences, Grantham-Allee 20, 53757 Sankt Augustin, Germany.
Ralf
R
Thiele
Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany.
Arndt
A
Borkhardt
Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
Michael
M
Hummel
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Hubert
H
Köster
Department of Pediatric Oncology, Hematology and Clinical Immunology, Center of Child and Adolescent Health, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany.
Ute
U
Fischer
caprotec bioanalytics GmbH, Magnusstraße 11, 12489 Berlin, Germany.
Mathias
M
Dreger
Institute of Pathology, Charité University Medicine, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany. Electronic address: volkhard.seitz@charite.de.
Volkhard
V
Seitz
D045744:Cell Line, Tumor; D019008:Drug Resistance, Neoplasm / Q000187:drug effects*; D055786:Gene Knockout Techniques; D053263:Gene Regulatory Networks / Q000187:drug effects; D056572:Histone Deacetylase Inhibitors / Q000494:pharmacology*; D006801:Humans; D006877:Hydroxamic Acids / Q000494:pharmacology*; D016393:Lymphoma, B-Cell / Q000473:pathology*; D013058:Mass Spectrometry; D009154:Mutation / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000378:metabolism*; D015203:Reproducibility of Results; D000077337:Vorinostat; D019061:src-Family Kinases / Q000378:metabolism*
D056572:Histone Deacetylase Inhibitors; D006877:Hydroxamic Acids; D011518:Proto-Oncogene Proteins; D000077337:Vorinostat; C053102:proto-oncogene proteins c-fgr; D019061:src-Family Kinases
B-cell lymphoma; Drug resistance; FGR; HDAC inhibitor; SAHA