Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation

Michael R. Green; Shingo Kihira; Chih Long Liu; Ramesh V. Nair; Raheleh Salari; Andrew J. Gentles; Jonathan Irish; Henning Stehr; Carolina Vicente-Dueñas; Isabel Romero-Camarero; Isidro Sanchez-Garcia; Sylvia K. Plevritis; Daniel A. Arber; Serafim Batzoglou; Ronald Levy; Ash A. Alizadeh

doi:10.1073/pnas.1501199112

New Research In

Contributed by Ronald Levy, January 22, 2015 (sent for review December 22, 2014; reviewed by Sattva Neelapu and Lisa Rimsza)

Significance

Follicular lymphoma (FL) is a disease characterized by multiple relapses that are linked by a common progenitor bearing only a subset of the mutations found within the tumor that presents clinically. Inability to cure this disease may therefore be linked to the failure of current therapies to clear these early tumor-propagating clones. Here we further define the genetic hallmarks of this disease and model the steps in evolution through phylogenetic analysis of serial tumor biopsies. This identified CREBBP mutations as early events in genome evolution that are enriched within tumor cell progenitors and provided evidence that these mutations act by allowing immune evasion. This highlights CREBBP mutations as an attractive therapeutic target in FL and provides insight into their pathogenic mechanism.

Abstract

Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are genetically characterized by B-cell leukemia/lymphoma 2 (BCL2) translocation and mutation of genes involved in chromatin modification. By analyzing purified tumor cells, we identified additional novel recurrently mutated genes and confirmed mutations of one or more chromatin modifier genes within 96% of FL tumors and two or more in 76% of tumors. We defined the hierarchy of somatic mutations arising during tumor evolution by analyzing the phylogenetic relationship of somatic mutations across the coding genomes of 59 sequentially acquired biopsies from 22 patients. Among all somatically mutated genes, CREBBP mutations were most significantly enriched within the earliest inferable progenitor. These mutations were associated with a signature of decreased antigen presentation characterized by reduced transcript and protein abundance of MHC class II on tumor B cells, in line with the role of CREBBP in promoting class II transactivator (CIITA)-dependent transcriptional activation of these genes. CREBBP mutant B cells stimulated less proliferation of T cells in vitro compared with wild-type B cells from the same tumor. Transcriptional signatures of tumor-infiltrating T cells were indicative of reduced proliferation, and this corresponded to decreased frequencies of tumor-infiltrating CD4 helper T cells and CD8 memory cytotoxic T cells. These observations therefore implicate CREBBP mutation as an early event in FL evolution that contributes to immune evasion via decreased antigen presentation.

Footnotes

↵¹To whom correspondence may be addressed. Email: arasha{at}stanford.edu or michael.green{at}unmc.edu.
↵²Present address: Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68106.
↵³Present address: Department of Cancer Biology, School of Medicine, Vanderbilt University, Nashville, TN 37232.

Author contributions: M.R.G., R.L., and A.A.A. designed research; M.R.G., S.K., J.I., C.V.-D., and I.R.-C. performed research; R.L. contributed new reagents/analytic tools; M.R.G., S.K., C.L.L., R.V.N., R.S., A.J.G., H.S., I.S.-G., S.K.P., D.A.A., S.B., R.L., and A.A.A. analyzed data; and M.R.G., R.L., and A.A.A. wrote the paper.
Reviewers: S.N., MD Anderson Cancer Center; and L.R., University of Arizona.
The authors declare no conflict of interest.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE56311).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1501199112/-/DCSupplemental.