Establishment of the TALE-code reveals aberrantly activated homeobox gene PBX1 in Hodgkin lymphoma

PLoS One. 2021 Feb 4;16(2):e0246603. doi: 10.1371/journal.pone.0246603. eCollection 2021.

Abstract

Homeobox genes encode transcription factors which regulate basic processes in development and cell differentiation and are grouped into classes and subclasses according to sequence similarities. Here, we analyzed the activities of the 20 members strong TALE homeobox gene class in early hematopoiesis and in lymphopoiesis including developing and mature B-cells, T-cells, natural killer (NK)-cells and innate lymphoid cells (ILC). The resultant expression pattern comprised eleven genes and which we termed TALE-code enables discrimination of normal and aberrant activities of TALE homeobox genes in lymphoid malignancies. Subsequent expression analysis of TALE homeobox genes in public datasets of Hodgkin lymphoma (HL) patients revealed overexpression of IRX3, IRX4, MEIS1, MEIS3, PBX1, PBX4 and TGIF1. As paradigm we focused on PBX1 which was deregulated in about 17% HL patients. Normal PBX1 expression was restricted to hematopoietic stem cells and progenitors of T-cells and ILCs but absent in B-cells, reflecting its roles in stemness and early differentiation. HL cell line SUP-HD1 expressed enhanced PBX1 levels and served as an in vitro model to identify upstream regulators and downstream targets in this malignancy. Genomic studies of this cell line therein showed a gain of the PBX1 locus at 1q23 which may underlie its aberrant expression. Comparative expression profiling analyses of HL patients and cell lines followed by knockdown experiments revealed NFIB and TLX2 as target genes activated by PBX1. HOX proteins operate as cofactors of PBX1. Accordingly, our data showed that HOXB9 overexpressed in HL coactivated TLX2 but not NFIB while activating TNFRSF9 without PBX1. Further downstream analyses showed that TLX2 activated TBX15 which operated anti-apoptotically. Taken together, we discovered a lymphoid TALE-code and identified an aberrant network around deregulated TALE homeobox gene PBX1 which may disturb B-cell differentiation in HL by reactivation of progenitor-specific genes. These findings may provide the framework for future studies to exploit possible vulnerabilities of malignant cells in therapeutic scenarios.

MeSH terms

  • B-Lymphocytes / metabolism
  • Cell Differentiation / physiology
  • Cell Line, Tumor
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Gene Regulatory Networks
  • Genes, Homeobox
  • Hematopoietic Stem Cells / metabolism
  • Hodgkin Disease / genetics*
  • Hodgkin Disease / metabolism*
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • Humans
  • Lymphocytes / metabolism
  • Myeloid Ecotropic Viral Integration Site 1 Protein / genetics
  • NFI Transcription Factors / genetics
  • NFI Transcription Factors / metabolism
  • Pre-B-Cell Leukemia Transcription Factor 1 / genetics*
  • Pre-B-Cell Leukemia Transcription Factor 1 / metabolism
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism

Substances

  • HOXB9 protein, human
  • Homeodomain Proteins
  • Myeloid Ecotropic Viral Integration Site 1 Protein
  • NFI Transcription Factors
  • NFIB protein, human
  • Pre-B-Cell Leukemia Transcription Factor 1
  • Repressor Proteins
  • TGIF1 protein, human
  • TLX2 protein, human
  • PBX1 protein, human

Grants and funding

The authors received no specific funding for this work.