SOX11 is a lineage-dependency factor and master epigenetic regulator in neuroblastoma

Abstract

The pediatric extra-cranial tumor neuroblastoma (NB) is characterised by a low mutation burden while copy number alterations are present in most high-risk cases. We identified SOX11 as a strong lineage dependency transcription factor in adrenergic NB based on recurrent chromosome 2p focal gains and amplifications, its specific expression in the normal sympatho-adrenal lineage and adrenergic NBs and its regulation by multiple adrenergic specific cis-interacting (super-)enhancers. Adrenergic NBs are strongly dependent on high SOX11 expression levels for growth and proliferation. Through genome-wide DNA-binding and transcriptome analysis, we identified and validated functional SOX11 target genes, several of which implicated in chromatin remodeling and epigenetic modification. SOX11 controls chromatin accessibility predominantly affecting distal adrenergic lineage-specific enhancers marked by binding sites of the adrenergic core regulatory circuitry. During normal sympathoblast differentiation we find expression of SOX11 prior to members of the adrenergic core regulatory circuitry. Given the broad control of SOX11 of multiple epigenetic regulatory complexes and its presumed pioneer factor function, we propose that adrenergic NB cells have co-opted the normal role of SOX11 as a crucial regulator of chromatin accessibility and cell identity.

Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma

“…No overlapping signatures were found in the up-regulated genes (Table S2). In contrast to the findings in neurons ( Piens et al, 2010 ; Μu et al, 2012 ), DCX promoter was not bound by SOX11 in NB cells ( Decaesteker et al, 2020 Preprint ). Also, SOX11 -KD IMR32_NM had different morphology, as compared with the DCX -KD cells ( Fig 3G ) and retained parental NNC/NCC angle distribution ( Fig 3H , top).…”

“…Rabbit anti-TRIO antibody (A304-269A) was from Bethyl Laboratories, rabbit anti-TIAM1 antibody (ST1070) was from Calbiochem, rabbit anti-SOX11 was from Millipore, mouse (GTU88), and rabbit anti-γ-tubulin (DQ-19) antibodies were from Sigma-Aldrich. The rabbit polyclonal antibody, SOX11-PAb, was custom made (Absea Biotechnology) against the immunogenic peptide p-SOX11 C-term DDDDDDDDDELQLQIKQEPDEEDEEPPHQQLLQPPGQQPSQLLRRYNVAKVPASPTLSSSAESPEGASLYDEVRAGATSGAGGGSRLYYSFKNITKQHPPPLAQPALSPASSRSVSTSSS ( Decaesteker et al, 2020 Preprint ). Mouse anti-Golgi apparatus (NB37-100) was from Merck Millipore.…”

“…100 nM of siRNA non-targeting control (siRNA NTC; Dharmacon) or siRNA SOX11 (Dharmacon) were transiently transfected using DharmaFect 2 (Thermo Fisher Scientific) according to the manufacturer’s guidelines. SOX11 expression was induced by doxycycline addition (0.1 μg/ml); and induction was assessed by WB for SOX11 ( Decaesteker et al, 2020 Preprint ). mCherry-gamma-tubulin-17, CyPet-RAC1, and DCX-RFP ( Tanaka et al, 2004 ) constructs were from Addgene repository.…”

MEIS2 Is an Adrenergic Core Regulatory Transcription Factor Involved in Early Initiation of TH-MYCN-Driven Neuroblastoma Formation

“…SOX11 , the locus which maps to the short arm of chromosome 2, which is often gained together with MYCN amplification in high-risk neuroblastoma, is a key oncogenic factor in multiple cancer entities including mantle cell lymphoma [ 65 ]. Furthermore, it is functionally connected to both early and late steps during neurogenesis, and we recently established a putative crucial role in adrenergic neuroblastoma cells for regulation of chromatin accessibility and cell identity [ 66 ].…”

From DNA Copy Number Gains and Tumor Dependencies to Novel Therapeutic Targets for High-Risk Neuroblastoma

“…Our team identified SOX11 as putative dependency gene through a search for focal gains and/or amplifications of chromosomal segments encompassing transcription factors with a putative or known role in normal (neuronal) development. Re-analysis of NB DNA copy number profiling data revealed the sympatho-adrenal lineage specific SOX11 gene in recurrent chromosome 2p focal gains and amplifications [111]. SOX11 is specifically expressed in adrenergic NBs and absent in mesenchymal NBs [111,112], two distinct superenhancer associated subtypes in NB [135,136].…”