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. 2010 Nov 24;33(5):685-98.
doi: 10.1016/j.immuni.2010.11.008.

Alternative promoter usage at the Notch1 locus supports ligand-independent signaling in T cell development and leukemogenesis

Pablo Gómez-del Arco  1 , Mariko Kashiwagi, Audrey F Jackson, Taku Naito, Jiangwen Zhang, Feifei Liu, Barbara Kee, Marc Vooijs, Freddy Radtke, Juan Miguel Redondo, Katia Georgopoulos
Affiliations

Alternative promoter usage at the Notch1 locus supports ligand-independent signaling in T cell development and leukemogenesis

Pablo Gómez-del Arco et al. Immunity. .

Abstract

Loss of the transcription factor Ikaros is correlated with Notch receptor activation in T cell acute lymphoblastic leukemia (T-ALL). However, the mechanism remains unknown. We identified promoters in Notch1 that drove the expression of Notch1 proteins in the absence of a ligand. Ikaros bound to both canonical and alternative Notch1 promoters and its loss increased permissive chromatin, facilitating recruitment of transcription regulators. At early stages of leukemogenesis, increased basal expression from the canonical and 5'-alternative promoters initiated a feedback loop, augmenting Notch1 signaling. Ikaros also repressed intragenic promoters for ligand-independent Notch1 proteins that are cryptic in wild-type cells, poised in preleukemic cells, and active in leukemic cells. Only ligand-independent Notch1 isoforms were required for Ikaros-mediated leukemogenesis. Notch1 alternative-promoter usage was observed during T cell development and T-ALL progression. Thus, a network of epigenetic and transcriptional regulators controls conventional and unconventional Notch signaling during normal development and leukemogenesis.

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Figures

Figure 1
Figure 1. Combined effects of Notch1 and Ikaros deletion on T cell development
(A) Thymocyte profiles of 3 weeks old wild-type (WT), Ikzf1-/-, Notch1-/- and Notch1-/-Ikzf1-/- littermates. The upper panel shows CD4 and CD8 staining, the middle the DN1 to DN4 staining of double negative (CD4−, CD8− and Thy1.2−) thymocytes for CD44 and CD25. The lower panel shows expression of TCRβ and CD5 in total thymocytes. Numbers indicate the percentage of cells in each subset. Red gate shows the DN2-DN3 intermediate accumulating in the Notch1-/- thymus. (B) Genomic PCR analysis of thymic deletion of the Notch1 locus by LckCre (C) Thymic cellularities in <1.5 month old mice (n> 5). (D) CD8+ SP cells shown in (A), were further evaluated for TCRβ and HSA expression.
Figure 2
Figure 2. The role of Notch signaling in-loss-of-Ikaros-mediated leukemogenesis
(A) Kaplan-Meier survival plot for mice with different Notch1 and Ikzf1 mutations. All WT (n=24) or Notch1-/- (n=15) mice remained healthy during observation (~6 months). Ikzf1+/- mice were also generally healthy (36/38). 11 out of the 12 Notch1-/-Ikzf1+/- died of leukemia. Of the 12 Ikzf1-/-, 1 survived, 2 died of anemia and the rest of leukemia. All Notch1-/-Ikzf1-/- (n=5) mice died during the first two months of study. (B) Thymocyte profiles of WT and 2 representative diseased Notch1-/-Ikzf1+/- mice, as described in Figure 1A. (C) Genomic PCR of leukemic clones deleted of the Notch1 canonical promoter and exon 1. (D) Semi-quantitative RT-PCR of E1c from mRNAs isolated from Notch1-/-Ikzf1+/- leukemic cells. Expression of E1a, Hes1 and Actb (control) was also detected in these cells. (E) Immunoblot analysis of whole thymocyte extracts at different stages of disease development with a Notch1 C-terminal (C-term) and Ikaros (Ik) antibodies. Right panel shows analysis of WT, pre-leukemic Ikzf1DN/+ and leukemic Notch1-/- Ikzf1+/- thymocytes using antibodies to Notch1 C-terminus and also to ICN (Val1744). (F) Notch1-/-Ikzf1+/- cell lines (1537 and 1218) were treated with γ-secretase inhibitors (GSI) and the growth was measured (See experimental procedures). Values of absorbance are represented as mean of triplicates from one representative experiment. The growth of an Ikzf1DN/+ (1891) GSI-resistant leukemic clone is also shown (G) Immunoblot analysis of cell-line extracts (as in E) and (H) expression of alternative Notch1 transcripts are shown. (I) Thymic cellularities of single and combined Ikzf1 and Rbpj mutants at <2 months of age (n>5) (J) Thymocyte profiles of WT, Ikzf1-/- and Rbpj-/-Ikzf1-/-. (K) Frequency of leukemic transformation (pink vs. green) in single and combined KO mice. All experiments were repeated at least three times, but those of F, G and H, which were done twice.
Figure 3
Figure 3. Mapping of alternative TSS at the Notch1 locus
(A) Promoter utilization at the Notch1 locus is shown. Green, black and red arrows demarcate the respective 5’ alternative, canonical and intragenic TSSs described in the text. cDNA probes are shown underneath relevant regions. Open rectangles depict canonical exons, a red rectangle the alternative E1a, and a black rectangle the alternative E1b. Two alternative polyadenylation sites in E34 are depicted by orange or green stars. (B, C) Expression of Notch1 transcripts and ICN in WT and leukemic cells derived from DKOs and Ikzf1DN/+ mutant mice. PolyA+ RNA and protein extracts were analyzed by probe hybridization (upper panels) and immunoblots (lower panel). To monitor Notch activation, the α-Val1744 Ab was used. Transcripts with distinct polyA sites are color-coded as in (A). All experiments were repeated at least three times.
Figure 4
Figure 4. Expression of Notch1 transcripts during T cell development and leukemogenesis
(A) Notch signaling during T cell development and stages of Ikaros-mediated leukemogenesis. Expression and signaling of canonical and alternative Notch1 isoforms is depicted during T cell development (DN3-SP) and leukemogenesis (Stages I-III). (B) Quantitative and (C) semi-quantitative RT-PCR using sorted DN3, DN4, and DP subsets from WT thymus and Ikzf1 mutant clones at stage I and III. Expression of Notch1 exon1 (E1c), exon1a (E1a) and Hes1 transcripts was determined in B and C. (D) RNA and (E) protein analysis of Notch1 transcripts and ICN during Ikaros-mediated leukemogenesis (SI-SIII). The arrow in (D) marks the E1a transcript and the star non-specific hybridization. Lane 2 from WT DN thymocytes was loaded with ~30% of the amount of RNA compared to lane 1 (~WT DP). (F) Quantitative RT-PCR analysis of E1a and E1c Notch1 transcripts in Ikzf1 mutant DP thymocytes at Stage I, II and III. (G) Quantitative RT-PCR analysis of total Notch1 (exons 33-34) in Rbpj-/-Ikzf1DN/+ DP thymocytes.
Figure 5
Figure 5. Ligand-independent signaling provided by alternative Notch1 isoforms
(A) Exon and protein domain composition of the canonical (E1c) and alternative Notch1 transcripts (E1a-E3 and E25, see also Figure S5). Notch1-translated isoforms are depicted with stars: black-300 kDa canonical (E1c FL and 6MT) and orange from exon 1a (E1a-E3 6MT) pro-proteins, green-M1615, pink-M1659, red-M1727, blue-M1796, M1845, M1848 and by processing with arrows: green-S1 site, yellow-S2 site, purple-S3 site. The construct substituted the PEST domain by a 6 MYC-tag is depicted 6MT and with the intact C-terminus FL. (B, C) The activity and cellular localization of the E1a-E3 transcript (E1a-E3 6MT) was compared to that of the canonical (E1c 6MT). Expression vectors were co-transfected with the RBP-Jκ pGALuc reporter into HEK 293 cells and assayed for Relative Luciferase Units-RLU (as light units measure in 10 s.) and recombinant protein production by immunoblot and immunofluorescence using antibodies to the c-Myc, the S2 (Val1711) and S3 (Val1744) epitopes as well as to a C-terminal domain. Notch1 proteins are demarcated by asterisks as in (A). A representative experiment out of three is shown. (D) Notch1 protein production and activity was also assessed in the presence (+) or absence (-) of GSI. The proteins generated by the alternative E25 transcript were tested for activity relative to the E1c FL. Reporter activity and protein analysis were performed as in (B). (E) Mutational analysis mapped a major as well as minor translation sites within the E25 transcript. Expression studies were performed as in B and D. Asterisks indicate distinct translation products as in (A). All experiments were repeated at least three times.
Figure 6
Figure 6. Loss of Ikaros binding to Notch1 locus affects the Notch1 chromatin environment
Peaks are shown for ChIP-Seq performed with anti-H3K27me3 (red), anti-H3K4me3 (blue), anti-H3K9/14ac (orange), anti-H3K36me3 (green), anti-Ikaros (purple and light blue), and anti-ICN (dark red). The Notch1 canonical promoter (black arrow), 5’ alternative promoter (green arrow) and intragenic alternative promoters (red arrows) are identified. (A) Histone modification status and Ikaros binding at Notch1 locus in WT DP thymocytes. Islands of H3K4me3 and H3K9/14ac (black vertical arrows), decorated the transcriptionally active E1c promoter and poised E1a promoter. Notch1 expression in DP thymocytes was confirmed by the H3K36me3 elongation mark. High confidence (purple, p-value 10-5), and lower confidence (light blue, p-value 10-3) Ikaros binding sites were identified at the promoters and at intragenic locations and validated by ChIP-PCR. Asterisk marks the internal control in duplex ChIP-PCR. (B) Histone modification status at the Notch1 locus in Ikaros null SII thymocytes that have not activated Notch signaling. (C) A direct comparison (equal tag numbers) of histone modifications at the E1c and E1a promoters. IkBS relative to methylation and acetylation islands are also indicated (D) Notch1 ICN binding at Notch1 at late stage III of leukemogenesis. Binding of ICN was examined by ChIP-seq and candidate ChIP at four Ikaros binding sites, at intron 15 (negative control) and at the Hes1 promoter (positive control). These experiments were repeated twice with similar results.
Figure 7
Figure 7. Ikaros and E2A co-regulate canonical and alternative Notch1 promoters
(A) Sequence analysis of the canonical and alternative promoter regions identified four promoter elements – CpG islands, TATA, CCAAT and GC boxes – and binding sites for E2A within or near regions of Ikaros binding. IkBSs sites are purple or light blue. Promoter elements and putative E2A sites are represented in blue (+ strand) or red (- strand). (B) Notch1 alternative transcripts and ICN protein were detected in Tcf3-/- leukemic cells. Exons in the vicinity of transcription start sites and 3’UTR are indicated with gray boxes. Table summarizes the usage of each TSS and 3’ UTRs.
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