Regulation of Heterochromatin Landscape in T-Cell Acute Lymphoblastic Leukemia

Abstract

Ikzf1 encodes a zinc finger, DNA-binding protein that functions as a tumor suppressor in acute lymphoblastic leukemia (ALL). Deletion and/or loss of Ikaros function results in the development of high-risk leukemia. In the nucleus, Ikaros forms complexes with histone deacetylase complex, NuRD, and it participates in the formation of heterochromatin. The role of Ikaros-mediated formation of heterochromatin in tumor suppression in leukemia is unknown. We determined global genomic occupancy of Ikaros, global heterochromatin distribution, chromatin accessibility, DNA methylation landscape, and gene expression in primary human T-cell ALL (T-ALL), as well as in mouse T-ALL to analyze how Ikaros regulates heterochromatin landscape and gene expression in T-ALL. Results showed that Ikaros DNA occupancy is essential for the recruitment of histone deacetylase 1 (HDAC1), Polycomb repressive complex 2 (PRC2) and formation of facultative heterochromatin, as well as the formation of constitutive heterochromatin (characterized by H3K9me3 occupancy). T-ALL cells with deletion of both Ikzf1 alleles have severely impaired HDAC1 DNA occupancy and reduced H3K27me3. Re-introduction of Ikzf1 via retroviral transduction resulted in the restoration of H3K27me3 facultative heterochromatin, along with HDAC1 DNA occupancy. The H3K27me3 genomic distribution following Ikzf1 re-introduction showed high homology to the H3K27me3 genomic distribution in normal thymocytes. Analysis of H3K9me3 genomic distribution showed that Ikzf1 deletion results in dramatic redistribution of H3K9me3 global occupancy, with reduced H3K9me3 occupancy at pericentromeric loci. Reintroduction of Ikzf1 enhances H3K9me3 enrichment in pericentromeric loci, as well as at the promoters of genes that are involves in cellular proliferation. Analysis of DNA methylation distribution showed that Ikzf1 expression regulates global DNA methylation landscape. The presence of facultative heterochromatin, with enrichment of H3K27me3, inversely correlated with DNA methylation. Global analysis of chromatin accessibility revealed that Ikaros binding resulted in the loss of chromatin accessibility at over 3400 previously-accessible chromatin sites. Dynamic analyses demonstrate the long-lasting effects of Ikaros's DNA binding on heterochromatin distribution and chromatin accessibility. Analysis of gene expression in T-ALL with both Ikzf1 alleles and in Ikzf1-defficient cells (from Ikzf1-defficient T-ALL, and from Ikzf1-wild-type T-ALL following Ikzf1 deletion by CRISPR) showed that Ikaros-induced redistribution of facultative and constitutive heterochromatin results in the repression of several genes that are critical for cell cycle progression, PI3K-AKT-mTOR, and WNT signaling pathway. In conclusion, results suggest that Ikaros' tumor suppressor function in T-ALL occurs via global regulation of the heterochromatin, DNA methylation landscape, and chromatin accessibility, as well as via epigenetic regulation of transcription of the genes that play essential roles in signaling pathways that promote cellular proliferation. Disclosures No relevant conflicts of interest to declare.

Significance of immunophenotypic, cytogenetic, and molecular markers in adult patients with T-cell lymphoblastic leukemia

“…По данным международных исследований, экспрессия матричной РНК Ikaros значительно снижена в когор те больных TОЛЛ с мутациями в NOTCH1 / FBXW7, при ингибировании же аберрантной передачи сигнала NOTCH отмечается восстановление эндогенной экс прессии Ikaros [28]. Исследователями из Китая и США была изучена роль Ikarosопосредованного лейкемогенеза [29,30]. Ikaros, повидимому, дейст вует как ингибитор и активатор транскрипции, вза имодействуя с различными ядерными факторами, связанными с эпигенетической регуляцией, или на прямую воздействуя на гены.…”

“…Ikaros ингиби рует Notchиндуцированную транскрипцию за счет противодействия эффекта Notch на активацию CSL (CBF1 / SuH / Lag1) посредством конкуренции с сайтом связывания ДНК CSL в области промотора и, таким образом, угнетает экспрессию генов. Вследствие это го делеции и мутации в гене IKZF1 приводят к блоку дифференцировки клеток [29,30].…”