A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation

Lazarian, Grégory; Yin, Shanye; Hacken, Elisa ten; Sewastianik, Tomasz; Uduman, Mohamed; Font-Tello, Alba; Gohil, Satyen; Li, Shuqiang; Kim, Ekaterina; Joyal, Heather; Billington, Leah; Witten, Elizabeth; Ma, Zheng; Huang, Teddy; Severgnini, Mariano; Lefebvre, Valérie; Rassenti, Laura Z.; Gutierrez, Catherine; Georgopoulos, Katia; Ott, Christopher J.; Wang, Lili; Kipps, Thomas J.; Burger, Jan A.; Livak, Kenneth J.; Neuberg, Donna; Baran‐Marszak, Fanny; Cymbalista, Florence; Carrasco, Ruben D.; Wu, Catherine J.

doi:10.1016/j.ccell.2021.02.003

Cited by 40 publications

(38 citation statements)

References 71 publications

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“…S5 ). Similar to our data, no defect of the PC-HC targeting was observed in B cells from mice with the L161R mutation (corresponding to human AIOLOS L162R), and increased density of nuclear dots was detected in the homozygous mice when compared with WT mice ( Lazarian et al, 2021 ). Mice with the L162R mutation showed enhanced BCR/NF-κB signaling, abnormal B cell differentiation, enhanced germinal center formation, and late development of a CLL-like disease at age 18–24 mo.…”

Section: Discussionsupporting

confidence: 91%

T and B cell abnormalities, pneumocystis pneumonia, and chronic lymphocytic leukemia associated with an AIOLOS defect in patients

Chang

Yamashita

Niemela

et al. 2021

Journal of Experimental Medicine

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AIOLOS/IKZF3 is a member of the IKAROS family of transcription factors. IKAROS/IKZF1 mutations have been previously associated with different forms of primary immunodeficiency. Here we describe a novel combined immunodeficiency due to an IKZF3 mutation in a family presenting with T and B cell involvement, Pneumocystis jirovecii pneumonia, and/or chronic lymphocytic leukemia. Patients carrying the AIOLOS p.N160S heterozygous variant displayed impaired humoral responses, abnormal B cell development (high percentage of CD21low B cells and negative CD23 expression), and abrogated CD40 responses. Naive T cells were increased, T cell differentiation was abnormal, and CD40L expression was dysregulated. In vitro studies demonstrated that the mutant protein failed DNA binding and pericentromeric targeting. The mutant was fully penetrant and had a dominant-negative effect over WT AIOLOS but not WT IKAROS. The human immunophenotype was recapitulated in a murine model carrying the corresponding human mutation. As demonstrated here, AIOLOS plays a key role in T and B cell development in humans, and the particular gene variant described is strongly associated with immunodeficiency and likely malignancy.

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Section: Discussionsupporting

confidence: 91%

T and B cell abnormalities, pneumocystis pneumonia, and chronic lymphocytic leukemia associated with an AIOLOS defect in patients

Chang

Yamashita

Niemela

et al. 2021

Journal of Experimental Medicine

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“…The somatic AIOLOS L162R mutation was repeatedly reported in CLL ( 25 ). AIOLOS L162R variant was not proven to be loss-of-function in DNA binding and PC-HC targeting abilities ( 27 , 30 ). Studies on the murine homologous variant Aiolos L161R suggested that this variant enhanced BCR and NF-κB signaling, contributing to the CLL-like disease development in aged mice.…”

Section: Discussion and Future Directionmentioning

confidence: 99%

“…Another Aiolos mutant mouse ( 30 ), a somatic hotspot mutation in AIOLOS (L162R) found in CLL patients, has been recently reported as a human disease model ( 30 ) ( Figure 1B ) ( 25 ). The B cell-conditional knock-in mouse model harboring the homologous variant L161R ( Cd19-Cre; Aiolos +/fl and Cd19-Cre; Aiolos fl/fl , hereafter designated as Aiolos +/Cd19-L161R and Aiolos Cd19-L161R/Cd19-L161R , respectively) was generated and studied.…”

Section: Murine Models Of Aiolos Variantsmentioning

confidence: 92%

“…The B cell-conditional knock-in mouse model harboring the homologous variant L161R ( Cd19-Cre; Aiolos +/fl and Cd19-Cre; Aiolos fl/fl , hereafter designated as Aiolos +/Cd19-L161R and Aiolos Cd19-L161R/Cd19-L161R , respectively) was generated and studied. In terms of binding to canonical consensus sequence and pericentromeric heterochromatin (PC-HC) targeting, the variant was not identified as loss-of-function ( 27 , 30 ).…”

Section: Murine Models Of Aiolos Variantsmentioning

confidence: 99%

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AIOLOS Variants Causing Immunodeficiency in Human and Mice

Yamashita

Morio

2022

Front. Immunol.

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AIOLOS is encoded by IKZF3 and is a member of the IKAROS zinc finger transcription factor family. Heterozygous missense variants in the second zinc finger of AIOLOS have recently been reported to be found in the families of patients with inborn errors of immunity. The AIOLOSG159R variant was identified in patients with B-lymphopenia and familial Epstein–Barr virus-associated lymphoma. Early B-cell progenitors were significantly reduced in the bone marrow of patients with AIOLOSG159R. Another variant, AIOLOSN160S was identified in the patients presented with hypogammaglobulinemia, susceptibility to Pneumocystis jirovecii pneumonia, and chronic lymphocytic leukemia. Patients with AIOLOSN160S had mostly normal B cell counts but showed increased levels of CD21lo B cells, decreased CD23 expression, and abrogated CD40 response. Both variants were determined to be loss-of-function. Mouse models harboring the corresponding patient’s variants recapitulated the phenotypes of the patients. AIOLOS is therefore a novel disease-causing gene in human adaptive immune deficiency.

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“…These studies have confirmed the CLL-driving roles of alterations such as mutated SF3B1 in conjunction with ATM deletion, and hotspot mutations in IKZF3, and altogether highlight the common and diverse mechanisms underlying CLL pathogenesis [i.e., dysregulation of B-cell receptor (BCR) signaling; refs. 3,4].…”

Section: Introductionmentioning

confidence: 99%

B Cell-Restricted Depletion of Dnmt3a Activates Notch Signaling and Causes Chronic Lymphocytic Leukemia

Yin

Biran

Kretzmer

et al. 2021

Blood

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Previous studies have revealed a critical role of methylation deregulation in the onset and progression of chronic lymphocytic leukemia (CLL). In mammalian cells, DNA methylation is dynamically established by the DNA methyltransferase 3 (DNMT3) family of de novo methyltransferases DNMT3A. Although mutations of DNMT3A are rarely observed in CLL, our RNA-sequencing (RNA-seq) analysis of 107 human CLLs show that low DNMT3A expression is associated with more aggressive disease, and supports a driving role of DNMT3A loss in CLL. To test this hypothesis, we generated a conditional knock-out mouse model with B cell-restricted deletion of Dnmt3a. Homozygous Dnmt3a depletion in B cells resulted in the development of CD5+ B cell leukemia mimicking human CLL with 100% penetrance at a median age of onset of 5.3 months, and heterozygous Dnmt3a depletion yielded a disease penetrance of 89% with a median onset at 18.5 months, confirming its role as a haplo-insufficient tumor suppressor. Given the known role of Dnmt3a as a de novo methyltransferase, we first evaluated the impact of Dnmt3a depletion on global DNA methylation in non-leukemic CD5+ B cells isolated from the peritoneal cavity by cell sorting (i.e. B1a cells) using reduced representation bisulfite sequencing (RRBS). We identified a set of differentially methylated regions (DMRs) (difference>0.2), mostly hypomethylated, in Dnmt3afl/fl versus WT B1a cells (473 hypomethylated, 19 hypermethylated). Genes with dysregulated methylation were highly enriched in pathways involved in immune response (e.g., Interferon-α signaling, JAK/STAT3 signaling) and proliferation (Wnt Signaling and Notch signaling). Given the prominent hypomethylation changes observed in Dnmt3a depleted B1a cells, we investigated whether these would lead to altered gene transcript expression. Using RNA-seq, we detected 460 downregulated and 168 upregulated genes in the Dnmt3afl/fl B1a cells compared to WT B1a cells (FDR<0.05, fold change >2). Consistent with the methylation data, differentially expressed genes were likewise enriched for JAK/STAT3 signaling, Wnt Signaling and Notch signaling, supporting a direct influence of dysregulated methylation on downstream signaling cascades. We investigated the changes in methylomes of the CLL cells arising from the Dnmt3afl/fl animals. Compared to WT B1a cells, Dnmt3afl/fl CLL cells generated 1335 hypomethylated and 2369 hypermethylated DMRs in. Focusing on genes that were hypomethylated in CLL compared to WT B1a cells, we found that these were highly enriched for several oncogenic signaling pathways including Notch signaling and Wnt Signaling, consistent with the pre-leukemia findings. RNA-seq analysis identified more upregulated (n=2801) than downregulated (n=1244) genes in CLL cells compared to WT B1a cells (FDR<0.05, FC>2), supporting a role of Dnmt3a depletion in transcriptional activation. We observed a general upregulation of Notch signaling genes and the downstream Notch targets, implicating Notch activation in this CLL mouse model. Of note, we showed Dnmt3a-depleted CLL cells to be highly sensitive to Notch inhibitor DAPT both in vitro and in a transplantable mouse model. Consistently, primary human CLL cells with low DNMT3A expression were more sensitive to DAPT than those with higher DNMT3A expression (P=0.005, Spearman correlation), despite similar sensitivity to ibrutinib and venetoclax. Together, our results have confirmed the causal role of Dnmt3a downregulation in CLL generation. We provide evidence in support of the interaction between Dnmt3a-dependent methylation changes and hyperactivation of Notch signaling in transcriptional reprogramming and transformation of B1a cells into CLL. Furthermore, we demonstrate differential sensitivity of DNMT3A high and low expressing primary CLLs to Notch inhibition, indicative of consistent dependencies of human and murine CLLs. Thus, the Dnmt3a models provides a unique opportunity for the study of non-mutational Notch activation, and a useful platform for the study of Notch-signaling targeted therapeutics. Disclosures Kipps: Abbott Laboratories: Consultancy, Research Funding; Celgene Corporation: Consultancy, Honoraria, Research Funding; Pharmacyclics LLC, an Abbvie Company: Consultancy, Honoraria, Other: Travel, Accommodations, Expenses, Research Funding, Speakers Bureau; Genentech, Inc.: Honoraria, Research Funding, Speakers Bureau; Gilead Sciences, Inc.: Honoraria, Research Funding; GlaxoSmithKline: Research Funding; MedImmune Inc: Research Funding; Moores Cancer Center: Current Employment; Oncternal Therapeutics, Inc.: Current holder of stock options in a privately-held company, Other: Stock or other ownership, Patents & Royalties: Cirmtuzumab was developed by Thomas J. Kipps in the Thomas J. Kipps laboratory and licensed by the University of California to Oncternal Therapeutics, Inc., which provided stock options and research funding to the Thomas J. Kipps laboratory., Research Funding; AbbVie: Consultancy, Honoraria, Other, Speakers Bureau; DAVAOncology: Consultancy, Honoraria, Other; DAVA Pharmaceuticals: Speakers Bureau; Bionest Partner: Other; Celgene: Consultancy, Honoraria, Other, Research Funding; Genetech: Honoraria, Other; Genentech-Roche: Consultancy; Gilead Sciences: Consultancy, Honoraria, Other, Speakers Bureau; Janssen: Consultancy, Honoraria, Other, Research Funding, Speakers Bureau; Roche: Honoraria, Other; MD Anderson Cancer Center: Research Funding; Velos: Research Funding; CRIM: Research Funding; Indy Hematology Review: Other; TG Therapeutics: Other; Verstem: Other, Speakers Bureau; University of California, San Diego: Current Employment; Pharmacyclics/AbbVie: Honoraria, Research Funding; Breast Cancer Research Foundation: Research Funding; SCOR - The Leukemia and Lymphoma Society: Research Funding; National Cancer Institute/NIH: Honoraria, Research Funding; Genentech/Roche: Honoraria; European Research Initiative on CLL (ERIC): Honoraria. Neuberg: Madrigal Pharmaceuticals: Other: Stock ownership; Pharmacyclics: Research Funding. Letai: Flash Therapeutics: Other: equity holding member of the scientific advisory board; Dialectic Therapeutics: Other: equity holding member of the scientific advisory board; Zentalis Pharmaceuticals: Other: equity holding member of the scientific advisory board. Wu: BioNTech: Current equity holder in publicly-traded company; Pharmacyclics: Research Funding.

show abstract

A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation

Cited by 40 publications

References 71 publications

T and B cell abnormalities, pneumocystis pneumonia, and chronic lymphocytic leukemia associated with an AIOLOS defect in patients

T and B cell abnormalities, pneumocystis pneumonia, and chronic lymphocytic leukemia associated with an AIOLOS defect in patients

AIOLOS Variants Causing Immunodeficiency in Human and Mice

B Cell-Restricted Depletion of Dnmt3a Activates Notch Signaling and Causes Chronic Lymphocytic Leukemia

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