Transcriptome analysis of primary adult B-cell lineage acute lymphoblastic leukemia identifies pathogenic variants and gene fusions, and predicts subtypes for in depth molecular diagnosis

BACKGROUND

B-cell acute lymphoblastic leukemia (B-ALL) is classified into subgroups based on known driver oncogenes and molecular lesions, including translocations and recurrent mutations. However, the current diagnostic tests do not identify subtypes or oncogenic lesions for all B-ALL samples, creating a heterogeneous B-ALL group of unknown subtypes.

METHODS

We sorted primary adult B-ALL cells and performed transcriptome analysis by bulk RNA sequencing (RNA-seq).

RESULTS

Transcriptomic analysis of an adult B-ALL cohort allowed the classification of four patient samples with subtypes that were not previously revealed by standard gene panels. The leukemia of two patients were of the DUX4 subtype and two were CRLF2+ Ph-like B-ALL. Furthermore, single nucleotide variant analysis detected the oncogenic NRAS-G12D, KRAS-G12D, and KRAS-G13D mutations in three of the patient samples, presenting targetable mutations. Additional oncogenic variants and gene fusions were uncovered, as well as multiple variants in the PDE4DIP gene across five of the patient samples.

CONCLUSION

We demonstrate that RNA-seq is an effective tool for precision medicine in B-ALL by providing comprehensive molecular profiling of leukemia cells, identifying subtype and oncogenic lesions, and stratifying patients for appropriate therapy.

Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance

Mutations in the gene encoding the zinc-finger transcription factor Ikaros (IKZF1) are found in patients with immunodeficiency, leukemia, and autoimmunity. Although Ikaros has a well-established function in modulating gene expression programs important for hematopoietic development, its role in other cell types is less well defined. Here, we uncover functions for Ikaros in thymic epithelial lineage development in mice and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both autoimmune regulator-positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, Ikaros shapes thymic mimetic cell diversity, and its deletion results in a marked expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations. Single-cell analysis reveals that Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.

Targeted engagement of β-catenin-Ikaros complexes in refractory B-cell malignancies

In most cell types, nuclear β-catenin functions as prominent oncogenic driver and pairs with TCF7-family factors for transcriptional activation of MYC. Surprisingly, B-lymphoid malignancies not only lacked expression and activating lesions of β-catenin but critically depended on GSK3β for effective β-catenin degradation. Our interactome studies in B-lymphoid tumors revealed that β-catenin formed repressive complexes with lymphoid-specific Ikaros factors at the expense of TCF7. Instead of MYC-activation, β-catenin was essential to enable Ikaros-mediated recruitment of nucleosome remodeling and deacetylation (NuRD) complexes for transcriptional repression of MYC. To leverage this previously unrecognized vulnerability of B-cell-specific repressive β-catenin-Ikaros-complexes in refractory B-cell malignancies, we examined GSK3β small molecule inhibitors to subvert β-catenin degradation. Clinically approved GSK3β-inhibitors that achieved favorable safety prof les at micromolar concentrations in clinical trials for neurological disorders and solid tumors were effective at low nanomolar concentrations in B-cell malignancies, induced massive accumulation of β-catenin, repression of MYC and acute cell death. Preclinical in vivo treatment experiments in patient-derived xenografts validated small molecule GSK3β-inhibitors for targeted engagement of lymphoid-specific β-catenin-Ikaros complexes as a novel strategy to overcome conventional mechanisms of drug-resistance in refractory malignancies.

HIGHLIGHTS

Unlike other cell lineages, B-cells express nuclear β-catenin protein at low baseline levels and depend on GSK3β for its degradation.In B-cells, β-catenin forms unique complexes with lymphoid-specific Ikaros factors and is required for Ikaros-mediated tumor suppression and assembly of repressive NuRD complexes. CRISPR-based knockin mutation of a single Ikaros-binding motif in a lymphoid MYC superenhancer region reversed β-catenin-dependent Myc repression and induction of cell death. The discovery of GSK3β-dependent degradation of β-catenin as unique B-lymphoid vulnerability provides a rationale to repurpose clinically approved GSK3β-inhibitors for the treatment of refractory B-cell malignancies.

GRAPHICAL ABSTRACT

Abundant nuclear β-cateninβ-catenin pairs with TCF7 factors for transcriptional activation of MYCB-cells rely on efficient degradation of β-catenin by GSK3βB-cell-specific expression of Ikaros factors Unique vulnerability in B-cell tumors: GSK3β-inhibitors induce nuclear accumulation of β-catenin.β-catenin pairs with B-cell-specific Ikaros factors for transcriptional repression of MYC.

Ikaros Regulates microRNA Networks in Acute Lymphoblastic Leukemia

The hematopoietic transcription factor Ikaros (IKZF1) regulates normal B cell development and functions as a tumor suppressor in precursor B cell acute lymphoblastic leukemia (B-ALL). MicroRNAs (miRNAs) are small regulatory RNAs that through post-transcriptional gene regulation play critical roles in intracellular processes including cell growth in cancer. However, the role of Ikaros in the regulation of miRNA expression in developing B cells is unknown. In this study, we examined the Ikaros-regulated miRNA targets using human IKZF1-mutated Ph+ B-ALL cell lines. Inducible expression of wild-type Ikaros (the Ik1 isoform) caused B-ALL growth arrest and exit from the cell cycle. Global miRNA expression analysis revealed a total of 31 miRNAs regulated by IK1, and ChIP-seq analysis showed that Ikaros bound to several Ik1-responsive miRNA genes. Examination of the prognostic significance of miRNA expression in B-ALL indicate that the IK1-regulated miRNAs hsa-miR-26b, hsa-miR-130b and hsa-miR-4649 are significantly associated with outcome in B-ALL. Our findings establish a potential regulatory circuit between the tumor-suppressor Ikaros and the oncogenic miRNA networks in IKZF1-mutated B-ALL. These results indicate that Ikaros regulates the expression of a subset of miRNAs, of which several may contribute to B-ALL growth.

ssvQC: an integrated CUT&RUN quality control workflow for histone modifications and transcription factors

OBJECTIVE

Among the different methods to profile the genome-wide patterns of transcription factor binding and histone modifications in cells and tissues, CUT&RUN has emerged as a more efficient approach that allows for a higher signal-to-noise ratio using fewer number of cells compared to ChIP-seq. The results from CUT&RUN and other related sequence enrichment assays requires comprehensive quality control (QC) and comparative analysis of data quality across replicates. While several computational tools currently exist for read mapping and analysis, a systematic reporting of data quality is lacking. Our aims were to (1) compare methods for using frozen versus fresh cells for CUT&RUN and (2) to develop an easy-to-use pipeline for assessing data quality.

RESULTS

We compared a workflow for CUT&RUN with fresh and frozen samples, and present an R package called ssvQC for quality control and comparison of data quality derived from CUT&RUN and other enrichment-based sequence data. Using ssvQC, we evaluate results from different CUT&RUN protocols for transcription factors and histone modifications from fresh and frozen tissue samples. Overall, this process facilitates evaluation of data quality across datasets and permits inspection of peak calling analysis, replicate analysis of different data types. The package ssvQC is readily available at https://github.com/FrietzeLabUVM/ssvQC .

Individual zinc finger domains of Ikaros have specific roles in regulating murine myeloid hematopoietic development

The Ikzf1 gene (encoding Ikaros) is essential for B cell development, but also plays important roles in the development of other hematopoietic lineages. Ikaros is a zinc finger (ZnF) transcription factor, with ZnF1 through ZnF4 involved in DNA binding, and ZnF5-ZnF6 required for dimerization. Previous work in our group has shown that germline deletion of the first or fourth ZnFs (ΔF1 and ΔF4 mice) resulted in different defects in lymphoid development. Here, we present our results from investigation of the roles of ZnF1 and ZnF4 in myeloid cell development.

Flow cytometry analysis of bone marrow (BM), peritoneal cavity, lung and spleen cells show that ΔF1 and ΔF4 mice have significantly altered levels of eosinophils, basophils, monocytes, and mast cells. Most importantly, the observed changes differ between the two mutants.

Interestingly, we observed a systemic increase in eosinophils in all tissues investigated in one of our ZnF-mutant mice. When culturing BM cells ex-vivo, we see that cells from the mutant mice proliferate at a higher rate than that of wt, and respond more actively to cytokine stimulation. Furthermore, ex vivo differentiation assay displayed a ZnF-dependent defect in mast cell/basophil development, and skewing towards eosinophil development, supporting the finding that ZnF1 and ZnF4 of Ikaros differentially regulate granulocyte development.

In addition to studying immune cell subsets and ex-vivo stimulation assays, we aim to sort granulocyte cell populations from the ΔF1 and ΔF4 mice and perform RNA-seq to investigate differential gene regulation. We conclude that Ikzf1 plays a role in the regulation of eosinophils, mast cells and basophils, and will present results to date.

Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

Abstract PO-62: Overcoming venetoclax resistance in B-cell malignancies by antagonism of stromal TGF-beta-mediated drug resistance

Novel targeted therapies have substantially improved the prognosis of patients with B-cell malignancies. However, a substantial fraction of patients relapse, even after initially achieving deep remissions. Many studies have characterized the interactions between tumor cells and their microenvironment as integral to leukemia/lymphoma homeostasis and for the provision of survival signals, also contributing to drug resistance (referred to as environment-mediated drug resistance [EMDR]). Therapeutic efforts to antagonize microenvironment-emanating survival cues have predominantly focused on perturbation of tumor cell adhesion enabling the physical displacement from protective niches. In an effort to address whether direct stromal targeting could more precisely mitigate EMDR, we antagonized stromal expressed PKC-beta, which we have previously shown to be a stroma-autonomous signaling pathway critical for the survival of malignant B cells (Lutzny et al., Cancer Cell 2013). The dependency on stroma PKC-b was uniformly found for acute (ALL) and chronic (CLL, MCL) B-cell malignancies. In particular, our data demonstrate that stroma PKC-b is of key importance for multidrug resistance of malignant B cells (Park et al., Science Trans Med 2020). Here we demonstrate novel mechanistic insights into stroma-mediated drug resistance in B-cell malignancies. We identified that stroma PKC-b drives a transcriptional program, activating TGF-b and BMP-signaling in tumor cells. Our data show that antagonizing stroma signals with TGF-b inhibitors abrogated upregulation of BCL-XL and overcomes stroma-dependent resistance to venetoclax. This activation operates in parallel to the activation of the transcription factor EB (TFEB) as a downstream target of PKC-b. Interference with these signaling pathways impairs plasma membrane integrity of MSCs by downregulation of numerous adhesion and signaling molecules (e.g., ADAM17), required for the reciprocal stabilization of BCL-XL in tumor cells. The significance of microenvironment PKC-b for drug resistance was demonstrated in vivo, using C57B/6 mice, diseased with EuTCL-1 driven B-cell tumors and treated with venetoclax in combination with or without enzastaurin (PKC-b inhibitor). Combined treatment significantly prolonged survival, based on PKC-b mediated impairment of lysosome biogenesis in vivo. Similarly, concurrent treatment of PKC-b inhibitors with chemotherapy also improved survival in an ALL-PDx model. Our data demonstrate that mitigating EMDR with small-molecule inhibitors of PKC-b or TGF-b signaling enhances the effectiveness of both targeted and nontargeted chemotherapies and, moreover, has the ability to overcome venetoclax resistance in B-cell malignancies in vivo. A clinical trial to test the dual inhibition of stroma and tumor cells in lymphoma patients is in preparation.

Citation Format: Eugene Park, Jingyu Chen, Andrew Moore, Maurizio Mangolini, Joseph R. Byod, Hilde Schjerven, James C. Williamson, Paul J. Lehner, Michael Leitges, Alexander Egle, Marc Schmidt-Supprian, Seth Frietze, Ingo Ringshausen. Overcoming venetoclax resistance in B-cell malignancies by antagonism of stromal TGF-beta-mediated drug resistance [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-62.

Ikaros regulates gene expression programs required for proper BCR-activation in mature B cells

The zinc-finger (ZnF) transcription factor Ikaros (encoded by Ikzf1) plays an essential role in regulating transcriptional programs required for B cell development, as Ikzf1null/null mice do not develop B cells. Ikaros contains two ZnF domains which function in DNA-binding and protein-protein interactions, respectively. Recently, mutations within the central DNA-binding ZnF domain of the IKZF1 gene has been linked to autoimmunity. Likewise, our murine model containing a germ-line deletion of the fourth ZnF (Ikzf1DF4/DF4) displays a B cell hyper-reactive (HR) phenotype, with B cells activated by anti-IgM without the requirement for a second co-stimulatory signal. Although Ikaros has been well-studied in early developing B cells, how loss-of-function mutations in Ikzf1 impacts downstream effector functions of mature B cells, remains largely unknown. Here, we investigated the role of Ikaros in regulating an epigenetic program required for co-stimulation-restricted activation of B cells. We utilized transcriptomic and epigenomic approaches (RNA-seq and ATAC-seq) to define transcriptional programs which dynamically change upon ex vivo stimulation and investigated their Ikaros-dependency. Interestingly, we found that the largest subset of genes deregulated between wt and Ikzf1DF4/DF4 B cells, occur prior to stimulation. In addition, CUT&RUN performed in wt B cells shows Ikaros binding to a large subset of genes expressed upon stimulation with anti-IgM and CD40L. Together, these results demonstrate that Ikaros regulates the transcriptional landscape of BCR-activated mature B cells. In the future, we will be integrating single cell RNA-seq analysis to investigate B cell heterogeneity in wt and Ikzf1DF4/DF4 B cells.

Stromal cell protein kinase C-β inhibition enhances chemosensitivity in B cell malignancies and overcomes drug resistance

Overcoming drug resistance remains a key challenge to cure patients with acute and chronic B cell malignancies. Here, we describe a stromal cell-autonomous signaling pathway, which contributes to drug resistance of malignant B cells. We show that protein kinase C (PKC)-β-dependent signals from bone marrow-derived stromal cells markedly decrease the efficacy of cytotoxic therapies. Conversely, small-molecule PKC-β inhibitors antagonize prosurvival signals from stromal cells and sensitize tumor cells to targeted and nontargeted chemotherapy, resulting in enhanced cytotoxicity and prolonged survival in vivo. Mechanistically, stromal PKC-β controls the expression of adhesion and matrix proteins, required for activation of phosphoinositide 3-kinases (PI3Ks) and the extracellular signal-regulated kinase (ERK)-mediated stabilization of B cell lymphoma-extra large (BCL-XL) in tumor cells. Central to the stroma-mediated drug resistance is the PKC-β-dependent activation of transcription factor EB, regulating lysosome biogenesis and plasma membrane integrity. Stroma-directed therapies, enabled by direct inhibition of PKC-β, enhance the effectiveness of many antileukemic therapies.

Ikaros mutations can bypass the requirement for second co-stimulatory signal and lead to break of B-cell tolerance

Autoimmunity is thought to arise due to a combination of genetic and environmental factors. IKZF1, encoding the Zinc finger (ZnF) transcription factor Ikaros, is implicated in human autoimmunity through GWAS and recent discovery of germline IKZF1 mutations in patients with autoimmune diseases. We have previously created mouse models with targeted deletions of Ikaros DNA-binding ZnF1 or ZnF4, and recently found that mice lacking Ikaros ZnF4 (Ik-dF4) displayed very high levels of autoreactive antibodies and elevated levels of the autoimmunity-associated cytokine IL-6 in serum at young age, while mice lacking ZnF1 did not. Furthermore, ex vivo stimulation of peripheral B cells with anti-IgM (aIgM) +/− CD40L revealed that Ik-dF4 B cells responded to BCR-stimulation alone (aIgM), while wt B cells required a second co-stimulatory signal (CD40L). To understand the underlying mechanism, we performed transcriptome profiling of these stimulated wt and Ik-dF4 B cells. Overall, the Ik-dF4 B cells displayed the same pattern of gene-expression changes as wt B cell upon activation by both signals (aIgM + CD40L). Further analysis revealed a set of genes selectively altered upon aIgM alone in Ik-dF4 B cells, and another set of genes that were aberrantly expressed in Ik-dF4 B cells at baseline. Pathway analysis suggest candidate mediators, and we have initiated functional studies. Preliminary results indicate that a small molecule inhibitor can block the aberrant activation with aIgM alone in Ik-dF4 B cells, while displaying only partial inhibition of the normal two-signal activation. Studies are actively ongoing to confirm these preliminary findings, and we will present our results to date at the meeting for how Ikaros regulates B cell tolerance.

Ikaros regulates chromatin landscape in mature B cells, and is critical for B cell tolerance

The zinc finger transcription factor Ikaros plays central roles in the gene regulatory programs associated with proper B cell development. While mutations in the IKZF1 gene have been implicated in autoimmune disease and various B cell malignancies, the resultant epigenetic and transcriptional alterations in Ikzf1-mutated B cells remain largely unknown. We recently found in mouse models that deletion of the fourth zinc finger domain in the Ikzf1 gene (Ikzf1ΔF4/ΔF4) results in a B cell hyper-reactive (HR) phenotype. We hypothesized that Ikaros is required to establish and maintain an epigenetic program for co-stimulatory activation of B cells. To test this hypothesis, we have generated genome-wide transcriptome and chromatin-accessibility profiles of wildtype and Ikzf1ΔF4/ΔF4naïve splenic B cells following ex vivo co-stimulatory activation. We found that Ikaros mutant B cells have an overall similar accessible chromatin landscape as wildtype, but Ikzf1ΔF4/ΔF4B cells exhibit deregulated chromatin structure at inflammatory gene pathways linked to B cell growth and survival. To then explore the direct Ikaros targets we determined the Ikaros chromatin binding sites by Cleavage Under Targets & Release Using Nuclease (CUT&RUN) in wildtype B cells. Integration of gene expression and chromatin binding data indicates that Ikaros has a role in the repression of gene targets associated with cell proliferation and inflammation. Our data supports the model that Ikaros antagonizes NFkB actions at inflammatory gene pathways. Overall, our results reveal distinct mechanisms of Ikaros in the regulation of inflammatory genes in mature B cells and defines altered pathways that may be responsible for the HR phenotype of Ikaros-mutated B cells.

Cell circuits between B cell progenitors and IL-7+ mesenchymal progenitor cells control B cell development

B cell development is characterized by well-defined transitions. Fistonich et al. demonstrate that two distinct cell circuits formed between proB, preB, and IL-7⁺ cells regulate the size and quality of B cell progenitors and control B cell development.

B cell progenitors require paracrine signals such as interleukin-7 (IL-7) provided by bone marrow stromal cells for proliferation and survival. Yet, how B cells regulate access to these signals in vivo remains unclear. Here we show that proB and IL-7⁺ cells form a cell circuit wired by IL-7R signaling, which controls CXCR4 and focal adhesion kinase (FAK) expression and restricts proB cell movement due to increased adhesion to IL-7⁺CXCL12^Hi cells. PreBCR signaling breaks this circuit by switching the preB cell behavior into a fast-moving and lower-adhesion state via increased CXCR4 and reduced FAK/α4β1 expression. This behavioral change reduces preB cell exposure to IL-7, thereby attenuating IL-7R signaling in vivo. Remarkably, IL-7 production is downregulated by signals provided by preB cells with unrepaired double-stranded DNA breaks and by preB acute lymphoblastic leukemic cells. Combined, these studies revealed that distinct cell circuits control the quality and homeostasis of B cell progenitors.

Ikaros establishes an epigenetic program required for proper two-signal activation of naive B cells

While there are many different types of autoimmune diseases, a common feature of chronic inflammatory diseases is the production of autoantibodies by B-cells. We and others have shown in mouse models that loss-of-function mutations in the transcription factor Ikaros (Ik) result in a hyper-reactive (HR) B-cell phenotype. In particular, naïve B-cells containing a targeted deletion in the Ikzf1 zinc finger domain (Ikzf1ΔF4/ΔF4) produce large quantities of autoantibodies and proliferate in the absence of a costimulatory signal. Ik is required for early lymphoid cell development and has been shown to regulate gene expression directly or through the recruitment of chromatin remodeling complexes. However, the epigenetic and transcriptional regulation by Ik in mature B-cells and its role in B-cell HR remain unknown. We hypothesized that Ik functions to establish and maintain an epigenetic program required for proper two-signal activation in naïve B-cells. We have generated whole transcriptome profiles of wildtype and Ikzf1ΔF4/ΔF4 cells and defined the gene expression program required for B-cell activation. A comparison of these profiles revealed distinct deficiencies in genes associated with the HR phenotype. Specifically, a variety of cell signaling pathways are derepressed in Ik-mutant B-cells. In addition, we have performed Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq), over the course of B-cell activation, to explore the altered chromatin structure in Ik-mutant B-cells. Together these results revealed transcriptional pathways required for proper B-cell activation and demonstrate how mutations in Ik contribute to B-cell HR.

Ikaros regulates B-cell tolerance

B-cell development and activation are tightly regulated at multiple steps to ensure a protective immune response, and at the same time avoiding harmful self-reactivity and autoimmunity. Ikaros is a transcription factor that is critical for B-cell development, as demonstrated by the complete lack of B-cells in Ikaros-null mice. Furthermore, Ikaros is shown to play important roles also at later stages of B-cell development, but the precise roles of Ikaros at different stages of B-cell development is still not fully understood. In recent years, Ikaros (encoded by the IKZF1 gene) has been linked to autoimmune disease in humans through both genome-wide association studies (GWAS) as well as recent reports of germline IKZF1 mutations in patients with autoimmune disease. However, the mechanisms underlying altered Ikaros function and the development of autoimmunity are not known. We previously developed Ikaros-mutant mouse models with targeted deletions of the exons encoding the DNA-binding zinc finger 1 (ZnF1) or ZnF4, and found that both mutants have B cells, but display selective partial defects at different stages of B-cell development. We recently found that the Ikzf1-ZnF4-mutant strain displays very high levels of serum Anti-Nuclear Antibodies (ANA) at young age, a hallmark of autoimmune disease. This indicates that Ikaros (and specifically exon 6 encoding ZnF4) is required to regulate B-cell tolerance, and we hypothesize that Ikaros regulates this, at least in part, by establishing a chromatin structure that sets restrictions on B-cell responses to limit autoreactive B cells. We are using our Ikaros-mutant mice to further study the role of Ikaros in B-cell development and tolerance, and will present our results to-date at the meeting.

Ikaros regulates epigenetic and transcriptional programs in progenitor B cell leukemia

Hematopoietic cell development is tightly controlled by a network of transcriptional and epigenetic regulators, many of which are mutated or have altered expression in hematological malignancies. Ikaros is a transcription factor that is critical for the proper development of several hematopoietic lineages, and essential for the B-cell lineage. It is recognized as a critical tumor suppressor in precursor B-cell lineage acute lymphoblastic leukemia (pre-B ALL), and is emerging to play roles also in other hematopoietic malignancies. In pre-B ALL, Ikaros mutations are particularly prevalent in the Ph+ (BCR-ABL1+) and ‘Ph-like’ subgroups of leukemia, and Ikaros mutations correlate with poor prognosis. To study the mechanisms of Ikaros tumor suppressor function, we developed a mouse model and a human model system with selective perturbation of Ikaros in Ph+ pre-B ALL cells. This has revealed conserved deregulated genes and pathways, and underscored the role of Ikaros in regulating progenitor-restricted gene programs. Furthermore, our recent studies have highlighted the role of Ikaros in regulation of chromatin structure, and revealed a novel role in epigenetic regulation. It is challenging to therapeutically target mutations in a tumor suppressor factor. It is therefore important to understand the mechanism of action and downstream targets to elucidate targetable vulnerabilities of the Ikaros-mutant leukemic cells. Investigating the tumor suppressor role of Ikaros in developing B cells also sheds light on its role in normal B cell development. We are using our newly established models of Ikaros-mutated pre-B ALL to study the underlying molecular mechanisms and downstream targets, and will present our results to-date at the meeting.

Ikaros Inhibits Group 3 Innate Lymphoid Cell Development and Function by Suppressing the Aryl Hydrocarbon Receptor Pathway

Group 3 innate lymphoid cells (ILC3s) expressing the transcription factor (TF) RORγt are important for the defense and homeostasis of host intestinal tissues. The zinc finger TF Ikaros, encoded by Ikzf1, is essential for the development of RORγt(+) fetal lymphoid tissue inducer (LTi) cells and lymphoid organogenesis, but its role in postnatal ILC3s is unknown. Here, we show that small-intestinal ILC3s had lower Ikaros expression than ILC precursors and other ILC subsets. Ikaros inhibited ILC3s in a cell-intrinsic manner through zinc-finger-dependent inhibition of transcriptional activity of the aryl hydrocarbon receptor, a key regulator of ILC3 maintenance and function. Ablation of Ikzf1 in RORγt(+) ILC3s resulted in increased expansion and cytokine production of intestinal ILC3s and protection against infection and colitis. Therefore, in contrast to being required for LTi development, Ikaros inhibits postnatal ILC3 development and function to regulate gut immune responses at steady state and in disease.

Abstract 93: Transcriptional control of glucocorticoid responses in leukemia

Glucocorticoids (GCs) are central to all major therapy regimens for pre-B cell-derived acute lymphoblastic leukemia (ALL), but have no activity in myeloid leukemia. Such divergent responses represent an empirically established clinical standard; however, neither the mechanism by which GCs induce cell death nor the biological basis for the distinct responses in B-cell and myeloid leukemias is clear. Studying patient-derived samples revealed that NR3C1 (glucocorticoid receptor) levels were 6- to 20-fold higher in pre-B ALL compared to chronic myeloid leukemia (CML). High levels of Nr3c1 were reduced upon B- to myeloid-lineage conversion, suggesting that regulation of NR3C1 expression and GC responsiveness depend on a B-cell transcriptional program. B-cell transcription factors (e.g. PAX5, IKZF1) are critical for B-cell development, yet they are genetically lesioned in more than 80% of pre-B ALL cases. Despite such high frequency, the significance of these inactivating lesions remains elusive. Combining ChIP-seq and RNA-seq analyses, we identified a novel B-cell transcriptional program for activation of NR3C1 and its transcriptional target TXNIP (a negative regulator of glucose uptake). Reconstitution of PAX5 or IKZF1 expression in haploinsufficient patient-derived pre-B ALL cells increased NR3C1 and TXNIP levels. Conversely, expression of dominant negative mutant of PAX5 or IKZF1 abolished NR3C1 expression. Loss of Nr3c1 or Txnip in murine BCR-ABL1-driven pre-B ALL cells resulted in survival advantage in competitive growth assays. Importantly, loss of Nr3c1 or Txnip significantly elevated glucose uptake, lactate production and cellular ATP levels. These findings suggest that GCs induce cell death by exacerbating glucose and energy depletion. Notably, reconstitution of PAX5 or IKZF1 rendered haploinsufficient patient-derived pre-B ALL cells more sensitive to dexamethasone (dex) treatment. In contrast, dominant-negative PAX5 or IKZF1 largely de-sensitized pre-B ALL cells expressing wildtype PAX5 or IKZF1. These findings suggest that B-cell transcription factors set the threshold for GC responsiveness in pre-B ALL. Since relapsed ALL cells often acquire GC resistance, drug-combinations may be useful to prevent GC-resistance. As expected, loss of Nr3c1 abrogated responses to GCs. Interestingly, loss of Txnip also largely rescued GC-induced cell death in pre-B ALL cells. On this basis, we tested drug interactions between GCs and TXNIP agonists, 3-O-methylglucose (3-OMG) and D-allose. Treating patient-derived GC-refractory pre-B ALL cells with 3-OMG or D-allose strongly synergized with GC-treatment. Collectively, our findings provide a mechanistic explanation for the empiric finding that GCs are effective in the treatment of B-cell but not myeloid malignancies, and identify TXNIP as a novel therapeutic target in pre-B ALL.

Note: This abstract was not presented at the meeting.

Citation Format: Lai N. Chan, Zhengshan Chen, Gang Xiao, Jae Woong Lee, Kadriye Nehir Cosgun, Huimin Geng, Valeria Cazzaniga, Hilde Schjerven, Ross A. Dickins, Markus Muschen. Transcriptional control of glucocorticoid responses in leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 93. doi:10.1158/1538-7445.AM2017-93

Antagonism of B cell enhancer networks by STAT5 drives leukemia and poor patient survival

The transcription factor STAT5 has a critical role in B cell acute lymphoblastic leukemia (B-ALL). How STAT5 mediates this effect is unclear. Here we found that activation of STAT5 worked together with defects in signaling components of the precursor to the B cell antigen receptor (pre-BCR), including defects in BLNK, BTK, PKCβ, NF-κB1 and IKAROS, to initiate B-ALL. STAT5 antagonized the transcription factors NF-κB and IKAROS by opposing regulation of shared target genes. Super-enhancers showed enrichment for STAT5 binding and were associated with an opposing network of transcription factors, including PAX5, EBF1, PU.1, IRF4 and IKAROS. Patients with a high ratio of active STAT5 to NF-κB or IKAROS had more-aggressive disease. Our studies indicate that an imbalance of two opposing transcriptional programs drives B-ALL and suggest that restoring the balance of these pathways might inhibit B-ALL.

Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL

Schjerven et al. compare mouse and human models of pre–B ALL to define conserved target genes and pathways of the tumor suppressor Ikaros, revealing CTNND1 and the early hematopoietic cell-surface receptors SPN (CD43) and CD34 as novel Ikaros targets that each confer oncogenic growth advantage.

Inactivation of the tumor suppressor gene encoding the transcriptional regulator Ikaros (IKZF1) is a hallmark of BCR-ABL1⁺ precursor B cell acute lymphoblastic leukemia (pre–B ALL). However, the mechanisms by which Ikaros functions as a tumor suppressor in pre–B ALL remain poorly understood. Here, we analyzed a mouse model of BCR-ABL1⁺ pre–B ALL together with a new model of inducible expression of wild-type Ikaros in IKZF1 mutant human BCR-ABL1⁺ pre–B ALL. We performed integrated genome-wide chromatin and expression analyses and identified Ikaros target genes in mouse and human BCR-ABL1⁺ pre–B ALL, revealing novel conserved gene pathways associated with Ikaros tumor suppressor function. Notably, genetic depletion of different Ikaros targets, including CTNND1 and the early hematopoietic cell surface marker CD34, resulted in reduced leukemic growth. Our results suggest that Ikaros mediates tumor suppressor function by enforcing proper developmental stage–specific expression of multiple genes through chromatin compaction at its target genes.

Analysis of Ikaros tumor suppressor function in BCR-ABL1+ pre-B ALL reveals conserved target genes and biological pathways

Inactivation of the transcriptional factor Ikaros (IKZF1) correlates with poor prognosis in progenitor B-cell acute lymphoblastic leukemia (pre-B ALL), and is a hallmark of the BCR-ABL1+ subgroup of pre-B ALL. Ikaros is a critical regulator of hematopoietic development and required for B-cell development, however the mechanisms by which Ikaros functions as a tumor suppressor in pre-B ALL remain poorly understood. We analyzed recently developed mouse models of BCR-ABL1+ pre-B ALL containing targeted deletions of Ikaros DNA-binding zinc finger domains together with a new model of inducible expression of WT Ikaros in IKZF1-mutant human BCR-ABL1+ pre-B ALL. We found that both the mouse and human Ikaros-mutated leukemic cells displayed a less mature cell surface phenotype and failed to downregulate the developmentally restricted cell surface receptors c-kit and CD34, respectively. In addition, Ctnnd1, a gene that is also expressed in earlier hematopoietic progenitor cells and normally downregulated as cells differentiate down the B-cell lineage, was found to be a conserved Ikaros target gene, with increased expression in Ikaros-mutated leukemic cells. RNA sequencing defined the Ikaros target genes in both mouse and human Ikaros-mutated pre-B ALL cells and revealed additional conserved target genes and biological functions. Loss of Ikaros tumor suppression was associated with deregulated adhesion pathways and stem-cell signatures. Furthermore, our results presented herein suggest that Ikaros mediates tumor suppressor function, at least in part, by enforcing proper developmental-stage specific expression of multiple genes involved in a network of cadherin-dependent, Rho-regulated Wnt/b-catenin pathways.

Role of the transcription factor Ikaros in development of autoimmune disease

The etiology of autoimmune disease is not fully understood, but disease development is believed to be due to a combination of genetic predispositions and environmental factors. Ikaros is a transcription factor that is an important regulator of hematopoiesis and critical for development of B cells. Recent genome wide association studies have found that several autoimmune diseases are associated with SNPs annotated to the Ikaros gene (IKZF1), as well as the closely related Ikaros family member Aiolos (IKZF3). Mouse models of autoimmunity are important research tools, and we recently reported the generation of two new Ikaros-mutant mice, with targeted deletions of the exons encoding the DNA-binding zinc finger 1 (ZnF1) or ZnF4 (Schjerven et al., 2013). These deletions did not abolish B-cell development, but rather illuminated differential roles of Ikaros at different stages of early B-cell development. Interestingly, we found that one of these mouse strains displayed very high levels of serum Anti-Nuclear Antibodies (ANA), indicative of autoimmune disease. Furthermore, we found by ex vivo studies that while wt spleen B cells require a “second signal” such as CD40L in addition to BCR stimulation (by anti-IgM), Ikaros-mutant B cells became activated and proliferated upon BCR stimulation alone without any externally added “second signal”. We hypothesize that Ikaros is important to limit autoimmunity and prevent auto reactive B cells by setting a requirement for the “second signal” in adaptive immune-recognition. Results will be presented from ongoing investigation using in vivo analysis of the autoimmune-related phenotype, and ex vivo analysis of Ikaros-dependent molecular mechanisms underlying the response to stimuli in B cells.

Targeting casein kinase II restores Ikaros tumor suppressor activity and demonstrates therapeutic efficacy in high-risk leukemia

Ikaros (IKZF1) is a tumor suppressor that binds DNA and regulates expression of its target genes. The mechanism of Ikaros activity as a tumor suppressor and the regulation of Ikaros function in leukemia are unknown. Here, we demonstrate that Ikaros controls cellular proliferation by repressing expression of genes that promote cell cycle progression and the phosphatidylinositol-3 kinase (PI3K) pathway. We show that Ikaros function is impaired by the pro-oncogenic casein kinase II (CK2), and that CK2 is overexpressed in leukemia. CK2 inhibition restores Ikaros function as transcriptional repressor of cell cycle and PI3K pathway genes, resulting in an antileukemia effect. In high-risk leukemia where one IKZF1 allele has been deleted, CK2 inhibition restores the transcriptional repressor function of the remaining wild-type IKZF1 allele. CK2 inhibition demonstrated a potent therapeutic effect in a panel of patient-derived primary high-risk B-cell acute lymphoblastic leukemia xenografts as indicated by prolonged survival and a reduction of leukemia burden. We demonstrate the efficacy of a novel therapeutic approach for high-risk leukemia: restoration of Ikaros tumor suppressor activity via inhibition of CK2. These results provide a rationale for the use of CK2 inhibitors in clinical trials for high-risk leukemia, including cases with deletion of one IKZF1 allele.

Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor

In this study, Arenzana et al. perform a detailed analysis of the functional abnormalities at five sequential stages of thymocyte development in an Ikaros mutant mouse strain followed by RNA-seq to document the gene expression changes seen in the mutant cells. By combining the quantitative power of the RNA-seq method with the analysis of five sequential stages of development, the findings demonstrate a unique function for Ikaros in supporting dynamic changes in gene expression during developmental transitions.

The DNA-binding protein Ikaros is a potent tumor suppressor and hematopoietic regulator. However, the mechanisms by which Ikaros functions remain poorly understood, due in part to its atypical DNA-binding properties and partnership with the poorly understood Mi-2/NuRD complex. In this study, we analyzed five sequential stages of thymocyte development in a mouse strain containing a targeted deletion of Ikaros zinc finger 4, which exhibits a select subset of abnormalities observed in Ikaros-null mice. By examining thymopoiesis in vivo and in vitro, diverse abnormalities were observed at each developmental stage. RNA sequencing revealed that each stage is characterized by the misregulation of a limited number of genes, with a strong preference for stage-specific rather than lineage-specific genes. Strikingly, individual genes rarely exhibited Ikaros dependence at all stages. Instead, a consistent feature of the aberrantly expressed genes was a reduced magnitude of expression level change during developmental transitions. These results, combined with analyses of the interplay between Ikaros loss of function and Notch signaling, suggest that Ikaros may not be a conventional activator or repressor of defined sets of genes. Instead, a primary function may be to sharpen the dynamic range of gene expression changes during developmental transitions via atypical molecular mechanisms that remain undefined.

STAT5 antagonism of B cell superenhancer networks initiates progenitor B cell leukemia and predicts patient survival (HEM1P.222)

B cell Acute Lymphoblastic Leukemia (B-ALL) arises from the transformation of progenitor B cells. The transcription factor STAT5 is required for transformation but how STAT5 mediates this effect is unclear. Previous studies suggested that STAT5 only acts to promote survival of progenitor B cells. However, other roles for STAT5 in B cell development and B-ALL have not been explored. Here we show that STAT5 activation drives leukemia in cooperation with defects in a linear signaling pathway emanating from the pre-BCR, including Blnk, Btk, Prkcb, Nfkb1, and Ikzf1. Using microarray analysis and ChIP-Seq we demonstrate that STAT5 disrupts the function of superenhancer binding transcription factor networks that normally promote B cell development. STAT5 versus NFkB or IKAROS binding to these enhancers largely had opposing effects on target gene expression. The antagonism between STAT5 and IKAROS or NFκB has direct clinical relevance as the balance between these transcription factors affects patient outcome; patients with high ratios of active STAT5 to NFκB or IKAROS had more aggressive disease characterized by shorter remission and decreased survival. Thus, our studies illustrate how modest perturbations in two opposing transcriptional programs can have dramatic consequences for B cell development and transformation and how the degree of antagonism between these transcriptional programs ultimately predicts patient outcome to therapy.

Ikaros tumor suppressor function in pre-B ALL: potential role of Ikaros target gene Ctnnd1 (IRM10P.621)

Ikaros is a zinc finger transcription factor required for B-cell development and proper hematopoiesis, and an important tumor suppressor in developing lymphocytes. To understand the mechanism of Ikaros tumor suppressor function and potentially develop new and improved targeted therapies, it is important to elucidate the downstream target genes involved. With this aim, we combine mouse models of pre-B ALL and in vitro culture of human patient-derived pre-B ALL cells. A mouse model with targeted deletion of the fourth DNA-binding zinc finger of Ikaros resulted in loss of tumor suppressor function, with a limited set of deregulated genes useful to narrow down the list of putative relevant Ikaros target genes (Schjerven et al., 2013). To specifically address the role of Ikaros as a tumor suppressor in human pre-B ALL, we developed TET-regulated Ikaros expression in human pre-B ALL cells. This enables us to test specific Ikaros target genes from the mouse model, and allows for genome-wide expression analysis by RNA-seq to elucidate all genes downstream of Ikaros in human pre-B ALL cells. To help distinguish direct from indirect target genes, we have mapped the genome-wide binding sites of Ikaros in these human pre-B ALL cells by ChIP-Seq. This approach has identified the Ikaros target gene Ctnnd1. Ongoing experiments explore the potential role of Ctnnd1 and test the current hypothesis that Ikaros-mediated repression of Ctnnd1 limits CyclinD levels and leukemic growth in pre-B ALL.

Identification of FOXM1 as a therapeutic target in B-cell lineage acute lymphoblastic leukaemia

Despite recent advances in the cure rate of acute lymphoblastic leukaemia (ALL), the prognosis for patients with relapsed ALL remains poor. Here we identify FOXM1 as a candidate responsible for an aggressive clinical course. We show that FOXM1 levels peak at the pre-B-cell receptor checkpoint but are dispensable for normal B-cell development. Compared with normal B-cell populations, FOXM1 levels are 2- to 60-fold higher in ALL cells and are predictive of poor outcome in ALL patients. FOXM1 is negatively regulated by FOXO3A, supports cell survival, drug resistance, colony formation and proliferation in vitro, and promotes leukemogenesis in vivo. Two complementary approaches of pharmacological FOXM1 inhibition-(i) FOXM1 transcriptional inactivation using the thiazole antibiotic thiostrepton and (ii) an FOXM1 inhibiting ARF-derived peptide-recapitulate the findings of genetic FOXM1 deletion. Taken together, our data identify FOXM1 as a novel therapeutic target, and demonstrate feasibility of FOXM1 inhibition in ALL.

Restriction of IL-22-producing T cell responses and differential regulation of regulatory T cell compartments by zinc finger transcription factor Ikaros

Proper immune responses are needed to control pathogen infection at mucosal surfaces. IL-22-producing CD4(+) T cells play an important role in controlling bacterial infection in the gut; however, transcriptional regulation of these cells remains elusive. In this study, we show that mice with targeted deletion of the fourth DNA-binding zinc finger of the transcription factor Ikaros had increased IL-22-producing, but not IL-17-producing, CD4(+) T cells in the gut. Adoptive transfer of CD4(+) T cells from these Ikaros-mutant mice conferred enhanced mucosal immunity against Citrobacter rodentium infection. Despite an intact in vivo thymic-derived regulatory T cell (Treg) compartment in these Ikaros-mutant mice, TGF-β, a cytokine well known for induction of Tregs, failed to induce Foxp3 expression in Ikaros-mutant CD4(+) T cells in vitro and, instead, promoted IL-22. Aberrant upregulation of IL-21 in CD4(+) T cells expressing mutant Ikaros was responsible, at least in part, for the enhanced IL-22 expression in a Stat3-dependent manner. Genetic analysis using compound mutations further demonstrated that the aryl hydrocarbon receptor, but not RORγt, was required for aberrant IL-22 expression by Ikaros-mutant CD4(+) T cells, whereas forced expression of Foxp3 was sufficient to inhibit this aberrant cytokine production. Together, our data identified new functions for Ikaros in maintaining mucosal immune homeostasis by restricting IL-22 production by CD4(+) T cells.

Selective requirement of Ikaros zinc fingers in Treg and Th17 fate decision. (P1137)

TGF-β is a common factor important for the differentiation of pro-inflammatory Th17 and anti-inflammatory inducible Treg cells. However, the precise molecular mechanisms underlying the fate decision of differentiating CD4+ T cells in the presence of TGF-β is poorly understood. Here, we show that distinctive N-terminal DNA-binding zinc fingers of Ikaros play essential roles in Treg and Th17 fate decision. Ikaros has a highly conserved DNA-binding domain near the N-terminus with four tandem zinc fingers. Zinc fingers 2 and 3 are required for stable binding to DNA, whereas fingers 1 and 4 appear to be important for differentially modulating binding properties to specific sites at target genes. Our data show that T cells lacking Ikaros zinc finger 4 but not 1 failed to differentiate into Foxp3+ Tregs upon TGF-β stimulation. Instead, TGF-β-skewed Ikaros zinc finger 4 mutant cells displayed aberrant upregulation of Th17-associated cytokines IL-17 and IL-22. IL-17 but not IL-22 upregulation is dependent on transcription factor RORγt. Aryl hydrocarbon receptor, an essential transcription factor required for IL-22 expression, was unexpectedly decreased. Together, our data uncover a novel selective requirement for Ikaros zinc fingers in the differentiation of Treg and Th17 cells and an intricate interplay among various transcription factors in programming Th17/Treg lineages. We are currently examining the role of Ikaros zinc finger 4 in infection and autoimmunity.

Role of Ikaros in hematopoiesis and tumor suppression: Selective functions of individual zinc fingers within the DNA-binding domain of Ikaros. (42.3)

Ikaros, a C2H2 zinc finger transcription factor, is a critical regulator of hematopoiesis and tumor suppression in the lymphoid lineage. The C2H2 zinc finger is the most prevalent DNA-binding motif in mammals, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, and to investigate in greater depth the role of Ikaros in hematopoiesis and tumor suppression, we generated mice lacking finger 1 or finger 4 of the 4-finger DNA-binding domain of Ikaros. Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice. Of particular relevance, fingers 1 and 4 contributed to distinct stages of B- and T-cell development and finger 4 was selectively required for tumor suppression in thymocytes and in a new model of BCR-ABL+ acute lymphoblastic leukemia. These results, combined with transcriptome profiling and DNA-binding analysis, reveal that different subsets of fingers within multi-finger transcription factors can modulate binding to different target sequences and regulate distinct target genes and biological functions. These novel mutant strains provide a powerful tool to elucidate Ikaros' role in hematopoiesis and tumor suppression. Furthermore, this study demonstrates that selective mutagenesis can facilitate efforts to elucidate the functions and mechanisms of action of this prevalent class of factors.

Regulation of the polymeric Ig receptor by signaling through TLRs 3 and 4: linking innate and adaptive immune responses

IgA Abs help to maintain homeostasis at mucosal surfaces by promoting defense mechanisms that protect against pathogens while suppressing inflammatory responses to commensal organisms and food Ags. The polymeric Ig receptor (pIgR) mediates transport of IgA across mucosal epithelial cells. We hypothesized that signaling through TLRs may up-regulate pIgR expression by intestinal epithelial cells and thus enhance IgA-mediated homeostasis. To test this hypothesis we treated the HT29 human intestinal epithelial cell line with dsRNA, a ligand for TLR3, or LPS, a ligand for TLR4. Both dsRNA and LPS up-regulated levels of pIgR mRNA and cell surface pIgR protein. By contrast, dsRNA but not LPS up-regulated expression of TLR3 and TLR4 mRNA. However, cell surface expression of both TLR3 and TLR4 was enhanced by treatment of HT29 cells with their respective ligands. Transfection of HT29 cells with wild-type and mutated promoter/enhancer plasmids suggested that TLR3 and TLR4 signal primarily through NF-kappaB to enhance transcription of pIgR mRNA. TLR3 signaling resulted in a more pronounced inflammatory response than did TLR4, as evidenced by up-regulation of the transcription factor IFN regulatory factor-1, chemokines IL-8 and RANTES, and the proinflammatory cytokine TNF. Signaling through LPS/TLR4 appears to up-regulate pIgR expression while minimizing proinflammatory responses, a mechanism that could promote IgA-mediated homeostasis in the presence of commensal Gram-negative bacteria.

De novo synthesized RelB mediates TNF-induced up-regulation of the human polymeric Ig receptor

Secretory Abs, which operate in a principally noninflammatory fashion, constitute the first line of acquired immune defense of mucosal surfaces. Such Abs are generated by polymeric Ig receptor (pIgR)-mediated export of dimeric IgA and pentameric IgM. TNF activates a proinflammatory gene repertoire in mucosal epithelial cells and also enhances pIgR expression. In this study we show that TNF-induced up-regulation of the human pIgR critically depends on an NF-kappa B site and flanking sequences within a 204-bp region of the first intron in the pIgR gene, a region largely overlapping with a recently characterized IL-4-responsive enhancer. The intronic NF-kappa B site was rapidly bound by NF-kappa B p65/p50 heterodimers present in nuclear extracts after TNF treatment of HT-29 cells, but a more delayed binding of RelB agreed better with the slow, protein synthesis-dependent, transcriptional activation of the pIgR gene. Overexpression of NF-kappa B p65 caused transient up-regulation of a pIgR-derived reporter gene, whereas overexpression of RelB showed a stronger and more sustained effect. Finally, we demonstrated that inhibition of endogenous RelB by RNA interference severely reduced the TNF responsiveness of our pIgR-derived reporter gene. Thus, TNF-induced signaling pathways required for up-regulated pIgR expression appear to differ from those of the proinflammatory gene repertoire.

Proinflammatory cytokines upregulate expression of calprotectin (L1 protein, MRP-8/MRP-14) in cultured human keratinocytes

BACKGROUND

Normal skin contains no epidermal calprotectin. In biopsies from various inflammatory skin disorders, however, this antimicrobial protein occurs in the cytoplasm of keratinocytes.

OBJECTIVES

To exclude the possibility of epidermal uptake of calprotectin from granulocytes and macrophages in diseased skin, we investigated whether cytokine-stimulated human keratinocytes can express calprotectin in vitro.

METHODS

Keratinocytes from healthy individuals were cultured in serum-free keratinocyte medium. The cells were stimulated with different cytokines [interferon (IFN)-gamma, tumour necrosis factor (TNF)-alpha, interleukin (IL)-1beta, IL-10 and IL-13], both separately and in various combinations. Cytoplasmic protein levels of calprotectin were measured by an enzyme-linked immunosorbent assay performed on fixed adherent keratinocytes, and mRNA expression was determined by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS

Calprotectin was produced by cytokine-stimulated keratinocytes, especially in response to combinations of the proinflammatory cytokines, which showed an additive upregulatory effect. When expression of mRNA for the light (MRP-8) and heavy (MRP-14) calprotectin chain was determined by RT-PCR, their respective levels were shown to be increased four- to ninefold and three- to fivefold after 24 h of combined stimulation with IFN-gamma and TNF-alpha. The time course of calprotectin production showed no significant elevation for the first 16 h but then increased and peaked after 36 h.

CONCLUSIONS

Cultured human keratinocytes stimulated with proinflammatory cytokines produce calprotectin, suggesting that epidermal expression of this antimicrobial protein in diseased skin reflects compartmentalized synthesis rather than uptake from dermal inflammatory cells.

Hepatocyte NF-1 and STAT6 cooperate with additional DNA-binding factors to activate transcription of the human polymeric Ig receptor gene in response to IL-4

Secretory IgA and IgM, which protect the mucosal surfaces, are generated by selective transport of locally produced polymeric (p)Igs through the epithelial barrier by the pIgR. The expression of this receptor, and hence the generation of secretory Igs, is modulated by numerous extracellular factors. We have previously identified a STAT6 site in intron 1 of the human pIgR gene that is required for the slow and de novo protein synthesis-dependent IL-4-mediated transcriptional activation of the gene. In this study, we show that this intronic IL-4-responsive enhancer is confined to a 250-bp region that is highly conserved in the murine pIgR gene. The enhancer was dependent on the cooperation between the STAT6 site and at least four additional DNA elements. EMSA experiments demonstrated binding by hepatocyte NF-1 to one of these DNA elements. Extensive overlap in the tissue distribution of hepatocyte NF-1 and pIgR suggests that this transcription factor contributes to tissue-specific pIgR expression. Changing the helical phase between the STAT6 site and downstream DNA elements greatly reduced the strength of the IL-4 response, suggesting that the precise organization of this enhancer is important for its proper function. Thus, several transcription factors cooperate in this enhanceosome to mediate IL-4 responsiveness in HT-29 epithelial cells.

A novel NF-kappa B/Rel site in intron 1 cooperates with proximal promoter elements to mediate TNF-alpha-induced transcription of the human polymeric Ig receptor

Secretory Abs constitute the first line of specific immune defense at mucosal surfaces. Such Abs are generated by the active transport of polymeric Ig (pIg) across secretory epithelia mediated by the pIgR, also known as transmembrane secretory component (SC). The proinflammatory cytokine TNF-alpha is a key mediator of host responses to infections, and it can stimulate protein synthesis-dependent transcriptional up-regulation of pIgR/SC in the HT-29 intestinal adenocarcinoma cell line. By reporter gene assay we identified a novel TNF-alpha-responsive region located within a 748-bp fragment in intron 1 of the human pIgR/SC gene which depended on an NF-kappaB/Rel site for full responsiveness. EMSAs demonstrated preferential binding of the NF-kappaB/Rel family member p65 (RelA) to this DNA element after TNF-alpha stimulation, with weaker and more delayed binding of p50. Furthermore, the TNF-alpha-responsive region in intron 1 required cooperation with DNA elements located in the proximal promoter region of the gene. Mutational analysis demonstrated that an IFN-stimulated response element near the transcriptional start site in exon 1 was involved in the TNF-alpha responsiveness. Thus, DNA elements located >4 kb apart were found to cooperate in TNF-alpha-induced pIgR/SC up-regulation. The intronic TNF-alpha-responsive enhancer overlapped with a recently identified IL-4-responsive enhancer. Several intronic DNA elements found to be functionally important in the human gene are highly conserved between the human and mouse pIgR/SC genes, suggesting the presence of a conserved cytokine-responsive enhancer region.

Mechanism of IL-4-mediated up-regulation of the polymeric Ig receptor: role of STAT6 in cell type-specific delayed transcriptional response

The polymeric IgR (pIgR) mediates transport of dimeric IgA and pentameric IgM across mucosal epithelia, thereby generating secretory Abs. Its expression is up-regulated at the transcriptional level by IL-4 in HT-29 cells. In this study, we demonstrate that IL-4 mediates up-regulation of human pIgR through a 554-bp IL-4-responsive enhancer in intron 1. Mutation of a binding site for STAT-6 within this region abolished IL-4-induced enhancement, while an adjacent putative C/EBP site was dispensable. IL-4 treatment induced binding of STAT6 to the intronic STAT6 site, but cooperation with nearby upstream and downstream DNA elements was required for IL-4 responsiveness. Furthermore, IL-4-mediated increased transcription of the pIgR-derived enhancer, like the endogenous pIgR gene, required de novo protein synthesis. Interestingly, a conditionally active form of STAT6 sufficed to activate a pIgR-derived enhancer in HT-29 cells, but not in Cos-1 cells, suggesting a requirement for cell type-specific factors. Thus, STAT6 activation mediates a delayed transcriptional enhancement of pIgR by induction of a de novo synthesized protein that cooperates with STAT6 itself bound to its cognate DNA element in intron 1. This mechanism may represent a general strategy for how pleiotropic cytokines elicit cell type-specific transcriptional responses.

Regulation of the formation and external transport of secretory immunoglobulins

Secretory IgA (SIgA) is the best defined effector component of the mucosal immune system. Generation of SIgA and secretory IgM (SIgM) in exocrine glands and mucous membranes depends on a fascinating cooperation between local plasma cells that produce polymeric IgA (pIgA, mainly dimers and some larger polymers) and pentameric IgM, and secretory epithelial cells that express the polymeric Ig receptor (pIgR)--also known as transmembrane secretory component. After release from the local plasma cells and diffusion through the stroma, pIgA and pentameric IgM become readily bound to pIgR, and are then actively transported across secretory epithelial cells for extrusion into external secretions after cleavage of pIgR. Much knowledge has recently been obtained at the molecular level about the regulation of pIgR-mediated transport of antibodies. This mechanism is of considerable biological interest because SIgA and SIgM form the first line of specific immunological defense against infectious agents and other harmful substances that may enter the body through the mucosae.

Mannuronan C-5-epimerases and their application for in vitro and in vivo design of new alginates useful in biotechnology

The industrially important polysaccharide alginate is a linear copolymer of beta-D-mannuronic acid (M) and alpha-L-guluronic acid (G). It is produced commercially by extraction from brown seaweeds, although some of the bacteria belonging to the genera Azotobacter and Pseudomonas also synthesize alginates. Alginates are synthesized as mannuronan, and varying amounts of the M residues in the polymer are then epimerized to G residues by mannuronan C-5-epimerases. The gel-forming, water-binding, and immunogenic properties of the polymer are dependent on the relative amount and sequence distribution of M and G residues. A family of seven calcium-dependent, secreted epimerases (AlgE1-7) from Azotobacter vinelandii have now been characterized, and in this paper the properties of all these enzymes are described. AlgE4 introduces alternating M and G residues into its substrate, while the remaining six enzymes introduce a mixture of continuous stretches of G residues and alternating sequences. Two of the enzymes, AlgE1 and AlgE3, are composed of two catalytically active domains, each introducing different G residue sequence patterns in alginate. These results indicate that the enzymes can be used for production of alginates with specialized properties.

E2F-mediated growth regulation requires transcription factor cooperation

Previous studies have indicated that the presence of an E2F site is not sufficient for G1/S phase transcriptional regulation. For example, the E2F sites in the E2F1 promoter are necessary, but not sufficient, to mediate differential promoter activity in G0 and S phase. We have now utilized the E2F1 minimal promoter to test several hypotheses that could account for these observations. To test the hypothesis that G1/S phase regulation is achieved via E2F-mediated repression of a strong promoter, a variety of transactivation domains were brought to the E2F1 minimal promoter. Although many of these factors caused increased promoter activity, growth regulation was not observed, suggesting that a general repression model is incorrect. However, constructs having CCAAT or YY1 sites or certain GC boxes cloned upstream of the E2F1 minimal promoter displayed E2F site-dependent regulation. Further analysis of the promoter activity suggested that E2F requires cooperation with another factor to activate transcription in S phase. However, we found that the requirement for E2F to cooperate with additional factors to achieve growth regulation could be relieved by bringing the E2F1 activation domain to the promoter via a Gal4 DNA binding domain. Our results suggest a model that explains why some, but not all, promoters that contain E2F sites display growth regulation.