GATA Transcription Research Articles

Immunohistochemical Analysis of GATA2 Expression in Endometrium and its Relationship with Hormone Receptor Expression in Benign and Premalignant Endometrial Disorders.

The GATA gene family encodes highly conserved zinc-finger transcription factors that facilitate the development and function of multiple organ systems including the uterus. In the endometrium, GATA2 functions in a positive autoregulatory loop with the progesterone receptor (PGR) and colocalizes with PGR on chromatin to promote PGR transcriptional programs. GATA2 also has PGR-independent functions that maintain endometrial cell identity, and GATA2 transcripts reportedly are down-regulated in endometrial disorders including endometriosis. This event is accompanied by a reciprocal increase in GATA6. Here, we applied custom anti-GATA2 monoclonal antibodies and performed GATA2 immunohistochemistry (IHC) on patient endometrial tissues corresponding to proliferative, secretory, inactive, and hormone-treated endometrium, as well as endometriosis and endometrial atypical hyperplasia/endometrioid intraepithelial neoplasia (EAH/EIN). We also performed IHC for the estrogen receptor, PGR, and GATA6 in relevant groups. The results reveal a tight correlation between GATA2 and PGR expression in the glandular and stromal cells of benign endometrium. GATA2 expression is markedly reduced in stromal but not glandular cells in endometriosis and EAH/EIN. This reduction in GATA2 expression does not lead to a detectable increase in GATA6 expression in endometriosis. Although average glandular GATA2 expression was preserved in endometriosis and EAH/EIN cases, its expression was decoupled from PGR, implying that alternative pathways regulate GATA2 levels in these disorders. Our findings indicate that GATA2 dysregulation is a feature of endometriosis and EAH/EIN, and support a model whereby loss of stromal GATA2 in these disorders contributes to their progesterone insensitivity.

GATA1 transcription factor targets the gene expression of B19 virus in HEK293 cell line

Backgrond/Aim: B19 virus (B19V) is a single strand DNA virus that has specific tropism to erythroid progenitor cells (EPCs). The virus enters to the cells via P antigen and coreseptors and induces infection and cell apoptosis. GATA1 has a high expression in EPC and is a critical transcription factor for the cells development and differentiation. As human EPCs are the main target of the virus infection that have high expression of GATA-1 as the critical transcription factor, the aim of this study was to investigate the effect of GATA1 cotransfection with B19V genome on expression of the viral mRNAs in HEK293 as non-permissive cell line to the virus that had no mRNA expression of GATA-1. Methods: HEK293 cells were transfected with pHI0 plasmid containing B19V genome and the plasmid of GATA1 genome. The quantity of B19V mRNAs (NS1, 7.5 kDa, 11 kDa) expression was evaluated after 24h of transfection. Results: The results showed a statistically significant increase in fold change expression of (NS1 ∽ 12.3, VP1 ∽ 27.6, 11kb protein ∽ 38) in cotransfected cells with GATA1 and B19 plasmids compare to control group (P<0.05). Conclusion: This research showed transfected cells with GATA1had elevation in expression of the B19V genes mRNAs in a non-permissive cell. This result may show a role of GATA1 as a critical transcription factor in support of the virus infection in EPCs. This suggests that GATA1 may potentially sport B19V replication or gene expression.

ALKBH5 governs human endoderm fate by regulating the DKK1/4-mediated Wnt/β-catenin activation.

N6-methyladenonsine (m6A) is ubiquitously distributed in mammalian mRNA. However, the precise involvement of m6A in early development has yet to be fully elucidated. Here, we report that deletion of the m6A demethylase ALKBH5 in human embryonic stem cells (hESCs) severely impairs definitive endoderm (DE) differentiation. ALKBH5-/- hESCs fail to undergo the primitive streak (PS) intermediate transition that precedes endoderm specification. Mechanistically, we show that ALKBH5 deficiency induces m6A hypermethylation around the 3' untranslated region (3'UTR) of GATA6 transcripts and destabilizes GATA6 mRNA in a YTHDF2-dependent manner. Moreover, GATA6 binds to the promoters of critical regulatory genes involved in Wnt/β-catenin signaling transduction, including the canonical Wnt antagonist DKK1 and DKK4, which are unexpectedly repressed upon the dysregulation of GATA6 mRNA metabolism. Remarkably, DKK1 and DKK4 both exhibit a pleiotropic effect in modulating the Wnt/β-catenin cascade and guard the endogenous signaling activation underlying DE formation as potential downstream targets of the ALKBH5-GATA6 regulation. Here, we unravel a role of ALKBH5 in human endoderm formation in vitro by modulating the canonical Wnt signaling logic through the previously unrecognized functions of DKK1/4, thus capturing a more comprehensive role of m6A in early human embryogenesis.

GATA2 downregulation contributes to pro-inflammatory phenotype and defective phagocytosis of pulmonary macrophages in chronic obstructive pulmonary disease.

Pulmonary macrophages from COPD patients are characterized by lower phagocytic and bactericidal activity whereas there is hypersecretion of pro-inflammatory cytokines. The prominent decline of GATA2 expression in pulmonary macrophages from COPD patients inspired us to figure out its role during COPD development. The expression levels of GATA2 were decreased in alveolar macrophages isolated from cigarette smoke (CS)-induced COPD mice and cigarette smoke extract (CSE)-treated macrophages. In vitro, both CSE and GATA2 knockdown via siRNAs elevated pro-inflammatory cytokines expression whereas inhibiting phagocytosis in macrophages. Integrated analysis of transcriptomics of GATA2-knockdown macrophages and the results of ChIP sequencing of GATA2 together with dual-luciferase reporter assay identified Abca1 and Pacsin1 as functional target genes of GATA2. Mechanistically, ABCA1 mediates the pro-inflammatory secretion phenotype and the dysfunction in early stage of phagocytosis of macrophages through TLR4/MyD88 and MEGF10/GULP1 pathways, respectively. PACSIN1/SUNJ1 partially mediates the disruption effects of GATA2 downregulation on maturation of phagolysosomes in macrophages. Together, our study suggests that GATA2 influences multiple functions of pulmonary macrophages by simultaneous transcriptional regulation of several target genes, contributing to the dysfunctions of pulmonary macrophages in response to CS, which provides an impetus for further investigations of GATA2 or other underappreciated transcription factors as regulatory hubs in COPD pathogenesis.

7657 Single Cell RNAseq And Omics Revealed Novel Role Of Liver Group 2 Innate Lymphocytes In Regulation Of Hepatic Gluconeogenesis

Abstract Disclosure: M. Fujimoto: None. T. Tanaka: None. Background: The liver is an important organ that maintains homeostasis of glucose metabolism in the body through gluconeogenesis. It is considered that gluconeogenesis in hepatocytes is particularly active around the portal vein. However, since excessive gluconeogenesis aggravates the pathogenesis of diabetes, it is necessary to elucidate the regulatory mechanism of gluconeogenesis. Although several studies revealed that group 2 innate lymphocytes (ILC2) contribute to blood glucose maintenance in adipose and pancreatic tissues, the contribution of liver ILC2s to glucose metabolism is unknown. This study aims to elucidate the contribution of liver ILC2s to glucose metabolism and its molecular mechanism. Methods: We administered IL-33, an endogenous ILC2 activator, to BALB/c and NSG mice, and measured fasting blood glucose levels and blood glucose elevation by gluconeogenic substrate pyruvate, and blood glucose levels in liver ILC2s transplanted NSG mice. Molecular mechanisms were analyzed by single cell-RNAseq (scRNA-seq) of liver ILC2s, lung ILC2s and hepatocytes, GATA3 transcription complex, ATAC-seq, GATA3-ChIP-seq, and Metabolomics of primary hepatocytes. Results: IL-33 strongly induced IL-13 production by liver ILC2s, lowered fasting blood glucose, and suppressed pyruvate-induced glucose elevation; these effects were not observed in NSG mice lacking immune cells including ILC2s. A hypoglycemic effect of IL-33 was observed in liver ILC2-transplanted NSG mice, but not in mice transplanted with IL-13-deficient ILC2s, suggesting the effect is IL-13-dependent. scRNA-seq results showed that liver ILC2s showed higher IL-13 expression than lung ILC2s, and IL-33 treatment suppressed the expression of gluconeogenic enzymes in the G6pc-high hepatocyte population. The interaction between liver ILC2s and G6pc-high hepatocytes via IL-13/IL-13 receptors was also demonstrated; co-culture of ILC2s with primary cultured hepatocytes resulted in decreased expression of hepatocyte gluconeogenic enzymes and accumulation of multiple gluconeogenic substrates. In addition, IL-13 neutralizing antibody treatment attenuated the effect of the decreased expression of gluconeogenic enzymes in hepatocytes. Transcription factor GATA3 complex analysis and GATA3-ChIPseq suggested binding of GATA3 of the AP-1 family (JunB) in liver ILC2s. Overexpression, knockdown, and scRNA-seq results suggest that AP1 may act in a GATA3-repressive manner in liver ILC2s. Discussion The functional characteristics of liver ILC2s, hepatocyte heterogeneity and subcluster were demonstrated by scRNA-seq, suggesting that liver ILC2s may directly suppress hepatocyte gluconeogenesis via IL-13. This may play a novel role in the homeostasis of hepatic glucose metabolism. Presentation: 6/1/2024

Molecular Interactions of the Pioneer Transcription Factor GATA3 With DNA.

The GATA3 transcription factor is a pioneer transcription factor that is critical in the development, proliferation, and maintenance of several immune cell types. Identifying the detailed conformational dynamics and interactions of this transcription factor, as well as its clinically important population variants will allow us to unravel its mode of action. In this study, we analyze the molecular interactions of the GATA3 transcription factor bound to dsDNA as well as three clinically important population variants by atomistic molecular dynamics simulations. We identify the effect of the variants on the DNA conformational dynamics and delineate the differences compared to the wildtype transcription factor that could be related to impaired function. We highlight the structural plasticity in the binding of the GATA3 transcription factor and identify important DNA-protein contacts. Although the DNA-protein contacts are persistent and appear to be stable, they exhibit nanosecond timescale fluctuations and several binding/unbinding events. Further, we identify differential DNA binding in the three variants and show that the N-terminal binding is reduced in two of the variants. Our results indicate that reduced minor groove width and DNA diameter are important hallmarks for the binding of GATA3. Our work is an important step towards understanding the functional dynamics of the GATA3 protein and its clinically significant population variants.

Alterations in CD4+ T Cell Cytokines Profile in Female Patients with Hashimoto's Thyroiditis Following Vitamin D Supplementation: A Double-blind, Randomized Clinical Trial.

Hashimoto's thyroiditis (HT) is an autoimmune disease characterized by the destruction of thyroid cells through immune processes involving T helper (Th)1 cytokines. This clinical trial investigates the impact of vitamin D supplementation on serum cytokine levels and gene expression in CD4+ T cells from HT patients, aiming to understand its effects on Th-1, Th-2, Th-17, and regulatory T (Treg) cell-associated factors. Female patients were randomly assigned in a double-blind design to either a vitamin D-supplemented group, which received cholecalciferol (1, 25(OH)2D3) at a dose of 50,000 IU, or the placebo group, which received a weekly placebo for a duration of three months. Serum cytokine levels were assessed using enzyme-linked immunosorbent assay (ELISA), while genes' expression levels were measured using real-time PCR. Serum 25-hydroxyvitamin D and levels exhibited a significant increase following vitamin D supplementation, in comparison to the placebo group. Additionally, the vitamin D supplementation resulted in a significant elevation of serum calcium (Ca) levels compared to baseline. In the vitamin D group, there was a significant decrease in both serum levels and expression of the interleukin (IL)-17 gene when compared to baseline, although no statistical difference was observed between the placebo and vitamin D groups. The gene expression of transforming growth factor-beta (TGFβ) was significantly increased in the vitamin D group compared to baseline, with no significant difference between the two study groups. Vitamin D treatment had no effect on serum levels of interferon-gamma (IFNϒ) and IL-4. While the gene expression of IL-4 in the vitamin D group did not exhibit a statistically significant increase, the level of GATA3 transcription factor increased significantly when compared to the placebo group. The expression of IFNϒ and transcription factors, T-bet, RORc, and forkhead box protein 3 (FOXP3) in genes did not show significant changes following vitamin D supplementation. The findings suggest that vitamin D supplementation may hold potential benefits for autoimmune diseases, such as HT. However, further longitudinal clinical trials are necessary to gain a more comprehensive understanding of the specific effects of vitamin D on HT.

The xenobiotic transporter ABCC4/MRP4 promotes epithelial mesenchymal transition in pancreatic cancer.

The xenobiotic transporter ABCC4/MRP4 is highly expressed in pancreatic ductal adenocarcinoma (PDAC) and correlates with a more aggressive phenotype and metastatic propensity. Here, we show that ABCC4 promotes epithelial-mesenchymal transition (EMT) in PDAC, a hallmark process involving the acquisition of mesenchymal traits by epithelial cells, enhanced cell motility, and chemoresistance. Modulation of ABCC4 levels in PANC-1 and BxPC-3 cell lines resulted in the dysregulation of genes present in the EMT signature. Bioinformatic analysis on several cohorts including tumor samples, primary patient-derived cultured cells, patient-derived xenografts, and cell lines, revealed a positive correlation between ABCC4 expression and EMT markers. We also characterized the ABCC4 cistrome and identified four candidate clusters in the distal promoter and intron one that showed differential binding of pro-epithelial FOXA1 and pro-mesenchymal GATA2 transcription factors in low ABCC4-expressing HPAF-II and high ABCC4-expressing PANC-1 xenografts. HPAF-II xenografts showed exclusive binding of FOXA1, and PANC-1 xenografts exclusive binding of GATA2, at ABCC4 clusters, consistent with their low and high EMT phenotype respectively. Our results underscore ABCC4/MRP4 as a valuable prognostic marker and a potential therapeutic target to treat PDAC subtypes with prominent EMT features, such as the basal-like/squamous subtype, characterized by worse prognosis and no effective therapies.

Identification of human host factors required for beta-defensin-2 expression in intestinal epithelial cells upon a bacterial challenge

The human intestinal tract is colonized with microorganisms, which present a diverse array of immunological challenges. A number of antimicrobial mechanisms have evolved to cope with these challenges. A key defense mechanism is the expression of inducible antimicrobial peptides (AMPs), such as beta-defensins, which rapidly inactivate microorganisms. We currently have a limited knowledge of mechanisms regulating the inducible expression of AMP genes, especially factors from the host required in these regulatory mechanisms. To identify the host factors required for expression of the beta-defensin-2 gene (HBD2) in intestinal epithelial cells upon a bacterial challenge, we performed a RNAi screen using a siRNA library spanning the whole human genome. The screening was performed in duplicate to select the strongest 79 and 110 hit genes whose silencing promoted or inhibited HBD2 expression, respectively. A set of 57 hits selected among the two groups of genes was subjected to a counter-screening and a subset was subsequently validated for its impact onto HBD2 expression. Among the 57 confirmed hits, we brought out the TLR5-MYD88 signaling pathway, but above all new signaling proteins, epigenetic regulators and transcription factors so far unrevealed in the HBD2 regulatory circuits, like the GATA6 transcription factor involved in inflammatory bowel diseases. This study represents a significant step toward unveiling the key molecular requirements to promote AMP expression in human intestinal epithelial cells, and revealing new potential targets for the development of an innovative therapeutic strategy aiming at stimulating the host AMP expression, at the era of antimicrobial resistance.

Affinity chromatography reveals direct binding of the GATA4–NKX2-5 interaction inhibitor (3i-1000) with GATA4

Heart failure is a serious medical condition with a poor prognosis. Current treatments can only help manage the symptoms and slow the progression of heart failure. However, there is currently no cure to prevent and reverse cardiac remodeling. Transcription factors are in a central role in various cellular processes, and in the heart, GATA4 and NKX2-5 transcription factors mediate hypertrophic responses and remodeling. We have identified compounds that modulate the synergistic interaction of GATA4 and NKX2-5 and shown that the most promising compound (1, 3i-1000) is cardioprotective in vitro and in vivo. However, direct evidence of its binding site and mechanism of action has not been available. Due to the disordered nature of transcription factors, classical target engagement approaches cannot be utilized. Here, we synthesized a small-molecule ligand-binding pulldown probe of compound 1 to utilize affinity chromatography alongside CETSA, AlphaScreen, and molecular modeling to study ligand binding. These results provide the first evidence of direct physical binding of compound 1 selectively to GATA4. While developing drugs that target transcription factors presents challenges, advances in technologies and knowledge of intrinsically disordered proteins enable the identification of small molecules that can selectively target transcription factors.

Abstract 4643: A novel epigenomic profiling assay reveals disease biology and therapeutic targets in gastro-esophageal cancer from 1 ml of plasma

Abstract INTRODUCTION: Gastro-esophageal adenocarcinoma (GEA) is an aggressive and heterogeneous disease with a poor prognosis. Targeted therapies have failed largely due to challenges associated with biopsy collection, tumor antigen heterogeneity, and accurately distinguishing transcriptionally distinct esophageal, GE junction or gastric tumor types. We developed a novel, multimodal liquid biopsy assay that profiles genome-wide transcriptional activation. Here, we deploy this assay to define clinically relevant insights in a cohort of GEA patients. METHODS: 1 ml of plasma from whole blood samples was used to assess genome-wide enhancer, promoter and DNA methylation loci in 11 GEA patients (Stage III: 1, Stage IV: 10) and 7 healthy volunteers. 6 patients were confirmed as HER2+ based on standard tissue IHC/ISH methods. ctDNA estimation was performed using the ichorCNA algorithm on low pass whole genome sequencing data. A multimodal HER2 classifier developed previously using genome-wide features including HER2 was used to predict HER2 status of the GEA samples. RESULTS: Epigenomic profiling and comparison of GEA and healthy volunteer plasma samples revealed distinct genome-wide transcriptional activation patterns associated with gastroesophageal adenocarcinoma, including (i) the characteristic upregulation of HER2, FGFR2 and VEGF (ii) SOX2, KLF4, GATA6 transcription factor circuitry, and (iii) DNA methylation at the CHFR and MGMT promoters. We then explored if epigenomic profiling of liquid biopsies could infer the activation status of antibody-drug conjugate (ADC) targets currently under investigation in GEA cancers. Simultaneous examination of multiple target genes including HER2, HER3, TROP2, CLDN18, CEACAM5 and MET demonstrated patient-specific differences and dynamic range in transcriptional activation of a subset of these target genes. Finally, we investigated if HER2 status could be assigned accurately and quantitatively from a liquid biopsy using the multimodal HER2 classifier. HER2 positivity by IHC was predicted accurately in 8/11 samples corresponding to an area under the ROC curve (AUC) greater than 0.85. Discordance between plasma and tissue HER2 calls could be partially attributed to variability associated with tumor site/section used for tissue collection, IHC staining, and time between biopsy collection and blood draw. CONCLUSIONS: We demonstrate the feasibility of comprehensive epigenomic profiling from low input volume of 1ml of plasma to provide a snapshot of the tumor’s transcriptional state to derive clinically actionable insights. The HER2 classifier overcomes several of the challenges with IHC profiling by providing a uniform and quantitative measurement of HER2 activation. This non-invasive assay provides an accurate reflection of tumor transcriptional biology that can inform optimal patient selection strategies. Citation Format: Jonathan Beagan, Aparna Gorthi, Anthony D'Ippolito, Travis Clark, Michael Coyne, Tyrone Tamakloe, Amy Donahue, Baovy Tran, Hyun-Hwan Jeong, Kristian Cibulskis, Hathairat Sawaengsri, Corrie A. Painter, Juliann Chmielecki, J Carl Barrett, Mosammat Faria Afreen, Aditya Pandey, Ilexa Ashley Schechter, Martin S. Taylor, Matthew R. Strickland, Matthew Eaton, Samuel J. Klempner. A novel epigenomic profiling assay reveals disease biology and therapeutic targets in gastro-esophageal cancer from 1 ml of plasma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4643.

MiR-1202 acts as anti-oncomiR in myeloid leukaemia by down-modulating GATA-1S expression.

Transient abnormal myelopoiesis (TAM) is a Down syndrome-related pre-leukaemic condition characterized by somatic mutations in the haematopoietic transcription factor GATA-1 that result in exclusive production of its shorter isoform (GATA-1S). Given the common hallmark of altered miRNA expression profiles in haematological malignancies and the pro-leukaemic role of GATA-1S, we aimed to search for miRNAs potentially able to modulate the expression of GATA-1 isoforms. Starting from an in silico prediction of miRNA binding sites in the GATA-1 transcript, miR-1202 came into our sight as potential regulator of GATA-1 expression. Expression studies in K562 cells revealed that miR-1202 directly targets GATA-1, negatively regulates its expression, impairs GATA-1S production, reduces cell proliferation, and increases apoptosis sensitivity. Furthermore, data from TAM and myeloid leukaemia patients provided substantial support to our study by showing that miR-1202 down-modulation is accompanied by increased GATA-1 levels, with more marked effects on GATA-1S. These findings indicate that miR-1202 acts as an anti-oncomiR in myeloid cells and may impact leukaemogenesis at least in part by down-modulating GATA-1S levels.

A novel frameshift variant of GATA3 (p.Ala17ProfsTer178) responsible for HDR syndrome in a Japanese family.

HDR syndrome is an autosomal dominant disorder characterized by hypoparathyroidism (H), deafness (D), and renal dysplasia (R) caused by genetic variants of the GATA3 gene. We present the case of a 38-year-old Japanese man with HDR syndrome who exhibited hypoparathyroidism, sensorineural deafness, renal dysfunction, severe symptomatic hypocalcemia with Chvostek's and Trousseau's signs, and QT prolongation on electrocardiography. He had a family history of deafness and hypocalcemia. Genetic testing revealed a novel GATA3 gene variant at exon 2 (c.48delC), which induces a frameshift resulting in termination at codon 178, causing HDR syndrome. We summarized 45 Japanese cases of HDR syndrome with regard to the mode of onset (familial or sporadic) and the age at diagnosis. In addition, we summarized all previous cases of HDR syndrome with GATA3 gene variants. Mapping of previously reported genetic variants in HDR syndrome revealed that most missense variants were observed at exons 4 and 5 regions in the GATA3 gene. These two regions contain zinc finger domains, demonstrating their functional importance in GATA3 transcription. This review of literature provides a useful reference for diagnosing HDR syndrome and predicting the related future manifestations.

Xpo-1 Antagonism Transcriptionally Reprograms and Is a Therapeutic Vulnerability in GATA-3 Driven T-Cell Lymphomas

Background: The transcription factor GATA-3, via the oncogenic transcriptional program it directs, is a bona fide proto-oncogene, and thus therapeutic target, in a subset of T-cell lymphomas (TCL). The eukaryotic translation initiation factor eIF4E, in complex with helicase and scaffolding factors, facilitates 40S ribosome and Met-tRNA recruitment, both of which are rate-limiting steps in the initiation of translation. Pathways that converge on eIF4E, including PI3K/AKT/mTOR-dependent phosphorylation of 4E-BP1, are frequently activated in GATA-3 PTCL. Within the nucleus, eIF4E specifically binds oncogenic mRNAs, and then forms a complex with a co-factor (LRPPRC) and the nuclear export receptor XPO1. In contrast to bulk mRNA, these eIF4E-bound mRNA are dependent upon XPO1 for nuclear export. Therefore, as we have shown that GATA-3 is oncogenic in T-cell lymphomas (TCL), we hypothesized that selective XPO1 inhibition may transcriptionally reprogram these TCL and is a novel therapeutic vulnerability. Methods: XPO1 expression was examined by immunohistochemistry or flow cytometry in TCL specimens and in TCL that emerge in multiple genetically engineered mouse (GEM) models. Transcripts that are eIF4e clients and dependent upon XPO-1 for nuclear export were identified in an unbiased manner by eIF4e RNA immunoprecipitation (eIF4e-RIP) and RNA-seq. The extent to which XPO1 antagonism transcriptionally reprograms TCL cells, and its value as a therapeutic strategy, was examined pharmacologically with selinexor in ex vivo and in vivo studies using primary TCL specimens and GEM/PDX models, respectively. Results: Among the PTCL cases (n=53) examined, XPO1 expression was observed in 62%, and was highly expressed in CTCL, particularly in patients with large cell transformation. We sought to further understand the extent to which XPO1 expression is associated with T-cell lymphomagenesis. We utilized multiple GEM TCL models in which Smarcb1 (SNF5) or PTEN were conditionally deleted in CD4 + T cells. In both GEM models, a significant increase in XPO-1 expression was associated with the emergence of a malignant clone. A significant reduction in cell viability and increased apoptosis was observed in TCL cell lines and primary specimens treated in vitro/ex vivo with selinexor. In both GEM models, and a PDX model, selinexor treatment similarly decreased TCL progression in vivo. Given these findings, we elected to examine XPO1's potential role in transporting oncogenic, and eIF4e client, transcripts. We performed eIF4e-RIP and RNA-seq in two representative cell lines. Gene set enrichment analysis utilizing the eIF4e client RNA identified demonstrated enrichment for pathways with an established role in TCL (e.g. TCR), including GATA-3. We subsequently performed eIF4e-RIP and quantified GATA-3 transcripts by qRT-PCR in cell lines (n=4), a PDX, and in primary SS specimens (n=2). Compatible with the RNA-seq data, significant enrichment in GATA-3 transcripts was observed. These findings imply that GATA-3 transcripts are dependent upon XPO1 for nuclear export. To directly examine this, the ratio of cytoplasmic to nuclear (C:N) GATA-3 transcripts were examined by qRT-PCR in cell lines treated with selinexor. A significant decrease in the C:N ratio was observed upon XPO1 inhibition, confirming that nuclear export of GATA-3 transcripts is XPO1 dependent. We similarly examined the extent to which GATA-3 target genes are eIF4e clients and XPO1 dependent for nuclear export. We had previously described GATA-3 target genes by integrated ChIP-seq/RNA-seq. Integration of this prior dataset with our eIF4e-RIP sequencing data demonstrated that ≈21-30% of previously described GATA-3 target genes were also eIF4e clients. We selected a few such targets, including ITK, for further validation. These GATA-3 targets were eIF4e clients and dependent upon XPO1 for nuclear export. Finally, we examined expression of these proteins in a diverse panel of T-cell lymphoma/leukemia cell lines and a primary SS specimen after brief exposure to selinexor, and compatible with our findings, a significant decrease in protein expression was observed. Conclusions: Collectively then, our findings demonstrate that XPO1 antagonism, by impairing the nuclear export of both GATA-3 and many of its target gene mRNA, is a novel strategy to transcriptionally reprogram and therapeutically target GATA-3 driven TCL.

Dysregulated expression of GATA2 and GATA6 transcription factors in adenomyosis: implications for impaired endometrial receptivity

To study the effect of adenomyosis on the localized expression of the GATA binding proteins 2 and 6 (GATA2 and GATA6) zinc-finger transcription factors that are involved in proliferation of hematopoietic and endocrine cell lineages, cell differentiation, and organogenesis, potentially leading to impaired endometrial implantation. Laboratory based experimental study. Academic hospital and laboratory. Human endometrial stromal cells (HESCs) of reproductive age patients, 18-45 years of age, with adenomyosis were compared with patients with no pathology and leiomyomatous uteri as controls (n = 4 in each group, respectively). Additionally, midsecretory phase endometrial sections were obtained from patients with adenomyosis and control patients with leiomyoma (n = 8 in each group, respectively). GATA2 and GATA6 immunohistochemistry and H-SCORE were performed on the midsecretory phase endometrial sections from adenomyosis and leiomyoma control patients (n = 8 each, respectively). Control and adenomyosis patient HESC cultures were treated with placebo or 10-8 M estradiol (E2), or decidualization media (EMC) containing 10-8 M E2, 10-7 M medroxyprogesterone acetate, and 5 × 10-5 M cAMP for 6 and 10 days. Additionally, control HESC cultures (n = 4) were transfected with scrambled small interfering RNA (siRNA) (control) or GATA2-specific siRNAs for 6 days while adenomyosis HESC cultures (n = 4) were transfected with human GATA2 expression vectors to silence or induce GATA2 overexpression. Immunohistochemistry was performed to obtain GATA2 and GATA6 H-SCORES in adenomyosis vs. control patient endometrial tissue. Expression of GATA2, GATA6, insulin-like growth factor-binding protein 1 (IGFBP1), prolactin (PRL), progesterone receptor (PGR), estrogen receptor 1 (ESR1), leukemia inhibitory factor (LIF), and Interleukin receptor 11 (IL11R) messenger RNA (mRNA) levels were analyzed using by qPCR with normalization to ACTB. Silencing and overexpression experiments also had the corresponding mRNA levels of the above factors analyzed. Western blot analysis was performed on isolated proteins from transfection experiments. Immunohistochemistry revealed an overall fourfold lower GATA2 and fourfold higher GATA6 H-SCORE level in the endometrial stromal cells of patients with adenomyosis vs. controls. Decidual induction with EMC resulted in significantly lower GATA2, PGR, PRL and IGFBP1 mRNA levels in HESC cultures from patients with adenomyosis patient vs. controls. Leukemia inhibitory factor and IL11R mRNA levels were also significantly dysregulated in adenomyosis HESCs compared with controls. . Silencing of GATA2 expression in control HESCs induced an adenomyosis-like state with significant reductions in GATA2, increases in GATA6 and accompanying aberrations in PGR, PRL, ESR1 and LIF levels. Conversely, GATA2 overexpression via vector in adenomyosis HESCs caused partial restoration of the defective decidual response with significant increases in GATA2, PGR, PRL and LIF expression. In-vivo and in-vitro experiment results demonstrate that there is an overall inverse relationship between endometrial GATA2 and GATA6 levels in patients with adenomyosis who have diminished GATA2 levels and concurrently elevated GATA6 levels. Additionally, lower GATA2 and higher GATA6 levels, together with aberrant levels of important receptors and implantation factors, such as ESR1, PGR, IGFBP1, PRL, LIF, and IL11R mRNA in HESCs from patients with adenomyosis or GATA2-silenced control HESCs, support impaired decidualization. These effects were partially restored with GATA2 overexpression in adenomyosis HESCs, demonstrating a potential therapeutic target.

GATA1 and GATA2 Sense/Antisense Transcriptional Switching in Early Hematopoietic Development

The GATA1 and GATA2 genes play essential roles in hematopoietic development. GATA1 is the master regulator of erythropoiesis and GATA2 is required for the expansion and survival of hematopoietic progenitor and stem cells, as well as the development of mast cells. A switch in GATA expression occurs during erythropoiesis, with silencing of the GATA2 gene and increased expression of GATA1. A GATA2 antisense transcript ( GATA2-AS1) has been associated with silencing of GATA2 expression. We have identified a novel GATA1 antisense promoter located in the first intron that opposes the GATA1 promoter and generates a spliced antisense transcript complementary to the SUV39H1 H3K9 methyltransferase gene. The competition between opposing sense and antisense promotersin the GATA1 and GATA2 genes may play a central role in the switching of GATA expression that occurs during hematopoiesis. To address this hypothesis, gene expression analysis of cells expressing sense versus antisense transcripts from the GATA1 or GATA2 genes was performed using 5'scRNAseq data from in vitro differentiated CD34 cells. Cells expressing only sense or only antisense GATA1 transcriptswere readily detected and comprised the majority (90%) of cells with GATA1 transcripts. Differential gene expression analysis of cells with GATA1 sense-only versus cells with GATA1 antisense-only showed association of sense transcription with erythrocyte genes, whereas antisense expression was associated with a mast cell phenotype and upregulation of GATA2 transcript levels. Conversely, GATA2 antisense expressing cells had increased GATA1 transcription and an erythrocyte phenotype, and GATA2 sense expressing cells demonstrated mast cell-specific gene expression. Single cell RNAseq analysis of HL60 cells induced to differentiate in vitro identified significant changes in GATA2 gene expression. Induction of granulocyte differentiation in HL60 cells treated with DMSO resulted in increased GATA2 antisense transcription, whereas PMA induction of monocyte differentiation was associated with increased GATA2 sense transcription. Taken together these results indicate a central role for sense/antisense promoter switching in hematopoiesis.

First-Hit SETBP1 Mutations Cause a Myeloproliferative Disorder with Bone Marrow Fibrosis

Somatic SETBP1 mutations are found in various myeloid disorders covering both myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS). To characterize the early steps of SETBP1-mediated leukemogenesis, we generated a conditional mouse model expressing SETBP1 G870S mutant in the entire hematopoietic tissue through Cre-mediated recombination driven by the Vav1 promoter. In all mice signs of a hematological disease appeared between 30 and 90 days: longitudinal analysis revealed accumulation of white blood cells (WBC) in virtually all heterozygous SETBP1 G870S mice, with a marked imbalance between the lymphoid and myeloid lineages in favor of the latter, and an increase in mature myeloid cells in absence of circulating blasts or non-segmented myeloid precursors. Kaplan-Meier analysis revealed a dramatic decrease in event-free survival in SETBP1 G870S mice. BM histology showed overt myeloid hyperplasia with fibrosis and no evidence of dysplasia except for the megakaryocytic lineage. Exploration of visceral organs highlighted the presence of severe hepatosplenomegaly with massive infiltration by myeloid elements, disruption of normal tissue architecture, and signs of extramedullary hematopoiesis. Single-cell RNA-sequencing (scRNA) on BM Lin - cells identified Mecom, Setbp1 and Hoxa9 among the top upregulated genes in SETBP1 G870S precursors. Pseudotime analysis of scRNA data revealed the presence of 261 spatially autocorrelated genes. Of them 158 were also differentially expressed in SETBP1 G870Svs control mice. Spi1, encoding for the master regulator of hematopoietic differentiation PU.1, was significantly upregulated in SETBP1 G870S precursors. PU.1 promotes the maturation of bone marrow early precursors towards the granulocytic/monocytic lineages by directly impairing the transcription of Gata2 and Gata1. In line with these data, Gata2 and Gata1 expression was profoundly suppressed in the early myeloid precursors of SETBP1 G870S mice, which associated with the down-modulation of markers of the erythroid lineage, such as the Carbonic Anhydrase 1, in the MEP differentiation branch. Ourmouse model recapitulates many clinical features of primary myelofibrosis (PMF). As up to 10% of PMF are triple-negative for the classical JAK2, CALR, and MPL mutations (TN-PMF), we set out to assess SETBP1 mutations in this context. We analyzed 36 TN-PMF patients by exome sequencing. In 29 we did not find any evidence of somatic mutations; in the remaining 7 (7/36; 19.4%) high VAF SETBP1 degron mutations were identified. In two patients SETBP1 was found as a single somatic variant, while in the others it coexisted with ASXL1, NRAS TET2 SRSF2, RIT1 CBL or CSF3R mutations. Notably, SETBP1 mutations were the only shared alterations among all seven patients. A markedly reduced overall survival was observed for SETBP1 positive patients, with a median survival time of 24 months (median survival not reached at 60 months for SETBP1 negative patients). To dissect the clonal architecture of SETBP1 positive TN-PMF at single-cell resolution, we applied single-cell targeted DNA sequencing on 3 SETBP1-mutated TN-PMF samples using the Tapestri technology, showing that, as opposite to MDS/MPN, in all TN-PMF cases SETBP1 is a very early clonal event. Therefore, our study suggests a clear partition of TN-PMF into two groups, the first one characterized by oncogenic, high VAF SETBP1 mutations accompanied by other oncogenic variants and poor prognosis and the other one characterized by no evidence of an active clonal process or of driver oncogenic events and much lower aggressiveness. SETBP1 positive TN-PMF disorders lie in a gray zone comprised between the MPN and MPN/MDS boundary. In MDS/MPN, SETBP1 mutations are often found as mid or late events. In contrast, we show here that in TN-PMF SETBP1 appears to be one of the earliest hits, therefore highlighting a potentially relevant biological difference occurring in the two subsets. In this context the presence of early SETBP1 mutations seems to promote the occurrence of a myeloid disorder characterized by the triad: leukocytosis without differentiation block or dysplasia, BM fibrosis and progressive splenomegaly, hence recapitulating many clinical features of overt or prefibrotic/early PMF and resembling the SETBP1 mouse model.

Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination

Previous studies of the murine Ly49 and human KIR gene clusters implicated competing sense and antisense promoters in the control of variegated gene expression. In the current study, an examination of transcription factor genes defines an abundance of convergent and divergent sense/antisense promoter pairs, suggesting that competing promoters may control cell fate determination. Differentiation of CD34+ hematopoietic progenitors invitro shows that cells with GATA1 antisense transcription have enhanced GATA2 transcription and a mast cell phenotype, whereas cells with GATA2 antisense transcription have increased GATA1 transcripts and an erythroblast phenotype. Detailed analyses of the AHR and RORC genes demonstrate the ability of competing promoters to act as binary switches and the association of antisense transcription with an immature/progenitor cell phenotype. These data indicate that alternative cell fates generated by promoter competition in lineage-determining transcription factors contribute to the programming of cell differentiation.

Determination of Plasmodium vivax and Plasmodium falciparum Malaria Exposure in Two Ethiopian Communities and Its Relationship to Duffy Expression.

Despite historical dogma that Duffy blood group negativity of human erythrocytes confers resistance to Plasmodium vivax blood stage infection, cases of P. vivax malaria and asymptomatic blood stage infection (subclinical malaria) have recently been well documented in Duffy-negative individuals throughout Africa. However, the impact of Duffy negativity on the development of naturally acquired immunity to P. vivax remains poorly understood. We examined antibody reactivity to P. vivax and P. falciparum antigens at two field sites in Ethiopia and assessed Duffy gene expression by polymerase chain reaction amplification and sequencing of the GATA-1 transcription factor-binding site of the Duffy antigen receptor for chemokines (DARC) gene promotor region that is associated with silencing of erythroid cell transcription and absent protein expression. Antibodies to three of the four P. vivax blood stage antigens examined, RBP2b, EBP2, and DBPIISal-1, were significantly lower (P < 0.001) in Duffy-negative individuals relative to Duffy-positive individuals. In stark contrast, no clear pattern was found across Duffy-negative and Duffy-positive genotypes for P. falciparum antibodies. We conclude that lack of erythroid Duffy expression is associated with reduced serologic responses, indicative of less naturally acquired immunity and less cumulative exposure to blood stage P. vivax parasites relative to Duffy positive individuals living in the same communities.

Comprehensive Analysis and Characterization of the GATA Gene Family, with Emphasis on the GATA6 Transcription Factor in Poplar.

GATA transcription factors are ubiquitously present in eukaryotic organisms and play a crucial role in multiple biological processes, such as plant growth, stress response, and hormone signaling. However, the study of GATA factors in poplar is currently limited to a small number of proteins, despite their evident functional importance. In this investigation, we utilized the most recent genome annotation and stringent criteria to identify 38 GATA transcription factor genes in poplar. Subsequently, we conducted a comprehensive analysis of this gene family, encompassing phylogenetic classification, protein characterization, analysis of promoter cis-acting elements, and determination of chromosomal location. Our examination of gene duplication events indicated that both tandem and segmental duplications have contributed to the expansion of the GATA gene family in poplar, with segmental duplication potentially being a major driving force. By performing collinearity analysis of genes across six different species, we identified 74 pairs of co-linear genes, which provide valuable insights for predicting gene functions from a comparative genomics perspective. Furthermore, through the analysis of gene expression patterns, we identified five GATA genes that exhibited differential expression in leaf-stem-root tissues and eight genes that were responsive to salt stress. Of particular interest was GATA6, which displayed strong induction by salt stress and overlapped between the two gene sets. We discovered that GATA6 encodes a nuclear-localized protein with transcription activation activity, which is continuously induced by salt stress in leaf and root tissues. Moreover, we constructed a co-expression network centered around GATA6, suggesting the potential involvement of these genes in the growth, development, and response to abiotic stress processes in poplar through cell transport systems and protein modification mechanisms, such as vesicle-mediated transport, intracellular transport, ubiquitination, and deubiquitination. This research provides a foundation for further exploration of the functions and mechanisms of GATA transcription factors in poplar.