Lineage-specific Transcription Factors Research Articles

Abstract PO4-16-03: Ectopic expression of lineage-specific transcription factors in Breast Cancer

Abstract Background: Lineage-specific transcription factors (LTFs) are purported to define cellular lineages and their expression could be used to identify subtypes of cancer. In many cancers, tuft cell differentiation appears to have prognostic impact. However, such differentiation has not been documented in breast cancer. Methods: We sought to study the fidelity of LTFs (MYOG, POU2F3, FOXA1, FOXA2, FOXA3, FOXJ1, HNF4A, HNF4G, SPIB, SOX8, GRHL1, GRHL2, and GRHL3) for their presence and prognostic impact in breast cancer. Single cell RNA data from GSE 161529, which contains 421,761 single cells, was downloaded and analyzed for the expression and co-expression of LTFs. The data was first subdivided based on ER+ and TNBC status. Analysis was performed using cells from 10ER+ samples and 4 TNBC samples. Cell clustering using Louvain’s method was run using all genes. Cell type assignment was then performed using well-known markers for both tumor and lymphocyte marker from existing publications. Further analysis was restricted to keratin expressing cells and to study the presence and co-expression of LTFs in the epithelial cells. KM-Plotter was employed to determine the prognostic value of these LTFs. The analysis was further stratified by expression of estrogen receptor positive and negative status. The endpoint of relapse free survival was used, as it provided data on the largest number of patients. Results: Single-cell analysis pipeline successfully identified distinct populations of tumor epithelial cells accompanied by various lymphocytes, including B cells, CD8+ T cells, CD4+ T cells, dendritic cells, and macrophages, in both ER+ tumors and TNBC tumor samples. We further confirmed the expression of the LTFs in the epithelial (keratin+) compartment. Expression of all LTFs (except MYOG, and FOXA2) was scattered in the different epithelial clusters. Further analysis of single LTFs showed differentiational co-expression based on ER+ status. POU2F3+/ER+ cells also co-expressed FOXA1 and GRHL1 while POU2F3+/ER- cells were GRHL1+ and (weak) SPIB+. The analysis of LTFs using KM-Plotter tool revealed their expression documenting multiple cell lineages in breast cancer; this was noted in ER+, HER2+ cancers and TNBCs. The directionality of the outcome (good or bad prognosis) varied with the specific TFs and subtype of breast cancer. High expression of POU2F3, and FOXA1, and SPIB were associated with better relapse-free survival (RFS) in ER+ breast cancer. POU2F3, FOXA2, FOXA3 were associated with worse RFS, whereas SPIB was with prognosis in ER- breast cancers. Conclusions: We for the first time document the expression of LTFs in breast cancer and their prognostic relevance based on ER+ and ERneg status. Expression of POU2F3, a marker of tuft cells which are known to regulate immune response, was noted to be associated with improved outcomes in ER+ tumors. Further characterization of the relevance of LTFs and their co-expression with respect to therapeutic response is ongoing. Citation Format: Sunil Badve, Jian Hu, Yu Zhang, Yesim Gokmen-Polar. Ectopic expression of lineage-specific transcription factors in Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-16-03.

Chromatin landscape instructs precise transcription factor regulome during embryonic lineage specification

Embryos, originating from fertilized eggs, undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Chromatin regulators, including transcription factors (TFs), play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass and trophectoderm of blastocysts, prompting inquiry into Tfap2c's function in post-lineage establishment. In this study, we delineate the dynamics of TFAP2C during the mouse peri-implantation stage and elucidate its collaboration with the key lineage regulators CDX2 and NANOG. Importantly, we propose that de novo formation of H3K9me3 in the extraembryonic ectoderm during implantation antagonizes TFAP2C binding to crucial developmental genes, thereby maintaining its lineage identity. Together, these results highlight the plasticity of the chromatin environment in designating the genomic binding of highly adaptable lineage-specific TFs and regulating embryonic cell fates.

Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation

Temporal regulation of super-enhancer (SE) driven transcription factors (TFs) underlies normal developmental programs. Neuroblastoma (NB) arises from an inability of sympathoadrenal progenitors to exit a self-renewal program and terminally differentiate. To identify SEs driving TF regulators, we use all-trans retinoic acid (ATRA) to induce NB growth arrest and differentiation. Time-course H3K27ac ChIP-seq and RNA-seq reveal ATRA coordinated SE waves. SEs that decrease with ATRA link to stem cell development (MYCN, GATA3, SOX11). CRISPR-Cas9 and siRNA verify SOX11 dependency, in vitro and in vivo. Silencing the SOX11 SE using dCAS9-KRAB decreases SOX11 mRNA and inhibits cell growth. Other TFs activate in sequential waves at 2, 4 and 8 days of ATRA treatment that regulate neural development (GATA2 and SOX4). Silencing the gained SOX4 SE using dCAS9-KRAB decreases SOX4 expression and attenuates ATRA-induced differentiation genes. Our study identifies oncogenic lineage drivers of NB self-renewal and TFs critical for implementing a differentiation program.

Single and mixture effects of bisphenol A and benzophenone-3 on in vitro T helper cell differentiation

Immune homeostasis is key to guarantee that the immune system can elicit effector functions against pathogens and at the same time raise tolerance towards other antigens. A disturbance of this delicate balance may underlie or at least trigger pathologies. Endocrine disrupting chemicals (EDCs) are increasingly recognized as risk factors for immune dysregulation. However, the immunotoxic potential of specific EDCs and their mixtures is still poorly understood. Thus, we aimed to investigate the effect of bisphenol A (BPA) and benzophenone-3 (BP-3), alone and in combination, on in vitro differentiation of T helper (TH)17 cells and regulatory T (Treg) cells.Naïve T cells were isolated from mouse lymphoid tissues and differentiated into the respective TH population in the presence of 0.001–10 μM BP-3 and/or 0.01–100 μM BPA. Cell viability, proliferation and the expression of TH lineage specific transcription factors and cytokines was measured by flow cytometry and CBA/ELISA. Moreover, the transcription of hormone receptors as direct targets of EDCs was quantified by RT-PCR.We found that the highest BPA concentration adversely affected TH cell viability and proliferation. Moreover, the general differentiation potential of both TH populations was not altered in the presence of both EDCs. However, EDC exposure modulated the emergence of TH17 and Treg cell intermediate states. While BPA and BP-3 promoted the development of TH1-like TH17 cells under TH17-differentiating conditions, TH2-like Treg cells occurred under Treg polarization. Interestingly, differential effects could be observed in mixtures of the two tested compounds compared with the individual compounds. Notably, estrogen receptor β expression was decreased under TH17-differentiating conditions in the presence of BPA and BP-3 as mixture. In conclusion, our study provides solid evidence for both, the immune disruptive potential and the existence of cumulative effects of real nature EDC mixtures on T cell in vitro differentiation.

Self-sufficient primary natural killer cells engineered to express T cell receptors and interleukin-15 exhibit improved effector function and persistence.

NK cells can be genetically engineered to express a transgenic T-cell receptor (TCR). This approach offers an alternative strategy to target heterogenous tumors, as NK:TCR cells can eradicate both tumor cells with high expression of HLA class I and antigen of interest or HLA class I negative tumors. Expansion and survival of NK cells relies on the presence of IL-15. Therefore, autonomous production of IL-15 by NK:TCR cells might improve functional persistence of NK cells. Here we present an optimized NK:TCR product harnessed with a construct encoding for soluble IL-15 (NK:TCR/IL-15), to support their proliferation, persistence and cytotoxic capabilities. Expression of tumor-specific TCRs in peripheral blood derived NK-cells was achieved following retroviral transduction. NK:TCR/IL-15 cells were compared with NK:TCR cells for autonomous cytokine production, proliferation and survival. NK:BOB1-TCR/IL-15 cells, expressing a HLA-B*07:02-restricted TCR against BOB1, a B-cell lineage specific transcription factor highly expressed in all B-cell malignancies, were compared with control NK:BOB1-TCR and NK:CMV-TCR/IL-15 cells for effector function against TCR antigen positive malignant B-cell lines in vitro and in vivo. Viral incorporation of the interleukin-15 gene into engineered NK:TCR cells was feasible and high expression of the TCR was maintained, resulting in pure NK:TCR/IL-15 cell products generated from peripheral blood of multiple donors. Self-sufficient secretion of IL-15 by NK:TCR cells enables engineered NK cells to proliferate in vitro without addition of extra cytokines. NK:TCR/IL-15 demonstrated a marked enhancement of TCR-mediated cytotoxicity as well as enhanced NK-mediated cytotoxicity resulting in improved persistence and performance of NK:BOB1-TCR/IL-15 cells in an orthotopic multiple myeloma mouse model. However, in contrast to prolonged anti-tumor reactivity by NK:BOB1-TCR/IL-15, we observed in one of the experiments an accumulation of NK:BOB1-TCR/IL-15 cells in several organs of treated mice, leading to unexpected death 30 days post-NK infusion. This study showed that NK:TCR/IL-15 cells secrete low levels of IL-15 and can proliferate in an environment lacking cytokines. Repeated in vitro and in vivo experiments confirmed the effectiveness and target specificity of our product, in which addition of IL-15 supports TCR- and NK-mediated cytotoxicity.

POU2F3-expressing intraepithelial small-cell carcinoma with mixed small-cell carcinoma and conventional-type urothelial carcinoma of the urinary bladder.

Based on lineage-specific transcription factors, small-cell neuroendocrine carcinoma (SmCC) of the urinary bladder has recently been subtyped into three molecular subtypes: ASCL1, NEUROD1 and POU2F3. The latter is a master transcriptional regulator of tuft cells (TCs) which are rare solitary cells found in various mucosal epithelia such as the gastrointestinal tract, but which have not been reported in the bladder. The POU2F3 subtype shows low or absent neuroendocrine marker expression. A case of mixed SmCC and conventional-type urothelial carcinoma (CUC) of the urinary bladder with POU2F3-expressing intraepithelial small-cell carcinoma in keeping with a tuft cell phenotype, arising in association with intestinal metaplasia (IM) is described. The presence of POU2F3-expressing cells in normal urothelium, cystitis cystica glandularis and IM of the urinary bladder is demonstrated in separate cases of cystitis cystica glandularis with IM. Also, POU2F3 expression is identified in a subset of bladder SmCC.

Abstract LB196: An atlas of accessible chromatin in advanced prostate cancer

Abstract Although androgen deprivation therapy (ADT) and second-generation Androgen Receptor (AR) signaling inhibitors (ARSIs) extend the survival of patients with metastatic castration-resistant prostate cancer (mCRPC), these tumors almost inevitably progress on these therapies. Prolonged usage of ADT and/or ARSI is associated with the development of treatment-associated transcriptional subtypes distinguished by alterations that affect the activity of the AR and neuroendocrine (NE) genes. Genomic and transcriptomic distinctions between the mCRPC subtypes are emerging. However, relatively little is known about the epigenome of the mCRPC transcriptional subtypes. We hypothesized that epigenetic mechanisms drive lineage plasticity in mCRPC by changing chromatin accessibility at regulatory loci for transcription factors (TFs) that affect downstream gene activity. In this study, we produced high-resolution chromatin accessibility maps linked to lineage-specific TF binding by performing Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on 70 mCRPC tissue biopsy samples from the SU2C/PCF West Coast Prostate Cancer Dream Team cohort. Here, we demonstrate that the global chromatin accessibility profile of mCRPC is unique and primarily correlated with the functional activity of AR. We comprehensively examined genome-wide TF occupancy signals in accessible chromatin regions and identified 203 TFs associated with mCRPC subtypes. Our findings indicated that different mCRPC subtypes exhibit a specific preference for certain TFs. The AR+NE- subtype showed a greater dependence on TFs, such as FOXA1, AR, and HOXB13, while the AR-NE+ subtype was more addicted to ASCL1 and NEUROD1. We found that a group of TFs including SP1, KLF5, and ZNF263 that bind to GC-rich sequences, are likely to play a major role in the regulation of the AR-NE- subtype. Most notably, we identified a potentially novel TF in prostate cancer, ZNF263, which is estimated to have a significant impact on gene activity in the AR-NE- subtype and may play a role in activating the targets of the MYC signaling pathway. Overall, our analysis of chromatin accessibility in mCRPC provides valuable insights into epigenetic changes that occur during mCRPC progression. Citation Format: Raunak Shrestha, Lisa N. Chesner, Meng Zhang, Stanley Zhou, Adam Foye, Arian Lundberg, Alana S. Weinstein, Martin Sjöström, Xiaolin Zhu, Thaidy Moreno-Rodriguez, Haolong Li, Joshi J. Alumkal, Rahul Aggarwal, Eric J. Small, Mathieu Lupien, David A. Quigley, Felix Y. Feng. An atlas of accessible chromatin in advanced prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB196.

Abstract 7327: Investigating the cell-type specific regulation of IRF4 and its role in lung cancer via a lung cancer risk-associated pleiotropic variant

Abstract Although smoking is a main risk factor for lung cancer, genetic factors also contribute to the risk, as shown by over 50 genomic loci identified by genome-wide association studies (GWAS). A recent cross-ancestry lung cancer GWAS identified a common germline variant, rs12203592 (C/T), in chr6p25.3 as a new signal, and quantitative trait loci (eQTL) colocalization analysis using lung and blood tissues (GTEx v8) identified IRF4 as a likely target of rs12203592. rs12203592 has previously been linked with diverse traits, including pigmentation phenotypes, smoking cessation, lymphoblastic leukemia, melanoma, and other skin cancers. rs12203592 also appears to have varied allelic effects in different cell types. Namely, the lung cancer risk-associated T allele is correlated with higher IRF4 expression in lung tissue and blood cells (GTEx v8) but lower expression in primary melanocytes (n = 106; Zhang et al). Since previous studies established the melanocyte-specific allelic function of this SNP through lineage-specific transcription factors (TFs), we hypothesized that cell-type-specific TFs mediate the observed allelic effect in different tissue/cell types and further contribute to the unique role of IRF4 in lung tumorigenesis. To identify these potential cell-type-specific regulators, we performed mass spectrometry using the nuclear extracts from three cell lines representing lung, blood, and melanocyte lineage. The results nominated the NF-kB and ZEB protein families as the most prominent T-specific binders in the A549 lung cancer cell line, which was validated by electromobility shift assays. Consistent with these findings, tissue-based SNP-gene interaction analysis demonstrated that the mRNA levels of NF-kB and ZEB family members (4 of 7 genes) were correlated with IRF4 expression with a significant interaction with rs12203592 in GTEx lung tissue (P < 0.017), where the correlation is mainly observed with the T allele. Notably, the SNP interaction was less pronounced in whole blood or melanocytes, and the correlation of these TFs and IRF4 expression was mainly observed with the C allele in melanocytes. To begin to establish the roles of these TFs and IRF4 in lung tumorigenesis and given that IRF4 was shown to promote endogenous DNA damage and proliferation of lung-lineage cell lines, we will investigate the roles of NF-kB and ZEB in IRF4 regulation in these contexts using knockdown and overexpression of these TFs. To further investigate lung cancer-specific IRF4 function, we will identify potential targets of IRF4 among lung cancer-associated functional variants established through our previous studies. This data will help elucidate the context-specific roles of IRF4 in lung cancer development and provide clues to gene regulation in a pleiotropic GWAS locus. Citation Format: Alexander Kane, Jinhu Yin, Erping Long, James Feng, Cathrin Gräwe, Harsh Patel, Jinyoung Byun, Christopher Amos, Kevin Brown, Jun Xia, Michiel Vermeulen, Jiyeon Choi. Investigating the cell-type specific regulation of IRF4 and its role in lung cancer via a lung cancer risk-associated pleiotropic variant [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 7327.

Abstract 5633: Unravelling the pleiotropic role of HNF4α in invasive mucinous adenocarcinoma of the lung (IMA)

Abstract IMA is a distinct subtype of lung adenocarcinoma (LUAD), marked by a cellular identity shift from a pulmonary to a gastric lineage with the loss of the pulmonary lineage specifier NKX2-1. This distinctive transformation underscores the complexity of lung cancer heterogeneity and highlights the critical role of lineage-specifying transcription factors in dictating tumor behavior. Notably, both human and murine models of IMA overexpress HNF4α, a known lineage specifier for gastric differentiation in the adult mouse mucosa. Also, concomitant deletion of Hnf4a and Nkx2-1 at tumor initiation impairs tumor growth and the extent of HNF4α in regulating IMA tumor growth, cellular identity and drug response remains unknown at large. Here, we utilized genetically engineered mouse models (GEMM) that relies on a sequential recombination strategy to delete Hnf4a in established tumors. We induce tumor formation through intratracheal delivery of Flp-O virus, activating the expression of mutant KRASG12D and Cre in lung epithelial cells. Tamoxifen administration recombines either Nkx2-1 alone (KN) or in combination with Hnf4a (KNH). We have extensively studied the phenotypic role of HNF4α in GEMM and organoids and identified gene sets regulated by HNF4α in IMA at the bulk level. To complement our findings, we profiled both the tumor and stromal compartments via scRNAseq analysis on our GEMM to gain insights into the cellular diversity within the tumor microenvironment (TME) and the role HNF4α plays. Additionally, we performed ChIPSeq in organoids to elucidate the genome occupancy of HNF4α and determine the mechanisms of gene regulation in IMA. We find that deletion of Hnf4a impairs tumor growth in GEMM and this is phenocopied in organoids. We identified numerous differentially expressed genes (DEGs) in KNH compared to KN and validated several DEGs in vivo. GSEA analysis reveals a significant involvement in regulating cellular identity and suggests a potential impact on anti-tumor immune responses. To this, our scRNAseq data revealed an enrichment of N2-TAN (tumor associated neutrophils) associated genes in KNH compared to KN, suggesting a nuanced interplay between HNF4α and the TME. Additionally, HNF4α exhibited dual functionality, acting as an activator and indirectly as a repressor by modulating the activity of other transcription factors like FOXA1. FOXA1 was found to bind de novo target genes following the loss of HNF4α. These findings so far collectively illuminate the multifaceted role of HNF4α in IMA, primarily driving tumorigenesis in a cell autonomous manner and secondarily skewing the TME towards a protumor via N2-TAN following loss of HNF4α in tumors. Citation Format: Headtlove Essel Dadzie, Gabriela Fort, Katherine Gillis, Pengshu Fang, Walter Orellana, Eric L. Snyder. Unravelling the pleiotropic role of HNF4α in invasive mucinous adenocarcinoma of the lung (IMA) [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 5633.

Abstract 6048: Targeting AR positive prostate cancer cells by the novel P300/CBP oral available PROTAC degrader

Abstract Background The Androgen Receptor (AR) serves as the core lineage-specific transcription factor for prostatic epithelial cells. Targeting AR is currently the most promising therapeutic strategy. However, the inevitable development of acquired resistance to anti-androgen treatments underscores the urgent need to devise new therapeutic strategies. Recent studies have revealed that in prostate cancer cells, AR is hijacked by oncogenic transcription factors, such as FOXA1 and HOXB13, which promiscuously bind to distinct enhancer sites, driving the progression of prostate cancer. This process leads to the formation of a substantially rewired AR cancer specific enhanceosome, requiring a variety of coregulators to exhibit oncogenic driver characteristics, which can be potential therapeutic targets for prostate cancer. Histone acetyltransferases (HATs) P300 and CBP are paralogs which play dominant roles in orchestrating high-order chromatin structures and transcription factor complexes by acetylating histone proteins at multiple residuals. Although accumulating evidence suggests that P300/CBP function as AR coregulator and targeting P300/CBP can markedly suppress AR-positive prostate cancer cell growth, including growth of castration-resistant prostate cancer (CRPC), most of the P300/CBP inhibitors have performed poorly in clinical trials. Methods We developed a novel P300/CBP dual oral available PROTAC degrader, namely CBPD-409. The on-target effects of CBPD-409 were assessed by quantitative proteomics (TMT-mass spectrometry) in prostate cancer cell lines. The RNA-seq analysis was conducted to investigate CBPD-409 effects on global transcriptome in prostate cancer cells. The cytotoxicity of CBPD-409 in multiple prostate cancer cell lines was examined by cell-titer-glo and incucyte assays. Conclusion In multiple cell lines, CBPD-409 exhibits remarked potency to degrade both P300 and CBP proteins in time and does dependent manner, without evident off-target effects. By employing CBPD-409, we demonstrate that degrading P300/CBP preferentially suppress AR+ prostate cancer cell growth. The global transcriptomic profiling in CBPD-409 treated prostate cancer cells revealed that loss of P300/CBP results in remarkedly downregulation of AR, Myc, FOXA1 and ERG signaling. Assessment of CBPD-409 cytotoxicity in a panel prostate cancer cell lines suggests that AR positive prostate cancer cells display highest sensitivity to CBPD-409. Citation Format: Jie luo, Abhijit Prolia, Yuanyuan Qiao, Jean Tian, Rahul Mannan, Somnath Mahapatra, Zhixiang Chen, Rithvik Seri, Shaomeng Wang, Arul Chinnaiyan. Targeting AR positive prostate cancer cells by the novel P300/CBP oral available PROTAC degrader [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 6048.

BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates.

Cell fate decisions are achieved with gene expression changes driven by lineage-specific transcription factors (TFs). These TFs depend on chromatin remodelers including the Brahma-related gene 1 (BRG1)-associated factor (BAF) complex to activate target genes. BAF complex subunits are essential for development and frequently mutated in cancer. Thus, interrogating how BAF complexes contribute to cell fate decisions is critical for human health. We examined the requirement for the catalytic BAF subunit BRG1 in neural progenitor cell (NPC) specification from human embryonic stem cells. During the earliest stages of differentiation, BRG1 was required to establish chromatin accessibility at neuroectoderm-specific enhancers. Depletion of BRG1 dorsalized NPCs and promoted precocious neural crest specification and enhanced neuronal differentiation. These findings demonstrate that BRG1 mediates NPC specification by ensuring proper expression of lineage-specific TFs and appropriate activation of their transcriptional programs.

Cell fate decision in erythropoiesis: Insights from multiomics studies

Every second, the body produces 2 million red blood cells through a process called erythropoiesis. Erythropoiesis is hierarchical in that it results from a series of cell fate decisions whereby hematopoietic stem cells progress toward the erythroid lineage. Single-cell transcriptomic and proteomic approaches have revolutionized the way we understand erythropoiesis, revealing it to be a gradual process that underlies a progressive restriction of fate potential driven by quantitative changes in lineage-specifying transcription factors. Despite these major advances, we still know very little about what cell fate decision entails at the molecular level. Novel approaches that simultaneously measure additional properties in single cells, including chromatin accessibility, transcription factor binding, and/or cell surface proteins are being developed at a fast pace, providing the means to exciting new advances in the near future. In this review, we briefly summarize the main findings obtained from single-cell studies of erythropoiesis, highlight outstanding questions, and suggest recent technological advances to address them.

STAT3 and SOX-5 induce BRG1-mediated chromatin remodeling of RORCE2 in Th17 cells

Retinoid-related orphan receptor gamma t (RORγt) is the lineage-specific transcription factor for T helper 17 (Th17) cells. Our previous study demonstrated that STAT3 likely participates in the activation of RORCE2 (a novel enhancer of the RORγt gene) in Th17 cells. However, the detailed mechanism is still unclear. Here, we demonstrate that both STAT3 and SOX-5 mediate the enhancer activity of RORCE2 in vitro. Deletion of the STAT3 binding site (STAT3-BS) in RORCE2 impaired RORγt expression and Th17 differentiation, resulting in reduced severity of experimental autoimmune encephalomyelitis (EAE). Mechanistically, STAT3 and SOX-5 bind the RORCE2 region and recruit the chromatin remodeling factor BRG1 to remodel the nucleosomes positioned at this region. Collectively, our data suggest that STAT3 and SOX-5 mediate the differentiation of Th17 cells through the induction of BRG1-mediated chromatin remodeling of RORCE2 in Th17 cells.

Parallel Evolution of Transcription Factors in Basal Metazoans.

Transcription factors (TFs) play a pivotal role as regulators of gene expression, orchestrating the formation and maintenance of diverse animal body plans and innovations. However, the precise contributions of TFs and the underlying mechanisms driving the origin of basal metazoan body plans, particularly in ctenophores, remain elusive. Here, we present a comprehensive catalog of TFs in 2 ctenophore species, Pleurobrachia bachei and Mnemiopsis leidyi, revealing 428 and 418 TFs in their respective genomes. In contrast, morphologically simpler metazoans have a reduced TF representation compared to ctenophores, cnidarians, and bilaterians: the sponge Amphimedon encodes 277 TFs, and the placozoan Trichoplax adhaerens encodes 274 TFs. The emergence of complex ctenophore tissues and organs coincides with significant lineage-specific diversification of the zinc finger C2H2 (ZF-C2H2) and homeobox superfamilies of TFs. Notable, the lineages leading to Amphimedon and Trichoplax exhibit independent expansions of leucine zipper (BZIP) TFs. Some lineage-specific TFs may have evolved through the domestication of mobile elements, thereby supporting alternative mechanisms of parallel TF evolution and body plan diversification across the Metazoa.

Delineating the Spectrum of Pituitary Adenoma Based on the WHO 2017 Classification.

The WHO 2017 classification of endocrine tumors incorporates lineage-specific transcription factors (TF) and hormone expression for the classification of pituitary adenoma (PA). There is paucity of reports describing the spectrum of PA based on this classification. The aim of this study was to delineate the spectrum of PA based on WHO 2017 classification of endocrine tumors. PA diagnosed in the year 2018 were studied. H and E and hormonal immunohistochemistry (IHC) for GH, PRL, ACTH, TSH, FSH, LH, CK, T-Pit and MIB-1 were performed and the results were analyzed. The cohort included 88 cases. M: F ratio was 2:1. Clinically, 22 (25%) were functional and 66 (75%) were non-functional adenomas. Amongst the clinically functional adenomas, GH secreting adenomas were the commonest (68%). Majority (83%) of non-functional adenomas were hormone positive with gonadotroph adenomas being the commonest (72.7%). Eleven (12.5%) PA were clinically and hormonally silent. Three of these showed intense nuclear T-Pit positivity, classifying them under silent corticotroph adenoma. Lineage of the remaining eight adenomas remained undetermined, since, IHC for Pit-1 and SF-1 was not performed. The aggressive adenomas identified by IHC included sparsely granulated somatotroph adenoma, Crooke cell adenoma, silent corticotroph adenoma, densely granulated lactotroph adenoma in men and constituted 17% of the PA. Four (4/88) cases were clinically invasive. A large majority of PA including aggressive adenomas can be identified by IHC. Addition of T-Pit helped to identify silent corticotroph adenoma. Pit -1 and SF-1 TF would help identify plurihormonal Pit-1 PA and null cell adenomas.

Prostate lineage-specific metabolism governs luminal differentiation and response to antiandrogen treatment

Lineage transitions are a central feature of prostate development, tumourigenesis and treatment resistance. While epigenetic changes are well known to drive prostate lineage transitions, it remains unclear how upstream metabolic signalling contributes to the regulation of prostate epithelial identity. To fill this gap, we developed an approach to perform metabolomics on primary prostate epithelial cells. Using this approach, we discovered that the basal and luminal cells of the prostate exhibit distinct metabolomes and nutrient utilization patterns. Furthermore, basal-to-luminal differentiation is accompanied by increased pyruvate oxidation. We establish the mitochondrial pyruvate carrier and subsequent lactate accumulation as regulators of prostate luminal identity. Inhibition of the mitochondrial pyruvate carrier or supplementation with exogenous lactate results in large-scale chromatin remodelling, influencing both lineage-specific transcription factors and response to antiandrogen treatment. These results establish reciprocal regulation of metabolism and prostate epithelial lineage identity.

The Influence of TET2 and/or DNMT3A Knockout on the 5hmC Levels and Growth Characteristics of Modified Human Primary CD4 T Cells after Activation

Angioimmunoblastic T-cell lymphoma (AITL) has a unique immunohistological profile featuring malignant CD4+ T follicular helper cells (Tfh) inter-mixed with an extensive infiltrate of multiple lineages of immune cells. The AITL tumor microenvironment (TME) classically features small or large B cells (variably Epstein-Barr Virus (EBV) positive), reactive CD8+ T-cells, plasma cells and proliferative high endothelial venules (HEVs). Common genetic mutations have been identified within the malignant Tfh clone in AITL including epigenetic modifiers TET2, DNMT3A, and IDH2. DNMT3A mutations in AITL occur at a frequency of 20-38.5%and most of the DNMT3A mutations occur together with TET2 mutations. Tet2/ Dnmt3a double-knockout mice show synergistic effects on the expression of lineage-specifying transcription factor genes via epigenetic mechanisms. However, it is still not clear how DNMT3A mutations enhance the effect of TET2 mutations on promoting AITL development. To investigate how TET2 and DNMT3A mutations interact in AITL development, we first generated TET2 and/or DNMT3A knockout human primary CD4-T cells with CRISPR-Cas9 mediated genome editing. TET proteins could oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmc) in replication- independent DNA demethylation. Unmethylated cytosine base can be methylated by the DNA methylation machinery (DNMT3A/B) to form 5mC, which in turn provides the substrate for TET enzymes to produce 5hmC. TET and DNMT family members are thus needed to be dynamically modulate the epigenome to maintain cellular homeostasis or alter cellular function or development. We found that in response to CD3/CD28 stimulation, WT CD4-T cells exhibited division mediated dilutional reduction in 5 hmC which was later reconstitution. However, in TET2 or DKO cells, this process was compromised, showing delayed global 5hmc levels recovery (Fig. 1A). We then investigated whether the changes in methylation dynamics would alter cellular function. When using CD3/CD28 beads stimulation (10 days/cycle), we found that after two cycles of stimulation, these CD4-T cells with different gene editing started showing distinct behaviors with proliferation and apoptosis when exposed to CD3/CD28 beads again. The TET2/ DNMT3A double knockout (DKO) CD4-T cells showed more rapid response in cell division and higher proliferation rate than the other three groups (Fig. 1B). Compared with WT cells, consistently higher apoptotic cells were found in DNMT3A-KO group, but not with either TET2-KO or DKO cells (Fig. 1C). Interestingly, withdraw of beads at the end of the 10 days cycle, DKO cells kept higher baseline proliferation level than WT cells (Fig. 1D). We then used autologous or allogeneic EBV transformed B-cell for stimulation of the CD4 T-cells after one or two cycles of CD3/28 beads stimulation, and different response kinetics were observed among these prior activated CD4-T cells with TET2 and/or DNMT3A mutations. DKO cells showed more rapid response in cell division and elevated percentages of replicated cells to either autologous or allogeneic B-cells compared with WT cells (Fig. 1E). An interesting aspect of this B/T interaction is that, even the autologous B-cells could activate a large percentage of the T-cell population, particularly in the DKO cells, so it is not likely due to specific antigen recognition but rather a non-specific stimulation by the B-cells, probably via one or more co-stimulatory molecules (ICOSL, CD86 or 4-1BBL). This may be relevant to in vivo evolution of the mutated T-cells with B-cells/activated B-cells providing support.

Epigenetic Regulation of Ameloblast Differentiation by HMGN Proteins

Dental enamel formation is coordinated by ameloblast differentiation, production of enamel matrix proteins, and crystal growth. The factors regulating ameloblast differentiation are not fully understood. Here we show that the high mobility group N (HMGN) nucleosomal binding proteins modulate the rate of ameloblast differentiation and enamel formation. We found that HMGN1 and HMGN2 proteins are downregulated during mouse ameloblast differentiation. Genetically altered mice lacking HMGN1 and HMGN2 proteins show faster ameloblast differentiation and a higher rate of enamel deposition in mice molars and incisors. In vitro differentiation of induced pluripotent stem cells to dental epithelium cells showed that HMGN proteins modulate the expression and chromatin accessibility of ameloblast-specific genes and affect the binding of transcription factors epiprofin and PITX2 to ameloblast-specific genes. Our results suggest that HMGN proteins regulate ameloblast differentiation and enamel mineralization by modulating lineage-specific chromatin accessibility and transcription factor binding to ameloblast regulatory sites.

Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity

Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.

Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells

Although lineage-specific genes have been identified in the mammary gland, little is known about the contribution of the 3D genome organization to gene regulation in the epithelium. Here, we describe the chromatin landscape of the three major epithelial subsets through integration of long- and short-range chromatin interactions, accessibility, histone modifications, and gene expression. While basal genes display exquisite lineage specificity via distal enhancers, luminal-specific genes show widespread promoter priming in basal cells. Cell specificity in luminal progenitors is largely mediated through extensive chromatin interactions with super-enhancers in gene-body regions in addition to interactions with polycomb silencer elements. Moreover, lineage-specific transcription factors appear to be controlled through cell-specific chromatin interactivity. Finally, chromatin accessibility rather than interactivity emerged as a defining feature of the activation of quiescent basal stem cells. This work provides a comprehensive resource for understanding the role of higher-order chromatin interactions in cell-fate specification and differentiation in the adult mouse mammary gland.