Profound Changes In Gene Expression Research Articles

Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells.

Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination of Lkb1 from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell-selective deletion of Lkb1 on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors (TFs) important for β-cell identity, such as FOXA, MAFA or RFX6, and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.

Abstract 3064: Distinct Regulatory Programs Govern Smooth Muscle Cell Fate In Atherosclerosis

Introduction: During atherosclerosis, some vascular smooth muscle cells (SMCs) undergo phenotypic modulation, de-differentiating and adopting a fibroblast-like (FMC) or a chondrocyte/osteoblast-like phenotype (CMC). Although FMCs and CMCs appear to occur in succession in single-cell RNAseq data, they occupy distinct locations within the lesion and are associated with protective and deleterious plaque features, respectively. Hypothesis: Smooth muscle cell transitions to FMC and CMC occur via discrete transcriptional pathways during atherosclerosis. Methods: We performed single-cell RNA-sequencing (scRNAseq) and assay for transposase-accessible chromatin with sequencing (ATAC-seq) on lineage-traced vascular SMCs isolated from the aortic root of ApoE mice (n=3). Our analysis included pseudotime and RNA velocity analyses of the scRNAseq data, which independently identified a subgroup of Vcam+Cd74+ modulated SMCs as a potential cell state from which FMCs and CMCs appear to originate, each following distinct trajectories. We explored lineage-specific gene expression using the TradeSeq R package and conducted Ingenuity Pathway Analysis on differentially expressed genes to identify relevant upstream transcription factors, which were assayed for lineage-specific motif accessibility. Results: Our analysis showed profound changes in gene expression between the two trajectories as well as differential activation and chromatin accessibility of specific transcription factors at the point where FMCs diverge from CMCs. Within the CMC lineage, we noted heightened activation and chromatin accessibility of transcription factors associated with cellular stress and inflammatory responses, including Tp53, Foxo4, and Irf1. In stark contrast, these factors exhibited diminished activity within the FMC lineage during the same pseudotime interval. Furthermore, coronary artery disease GWAS transcription factors Twist1 and Tcf21 displayed differential motif accessibility over the FMC and CMC trajectories. Conclusions: Our study provides valuable insights into the regulatory mechanisms governing SMC phenotypic transitions in atherosclerosis, and further underscores the importance of GWAS genes in influencing these transitions.

Effects of senescence on the tumour microenvironment and response to therapy.

Cellular senescence is a state of durable cell arrest that has been identified both in vitro and in vivo. It is associated with profound changes in gene expression and a specific secretory profile that includes pro-inflammatory cytokines, growth factors and matrix-remodelling enzymes, referred to as the senescence-associated secretory phenotype (SASP). In cancer, senescence can have anti- or pro-tumour effects. On one hand, it can inhibit tumour progression in a cell autonomous manner. On the other hand, senescence can also promote tumour initiation, progression, metastatic dissemination and resistance to therapy in a paracrine manner. Therefore, despite efforts to target senescence as a potential strategy to inhibit tumour growth, senescent cancer and microenvironmental cells can eventually lead to uncontrolled proliferation and aggressive tumour phenotypes. This can happen either through overcoming senescence growth arrest or through SASP-mediated effects in adjacent tumour cells. This review will discuss how senescence affects the tumour microenvironment, including extracellular matrix remodelling, the immune system and the vascular compartment, to promote tumourigenesis, metastasis and resistance to DNA-damaging therapies. It will also discuss current approaches used in the field to target senescence: senolytics, improving the immune clearance of senescent cells and targeting the SASP.

Chemical Inhibition of Bromodomain Proteins in Insect-Stage African Trypanosomes Perturbs Silencing of the Variant Surface Glycoprotein Repertoire and Results in Widespread Changes in the Transcriptome.

The eukaryotic protozoan parasite Trypanosoma brucei is transmitted by the tsetse fly to both humans and animals, where it causes a fatal disease called African trypanosomiasis. While the parasite lacks canonical DNA sequence-specific transcription factors, it does possess histones, histone modifications, and proteins that write, erase, and read histone marks. Chemical inhibition of chromatin-interacting bromodomain proteins has previously been shown to perturb bloodstream specific trypanosome processes, including silencing of the variant surface glycoprotein (VSG) genes and immune evasion. Transcriptomic changes that occur in bromodomain-inhibited bloodstream parasites mirror many of the changes that occur as parasites developmentally progress from the bloodstream to the insect stage. We performed transcriptome sequencing (RNA-seq) time courses to determine the effects of chemical bromodomain inhibition in insect-stage parasites using the compound I-BET151. We found that treatment with I-BET151 causes large changes in the transcriptome of insect-stage parasites and also perturbs silencing of VSG genes. The transcriptomes of bromodomain-inhibited parasites share some features with early metacyclic-stage parasites in the fly salivary gland, implicating bromodomain proteins as important for regulating transcript levels for developmentally relevant genes. However, the downregulation of surface procyclin protein that typically accompanies developmental progression is absent in bromodomain-inhibited insect-stage parasites. We conclude that chemical modulation of bromodomain proteins causes widespread transcriptomic changes in multiple trypanosome life cycle stages. Understanding the gene-regulatory processes that facilitate transcriptome remodeling in this highly diverged eukaryote may shed light on how these mechanisms evolved. IMPORTANCE The disease African trypanosomiasis imposes a severe human and economic burden for communities in sub-Saharan Africa. The parasite that causes the disease is transmitted to the bloodstream of a human or ungulate via the tsetse fly. Because the environments of the fly and the bloodstream differ, the parasite modulates the expression of its genes to accommodate two different lifestyles in these disparate niches. Perturbation of bromodomain proteins that interact with histone proteins around which DNA is wrapped (chromatin) causes profound changes in gene expression in bloodstream-stage parasites. This paper reports that gene expression is also affected by chemical bromodomain inhibition in insect-stage parasites but that the genes affected differ depending on life cycle stage. Because trypanosomes diverged early from model eukaryotes, an understanding of how trypanosomes regulate gene expression may lend insight into how gene-regulatory mechanisms evolved. This could also be leveraged to generate new therapeutic strategies.

Abstract 4744: Epigenetic reprogramming induced by lipids fosters mammary cell plasticity in non-transformed breast epithelial cells

Abstract Introduction. Lipid exposure of non-transformed breast epithelial cells results in increased flux modifications, and profound changes in gene expression. The upregulated genes are involved in stemness, neural development, and neural crest pathways. Neural genes are highly expressed in an estrogen receptor negative breast cancer (ERnegBC): the triple negative subtype. We aim to identify mechanisms that link lipids and epigenetic reprogramming to the genesis of ERnegBC. Methods. Non-transformed MCF-10A cells exposed to octanoic acid (OA) were utilized for U13C-glucose tracing. S-adenosylmethionine (SAM), 2-HG and other metabolites were analyzed following treatment with OA ± PHGDH inhibitor. CUT&RUN for H3K4me3 and H3K27me3 was performed, and genes affected by OA (PMID: 28263391) were compared with OA-responsive peaks. OA-induced genes with CUT&RUN peaks were measured in breast organoids derived from reduction mammoplasty samples exposed to OA. The Aldefluour assay was used to identify stem-like (ALDH+) cells. Results. U13C-glucose tracing in presence of OA showed decreased glucose uptake, glycolysis and pentose phosphate pathway flux, with little effect on the TCA cycle. One-carbon (1C)-THF was redirected to the methionine cycle increasing flux to methylation. The methyl donor SAM and the demethylase inhibitor 2-HG increased after 15- and 30-min OA exposure, respectively; PHGDH inhibitor blocked these increases likely via effects on 1C metabolism. H3K4me3 CUT&RUN revealed 661 differential peaks (FDR < 0.05) comparing OA to control. The genes associated with these peaks are involved in neuron differentiation, neural crest, EMT and neural genes expressed in ERnegBC. 73% of H3K4me3 OA-associated peaks were in regulatory regions of OA-induced genes (FDR < 0.01), including NGFR (log2FC = 11.7), NGF (log2FC = 8), NTRK1 (log2FC = 2.1). OA-induced genes with enriched H3K4me3 peaks were also upregulated in breast organoids exposed to OA, such as NGFR (FC = 2.2), NGF (FC = 4.7), NTRK1 (FC = 6.6). Motif analysis revealed an overrepresentation of transcription factors (p < 0.05) associated with EMT (Zeb1, Slug), neural functions (E2A, AP1, JunB), neuronal-injury (Atf3) and stress response (Chop, Atf4). Twelve H3K27me3 peaks were enriched in control (FDR < 0.05) and associated with increased gene expression in OA, among them were LGR6 (log2FC = 1.9), a gene associated with ERnegBC and PLAG1 (log2FC = 2.8) a stem cell marker. ALDH+ cells’ percentage increased by at least 10% after OA exposure. Conclusions. Lipid exposure affects the production of SAM and 2-HG, which results in epigenetic fostered plasticity, leading to reprogramming/selecting cells with a multi-potential embryonic or stem-like state and/or differentiation to a neural/neural crest-like state which may facilitate ERnegBC genesis. Citation Format: Mariana Bustamante Eduardo, Gannon Cottone, Shiyu Liu, Seema Khan, Susan Clare. Epigenetic reprogramming induced by lipids fosters mammary cell plasticity in non-transformed breast epithelial cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4744.

Experimental life history evolution results in sex-specific evolution of gene expression in seed beetles.

The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in ageing, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of ageing in each sex.

Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression

Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.

Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers.

Cancer is a disease of gene dysregulation, where cells acquire somatic and epigenetic alterations that drive aberrant cellular signaling. These alterations adversely impact transcriptional programs and cause profound changes in gene expression. Interpreting somatic alterations within context-specific transcriptional programs will facilitate personalized therapeutic decisions but is a monumental task. Toward this goal, we develop a partially interpretable neural network model called Chromatin-informed Inference of Transcriptional Regulators Using Self-attention mechanism (CITRUS). CITRUS models the impact of somatic alterations on transcription factors and downstream transcriptional programs. Our approach employs a self-attention mechanism to model the contextual impact of somatic alterations. Furthermore, CITRUS uses a layer of hidden nodes to explicitly represent the state of transcription factors (TFs) to learn the relationships between TFs and their target genes based on TF binding motifs in the open chromatin regions of tumor samples. We apply CITRUS to genomic, transcriptomic, and epigenomic data from 17 cancer types profiled by The Cancer Genome Atlas. CITRUS predicts patient-specific TF activities and reveals transcriptional program variations between and within tumor types. We show that CITRUS yields biological insights into delineating TFs associated with somatic alterations in individual tumors. Thus, CITRUS is a promising tool for precision oncology.

Epigenetic Modulation of Opioid Receptors by Drugs of Abuse.

Chronic exposure to drugs of abuse produces profound changes in gene expression and neural activity associated with drug-seeking and taking behavior. Dysregulation of opioid receptor gene expression is commonly observed across a variety of abused substances including opioids, cocaine, and alcohol. Early studies in cultured cells showed that the spatial and temporal gene expression of opioid receptors are regulated by epigenetic mechanisms including DNA and histone modifications and non-coding RNAs. Accumulating evidence indicate that drugs of abuse can modulate opioid receptor gene expression by targeting various epigenetic regulatory networks. Based on current cellular and animal models of substance use disorder and clinical evidence, this review summarizes how chronic drug exposure alters the gene expression of mu, delta, kappa, and nociceptin receptors via DNA and histone modifications. The influence of drugs of abuse on epigenetic modulators, such as non-coding RNAs and transcription factors, is also presented. Finally, the therapeutic potential of manipulating epigenetic processes as an avenue to treat substance use disorder is discussed.

SET domain containing 2 (SETD2) influences metabolism and alternative splicing during myogenesis.

Epigenetic regulatory mechanisms are increasingly recognized as crucial determinants of cellular specification and differentiation. During muscle cell differentiation (myogenesis), extensive remodelling of histone acetylation and methylation occurs. Several of these histone modifications aid in the expression of muscle-specific genes and the silencing of genes that block lineage commitment. Therefore, the identification of new epigenetic regulatory mechanisms is of high interest. Still, the functional relevance of numerous histone modifications during myogenesis remain completely uncertain. In this study, we focus on the function of H3K36me3 and its epigenetic writer, SET domain containing 2 (SETD2), in the context of muscle cell differentiation. We first observed that SETD2 expression increases during myogenesis. Targeted depletion of SETD2 in undifferentiated (myoblasts) and differentiated (myotubes) muscle cells reduced H3K36me3 levels and induced profound changes in gene expression and slight alterations in alternative splicing, as determined by deep RNA-sequencing analysis. Enzymes that function in metabolic pathways were upregulated in response to SETD2 depletion. Furthermore, we demonstrated that upregulation of several glycolytic enzymes was associated with an increase in intracellular pyruvate levels in SETD2-depleted cells, indicating a novel role for SETD2 in metabolic programming during myogenesis. Together, our results provide new insight into the signalling pathways controlled by chromatin-modifying enzymes and their associated histone modifications during muscle cell differentiation.

Abstract 3508: Exosome-mediated delivery of antisense oligonucleotides targeting C/EBPβ reprograms tumor-associated macrophages and induces potent single agent anti-tumor activity

Abstract Background: Tumor-associated macrophages (TAMs) and myeloid derived suppressor cells (MDSCs) promote an immunosuppressive milieu by inhibiting T-cell activation and recruitment, leading to resistance to immune checkpoint therapies. Interleukin 10 (IL10) and prostaglandin E2 (PGE2) promote tumor initiation and spread, in part, through TAM polarization and MDSC recruitment. C/EBPβ is a critical transcription factor that regulates the immunosuppressive state of TAMs and MDSCs and is activated by IL10 and PGE2 signaling. We developed a proprietary engineered exosome loaded with antisense oligonucleotides (ASOs) targeting C/EBPβ (exoASO-C/EBPβ), that selectively delivers ASO to TAMs and MDSCs, thereby inhibiting C/EBPβ expression and inducing reprogramming from an immunosuppressive (M2) to a pro-inflammatory (M1) phenotype. Results: exoASO-C/EBPβ demonstrated dose-dependent target gene knockdown (KD) in primary human M2 macrophages in vitro with a 2-fold higher potency (IC50) compared to free ASO. C/EBPβ KD resulted in profound changes in gene expression and cytokine secretion profile consistent with reprogramming to a M1 phenotype. exoASO-C/EBPβ induced a significant induction of pro-inflammatory cytokines, in M2 macrophages generated with IL10 or PGE2, both of which show prominent activation of the C/EBPβ pathway. Biodistribution in tumor-bearing mice (IT and IV) demonstrate selective uptake by MDSCs and TAMs. Intra-tumoral (IT) administration of exoASO-C/EBPβ in CT26 tumors resulted in a significantly higher KD of C/EBPβ in tumor-associated CD11b+ cells, as compared to CD11b- cells. Additionally, exoASO-C/EBPβ induced changes in Nos2, CD206 and Csf1r mRNA expression in CD11b+ cells, demonstrating in vivo M2 to M1 reprogramming. Furthermore, IT microinjections of exoASO-C/EBPβ in YUMM1.7 tumor-bearing mice resulted in a significant induction of pro-inflammatory M1 markers TNFα and iNOS, in contrast, free C/EBPβ ASO showed limited increase in M1 markers. exoASO-C/EBPβ administered IT as a single agent demonstrated significant anti-tumor activity in multiple tumor models including: the CT26-colorectal cancer (60% complete responses (CRs)), MB49-bladder cancer (70% CRs) and B16F10-melanoma (30% CRs). Combination treatment with anti-PD1 in all these models further increased the anti-tumor efficacy. Finally, we used a myeloid cell specific C/EBPβ/PGE2/IL10 gene signature to identify cancer indications where exoASO-C/EBPβ therapy might have the most therapeutic significance. Conclusion: exoASO-C/EBPβ is a novel therapeutic candidate that selectively targets and attenuates a critical transcription factor in immunosuppressive myeloid cells, resulting in reprogramming of TAMs and potent anti-tumor activity across multiple TAM-rich mouse models as a monotherapy. Citation Format: Sushrut Kamerkar, Charan Leng, Olga Burenkova, SuChul Jang, Kelvin Zhang, Yanyan Liu, William Dahlberg, Kyriakos Economides, Timothy Soos, Dalia Burzyn, Sriram Sathyanarayanan. Exosome-mediated delivery of antisense oligonucleotides targeting C/EBPβ reprograms tumor-associated macrophages and induces potent single agent anti-tumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3508.

Abstract 5675: Pathological crosstalk between osteocytes and breast cancer cells in bone metastasis

Abstract Bone provides an ideal niche for breast cancer cells (BCa) to reside and proliferate and is a frequent site of BCa metastasis. Osteocytes are the most abundant skeletal cells and permanent residents of bone. However, the role of osteocytes in BCa bone metastasis remains understudied. Here, we investigated the crosstalk between metastatic BCa cells and osteocytes. In vitro cultures revealed that conditioned media (CM) derived from metastatic E0771 BCa cells decreased by 50% the number of alive MLO-A5 and MLO-Y4 osteocyte-like cell lines. BCa cells modestly increased osteocyte apoptosis (2% vs. 6%, alone vs. exposed to BCa, respectively). Treatment with DEVD, a caspase 3 inhibitor, blocked osteocyte apoptosis but did not prevent the decrease in osteocytes induced by BCa. Thus, we studied osteocyte senescence, a process that causes irreversible cell cycle arrest and profound changes in gene expression. We found that BCa-CM upregulated the expression of markers of senescence markers (p16, p21) and senescence-associated secretory phenotype (Mmp13, Mmp9, Vcam-1) in osteocyte-like cell lines. Similarly, BCa-CM increased the expression of senescent markers in ex vivo bone organ cultures containing primary osteocytes. Osteocytes increased BCa cell proliferation by increasing cyclin D1 expression Through both cell-to-cell interactions and secretion of soluble factors., osteocytes increased BCa cell proliferation by increasing cyclin D1 expression. Moreover, osteocyte-derived CM stimulated BCa cells migration and invasion capabilities and upregulated the expression of genes involved in migration (Vcam-1 and N-cadherin). Co-culture with stromal cells also stimulated BCa cell proliferation, invasion, and migration. However, the increases induced by stromal cells were four-fold lower than those seen with osteocytes. Overall, our results suggest that BCa cells reprogram osteocytes, which acquire a senescent phenotype, whereas osteocytes produce factors that stimulate tumor growth, migration, and invasion. Together, these findings support the existence of a crosstalk between osteocytes and BCa cells in the metastatic niche that favors the progression of breast cancer in bone. Future studies are warranted to examine the contribution of osteocyte senescence and osteocytes-derived factors in animal models of breast cancer metastasis. Citation Format: Manish Adhikari, Hayley Sabol, Aric anloague, Sharmin Khan, Jesus Delgado-Calle. Pathological crosstalk between osteocytes and breast cancer cells in bone metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5675.

Single-cell transcriptomics uncovers the impacts of titanium dioxide nanoparticles on human bone marrow stromal cells

Titanium dioxide nanoparticles (TiO2 NPs) have attracted substantial attention in various applications, including environmental remediation and nanomedicine. A detailed understanding of the toxicity of TiO2 NPs and the underlying mechanisms is fundamental to further development of their environmental and biomedical applications. Herein, we determined the changes in the transcriptional profile of human bone marrow stromal cells (BMSCs) after a set of different sized TiO2 NPs exposure using single-cell RNA-seq (scRNA-seq). By taking advantage of sensitivity of scRNA-seq, we found that TiO2 NPs exposure led to profound changes in gene expression and DNA damage signaling played a pivotal role in cellular responses to TiO2 NPs exposure. Smaller TiO2 NPs (5, 14 nm) led to a response similar to antivirus defense, and bigger TiO2 NPs (54, 135, and 228 nm) induced proliferation and differentiation changes in transcriptional levels. Validation experiments on representative genes showed that some genes might be served as biomarkers of TiO2 NPs exposure. Furthermore, in vitro and in vivo analyses showed remarkable over-production of reactive oxygen species (ROS) but did not affect osteogenic differentiation potential in BMSCs. The results unveiled landscape changes in transcriptomes in BMSCs induced by TiO2 NPs, which provides new insights into toxicity assessments of nanomaterials.

Profound gene expression changes in the epithelial monolayer of active ulcerative colitis and Crohn's disease.

In recent years it has become apparent that the epithelium is highly involved in inflammatory bowel disease (IBD) pathophysiology. The majority of gene expression studies of IBD are generated from heterogeneous biopsies, providing no distinction between immune cells, the epithelium and other mucosal cells. By using laser capture microdissection (LCM) coupled with RNA sequencing, we aimed to characterize the expressional changes of the isolated colonic epithelial monolayer from ulcerative colitis (UC) and Crohn’s disease (CD) patients compared to healthy controls (HC). The analysis identified 3706 genes as differentially expressed between active IBD epithelium and HC. Weighted gene co-expression network analysis was used to stratify genes into modules, which were subsequently characterized using enrichment analysis. Our data show a distinct upregulation of the antigen presentation machinery during inflammation, including major histocompatibility complex class II molecules (e.g. HLA-DPA1, HLA-DPB1, HLA-DRA) and key transcription factors/activators (STAT1, IRF1, CIITA). We also see an epithelial downregulation of retinoic acid-responsive nuclear receptors (RARA, RARB, RXRA), but upregulation of retinoid-metabolizing enzymes (RDH11, ALDH1A2, ALDH1A3), which together suggest a perturbation of epithelial vitamin A signaling during active IBD. Lastly, we identified a cluster of stress-related genes, including activator protein 1 components JUNB and ATF3, as significantly upregulated in active UC but not in CD, revealing an interesting aspect of IBD heterogeneity. The results represent a unique resource for enhanced understanding of epithelial involvement in IBD inflammation and is a valuable tool for further studies on these processes.

Abstract P5-05-05: Unraveling the mechanism of Lipid-induced malignant transformation in non-transformed breast epithelial cells

Abstract Introduction. With the goal of defining the in-breast environment that facilitates the development of estrogen receptor negative (ER-) breast cancer (BC), we have previously identified a set of genes involved in lipid metabolism with increased expression in the contralateral unaffected breast of women with ER- BC (PMID: 28263391). MCF-10A cells exposed to lipids in vitro display profound changes in gene expression, chromatin packing density, chromatin accessibility and histone posttranslational modifications (PTMs). In addition, flux through thirty-eight metabolic reactions was significantly increased by this exposure, including those of the electron transport chain (ETC). However, the mechanisms by which lipids induce molecular changes that result in epigenomic reprogramming, and potentially promote malignant transformation remain to be elucidated. We hypothesized that dysfunction of the ETC and increased serine, glycine, one carbon (SGOC) metabolism pathway activity play a role in the modulation of epigenetics. Methods. To interrogate potential mechanisms that link lipids to ER- BC genesis, estrogen and progesterone receptor negative MCF-10A cells were cultured in MEBM/MEGM and exposed to vehicle, octanoic acid (C8) or linoleic acid (C18) for 24 hours. Histone PTMs were assayed by liquid chromatography-mass spectrometry. Gene expression was measured by RNA-seq and differentially expressed genes between vehicle and lipid treated groups were identified using the DESeq2 R package. ATAC-seq was performed to study chromatin accessibility. MCF-10A cells were exposed to C8 in presence or absence of inhibitors of Complex I (Metformin) and Complex III (Antimycin A) of the ETC. Real-time qPCR was performed to measure epigenetic modulators, Unfolded Protein Response (UPR) pathway and SGOC metabolism genes. Results. Histone PTMs changed significantly following 24 hours exposure to C8 or C18. Exposure to C8 resulted in the modulation of the expression of genes involved in the UPR/recognition of mitochondrial dysfunction (ATF4), de novo serine biosynthesis (PHGDH, PSAT1, SPH) and one-carbon metabolism (SHMT2, MTHFD2) pathways as well as numerous genes coding for epigenetic modulators. Upon C18 exposure, the binding motif for ATF4 was among the most significantly enriched motifs in the open chromatin regions and p53 was among the motifs with significantly decreased accessibility. Interestingly ATF4 actives PHGDH expression while p53 suppresses it. Exposure to C8 in presence of ETC inhibitors affected gene expression in the same direction as lipid exposure and co-treatment had an additive effect. Fatty acid oxidation and inhibition of the ETC increased the expression of PHGDH: C8, 2.6-fold (p-value = 0.005); Metformin, 2.3-fold (p-value = 0.0052); Antimycin A, 5.1-fold (p-value < 0.0001); C8 plus Metformin, 5.3-fold (p-value < 0.0001), and C8 plus Antimycin A, 5.2-fold (p-value < 0.0001). Conclusions. The modulation of epigenetic effectors does not appear to be a consequence of increased flux through the ETC but rather a consequence of increased SGOC metabolism, and the methionine cycle. Our in vitro model shows that lipid-induced stress increases ATF4 expression. ATF4 controls the expression of PHGDH, PSAT1, SPH, SHMT2 and MTHFD2 which influences epigenetics through S-adenosyl methionine production, the major methyl donor. PHGDH overexpression appears to be the key in our model as it has been associated with ER- BC and its engineered overexpression in non-transformed breast cells causes alterations associated with malignant transformation. The increase in PDGDH expression is hypothesized to compensate for mitochondrial dysfunction and to restore redox homeostasis by producing precursors that can be used for the production of antioxidants, such as glutathione. Citation Format: Mariana Bustamante Eduardo, Shivangi Yadav, Seema Khan, Susan Clare. Unraveling the mechanism of Lipid-induced malignant transformation in non-transformed breast epithelial cells [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-05-05.

2D-DIGE proteomic analysis of blood plasma reveals changes in immune- and stress-associated proteins following hormonal stimulation of carp males

In carp aquaculture, hormonal manipulation with an analog of GnRH (Ovopel) and carp pituitary extract (CPE), which act at different levels of the hypothalamic-pituitary-gonadal axis, is a routine practice to enhance sperm production. Our recent studies revealed that hormonal stimulation of male carp was associated with changes in the seminal plasma proteome, including blood origin proteins. Here, we explored whether Ovopel and CPE could affect the blood proteome of male carp. Both preparations induced increases in semen volume, total number of sperm, and testosterone level. However, hormonal stimulation did not affect the plasma cortisol and glucose levels. A comparative proteomic analysis of carp blood plasma between the control (PBS) and the hormonally treated males revealed significant changes (>1.2 <−1.2-fold change, P < 0.05) in the abundance of 30 spots (14 up- and 16 downregulated) and 44 spots (28 up- and 16 downregulated) upon CPE and Ovopel treatment, respectively. The most significantly affected pathways were acute phase response signaling, the coagulation system, LXR/RXR and FXR/RXR activation; however, there were different sets of proteins in Ovopel- and CPE-treated males. The majority of differentially abundant proteins were involved in the regulation of the immune defense response, the response to stress, and complement activation. Moreover hormonal stimulation with CPE markedly increased the bactericidal activity of blood and both preparations caused profound changes in gene expression in hematopoietic organs. This work is important in understanding the biological processes behind the protein-based response to hormonal stimulation of sperm production in fish.

Pervasive compartment-specific regulation of gene expression during homeostatic synaptic scaling

Synaptic scaling is a form of homeostatic plasticity which allows neurons to adjust their action potential firing rate in response to chronic alterations in neural activity. Synaptic scaling requires profound changes in gene expression, but the relative contribution of local and cell-wide mechanisms is controversial. Here we perform a comprehensive multi-omics characterization of the somatic and process compartments of primary rat hippocampal neurons during synaptic scaling. We uncover both highly compartment-specific and correlating changes in the neuronal transcriptome and proteome. Whereas downregulation of crucial regulators of neuronal excitability occurs primarily in the somatic compartment, structural components of excitatory postsynapses are mostly downregulated in processes. Local inhibition of protein synthesis in processes during scaling is confirmed for candidate synaptic proteins. Motif analysis further suggests an important role for trans-acting post-transcriptional regulators, including RNA-binding proteins and microRNAs, in the local regulation of the corresponding mRNAs. Altogether, our study indicates that, during synaptic scaling, compartmentalized gene expression changes might co-exist with neuron-wide mechanisms to allow synaptic computation and homeostasis.

Endothelial Reprogramming Stimulated by Oncostatin M Promotes Inflammation and Tumorigenesis in VHL-Deficient Kidney Tissue.

Clear-cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma (RCC), and its progression has been linked to chronic inflammation. About 70% of the ccRCC cases are associated with inactivation of the von Hippel-Lindau (VHL) tumor-suppressor gene. However, it is still not clear how mutations in VHL, encoding the substrate-recognition subunit of an E3 ubiquitin ligase that targets the alpha subunit of hypoxia-inducible factor-α (HIFα), can coordinate tissue inflammation and tumorigenesis. We previously generated mice with conditional Vhlh knockout in kidney tubules, which resulted in severe inflammation and fibrosis in addition to hyperplasia and the appearance of transformed clear cells. Interestingly, the endothelial cells (EC), although not subject to genetic manipulation, nonetheless showed profound changes in gene expression that suggest a role in promoting inflammation and tumorigenesis. Oncostatin M (OSM) mediated the interaction between VHL-deficient renal tubule cells and the ECs, and the activated ECs in turn induced macrophage recruitment and polarization. The OSM-dependent microenvironment also promoted metastasis of exogenous tumors. Thus, OSM signaling initiates reconstitution of an inflammatory and tumorigenic microenvironment by VHL-deficient renal tubule cells, which plays a critical role in ccRCC initiation and progression. SIGNIFICANCE: A novel mechanism of cross-talk between ECs and VHL-deficient kidney tubules that stimulates inflammation and tumorigenesis is discovered, suggesting OSM could be a potential target for ccRCC intervention.

HCV eradication with IFN-based therapy does not completely restore gene expression in PBMCs from HIV/HCV-coinfected patients

ObjectiveTo evaluate the impact of hepatitis C virus (HCV) elimination via interferon (IFN)-based therapy on gene expression profiles related to the immune system in HIV/HCV-coinfected patients.MethodsWe conducted a prospective study in 28 HIV/HCV-coinfected patients receiving IFN-based therapy at baseline (HIV/HCV-b) and week 24 after sustained virological response (HIV/HCV-f). Twenty-seven HIV-monoinfected patients (HIV-mono) were included as a control. RNA-seq analysis was performed on peripheral blood mononuclear cells (PBMCs). Genes with a fold-change (FC) ≥ 1.5 (in either direction) and false discovery rate (FDR) ≤ 0.05 were identified as significantly differentially expressed (SDE).ResultsHIV/HCV-b showed six SDE genes compared to HIV-mono group, but no significantly enriched pathways were observed. For HIV/HCV-f vs. HIV/HCV-b, we found 58 SDE genes, 34 upregulated and 24 downregulated in the HIV/HCV-f group. Of these, the most overexpressed were CXCL2, PDCD6IP, ATP5B, IGSF9, RAB26, and CSRNP1, and the most downregulated were IFI44 and IFI44L. These 58 SDE genes revealed two significantly enriched pathways (FDR < 0.05), one linked to Epstein-Barr virus infection and another related to p53 signaling. For HIV/HCV-f vs. HIV-mono group, we found 44 SDE genes that revealed 31 enriched pathways (FDR < 0.05) related to inflammation, cancer/cell cycle alteration, viral and bacterial infection, and comorbidities associated with HIV/HCV-coinfection. Five genes were overrepresented in most pathways (JUN, NFKBIA, PIK3R2, CDC42, and STAT3).ConclusionHIV/HCV-coinfected patients who eradicated hepatitis C with IFN-based therapy showed profound gene expression changes after achieving sustained virological response. The altered pathways were related to inflammation and liver-related complications, such as non-alcoholic fatty liver disease and hepatocellular carcinoma, underscoring the need for active surveillance for these patients.

Autocrine Leukemia Inhibitory Factor Promotes Esophageal Squamous Cell Carcinoma Progression via Src Family Kinase-Dependent Yes-Associated Protein Activation.

The IL6 family of cytokines, including IL6 and leukemia-inhibitory factor (LIF), are induced during inflammation and are also expressed in many types of cancer where they play an important role in tumor development. IL6 family cytokines mainly activate the JAK-STAT3 pathway via the coreceptor, gp130, and IL6 is known to activate the Src family kinase (SFK)-Yes-associated protein (YAP) pathway. The current study investigated the role of autocrine LIF in human esophageal squamous cell carcinoma (ESCC) that highly expresses LIF. LIF knockdown had various effects on cancer cells, including profound changes in gene expression, suppression of cell proliferation, migration/invasion and sphere formation, and induction of apoptosis. Similar to IL6, LIF activated the SFK-YAP pathway as well as the JAK-STAT3 pathway. LIF-induced YAP activation was more important for cancer cell proliferation than LIF-induced STAT3 activation, and concomitant YAP and STAT3 activation completely compensated for the role of LIF in human ESCC growth. We also confirmed that SFK activation and LIF expression were correlated with YAP activation in human ESCC clinical samples. Furthermore, simultaneous inhibition of the SFK-YAP and JAK-STAT3 pathways in human ESCC cells was more effective at suppressing cell proliferation than single inhibition, and autocrine LIF signaling promoted human ESCC growth in vivo. Therefore, the LIF-SFK-YAP axis may represent a new therapeutic target for human ESCC. IMPLICATIONS: Autocrine LIF signaling promotes human ESCC progression via SFK-dependent YAP activation and is a new potential target of treatment for human ESCC.