Brd4-bound enhancers drive cell intrinsic sex differences in glioblastoma

Brd4-bound enhancers drive cell-intrinsic sex differences in glioblastoma

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2017148118 ◽

2021 ◽

Vol 118 (16) ◽

pp. e2017148118

Author(s):

Najla Kfoury ◽

Zongtai Qi ◽

Briana C. Prager ◽

Michael N. Wilkinson ◽

Lauren Broestl ◽

...

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Stem Cell ◽

Cell Function ◽

Expression Patterns ◽

Tumor Biology ◽

Male And Female ◽

Bet Inhibitors ◽

Human Gbm

Sex can be an important determinant of cancer phenotype, and exploring sex-biased tumor biology holds promise for identifying novel therapeutic targets and new approaches to cancer treatment. In an established isogenic murine model of glioblastoma (GBM), we discovered correlated transcriptome-wide sex differences in gene expression, H3K27ac marks, large Brd4-bound enhancer usage, and Brd4 localization to Myc and p53 genomic binding sites. These sex-biased gene expression patterns were also evident in human glioblastoma stem cells (GSCs). These observations led us to hypothesize that Brd4-bound enhancers might underlie sex differences in stem cell function and tumorigenicity in GBM. We found that male and female GBM cells exhibited sex-specific responses to pharmacological or genetic inhibition of Brd4. Brd4 knockdown or pharmacologic inhibition decreased male GBM cell clonogenicity and in vivo tumorigenesis while increasing both in female GBM cells. These results were validated in male and female patient-derived GBM cell lines. Furthermore, analysis of the Cancer Therapeutic Response Portal of human GBM samples segregated by sex revealed that male GBM cells are significantly more sensitive to BET (bromodomain and extraterminal) inhibitors than are female cells. Thus, Brd4 activity is revealed to drive sex differences in stem cell and tumorigenic phenotypes, which can be abrogated by sex-specific responses to BET inhibition. This has important implications for the clinical evaluation and use of BET inhibitors.

Download Full-text

In vivo effects of olive oil and trans-fatty acids on miR-134, miR-132, miR-124-1, miR-9-3 and mTORC1 gene expression in a DMBA-treated mouse model

PLoS ONE ◽

10.1371/journal.pone.0246022 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0246022

Author(s):

Richard Molnar ◽

Laszlo Szabo ◽

Andras Tomesz ◽

Arpad Deutsch ◽

Richard Darago ◽

...

Keyword(s):

Gene Expression ◽

Fatty Acids ◽

Cell Membrane ◽

Olive Oil ◽

Trans Fatty Acids ◽

Expression Patterns ◽

Tumor Biology ◽

The Many ◽

In Vivo Effects

Both the intake of beneficial olive oil and of harmful trans-fatty acids (TFAs) in consumed foods are of great significance in tumor biology. In our present study we examined the effects they exert on the expression patterns of miR-134, miR-132, miR-124-1, miR-9-3 and mTOR in the liver, spleen and kidney of mice treated with 7,12-dimethylbenz [a] anthracene (DMBA). Feeding of TFA-containing diet significantly increased the expression of all studied miRs and mTORC1 in all organs examined, except the expression of mTORC1 in the spleen and kidney. Diet containing olive oil significantly reduced the expression of miR-124-1, miR-9-3 and mTORC1 in the liver and spleen. In the kidney, apart from the mTORC1 gene, the expression of all miRs examined significantly decreased compared to the DMBA control. According to our results, the cell membrane protective, antioxidant, and anti-inflammatory effects of olive oil and the cell membrane damaging, inflammatory, and carcinogenic properties of TFA suggest negative feedback regulatory mechanisms. In contrast to our expectations, mTORC1 gene expression in the kidney has not been shown to be an appropriate biomarker–presumably, because the many complex effects that regulate mTOR expression may quench each other.

Download Full-text

A Comparison of Gene Expression Signatures from Breast Tumors and Breast Tissue Derived Cell Lines

Disease Markers ◽

10.1155/2001/850531 ◽

2001 ◽

Vol 17 (2) ◽

pp. 99-109 ◽

Cited By ~ 83

Author(s):

Douglas T. Ross ◽

Charles M. Perou

Keyword(s):

Gene Expression ◽

Cell Line ◽

Cell Lines ◽

Cell Biology ◽

Expression Patterns ◽

Tumor Biology ◽

Clinical Samples ◽

Analysis Tool

Cell lines derived from human tumors have historically served as the primary experimental model system for exploration of tumor cell biology and pharmacology. Cell line studies, however, must be interpreted in the context of artifacts introduced by selection and establishment of cell linesin vitro. This complication has led to difficulty in the extrapolation of biology observed in cell lines to tumor biologyin vivo. Modern genomic analysis tool like DNA microarrays and gene expression profiling now provide a platform for the systematic characterization and classification of both cell lines and tumor samples. Studies using clinical samples have begun to identify classes of tumors that appear both biologically and clinically unique as inferred from their distinctive patterns of expressed genes. In this review, we explore the relationships between patterns of gene expression in breast tumor derived cell lines to those from clinical tumor specimens. This analysis demonstrates that cell lines and tumor samples have distinctive gene expression patterns in common and underscores the need for careful assessment of the appropriateness of any given cell line as a model for a given tumor subtype.

Download Full-text

Socs2 Is Dispensable for BCR/ABL1-Induced Chronic Myeloid Leukemia-Like Disease in Mice and for Normal Hematopoietic Stem Cell Function,

Blood ◽

10.1182/blood.v118.21.3743.3743 ◽

2011 ◽

Vol 118 (21) ◽

pp. 3743-3743

Author(s):

Nils Hansen ◽

Helena Agerstam ◽

Martin Wahlestedt ◽

Mats Ehinger ◽

Petra Johnels ◽

...

Keyword(s):

Gene Expression ◽

Stem Cell ◽

Myeloid Leukemia ◽

Cell Function ◽

Cytokine Signaling ◽

Wild Type ◽

Hematopoietic Stem ◽

Cell Counts ◽

Blood Cell Counts

Abstract Abstract 3743 Background: The P210 BCR/ABL1 fusion protein initiates signaling through several down stream pathways such as STAT5, PI3K, AKT, RAS, and WNT. However, only few down stream mediators have so far been thoroughly studied in vivo in the context of BCR/ABL1-mediated induction of CML-like disorder in mice deficient for the specific genes. Suppressor of cytokine signaling 2 (SOCS2) is known as a feedback inhibitor of cytokine signaling, a negative regulator of the STAT5 pathway, and is markedly upregulated in primary bone marrow cells from patients with chronic myeloid leukemia (CML). However, it has not been clear whether SOCS2 is involved in BCR/ABL1 induced cell transformation or whether it is important for normal hematopoietic stem cell (HSC) function. Methods: To evaluate the stem cell function of Socs2, HSCs from wild type and Socs2 deficient mice were competitively transplanted into lethally irradiated recipients. Blood chimerism and lineage distribution were analyzed by flow cytometry at 4 and 18 weeks after transplantation. To investigate the potential role of Socs2 in CML, c-kit enriched Socs2(−/−) and wild type cells were transduced with a BCR/ABL1 expressing retroviral vector and transplanted into lethally irradiated recipients. The in vivo development of malignant disease was analyzed by peripheral blood cell counts and, upon euthanization, by flow cytometry and histopathology. Socs family gene expression was assessed by Q-RT/PCR and Stat5 phosphorylation by Western blotting on BCR-ABL1 expressing cells. Results: Although Socs2 was previously found to be upregulated in long-term repopulating HSCs by gene expression arrays, Socs2 deficient HSCs were indistinguishable from wild type HSCs when challenged in competitive bone marrow transplantation. Furthermore, when expressing BCR/ABL1, both Socs2 deficient and wild type cells induced a CML-like disease with an average survival of three weeks after transplantation. The leukemic mice suffered from elevated white blood cell counts and splenomegaly. To investigate if other Socs family members were upregulated to compensate for the Socs2 deficiency, we compared the expression of the Socs gene family members in Socs2(−/−) with wild type, leukemic cells. The expression levels of all other Socs genes were similar between Socs2(−/−) and Socs2 wt cells, suggesting that compensatory mechanisms of other Socs genes do not account for the lack of Socs2 function. In addition, the finding that the phosphorylation of Stat5 was unaffected in Socs2(−/−) cells indicates that BCR/ABL1-induced Stat5-phosphorylation is insensitive to Socs2 levels. Conclusions: Collectively, our results clarify that Socs2 is dispensable for normal HSC function and for BCR/ABL1-induced CML-like disease. Disclosures: No relevant conflicts of interest to declare.

Download Full-text

The histone H2A deubiquitinase Usp16 regulates hematopoiesis and hematopoietic stem cell function

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1517041113 ◽

2015 ◽

Vol 113 (1) ◽

pp. E51-E60 ◽

Cited By ~ 34

Author(s):

Yue Gu ◽

Amanda E. Jones ◽

Wei Yang ◽

Shanrun Liu ◽

Qian Dai ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Stem Cell ◽

Hematopoietic Stem Cell ◽

Ubiquitin Ligase ◽

Cell Function ◽

Lymphoid Organ ◽

Histone H2a ◽

Hematopoietic Stem

Epigenetic mechanisms play important regulatory roles in hematopoiesis and hematopoietic stem cell (HSC) function. Subunits of polycomb repressive complex 1 (PRC1), the major histone H2A ubiquitin ligase, are critical for both normal and pathological hematopoiesis; however, it is unclear which of the several counteracting H2A deubiquitinases functions along with PRC1 to control H2A ubiquitination (ubH2A) level and regulates hematopoiesis in vivo. Here we investigated the function of Usp16 in mouse hematopoiesis. Conditional deletion of Usp16 in bone marrow resulted in a significant increase of global ubH2A level and lethality. Usp16 deletion did not change HSC number but was associated with a dramatic reduction of mature and progenitor cell populations, revealing a role in governing HSC lineage commitment. ChIP- and RNA-sequencing studies in HSC and progenitor cells revealed that Usp16 bound to many important hematopoietic regulators and that Usp16 deletion altered the expression of genes in transcription/chromosome organization, immune response, hematopoietic/lymphoid organ development, and myeloid/leukocyte differentiation. The altered gene expression was partly rescued by knockdown of PRC1 subunits, suggesting that Usp16 and PRC1 counterbalance each other to regulate cellular ubH2A level and gene expression in the hematopoietic system. We further discovered that knocking down Cdkn1a (p21cip1), a Usp16 target and regulated gene, rescued the altered cell cycle profile and differentiation defect of Usp16-deleted HSCs. Collectively, these studies identified Usp16 as one of the histone H2A deubiquitinases, which coordinates with the H2A ubiquitin ligase PRC1 to regulate hematopoiesis, and revealed cell cycle regulation by Usp16 as key for HSC differentiation.

Download Full-text

Compendium of Methods to Uncover RNA-Protein Interactions In Vivo

Methods and Protocols ◽

10.3390/mps4010022 ◽

2021 ◽

Vol 4 (1) ◽

pp. 22

Author(s):

Mrinmoyee Majumder ◽

Viswanathan Palanisamy

Keyword(s):

Gene Expression ◽

Protein Interactions ◽

Rna Binding ◽

Rna Binding Proteins ◽

Expression Patterns ◽

Control Of Gene Expression ◽

Regulatory Pathways ◽

Advantages And Disadvantages ◽

Protein Nucleic Acid

Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.

Download Full-text

Set1 Targets Genes with Essential Identity and Tumor-Suppressing Functions in Planarian Stem Cells

Genes ◽

10.3390/genes12081182 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1182

Author(s):

Prince Verma ◽

Court K. M. Waterbury ◽

Elizabeth M. Duncan

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Mammalian Cells ◽

Cell Function ◽

Genotoxic Stress ◽

Specific Gene ◽

Cell Identity ◽

Chromatin Signature ◽

Lysine Methyltransferase

Tumor suppressor genes (TSGs) are essential for normal cellular function in multicellular organisms, but many TSGs and tumor-suppressing mechanisms remain unknown. Planarian flatworms exhibit particularly robust tumor suppression, yet the specific mechanisms underlying this trait remain unclear. Here, we analyze histone H3 lysine 4 trimethylation (H3K4me3) signal across the planarian genome to determine if the broad H3K4me3 chromatin signature that marks essential cell identity genes and TSGs in mammalian cells is conserved in this valuable model of in vivo stem cell function. We find that this signature is indeed conserved on the planarian genome and that the lysine methyltransferase Set1 is largely responsible for creating it at both cell identity and putative TSG loci. In addition, we show that depletion of set1 in planarians induces stem cell phenotypes that suggest loss of TSG function, including hyperproliferation and an abnormal DNA damage response (DDR). Importantly, this work establishes that Set1 targets specific gene loci in planarian stem cells and marks them with a conserved chromatin signature. Moreover, our data strongly suggest that Set1 activity at these genes has important functional consequences both during normal homeostasis and in response to genotoxic stress.

Download Full-text

Gene networks underlying functional sex in Sparidae (Pisces, Teleostei)

10.12681/eadd/44179 ◽

2018 ◽

Author(s):

Αλέξανδρος Τσακογιάννης

Keyword(s):

Gene Expression ◽

Sex Determination ◽

Gene Networks ◽

Expression Patterns ◽

Gene Families ◽

Male And Female ◽

Dentex Dentex ◽

The Common ◽

Model Fish Species ◽

Model Fish

The differences between sexes and the concept of sex determination have always fascinated, yet troubled philosophers and scientists. Among the animals that reproduce sexually, teleost fishes show a very wide repertoire of reproductive modes. Except for the gonochoristic species, fish are the only vertebrates in which hermaphroditism appears naturally. Hermaphroditism refers to the capability of an organism to reproduce both as male and female in its life cycle and there are various forms of it. In sequential hermaphroditism, an individual begins as female first and then can change sex to become male (protogyny), or vice versa (protandry). The diverse sex-phenotypes of fish are regulated by a variety of sex determination mechanisms, along a continuum of environmental and heritable factors. The vast majority of sexually dimorphic traits result from the differential expression of genes that are present in both sexes. To date, studies regarding the sex-specific differences in gene expression have been conducted mainly in sex determination systems of model fish species that are well characterized at the genomic level, with distinguishable heteromorphic sex chromosomes, exhibiting genetic sex determination and gonochorism. Among teleosts, the Sparidae family is considered to be one of the most diversified families regarding its reproductive systems, and thus is a unique model for comparative studies to understand the molecular mechanisms underlying different sexual motifs. In this study, using RNA sequencing, we studied the transcriptome from gonads and brains of both sexes in five sparid species, representatives of four different reproductive styles. Specifically, we explored the sex-specific expression patterns of a gonochoristic species: the common dentex Dentex dentex, two protogynous hermaphrodites: the red porgy Pagrus pagrus and the common pandora Pagellus erythrinus, the rudimentary hermaphrodite sharpsnout seabream Diplodus puntazzo, and the protandrous gilthead seabream Sparus aurata. We found minor sex-related expression differences indicating a more homogeneous and sexually plastic brain, whereas there was a plethora of sex biased gene expression in the gonads. The functional divergence of the two gonadal types is reflected in their transcriptomic profiles, in terms of the number of genes differentially expressed, as well as the expression magnitude (i.e. fold-change differences). The observation of almost double the number of up-regulated genes in males compared to females indicates a male-biased expression tendency. Focusing on the pathways and genes implicated in sex determination/differentiation, we aimed to unveil the molecular pathways through which these non-model fish species develop a masculine or a feminine character. We observed the implicated pathways and major gene families (e.g. Wnt/b-catenin pathway and Retinoic-acid signaling pathway, Notch, TGFβ) behind sex-biased expression and the recruitment of known sex-related genes either to male or female type of gonads in these fish. (e.g Dmrt1, Sox9, Sox3, Cyp19a, Filgla, Ctnnb1, Gsdf9, Stra6 etc.). We also carefully investigated the presence of genes reported to be involved in sex determination/differentiation mechanisms in other vertebrates and fish and compared their expression patterns in the species under study. The expression profiling exposed known candidate molecular-players/genes establishing the common female (Cyp19a1, Sox3, Figla, Gdf9, Cyp26a, Ctnnb1, Dnmt1, Stra6) and male identity (Dmrt1, Sox9, Dnmt3aa, Rarb, Raraa, Hdac8, Tdrd7) of the gonad in these sparids. Additionally, we focused on those contributing to a species-specific manner either to female (Wnt4a, Dmrt2a, Foxl2 etc.) or to male (Amh, Dmrt3a, Cyp11b etc.) characters, and discussed the expression patterns of factors that belong to important pathways and/or gene families in the SD context, in our species gonadal transcriptomes. Taken together, most of the studied genes form part of the cascade of sex determination, differentiation, and reproduction across teleosts. In this study, we focused on genes that are active when sex is established (sex-maintainers), revealing the basic “gene-toolkit” & gene-networks underlying functional sex in these five sparids. Comparing related species with alternative reproductive styles, we saw different combinations of genes with conserved sex-linked roles and some “handy” molecular players, in a “partially- conserved” or “modulated” network formulating the male and female phenotype. The knowledge obtained in this study and tools developed during the process have set the groundwork for future experiments that can improve the sex control of this species and help the in-deep understanding the complex process of sex differentiation in the more flexible multi-component systems as these studied here.

Download Full-text

Loss of FancC Function Results in Decreased Hematopoietic Stem Cell Repopulating Ability

Blood ◽

10.1182/blood.v94.1.1.413k03_1_8 ◽

1999 ◽

Vol 94 (1) ◽

pp. 1-8 ◽

Cited By ~ 114

Author(s):

Laura S. Haneline ◽

Troy A. Gobbett ◽

Rema Ramani ◽

Madeleine Carreau ◽

Manuel Buchwald ◽

...

Keyword(s):

Stem Cell ◽

Hematopoietic Stem Cell ◽

Cell Function ◽

Genetic Disorder ◽

Test Cell ◽

Hematopoietic Stem ◽

Murine Homologue ◽

Complex Genetic Disorder

Fanconi anemia (FA) is a complex genetic disorder characterized by progressive bone marrow (BM) aplasia, chromosomal instability, and acquisition of malignancies, particularly myeloid leukemia. We used a murine model containing a disruption of the murine homologue ofFANCC (FancC) to evaluate short- and long-term multilineage repopulating ability of FancC −/− cells in vivo. Competitive repopulation assays were conducted where “test”FancC −/− or FancC +/+ BM cells (expressing CD45.2) were cotransplanted with congenic competitor cells (expressing CD45.1) into irradiated mice. In two independent experiments, we determined that FancC −/− BM cells have a profound decrease in short-term, as well as long-term, multilineage repopulating ability. To determine quantitatively the relative production of progeny cells by each test cell population, we calculated test cell contribution to chimerism as compared with 1 × 105 competitor cells. We determined that FancC −/− cells have a 7-fold to 12-fold decrease in repopulating ability compared with FancC +/+cells. These data indicate that loss of FancC function results in reduced in vivo repopulating ability of pluripotential hematopoietic stem cells, which may play a role in the development of the BM failure in FA patients. This model system provides a powerful tool for evaluation of experimental therapeutics on hematopoietic stem cell function.

Download Full-text

Enforced dimerization between XBP1s and ATF6f enhances the protective effects of the unfolded protein response (UPR) in models of neurodegeneration

10.1101/2020.11.17.387480 ◽

2020 ◽

Author(s):

René L. Vidal ◽

Denisse Sepulveda ◽

Paulina Troncoso-Escudero ◽

Paula Garcia-Huerta ◽

Constanza Gonzalez ◽

...

Keyword(s):

Gene Expression ◽

Unfolded Protein Response ◽

Target Genes ◽

Cell Function ◽

Alpha Synuclein ◽

Protective Effects ◽

Unfolded Protein ◽

The Unfolded Protein Response ◽

Protein Response

AbstractAlteration to endoplasmic reticulum (ER) proteostasis is observed on a variety of neurodegenerative diseases associated with abnormal protein aggregation. Activation of the unfolded protein response (UPR) enables an adaptive reaction to recover ER proteostasis and cell function. The UPR is initiated by specialized stress sensors that engage gene expression programs through the concerted action of the transcription factors ATF4, ATF6f, and XBP1s. Although UPR signaling is generally studied as unique linear signaling branches, correlative evidence suggests that ATF6f and XBP1s may physically interact to regulate a subset of UPR-target genes. Here, we designed an ATF6f-XBP1s fusion protein termed UPRplus that behaves as a heterodimer in terms of its selective transcriptional activity. Cell-based studies demonstrated that UPRplus has stronger an effect in reducing the abnormal aggregation of mutant huntingtin and alpha-synuclein when compared to XBP1s or ATF6 alone. We developed a gene transfer approach to deliver UPRplus into the brain using adeno-associated viruses (AAVs) and demonstrated potent neuroprotection in vivo in preclinical models of Parkinson’s and Huntington’s disease. These results support the concept where directing UPR-mediated gene expression toward specific adaptive programs may serve as a possible strategy to optimize the beneficial effects of the pathway in different disease conditions.

Download Full-text