Ido Goldstein

Hebrew University of Jerusalem | HUJI · Institute of Biochemistry, Food Science and Nutrition

Disclosure: D. Goldberg: None. I. Goldstein: None. Most animals are well equipped to endure prolonged fasting periods by converting energy stores into available biochemical fuel. This is achieved by the hepatic production of two fuel types supplying other tissues: glucose (originating from gluconeogenesis or glycogen breakdown) and ketone bodies (p...

The accessibility of different chromatin regions to transcription factors and other DNA-binding proteins is a critical determinant of cell function. Here, we detail a modified assay for transposase-accessible chromatin sequencing (ATAC-seq) protocol which measures chromatin accessibility genome wide. We describe nuclei isolation, tagmentation, PCR...

During fasting, hepatocytes produce glucose in response to hormonal signals. Glucagon and glucocorticoids are principal hormones secreted during fasting that cooperate in regulating glucose production via increasing hepatic gluconeogenesis. However, how these hormone signals are integrated in hepatocytes and translated to a biological output is unk...

During fasting, hepatocytes produce glucose in response to hormonal signals. Glucagon and glucocorticoids are principal fasting hormones that cooperate in regulating glucose production via gluconeogenesis. However, how these hormone signals are integrated and interpreted to a biological output is unknown. Here, we use genome-wide profiling of gene...

BACKGROUND & AIMS Gluconeogenesis from amino acids (AAs) maintains glucose homeostasis during fasting. While glucagon is known to regulate AA catabolism, the contribution of other hormones to it and the scope of transcriptional regulation dictating AA catabolism are unknown. We explored the role of the fasting hormones glucagon and glucocorticoids...

Primary hepatocytes are a vital tool in various biomedical research disciplines, serving as an ex vivo model for liver physiology. Obtaining high yields of viable primary mouse hepatocytes is technically challenging, limiting their use. Here, we present an improved protocol based on the classic two-step collagenase perfusion technique. The liver is...

The cytokines interleukin 1β and 6 (IL-1β, IL-6) mediate the acute phase response (APR). In liver, they regulate the secretion of acute phase proteins. Using RNA-seq in primary hepatocytes, we show that these cytokines regulate transcription in a bifurcated manner, leading to both synergistic and antagonistic gene expression. By mapping changes in...

Upon lowered blood glucose occurring during fasting, glucagon is secreted from pancreatic islets, exerting various metabolic effects to normalize glucose levels. A significant portion of these effects are mediated by glucagon-activated transcription factors (TFs) in liver. Glucagon directly activates several TFs via immediate cAMP- and calcium-depe...

During inflammation, the liver responds to pro-inflammatory signals by producing and secreting acute phase reactants (APR) involved in the inflammatory process. The notable increase in the level of these proteins is due to transcriptional induction that is jointly mediated by the pro-inflammatory cytokines IL-1β, TNFα and IL-6. Although critical to...

Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome‐wide methodologies, including chromatin immunoprecipitation (ChIP‐seq), DNase‐I hypersensitivity (DNase‐seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (...

In response to activating signals, transcription factors (TFs) bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint). Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif...

Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understands how this complex network regulates the metabolic response to fasting we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibili...

Earlier reported small interfering RNA (siRNA) high-throughput screens, identified seven-transmembrane superfamily member 3 (TM7SF3) as a novel inhibitor of pancreatic β-cell death. Here we show that TM7SF3 maintains protein homeostasis and promotes cell survival through attenuation of ER stress. Overexpression of TM7SF3 inhibits caspase 3/7 activa...

The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1 (FoxA1) are significant factors in breast cancer progression. FoxA1 has been implicated in establishing ER-binding patterns though its unique ability to serve as a pioneer factor. However, the molecular interplay between ER, GR, and FoxA1 requires further investiga...

An elaborate metabolic response to fasting is orchestrated by the liver and is heavily reliant on transcriptional regulation. In response to hormones (glucagon, glucocorticoids) many transcription factors (TFs) are activated and regulate various genes involved in metabolic pathways aimed at restoring homeostasis: gluconeogenesis, fatty acid oxidati...

The tumor-suppressor p53 is a transcription factor that prevents cancer development and is involved in regulation of various physiological processes. This is mediated both by induction of cell cycle arrest and apoptosis and by controlling the expression of a plethora of target genes, including secreted proteins. It has been demonstrated that p53 ma...

p53 loss of heterozygosity (p53LOH) is frequently observed in Li-Fraumeni syndrome (LFS) patients who carry a mutant (Mut) p53 germ-line mutation. Here, we focused on elucidating the link between p53LOH and tumor development in stem cells (SCs). Although adult mesenchymal stem cells (MSCs) robustly underwent p53LOH, p53LOH in induced embryonic plur...

Cancer associated fibroblasts (CAFs) are a subpopulation of cells that reside within the tumor microenvironment and promotes the transformation process by encouraging tumor growth, angiogenesis, inflammation, and metastasis. CAF-specific proteins serve as both prognostic markers and targets for anticancer drugs. With the growing interest in CAFs, s...

Mutations in the p53 tumor suppressor protein are highly frequent in tumors and often endow cells with tumorigenic capacities. We sought to examine a possible role for mutant p53 in the cross-talk between cancer cells and their surrounding stroma, which is a crucial factor affecting tumor outcome. Here we present a novel model which enables individ...

(Related to Figure 2) The interferon pathway is up regulated in some but not all pairs of CAFs and lung carcinoma cells. (A–C) CAFs were co-cultured with the designated carcinoma cells lines and with each other. Shown is a QRT-PCR for MX1. * denotes P<0.05. (TIF)

(Related to Figure 5) IFNβ attenuates WIG1 in mouse B-cells. (A) In a microarray retrieved from [41] mouse B cells were treated with IFNβ. Shown is the average WIG1 expression of four replicates. p = 0.003. (TIF)

QRT-PCR primers. (DOCX)

(Related to Figure 1) The effect of the sorting procedure on stromal and cancer cells. QRT-PCR was performed and relative expression of GFP and dsRed following the second sort is shown (A). GFP labeled cells are written in green and dsRed labeled cells are written in red. Parentheses denote the adjacent population that was not collected. (B)The des...

(Related to Figure 4) SOCS1 mediates mutant p53 attenuating effect on CXCL11 following IFNβ treatment. (A) H1299175 cells were introduced with RNAi against Lacz as a control or SOCS1and treated with IFNβ for 24 h. Shown is QRT-PCR for SOCS1 and MX1 expression. (TIF)

(Related to Figure 3) MX1 is attenuated by mutant p53 following IFNβ treatment. (A) A549 were introduced with an empty vector or mutant p53 (R175H) vector, and treated with IFNβ for 24 h. Shown is a QRT-PCR for MX1. (B) SKBR3 which express endogenous mutant p53 (R175H) were introduced with shRNA vector targeting non-human sequence and mutant p53 an...

The p53 tumor suppressor protein is a transcription factor that initiates transcriptional programs aimed at inhibiting carcinogenesis. p53 represses metabolic pathways that support tumor development (such as glycolysis and the pentose phosphate pathway (PPP)) and enhances metabolic pathways that are considered counter-tumorigenic such as fatty acid...

Cytochrome P450 enzymes (P450) are abundantly expressed in the human liver where they hydroxylate organic substrates. In a microarray screen performed in human liver cells, we found a group of eleven P450 genes whose expression was induced by p53 (CYP3A4, CYP3A43, CYP3A5, CYP3A7, CYP4F2, CYP4F3, CYP4F11, CYP4F12, CYP19A1, CYP21A2 and CYP24A1). The...

Uncontrolled accumulation of reactive oxygen species (ROS) causes oxidative stress and induces harmful effects. Both high ROS levels and p53 mutations are frequent in human cancer. Mutant p53 forms are known to actively promote malignant growth. However, no mechanistic details are known about the contribution of mutant p53 to excessive ROS in cance...

Both cellular and systemic metabolism of lipids are paramount for homeostasis, and their malfunction leads to devastating pathologies. Recently, exciting findings have linked the p53 tumor suppressor to the regulation of lipid metabolism. Here, we summarize these findings showing a clear role for p53 in enhancing lipid catabolism while inhibiting i...

The theoretical framework for the field of cancer research is based on two main principles. The first is that cancer advances in a stepwise manner, with each alteration driving cells further toward a malignant state. Second, to cure cancer we must target only cancer-specific properties. Here, we analyze the birth and propagation of the cancer resea...

Concomitant expression of mutant p53 and oncogenic Ras, leading to cellular transformation, is well documented. However, the mechanisms by which the various mutant p53 categories cooperate with Ras remain largely obscure. From this study we suggest that different mutant p53 categories cooperate with H-Ras in different ways to induce a unique expres...

In this study we aimed at characterizing the regulation of hepatic metabolic pathways by the p53 transcription factor. Analysis of gene expression following alteration of p53 status in several human- and mouse-derived cells using microarray analysis, quantitative real-time PCR, chromatin immunoprecipitation, and reporter gene assays. A functional a...

Comment on: Sohr S, et al. Cell Cycle 2011; 10:3758-67.

Compelling evidences have rendered the tumor microenvironment a crucial determinant in cancer outcome. Activating transcription factor 3 (ATF3), a stress response transcription factor, is known to have a dichotomous role in tumor cells, acting either as a tumor suppressor or an oncogene in a context-dependent manner. However, its expression and pos...

The formation of tumor metastasis. LHSR T/ERG tumor metastasized into the murine lung and stained for AR (right hand side) compared to the normal lung of the LHSR mouse (left hand side) (X400 Magnification). Arrow in the LHSR T/ERG panel indicates lung metastasis. (TIF)

Tumor incidence summary. (TIF)

EP-AR and LHSR exhibit identical chromosomal characteristics as their TMPRSS2/ERG expressing counterparts. The designated cell cultures were subjected to SKY analysis. (A) Most recurrent features are shown in a table. (B) Representative images of the chromosomal features, recurrent features are circled in white. (TIF)

ERG binding sites in various promoters. (A) The ETS transcription family binding site sequence. (B) ∼2000 base pairs up stream to the translation start site of the gene of interest were analyzed using ‘MatInspector’ Algorithm by ‘Genomatix’. ERG putative binding sites which passed a threshold of >0.96 matrix similarity and a core similarity of 1 ar...

Primers list. (DOC)

Prostate cancer is the most common non-dermatologic malignancy in men in the Western world. Recently, a frequent chromosomal aberration fusing androgen regulated TMPRSS2 promoter and the ERG gene (TMPRSS2/ERG) was discovered in prostate cancer. Several studies demonstrated cooperation between TMPRSS2/ERG and other defective pathways in cancer progr...

The transcription factor p53 functions not only to suppress tumorigenesis but also to maintain normal development and homeostasis. Although p53 was implicated in different aspects of fertility, including spermatogenesis and implantation, the mechanism underlying p53 involvement in spermatogenesis is poorly resolved. In this study we describe the id...

Three decades of p53 research have led to many advances in understanding the basic biology of normal and cancer cells. Nonetheless, the detailed functions of p53 in normal cells, and even more so in cancer cells, remain obscure. A major breakthrough is the realization that mutant p53 has a life of its own: it contributes to cancer not only through...

Partial gain of chromosome arm 17q is an abundant aberrancy in various cancer types such as lung and prostate cancer with a prominent occurrence and prognostic significance in neuroblastoma--one of the most common embryonic tumors. The specific genetic element/s in 17q responsible for the cancer-promoting effect of these aberrancies is yet to be de...

In this study, we focus on the analysis of a previously identified cancer-related gene signature (CGS) that underlies the cross talk between the p53 tumor suppressor and Ras oncogene. CGS consists of a large number of known Ras downstream target genes that were synergistically upregulated by wild-type p53 loss and oncogenic H-Ras(G12V) expression....

The human 1-8 interferon inducible gene family consists of at least 3 functional genes; 9-27, 1-8D and 1-8U, which are all linked on an 18-kb fragment of chromosome 11 and are highly homologous. It has recently been shown by us and others that the 1-8D gene is overexpressed in colon carcinoma. Here, we show, by sequence comparison of the 1-8D in pa...

Comment on: Characterization of a new cancer-associated mutant of p53 with a missense mutation (K351N) in the tetramerization domain. Muscolini M, et al. Cell Cycle 2009; 8:In press.

Supplementary Information

Supplementary Dataset 1

Supplementary Dataset 2

Supplementary Dataset 3

Supplementary Dataset 4

Supplementary Dataset 5

Fibroblasts located adjacent to the tumor [cancer-associated fibroblasts (CAFs)] that constitute a large proportion of the cancer-associated stroma facilitate the transformation process. In this study, we compared the biological behavior of CAFs that were isolated from a prostate tumor to their normal-associated fibroblast (NAF) counterparts. CAFs...

Normal cell growth is governed by a complicated biological system, featuring multiple levels of control, often deregulated in cancers. The role of microRNAs (miRNAs) in the control of gene expression is now increasingly appreciated, yet their involvement in controlling cell proliferation is still not well understood. Here we investigated the mammal...