Proximal Gene Expression Research Articles

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma.

The contributions of coding mutations to tumorigenesis are relatively well known; however, little is known about somatic alterations in noncoding DNA. Here we describe GECCO (Genomic Enrichment Computational Clustering Operation) to analyze somatic noncoding alterations in 308 pancreatic ductal adenocarcinomas (PDAs) and identify commonly mutated regulatory regions. We find recurrent noncoding mutations are enriched in PDA pathways, including axon guidance and cell adhesion, and novel processes including transcription and homeobox genes. We identify mutations in protein binding sites correlating with differential expression of proximal genes and experimentally validate effects of mutations on expression. We developed an expression modulation score that quantifies the strength of gene regulation imposed by each class of regulatory elements, and find the strongest elements are most frequently mutated, suggesting a selective advantage. Our detailed single-cancer analysis of noncoding alterations identifies regulatory mutations as candidates for diagnostic and prognostic markers, and suggests novel mechanisms for tumor evolution.

Cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture

Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most ofthese transcripts remain undetermined. We investigated the regulatory roles of a high-confidence andreproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci. Their enrichment in enhancer-like chromatin signatures, interactions with nearby trait-relevant protein-coding loci, and preferential location at topologically associated domain (TAD) boundaries provide evidence that TR-lincRNAs likely regulate proximal trait-relevant gene expression in cis by modulating local chromosomal architecture. This is consistent with the positive and significant correlation found between TR-lincRNA abundance and intra-TAD DNA-DNA contacts. Our results provide insights into the molecular mode of action by which TR-lincRNAs contribute to complex human traits.

Retinoic acid receptor regulation of epimorphic and homeostatic regeneration in the axolotl.

Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we target specific retinoic acid receptors (RARs) to either PD duplicate (RA treatment or RARγ agonist) or truncate (RARβ antagonist) regenerating limbs. RARE-EGFP reporter axolotls showed divergent reporter activity in limbs undergoing PD duplication versus truncation, suggesting differences in patterning and skeletal regeneration. Transcriptomics identified expression patterns that explain PD duplication, including upregulation of proximal homeobox gene expression and silencing of distal-associated genes, whereas limb truncation was associated with disrupted skeletal differentiation. RARβ antagonism in uninjured limbs induced a loss of skeletal integrity leading to long bone regression and loss of skeletal turnover. Overall, mechanisms were identified that regulate the multifaceted roles of RARs in the salamander limb including regulation of skeletal patterning during epimorphic regeneration, skeletal tissue differentiation during regeneration, and homeostatic regeneration of intact limbs.

Radiographic endophenotyping in hip osteoarthritis improves the precision of genetic association analysis

ObjectiveOsteoarthritis (OA) has a strong genetic component but the success of previous genome-wide association studies (GWAS) has been restricted due to insufficient sample sizes and phenotype heterogeneity. Our aim was...

Abstract A27: Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma

Abstract Pancreatic ductal adenocarcinoma (PDA) is a highly lethal malignancy with a 5-year survival rate of 6%, due in part to therapy resistance and late stage at diagnosis. A detailed understanding of the molecular alterations underlying PDA is required to uncover mechanisms of tumorigenesis and enable development of more effective therapies. As such, large-scale exome sequencing efforts have revealed genes (KRAS, TP53, CDKN2A, SMAD4) and pathways (Wnt/Notch, TGFβ, axon guidance, cell adhesion) important for PDA progression. However, the exome comprises less than 2% of the human genome. Whole-genome sequencing analyses have uncovered a somatic mutation rate of 1 mutation per megabase in PDA. Therefore, PDA tumors carry thousands of somatic mutations per genome, mostly located in noncoding regions, the vast majority of which are completely uncharacterized. While the contributions of coding mutations to tumorigenesis are relatively well known, few studies have detailed alterations in noncoding DNA. Here we describe a new computational pipeline, GECCO (Genomic Enrichment Computational Clustering Operation) to analyze somatic noncoding alterations in 308 pancreatic ductal adenocarcinomas (PDA) and systematically identify commonly mutated putative regulatory regions. We find that recurrent somatic noncoding regulatory mutations are present in PDA but uncommon near canonical PDA genes. Instead, using GECCO we find that the regulatory mutations are enriched in known PDA pathways, including axon guidance and cell adhesion, and novel processes including transcriptional regulation and homeobox genes. We identify mutations in specific protein binding sites that correlate with significant differential expression of proximal genes. Furthermore, to explore the effects of these candidate mutations on gene expression, we developed an expression modulation score that quantifies the strength of gene regulation imposed by each class of regulatory elements. Surprisingly, we find that the strongest regulatory elements are also the most frequently mutated, suggesting a selective advantage for mutations in these regions. Our analysis provides a detailed single-cancer view of noncoding alterations in tumorigenesis, identifies recurrent regulatory mutations as new candidates for diagnostic and prognostic markers, and suggests novel mechanisms for tumor genome evolution. Citation Format: Michael E. Feigin, Tyler Garvin, Peter Bailey, Nicola Waddell, David K. Chang, Shimin Shuai, Steven Gallinger, John D. McPherson, Sean M. Grimmond, Ekta Khurana, Lincoln D. Stein, Andrew V. Biankin, Michael C. Schatz, David A. Tuveson.{Authors}. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A27.

SY1425 (tamibarotene) Induces Profound Transcriptional Changes in AML Tumors with High Retinoic Acid Receptor Alpha

Retinoic acid receptor alpha (RARα) regulates myeloid differentiation and proliferation through the regulation of specific sets of genes. When unbound by a ligand, RARα is a repressive transcription factor while in its ligand-bound state it functions as a transcriptional activator. Previously, blast cells from a subset of individuals with non-APL AML were found to have a super-enhancer (SE), as revealed by H3K27 acetyl ChIP-Seq, associated with the RARA locus (hereafter called RARA-high), suggesting that tumor cell proliferation may have a dependency on RARA that can be exploited for therapeutic benefit. SEs are exceptionally large, highly active chromatin regions that are densely occupied by transcription factors and have been implicated in oncogene expression. Indeed, RARA-high non-APL AML cell lines showed >1000-fold increased sensitivity compared to RARA-low cells to the potent and selective RARα agonist SY-1425 (tamibarotene) as well as efficacy in non-APL AML patient derived xenograft models with a dependency on RARA.Since RARα is a transcription factor and the direct target of SY-1425, we investigated the change SY-1425 had on the transcriptional program of non-APL AML cell lines and the mechanism underlying those changes. Expression profiling on a panel of AML cell lines revealed that RARA-high AML cell lines had profound transcriptional changes in response to SY-1425, with 437 genes significantly changed, while RARA-low cell lines did not show significant gene expression changes. Gene set enrichment analysis (GSEA) of three RARA-high AML cell lines revealed that the genes upregulated by SY-1425 in the RARA-high cells are associated with immune signaling, interferon induction, protein secretion, and pathways associated with complement, MHC and integrin functions, all pathways indicative of more differentiated blood cells. Signatures downregulated by SY-1425 include MYC target genes. These findings are consistent with SY-1425 increasing the expression of genes involved in differentiation and decreasing those involved in proliferation. Genome-wide ChIP-Seq analysis revealed an increase in H3K27 acetylation at loci found to have strong RARα peaks as well as increased expression of those genes upon treatment with SY-1425. Together, these data support a model in which RARα binding nucleates functional enhancers in response to SY-1425 thereby upregulating proximal target gene expression and promotion of differentiation.The gene expression and epigenomic responses of RARA-high AML cell lines to SY-1425 were found to be similar to the responses of an APL cell line (NB-4) to retinoids or SY-1425. Gene sets identified in response to either retinoid treatment or genetic perturbation, such as forced expression or RAR-fusions or knockdown, matched the gene sets identified in RARA-high AML cell lines. Furthermore, the quantitative response of both NB-4 and RARA-high AML cell lines to SY-1425 was found to be similar. Across the genome, RARα binding was highly conserved between NB-4 and RARA-high AML cell lines with less overlap with the RARA-low cell lines. For example, the transcriptional and H3K27 acetylation alterations at the known PML-RARα target gene TGM2 following retinoid treatment was similar in NB-4 and the RARA- high cell lines. This locus also had a strong RARα binding site that is conserved among the cell lines and co-localized with a strong H3K27 acetylation peak. Consistent with the pattern of occupancy of RARα on the genome, the transcriptional response of the RARA enhancer-high cell lines to SY-1425 treatment was similar to the response of APL ex-vivo patient samples to retinoic acid treatment. These data support a model of a common biological response to retinoids between cells with the RARA-PML translocation in APL and cells with the RARA SE in AML. The mechanistic studies described here support the therapeutic potential of SY-1425 in myeloid leukemia patients who have a SE associated with RARA. A biomarker directed clinical trial of SY-1425, a potent and selective RARα agonist, in a subset of AML and MDS patients with an altered RARA locus (clinicaltrials.gov, NCT02807558) is supported by these data. DisclosuresFiore:Syros Pharmaceuticals: Employment, Equity Ownership. McKeown:Syros Pharmaceuticals: Employment, Equity Ownership. Lee:Syros Pharmaceuticals: Employment, Equity Ownership. Eaton:Syros Pharmaceuticals: Employment, Equity Ownership. Fritz:Syros Pharmaceuticals: Employment, Equity Ownership.

The Chromatin of Candida albicans Pericentromeres Bears Features of Both Euchromatin and Heterochromatin.

Centromeres, sites of kinetochore assembly, are important for chromosome stability and integrity. Most eukaryotes have regional centromeres epigenetically specified by the presence of the histone H3 variant CENP-A. CENP-A chromatin is often surrounded by pericentromeric regions packaged into transcriptionally silent heterochromatin. Candida albicans, the most common human fungal pathogen, possesses small regional centromeres assembled into CENP-A chromatin. The chromatin state of C. albicans pericentromeric regions is unknown. Here, for the first time, we address this question. We find that C. albicans pericentromeres are assembled into an intermediate chromatin state bearing features of both euchromatin and heterochromatin. Pericentromeric chromatin is associated with nucleosomes that are highly acetylated, as found in euchromatic regions of the genome; and hypomethylated on H3K4, as found in heterochromatin. This intermediate chromatin state is inhibitory to transcription and partially represses expression of proximal genes and inserted marker genes. Our analysis identifies a new chromatin state associated with pericentromeric regions.

352 Allelic series for an EDC enhancer generated by CRISPR/Cas9 genome editing identifies an enhancer requirement for proximal gene expression and efficient wound healing

The epidermal-specific 923 enhancer is involved in dynamic chromatin remodelling and activation of the Epidermal Differentiation Complex (EDC) locus. To test the function of 923 during epidermal development, we used the CRISPR/Cas9 genome editing system to generate multiple 923 genetic alleles using 2 guide RNAs and 2 loxP ssODNs targeted to the mouse 923 locus. Germline transmission of 2 independent 923 global deletions [923dela, 923delb], one 923 inversion [923inv], and one floxed 923 was confirmed with at least 4 rounds of C57BL/6 backcrosses to exclude off-target effects for each allele. 923inv enabled the study of the effect of enhancer directionality on developmental EDC activation. 923dela-/-, 923delb-/-, and 923inv-/- mice are fertile, viable, and appear normal. No significant changes in the EDC gene expression of newborn 923inv-/- skin were observed, consistent with the direction-independent function of classical enhancers. However, a dose-dependent decrease in the expression of the EDC genes proximal to 923 (involucrin (Ivl), Sprr3, and Sprr2d) was identified in the heterozygous and homozygous mice of the 2 independent 923 deletions (923dela, 923delb). Coincident with this finding and contrary to previous studies of Ivl KO mice, we also observed a dose-dependent and concomitant upregulation of loricrin and Flg-like gene family members (filaggrin, filaggrin-2, hornerin, and repetin) in the EDC, as well as envoplakin (Evpl) and periplakin (Ppl) that, with Ivl, form the cornified envelope (CE) scaffold. Delayed wound closure in both 923del-/- lines (F2) was also noted. Thus, we find that 923 is required for proximal gene expression (Ivl, Sprr3, Sprr2d) and recovery of the skin barrier after perturbation, and elucidate a distinct molecular signature for upregulation of the Flg-like gene family and CE scaffold components to maintain barrier integrity in the context of loss of 923 enhancer and downstream Ivl expression.

Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality.

Formation of nucleosome free region (NFR) accompanied by specific histone modifications at flanking nucleosomes is an important prerequisite for enhancer and promoter activity. Due to this process, active regulatory elements often exhibit a distinct shape of histone signal in the form of a peak-valley-peak (PVP) pattern. However, different features of PVP patterns and their robustness in predicting active regulatory elements have never been systematically analyzed. Here, we present PARE, a novel computational method that systematically analyzes the H3K4me1 or H3K4me3 PVP patterns to predict NFRs. We show that NFRs predicted by H3K4me1 and me3 patterns are associated with active enhancers and promoters, respectively. Furthermore, asymmetry in the height of peaks flanking the central valley can predict the directionality of stable transcription at promoters. Using PARE on ChIP-seq histone modifications from four ENCODE cell lines and four hematopoietic differentiation stages, we identified several enhancers whose regulatory activity is stage specific and correlates positively with the expression of proximal genes in a particular stage. In conclusion, our results demonstrate that PVP patterns delineate both the histone modification landscape and the transcriptional activities governed by active enhancers and promoters, and therefore can be used for their prediction. PARE is freely available at http://servers.binf.ku.dk/pare.

Understanding super-enhancers.

Super-enhancers are defined as cluster of enhancers with dense TF binding, which can activate proximal cell-identity gene expression. Here we review the identification, functional significance of super-enhancers, and their relationships with cancer. With the current intense interests in super-enhancers, more super-enhancers will be defined and studied in different cell types and tissues and in different developmental and biological contexts to reveal molecular mechanisms of their functions.

Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans.

Only few systematic studies on the contribution of copy number variation to gene expression variation have been published to date. Here we identify effects of copy number variable regions (CNVRs) on nearby gene expression by investigating 909 CNVRs and expression levels of 12059 nearby genes in white blood cells from Mexican-American participants of the San Antonio Family Heart Study. We empirically evaluate our ability to detect the contribution of CNVs to proximal gene expression (presumably in cis) at various window sizes (up to a 10 Mb distance) between the gene and CNV. We found a ~1-Mb window size to be optimal for capturing cis effects of CNVs. Up to 10% of the CNVs in this study were found to be significantly associated with the expression of at least one gene within their vicinity. As expected, we find that CNVs that directly overlap gene sequences have the largest effects on gene expression (compared with non-overlapping CNVRs located nearby), with positive correlation (except for a few exceptions) between estimated genomic dosage and expression level. We find that genes whose expression level is significantly influenced by nearby CNVRs are enriched for immunity and autoimmunity related genes. These findings add to the currently limited catalog of CNVRs that are recognized as expression quantitative trait loci, and have implications for future study designs as well as for prioritizing candidate causal variants in genomic regions associated with disease.

Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease.

We conducted a meta analysis of Parkinson’s disease genome-wide association studies using a common set of 7,893,274 variants across 13,708 cases and 95,282 controls. Twenty-six loci were identified as genome-wide significant; these and six additional previously reported loci were then tested in an independent set of 5,353 cases and 5,551 controls. Of the 32 tested SNPs, 24 replicated, including 6 novel loci. Conditional analyses within loci show four loci including GBA, GAK/DGKQ, SNCA, and HLA contain a secondary independent risk variant. In total we identified and replicated 28 independent risk variants for Parkinson disease across 24 loci. While the effect of each individual locus is small, a risk profile analysis revealed a substantial cummulative risk in a comparison highest versus lowest quintiles of genetic risk (OR=3.31, 95% CI: 2.55, 4.30; p-value = 2×10−16). We also show 6 risk loci associated with proximal gene expression or DNA methylation.

PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression.

Chromatin regulators play an important role in the development of human diseases. In this study, we focused on Plant Homeo Domain Finger protein 8 (PHF8), a chromatin regulator that has attracted special concern recently. PHF8 is a histone lysine demethylase ubiquitously expressed in nuclei. Mutations of PHF8 are associated with X-linked mental retardation. It usually functions as a transcriptional co-activator by associating with H3K4me3 and RNA polymerase II. We found that PHF8 may associate with another regulator, REST/NRSF, predominately at promoter regions via studying several published PHF8 chromatin immunoprecipitation-sequencing (ChIP-Seq) datasets. Our analysis suggested that PHF8 not only activates but may also repress gene expression.

Chromatin landscapes of retroviral and transposon integration profiles.

The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected integrations in the mouse genome for the Sleeping Beauty (SB) and piggyBac (PB) transposons, and the Mouse Mammary Tumor Virus (MMTV). We analyzed (epi)genomic features to generate bias maps at both local and genome-wide scales. MMTV showed a remarkably uniform distribution of integrations across the genome. More distinct preferences were observed for the two transposons, with PB showing remarkable resemblance to bias profiles of the Murine Leukemia Virus. Furthermore, we present a model where target site selection is directed at multiple scales. At a large scale, target site selection is similar across systems, and defined by domain-oriented features, namely expression of proximal genes, proximity to CpG islands and to genic features, chromatin compaction and replication timing. Notable differences between the systems are mainly observed at smaller scales, and are directed by a diverse range of features. To study the effect of these biases on integration sites occupied under selective pressure, we turned to insertional mutagenesis (IM) screens. In IM screens, putative cancer genes are identified by finding frequently targeted genomic regions, or Common Integration Sites (CISs). Within three recently completed IM screens, we identified 7%–33% putative false positive CISs, which are likely not the result of the oncogenic selection process. Moreover, results indicate that PB, compared to SB, is more suited to tag oncogenes.

A Footnote to the Evolution of Digits

A Footnote to the Evolution of Digits

Hallmarks of Aromatase Inhibitor Drug Resistance Revealed by Epigenetic Profiling in Breast Cancer

Aromatase inhibitors are the major first-line treatment of estrogen receptor-positive breast cancer, but resistance to treatment is common. To date, no biomarkers have been validated clinically to guide subsequent therapy in these patients. In this study, we mapped the genome-wide chromatin-binding profiles of estrogen receptor α (ERα), along with the epigenetic modifications H3K4me3 and H3K27me3, that are responsible for determining gene transcription (n = 12). Differential binding patterns of ERα, H3K4me3, and H3K27me3 were enriched between patients with good or poor outcomes after aromatase inhibition. ERα and H3K27me3 patterns were validated in an additional independent set of breast cancer cases (n = 10). We coupled these patterns to array-based proximal gene expression and progression-free survival data derived from a further independent cohort of 72 aromatase inhibitor-treated patients. Through this approach, we determined that the ERα and H3K27me3 profiles predicted the treatment outcomes for first-line aromatase inhibitors. In contrast, the H3K4me3 pattern identified was not similarly informative. The classification potential of these genes was only partially preserved in a cohort of 101 patients who received first-line tamoxifen treatment, suggesting some treatment selectivity in patient classification.

689 Evaluation of the Second Generation Colon Capsule Endoscopy (CCE-2) in Pediatric Ulcerative Colitis (UC)

Background: Obesity is defined as a chronic low-level inflammatory condition characterized by high levels of circulating IL-6 and LPS and increases the risk of colon cancer development. Aim: We aimed to investigate the mechanism of obesity enhanced colon tumorigenesis in a murine model of diet-induced obesity. Method: Mice were fed either a control diet (10% calories from fat) or a high fat (HF) diet (60% calories from fat) and colonic tumors were induced by intraperitoneal injection of the genotoxic compound azoxymethane (AOM) followed by 2 rounds of oral dextran-sodium sulfate (DSS). Proximal and distal colon tissue was assessed for gene expression of inflammatory markers by qRT-PCR. The mesenteric fat was similarly assessed. The macrophage infiltrate in mesenteric fat was measured by immunohistochemistry staining for CD68. Bacterial translocation of live bacteria to the mesenteric lymph nodes (MLN) and spleen was determined using culture-dependent techniques. Results: Mice fed a HF diet for 10 weeks gained significantly more weight during the course of the experiment compared to mice fed a lean diet. They also had increased proximal colon gene expression of inflammatory mediators including tnfa, nos2 and il1b which was not observed distally. However, increased proximal gene expression did not lead to overt inflammation in the colon as determined by histological grading. Feeding a HF diet also resulted in mesenteric adipose tissue gene expression of tnfa and il1b and increased infiltration of CD68+ macrophages. Mice fed a HF diet and given AOM-DSS had an increased number of colonic tumors compared to control diet fed mice. However, there were few differences in inflammatory gene expression between the control diet or HF diet fed mice given AOM-DSS, and this observation extended to cytokine protein secretion from distal colon explant supernatants. The highest levels of live bacteria were recovered from the MLN of mice fed a HF diet and given AOM-DSS. Macrophages isolated from the mesenteric fat of mice fed a HF diet did not robustly respond to LPS stimulation, while those isolated from mice fed a HF diet and given AOM-DSS had increased baseline cytokine secretion that was further enhanced by LPS stimulation. Conclusion: Obesity increases tumor formation in a model of inflammation-induced colon cancer. Obesity itself induces inflammation of the colon and mesenteric fat. Mesenteric fat-associated macrophages from obese tumor bearing mice are primed to respond to LPS or translocated bacteria leading to an increase in local and systemic inflammation. We believe our results highlight the yet unknown role of mesenteric fat as a rheostat for intestinal and systemic inflammatory states.

688 Obesity Induces Colonic and Mesenteric Fat Inflammation and Promotes Tumorigenesis in a Model of Murine Colon Cancer

Background: Obesity is defined as a chronic low-level inflammatory condition characterized by high levels of circulating IL-6 and LPS and increases the risk of colon cancer development. Aim: We aimed to investigate the mechanism of obesity enhanced colon tumorigenesis in a murine model of diet-induced obesity. Method: Mice were fed either a control diet (10% calories from fat) or a high fat (HF) diet (60% calories from fat) and colonic tumors were induced by intraperitoneal injection of the genotoxic compound azoxymethane (AOM) followed by 2 rounds of oral dextran-sodium sulfate (DSS). Proximal and distal colon tissue was assessed for gene expression of inflammatory markers by qRT-PCR. The mesenteric fat was similarly assessed. The macrophage infiltrate in mesenteric fat was measured by immunohistochemistry staining for CD68. Bacterial translocation of live bacteria to the mesenteric lymph nodes (MLN) and spleen was determined using culture-dependent techniques. Results: Mice fed a HF diet for 10 weeks gained significantly more weight during the course of the experiment compared to mice fed a lean diet. They also had increased proximal colon gene expression of inflammatory mediators including tnfa, nos2 and il1b which was not observed distally. However, increased proximal gene expression did not lead to overt inflammation in the colon as determined by histological grading. Feeding a HF diet also resulted in mesenteric adipose tissue gene expression of tnfa and il1b and increased infiltration of CD68+ macrophages. Mice fed a HF diet and given AOM-DSS had an increased number of colonic tumors compared to control diet fed mice. However, there were few differences in inflammatory gene expression between the control diet or HF diet fed mice given AOM-DSS, and this observation extended to cytokine protein secretion from distal colon explant supernatants. The highest levels of live bacteria were recovered from the MLN of mice fed a HF diet and given AOM-DSS. Macrophages isolated from the mesenteric fat of mice fed a HF diet did not robustly respond to LPS stimulation, while those isolated from mice fed a HF diet and given AOM-DSS had increased baseline cytokine secretion that was further enhanced by LPS stimulation. Conclusion: Obesity increases tumor formation in a model of inflammation-induced colon cancer. Obesity itself induces inflammation of the colon and mesenteric fat. Mesenteric fat-associated macrophages from obese tumor bearing mice are primed to respond to LPS or translocated bacteria leading to an increase in local and systemic inflammation. We believe our results highlight the yet unknown role of mesenteric fat as a rheostat for intestinal and systemic inflammatory states.

Apolipoprotein C-I is an APOE genotype-dependent suppressor of glial activation

BackgroundInheritance of the human ϵ4 allele of the apolipoprotein (apo) E gene (APOE) significantly increases the risk of developing Alzheimer’s disease (AD), in addition to adversely influencing clinical outcomes of other neurologic diseases. While apoE isoforms differentially interact with amyloid β (Aβ), a pleiotropic neurotoxin key to AD etiology, more recent work has focused on immune regulation in AD pathogenesis and on the mechanisms of innate immunomodulatory effects associated with inheritance of different APOE alleles. APOE genotype modulates expression of proximal genes including APOC1, which encodes a small apolipoprotein that is associated with Aβ plaques. Here we tested the hypothesis that APOE-genotype dependent innate immunomodulation may be mediated in part by apoC-I.MethodsApoC-I concentration in cerebrospinal fluid from control subjects of differing APOE genotypes was quantified by ELISA. Real-time PCR and ELISA were used to analyze apoC-I mRNA and protein expression, respectively, in liver, serum, cerebral cortex, and cultured primary astrocytes derived from mice with targeted replacement of murine APOE for human APOE ϵ3 or ϵ4. ApoC-I direct modulation of innate immune activity was investigated in cultured murine primary microglia and astrocytes, as well as human differentiated macrophages, using specific toll-like receptor agonists LPS and PIC as well as Aβ.ResultsApoC-I levels varied with APOE genotype in humans and in APOE targeted replacement mice, with ϵ4 carriers showing significantly less apoC-I in both species. ApoC-I potently reduced pro-inflammatory cytokine secretion from primary murine microglia and astrocytes, and human macrophages, stimulated with LPS, PIC, or Aβ.ConclusionsApoC-I is immunosuppressive. Our results illuminate a novel potential mechanism for APOE genotype risk for AD; one in which patients with an ϵ4 allele have decreased expression of apoC-I resulting in increased innate immune activity.

Association of genetic variants in the NLRP3 region with expression of proximal genes and myocardial infarction

Association of genetic variants in the NLRP3 region with expression of proximal genes and myocardial infarction