Jason X. Cheng

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Genome-scale studies have revealed extensive, cell type-specific colocalization of transcription factors, but the mechanisms underlying this phenomenon remain poorly understood. Here, we demonstrate in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions. PU.1 binding initiates nucleosome remodeling, followed by H3K4 monomethylation at large numbers of genomic regions associated with both broadly and specifically expressed genes. These locations serve as beacons for additional factors, exemplified by liver X receptors, which drive both cell-specific gene expression and signal-dependent responses. Together with analyses of transcription factor binding and H3K4me1 patterns in other cell types, these studies suggest that simple combinations of lineage-determining transcription factors can specify the genomic sites ultimately responsible for both cell identity and cell type-specific responses to diverse signaling inputs.

Renal medullary carcinoma : rhabdoid features and the absence of INI1 expression as markers of aggressive behavior

Renal medullary carcinoma is a rare, well-recognized highly aggressive tumor of varied histopathology, which occurs in young patients with sickle cell trait or disease. Rhabdoid elements, occasionally seen in high-grade renal tumors including renal medullary carcinoma, possibly represent a pathologic marker of aggressive behavior. INI1 (hSNF5/SMARCB1/BAF47) is a highly conserved factor in the ATP-dependent chromatin-modifying complex. Loss of this factor in mice results in aggressive rhabdoid tumors or lymphomas. In humans, the loss of INI1 expression has been reported in pediatric renal rhabdoid tumors, central nervous system atypical teratoid/rhabdoid tumors and epithelioid sarcomas, a possible primary soft tissue rhabdoid tumor. This study compares five renal medullary carcinomas with 10 high-grade renal cell carcinomas (five with rhabdoid features), two urothelial carcinomas and two pediatric renal rhabdoid tumors. All five renal medullary carcinomas, irrespective of histopathology, showed complete loss of INI1 expression similar to that seen in pediatric renal rhabdoid tumors. In contrast, all renal cell carcinomas or urothelial carcinomas, including those with histological rhabdoid features, expressed INI1. Clinically, all five of the patients with renal medullary carcinoma and the two patients with rhabdoid tumors presented with extra-renal metastases at the time of diagnosis. This study demonstrates that renal medullary carcinoma and renal rhabdoid tumor share a common molecular/genetic alteration, which is closely linked to their aggressive biological behavior. However, the absence of INI1 expression is not necessarily predictive of rhabdoid histopathology but remains associated with aggressive behavior in renal medullary carcinoma.

A Recurrent Network Involving the Transcription Factors PU.1 and Gfi1 Orchestrates Innate and Adaptive Immune Cell Fates

The transcription factor PU.1, encoded by the Sfpi1 gene, functions in a graded manner to regulate macrophage versus B cell generation; its higher concentration favors the macrophage fate. We demonstrated that Gfi1 reciprocally promoted B cell fate choice at the expense of myeloid progeny. Gfi1(-/-) multipotential progenitors (MPPs) were unable to constrain the expression of PU.1 because Gfi1 functioned to repress the Sfpi1 gene by displacing PU.1 from positive autoregulatory elements. Attenuating a transcriptional module composed of PU.1 and Egr suppressed the B lineage developmental defects of Gfi1(-/-) MPPs. Finally Ikaros, a transcription factor required for B cell development, promoted Gfi1 and antagonized PU.1 expression in MPPs. Our results reveal that a core transcriptional regulatory network used for directing cell fate choice in the innate immune system has been co-opted by Ikaros to orchestrate B lymphocyte generation. These findings have important implications for the evolution of the adaptive immune system.

Tumor Necrosis Factor-induced Long Myosin Light Chain Kinase Transcription Is Regulated by Differentiation-dependent Signaling Events CHARACTERIZATION OF THE HUMAN LONG MYOSIN LIGHT CHAIN KINASE PROMOTER

Myosin light chain kinase (MLCK) is expressed as long and short isoforms from unique transcriptional start sites within a single gene. Tumor necrosis factor (TNF) augments intestinal epithelial long MLCK expression, which is critical to cytoskeletal regulation. We found that TNF increases long MLCK mRNA transcription, both in human enterocytes in vitro and murine enterocytes in vivo.5′-RACE identified two novel exons, 1A and 1B, which encode alternative long MLCK transcriptional start sites. Chromatin immunoprecipitation (ChIP) and site-directed mutagenesis identified two essential Sp1 sites upstream of the exon 1A long MLCK transcriptional start site. Analysis of deletion and truncation mutants showed that a 102-bp region including these Sp1 sites was necessary for basal transcription. A promoter construct including 4-kb upstream of exon 1A was responsive to TNF, AP-1, or NFκB, but all except NFκB responses were absent in a shorter 2-kb construct, and all responses were absent in a 1-kb construct. Electrophoretic mobility shift assays, ChIP, and site-directed mutagenesis explained these data by identifying three functional AP-1 sites between 2- and 4-kb upstream of exon 1A and two NFκB sites between 1- and 2-kb upstream of exon 1A. Analysis of differentiating epithelia showed that only well differentiated enterocytes activated the 4-kb long MLCK promoter in response to TNF, and consensus promoter reporters demonstrated that TNF-induced NFκB activation decreased during differentiation while TNF-induced AP-1 activation increased. Thus either AP-1 or NFκB can up-regulate long MLCK transcription, but the mechanisms by which TNF up-regulates intestinal epithelial long MLCK transcription from exon 1A are differentiation-dependent.

Anti-adipogenic regulation underlies hepatic stellate cell transdifferentiation

Cirrhosis is the most important consequence of alcoholic liver disease for which liver transplantation is the only treatment option available. Transdifferentiation of hepatic stellate cells (HSC) to myofibroblastic cells (MF) is a central event in liver fibrogenesis, and understanding molecular mechanisms that underlie this cellular event provides pivotal insights into development of new therapeutic modalities for cirrhosis. To this end, the authors proposed several years ago that transdifferentiation of quiescent HSC to MF may be causally associated with transcriptional regulation known for adipocyte–preadipocytic fibroblast dedifferentiation. In support of this notion, the authors showed that adipogenic transcription factors and their downstream adipocyte specific genes are expressed abundantly in quiescent HSC and that this expression profile is lost in HM. Further, gain‐of‐function manipulations for adipogenic transcription factors such as peroxisome proliferator‐activated receptor‐γ (PPAR‐γ) and sterol regulatory element binding protein‐1c have been shown to reverse culture‐induced MF to quiescent HSC. The authors also demonstrated that tumor necrosis factor‐α and Wnt, known mediators of anti‐adipogenesis, also suppress the activity of PPAR‐γ and contribute to HSC‐MF transdifferentiation. These results reinforce the concept of adipogenic regulation essential to the quiescent phenotype and the loss of such regulation underlying HSC‐HM transdifferentiation. They also provide insights into the molecular basis for the use of PPAR‐γ agonists, which has been advocated for treatment of liver fibrosis.

Responses of Four Yeast Genes to Changes in the Transcriptional Machinery Are Determined by Their Promoters

Many yeast genes are distinguished by their specific requirements for different components of the transcriptional machinery. Here we examine four genes that fall into two classes as defined by their dependence on specific components of the transcriptional machinery. We describe a series of hybrid constructs, each of which bears activator binding sites that are associated with a promoter other than that with which they are usually affiliated. We examine expression of these reporters in strains bearing three modifications of the transcriptional machinery. Our results indicate that, in each of these cases, the promoter (and not the activator) determines which components of the transcriptional machinery are required. These and additional results, including those of others, clarify how disparate activators can work at many different promoters.

Fat paradox of steatohepatitis.

Alcoholic and non‐alcoholic steatohepatitis (ASH and NASH) constitute two major types of chronic liver disease with worldwide prevalence and are histologically indistinguishable with shared pathogenetic mechanisms. More importantly, they have synergistic interactions for liver pathology. Comparative studies on ASH and NASH have been hampered by the use of different animal models with confounding variables, particularly those with extreme genetic, toxic, and malnutrition etiologies. The mouse intragastric model circumvents these problems and reproduces the natural course and etiological background of ASH and NASH. Further, our recent work reproduces a profound synergism between the two in the model. Intracellular accumulation of neural lipids is a hallmark biochemical feature of ASH and NASH. Although impaired lipid oxidation and export may contribute to this pathological change, enhanced lipogenic regulation is frequently encountered, as characterized by induction of lipogenic or adipogenic transcription factors (peroxisome proliferator‐activated receptor [PPARγ], liver X receptor α[LXRα], sterol‐regulatory element‐binding protein‐1c [SREBP‐1c]). In contrast, we have recently defined transdifferentiation of hepatic stellate cells (HSC), a pivotal event in liver fibrogenesis, as an ‘antilipogenic’ or ‘anti‐adipogenic’ phenomenon. Thus, there is an apparent paradox between hepatocytes and HSC in steatohepatitis in terms of the outcome of lipogenic regulation. Our recent work suggests that defective insulin signaling in activated HSC may be responsible for this paradox. Further, activated Wnt signaling is implicated in ‘anti‐adipogenic’ stellate cell transdifferentiation in liver fibrogenesis.

Glucose Transporter Expression in an Avian Nectarivore: The Ruby-Throated Hummingbird (Archilochus colubris)

Glucose transporter (GLUT) proteins play a key role in the transport of monosaccharides across cellular membranes, and thus, blood sugar regulation and tissue metabolism. Patterns of GLUT expression, including the insulin-responsive GLUT4, have been well characterized in mammals. However, relatively little is known about patterns of GLUT expression in birds with existing data limited to the granivorous or herbivorous chicken, duck and sparrow. The smallest avian taxa, hummingbirds, exhibit some of the highest fasted and fed blood glucose levels and display an unusual ability to switch rapidly and completely between endogenous fat and exogenous sugar to fuel energetically expensive hovering flight. Despite this, nothing is known about the GLUT transporters that enable observed rapid rates of carbohydrate flux. We examined GLUT (GLUT1, 2, 3, & 4) expression in pectoralis, leg muscle, heart, liver, kidney, intestine and brain from both zebra finches (Taeniopygia guttata) and ruby-throated hummingbirds (Archilochus colubris). mRNA expression of all four transporters was probed using reverse-transcription PCR (RT-PCR). In addition, GLUT1 and 4 protein expression were assayed by western blot and immunostaining. Patterns of RNA and protein expression of GLUT1-3 in both species agree closely with published reports from other birds and mammals. As in other birds, and unlike in mammals, we did not detect GLUT4. A lack of GLUT4 correlates with hyperglycemia and an uncoupling of exercise intensity and relative oxidation of carbohydrates in hummingbirds. The function of GLUTs present in hummingbird muscle tissue (e.g. GLUT1 and 3) remain undescribed. Thus, further work is necessary to determine if high capillary density, and thus surface area across which cellular-mediated transport of sugars into active tissues (e.g. muscle) occurs, rather than taxon-specific differences in GLUT density or kinetics, can account for observed rapid rates of sugar flux into these tissues.

Assessment of the Quality of Glaucoma Referral Letters Based on a Survey of Glaucoma Specialists and a Glaucoma Guideline

OBJECTIVE To assess the quality of glaucoma referral letters and to report on the results of a survey of glaucoma specialists about referral letter content. DESIGN Cross-sectional study. PARTICIPANTS A survey of 135 glaucoma specialists and audit of 200 consecutive referral letters to a tertiary glaucoma unit. METHODS An online questionnaire was sent to members of the Canadian and American Glaucoma Societies asking what they considered the most important data to be included in a glaucoma referral. Consecutive referral letters to a tertiary glaucoma unit were assessed for legibility and content on the basis of the survey results and information items in current guidelines. MAIN OUTCOME MEASURES Survey outcome and proportion of included content items in referral letters. RESULTS The survey revealed that the top 5 most important data that glaucoma specialists would like to be included in a referral letter for progressive glaucoma were serial visual fields (VFs), current glaucoma therapy, current intraocular pressure (IOP), maximum IOP, and serial disc imaging. These items often were omitted in the referral letters audited. A total of 200 referral letters were assessed, 46% from ophthalmologists, 42% from optometrists, 10% from family practitioners, and 2% from other sources. Reasons for referral were diagnosis of glaucoma (37%), unstable glaucoma (25%), angle assessment (17%), and others (21%). Some 26% of the referral letters were deemed illegible (18% from ophthalmologists vs. 6% from optometrists; P< 0.01). Degree of urgency was mentioned in 27% of referrals. Optometrists were more likely than ophthalmologists to provide visual acuity (VA), IOP, refraction, and VFs (P< 0.01 for each). Some 24% of referrals for progression included more than 10 of the 14 information points suggested by the Canadian glaucoma guidelines, and 34% included fewer than 8 of the 14 points. CONCLUSIONS Referral letters frequently did not include important information, with 34% of referral letters deemed substandard. Optometrist referrals were better than ophthalmologist referrals in terms of content and legibility. A checklist of clinical details for referring physicians is suggested, which includes maximum and current IOP, disc evaluation, serial VFs, and serial disc imaging.

Inhibition of WNT signaling in the bone marrow niche prevents the development of MDS in the Apc del/+ MDS mouse model

There is accumulating evidence that functional alteration(s) of the bone marrow (BM) microenvironment contribute to the development of some myeloid disorders, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). In addition to a cell-intrinsic role of WNT activation in leukemia stem cells, WNT activation in the BM niche is also thought to contribute to the pathogenesis of MDS and AML. We previously showed that the Apc-haploinsufficient mice (Apcdel/+ ) model MDS induced by an aberrant BM microenvironment. We sought to determine whether Apc, a multifunctional protein and key negative regulator of the canonical β-catenin (Ctnnb1)/WNT-signaling pathway, mediates this disease through modulating WNT signaling, and whether inhibition of WNT signaling prevents the development of MDS in Apcdel/+ mice. Here, we demonstrate that loss of 1 copy of Ctnnb1 is sufficient to prevent the development of MDS in Apcdel/+ mice and that altered canonical WNT signaling in the microenvironment is responsible for the disease. Furthermore, the US Food and Drug Administration (FDA)-approved drug pyrvinium delays and/or inhibits disease in Apcdel/+ mice, even when it is administered after the presentation of anemia. Other groups have observed increased nuclear CTNNB1 in stromal cells from a high frequency of MDS/AML patients, a finding that together with our results highlights a potential new strategy for treating some myeloid disorders.