Publications by authors named "Stefano Monti"

94 Publications

A Data-Driven Transcriptional Taxonomy of Adipogenic Chemicals to Identify White and Brite Adipogens.

Environ Health Perspect 2021 Jul 29;129(7):77006. Epub 2021 Jul 29.

Boston University Superfund Research Program, Boston University, Massachusetts, USA.

Background: Chemicals in disparate structural classes activate specific subsets of the transcriptional programs of peroxisome proliferator-activated receptor- () to generate adipocytes with distinct phenotypes.

Objectives: Our objectives were to ) establish a novel classification method to predict ligands and modifying chemicals; and ) create a taxonomy to group chemicals on the basis of their effects on transcriptome and downstream metabolic functions. We tested the hypothesis that environmental adipogens highly ranked by the taxonomy, but segregated from therapeutic ligands, would induce white but not brite adipogenesis.

Methods: 3T3-L1 cells were differentiated in the presence of 76 chemicals (negative controls, nuclear receptor ligands known to influence adipocyte biology, potential environmental ligands). Differentiation was assessed by measuring lipid accumulation. mRNA expression was determined by RNA-sequencing (RNA-Seq) and validated by reverse transcription-quantitative polymerase chain reaction. A novel classification model was developed using an amended random forest procedure. A subset of environmental contaminants identified as strong agonists were analyzed by their effects on lipid handling, mitochondrial biogenesis, and cellular respiration in 3T3-L1 cells and human preadipocytes.

Results: We used lipid accumulation and RNA-Seq data to develop a classification system that ) identified agonists; and ) sorted chemicals into likely white or brite adipogens. Expression of was the most efficacious indicator of strong activation. 3T3-L1 cells treated with two known environmental ligands, tetrabromobisphenol A and triphenyl phosphate, which sorted distinctly from therapeutic ligands, had higher expression of white adipocyte genes but no difference in and expression, and higher fatty acid uptake but not mitochondrial biogenesis. Moreover, cells treated with two chemicals identified as highly ranked agonists, tonalide and quinoxyfen, induced white adipogenesis without the concomitant health-promoting characteristics of brite adipocytes in mouse and human preadipocytes.

Discussion: A novel classification procedure accurately identified environmental chemicals as ligands distinct from known -activating therapeutics.

Conclusion: The computational and experimental framework has general applicability to the classification of as-yet uncharacterized chemicals. https://doi.org/10.1289/EHP6886.
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http://dx.doi.org/10.1289/EHP6886DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8320370PMC
July 2021

Yap/Taz inhibit goblet cell fate to maintain lung epithelial homeostasis.

Cell Rep 2021 Jul;36(2):109347

Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA. Electronic address:

Proper lung function relies on the precise balance of specialized epithelial cells that coordinate to maintain homeostasis. Herein, we describe essential roles for the transcriptional regulators YAP/TAZ in maintaining lung epithelial homeostasis, reporting that conditional deletion of Yap and Wwtr1/Taz in the lung epithelium of adult mice results in severe defects, including alveolar disorganization and the development of airway mucin hypersecretion. Through in vivo lineage tracing and in vitro molecular experiments, we reveal that reduced YAP/TAZ activity promotes intrinsic goblet transdifferentiation of secretory airway epithelial cells. Global gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggest that YAP/TAZ act cooperatively with TEA domain (TEAD) transcription factors and the NuRD complex to suppress the goblet cell fate program, directly repressing the SPDEF gene. Collectively, our study identifies YAP/TAZ as critical factors in lung epithelial homeostasis and offers molecular insight into the mechanisms promoting goblet cell differentiation, which is a hallmark of many lung diseases.
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http://dx.doi.org/10.1016/j.celrep.2021.109347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8346236PMC
July 2021

Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.

Nucleic Acids Res 2021 Sep;49(17):e98

Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA.

As high-throughput genomics assays become more efficient and cost effective, their utilization has become standard in large-scale biomedical projects. These studies are often explorative, in that relationships between samples are not explicitly defined a priori, but rather emerge from data-driven discovery and annotation of molecular subtypes, thereby informing hypotheses and independent evaluation. Here, we present K2Taxonomer, a novel unsupervised recursive partitioning algorithm and associated R package that utilize ensemble learning to identify robust subgroups in a 'taxonomy-like' structure. K2Taxonomer was devised to accommodate different data paradigms, and is suitable for the analysis of both bulk and single-cell transcriptomics, and other '-omics', data. For each of these data types, we demonstrate the power of K2Taxonomer to discover known relationships in both simulated and human tissue data. We conclude with a practical application on breast cancer tumor infiltrating lymphocyte (TIL) single-cell profiles, in which we identified co-expression of translational machinery genes as a dominant transcriptional program shared by T cells subtypes, associated with better prognosis in breast cancer tissue bulk expression data.
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http://dx.doi.org/10.1093/nar/gkab552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8464061PMC
September 2021

Evaluating the Homogeneity of Surface Features Induced by Impact-Based Surface Treatments.

Materials (Basel) 2021 Jun 22;14(13). Epub 2021 Jun 22.

Department of Mechanical Engineering, Politecnico di Milano, 20156 Milan, Italy.

Impact surface treatments are well-known for their efficiency in enhancing the mechanical properties of metallic materials, especially under cyclic loadings. These processes, which encompass a wide range of surface treatments based on repetitive impacts of tools of various types, induce surface plastic deformation, compressive residual stresses, and grain refinement alter the surface roughness as a side effect. Thus, it is essential to have suitable indexes to quantify the surface features caused by the typically random nature of these treatments. Herein, we evaluated the rationality of using standard roughness parameters for describing the morphological characteristics of surfaces treated by shot peening as a representative and widely used treatment of the category. A detailed numerical model of the peening process was developed. The output data were elaborated to extract the surface roughness parameters following the standard procedures. The results revealed the validity of the surface roughness parameters to describe the topography of material treated with adequate surface coverage, also highlighting the necessity to use a set of parameters rather than the common practice of relying on single parameters. Not considering a comprehensive set of amplitude and spacing parameters can result in significant, inconsistent, and misleading results while comparing the performance of surfaces.
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http://dx.doi.org/10.3390/ma14133476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269480PMC
June 2021

Gene expression alterations in salivary gland epithelia of Sjögren's syndrome patients are associated with clinical and histopathological manifestations.

Sci Rep 2021 05 27;11(1):11154. Epub 2021 May 27.

Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, USA.

Sjögren's syndrome (SS) is a complex autoimmune disease associated with lymphocytic infiltration and secretory dysfunction of salivary and lacrimal glands. Although the etiology of SS remains unclear, evidence suggests that epithelial damage of the glands elicits immune and fibrotic responses in SS. To define molecular changes underlying epithelial tissue damage in SS, we laser capture microdissected (LCM) labial salivary gland epithelia from 8 SS and 8 non-SS controls for analysis by RNA sequencing (RNAseq). Computational interrogation of gene expression signatures revealed that, in addition to a division of SS and non-SS samples, there was a potential intermediate state overlapping clustering of SS and non-SS samples. Differential expression analysis uncovered signaling events likely associated with distinct SS pathogenesis. Notable signals included the enrichment of IFN-γ and JAK/STAT-regulated genes, and the induction of genes encoding secreted factors, such as LTF, BMP3, and MMP7, implicated in immune responses, matrix remodeling and tissue destruction. Identification of gene expression signatures of salivary epithelia associated with mixed clinical and histopathological characteristics suggests that SS pathology may be defined by distinct molecular subtypes. We conclude that gene expression changes arising in the damaged salivary epithelia may offer novel insights into the signals contributing to SS development and progression.
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http://dx.doi.org/10.1038/s41598-021-90569-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159963PMC
May 2021

Effect of longevity genetic variants on the molecular aging rate.

Geroscience 2021 06 4;43(3):1237-1251. Epub 2021 May 4.

Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA.

We conducted a genome-wide association study of 1320 centenarians from the New England Centenarian Study (median age = 104 years) and 2899 unrelated controls using >9 M genetic variants imputed to the HRC panel of ~65,000 haplotypes. The genetic variants with the most significant associations were correlated to 4131 proteins that were profiled in the serum of a subset of 224 study participants using a SOMAscan array. The genetic associations were replicated in a genome-wide association study of 480 centenarians and ~800 controls of Ashkenazi Jewish descent. The proteomic associations were replicated in a proteomic scan of approximately 1000 Ashkenazi Jewish participants from a third cohort. The analysis replicated a protein signature associated with APOE genotypes and confirmed strong overexpression of BIRC2 (p < 5E-16) and under-expression of APOB in carriers of the APOE2 allele (p < 0.05). The analysis also discovered and replicated associations between longevity variants and slower changes of protein biomarkers of aging, including a novel protein signature of rs2184061 (CDKN2A/CDKN2B in chromosome 9) that suggests a genetic regulation of GDF15. The analyses showed that longevity variants correlate with proteome signatures that could be manipulated to discover healthy-aging targets.
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http://dx.doi.org/10.1007/s11357-021-00376-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190315PMC
June 2021

Inclined and multi-directional surface impacts accelerate biodegradation and improve mechanical properties of pure iron.

J Mech Behav Biomed Mater 2021 07 2;119:104476. Epub 2021 Apr 2.

Department of Mechanical Engineering, Politecnico di Milano, Milan, Italy.

Impact based surface treatments with adequate kinetic energy have favorable effects on promoting cell-substrate interactions, reducing bacterial adhesion, and enhancing fatigue performance of metallic biomaterials. Here, we used both numerical and experimental approaches to evaluate the potential of these treatments for addressing the major issue associated with the application of pure iron in biomedical implants, i.e. its low corrosion rate. Despite the efficiency of impact based surface treatments in modulating the degradation rate of pure iron, the maximum reported depth of the affected surface layer is still limited, even when extreme process parameters are used. To address this issue, herein, two impact based treatments were adjusted to trigger the dislocation activities that facilitate grain refinement in pure iron using multi-directional inclined impacts. An alternative approach of severe shot peening (SSP) was developed and compared with ultrasonic shot peening (USP). The effect of both treatments and variations of their key parameters were analyzed considering the significant role of shear bands and dislocation cells in the grain refinement mechanism of pure α-iron. Microstructural, mechanical and electrochemical properties of the treated material were analyzed. The observations showed extension of the grain refined layers for the specimens subjected to multidirectional oblique impacts compared to the ones treated in the classic manner using normal impacts. The results imply that by adapting peening parameters, it would be possible to effectively create a thick surface layer with properties that can accelerate the biodegradation of pure iron boosting its potential to meet clinical requirements for temporary hard tissue implants.
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http://dx.doi.org/10.1016/j.jmbbm.2021.104476DOI Listing
July 2021

animalcules: interactive microbiome analytics and visualization in R.

Microbiome 2021 03 28;9(1):76. Epub 2021 Mar 28.

Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.

Background: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data.

Results: To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface.

Conclusions: We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html . Video abstract.
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http://dx.doi.org/10.1186/s40168-021-01013-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006385PMC
March 2021

Protein signatures of centenarians and their offspring suggest centenarians age slower than other humans.

Aging Cell 2021 02 29;20(2):e13290. Epub 2021 Jan 29.

Geriatric Section, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA.

Using samples from the New England Centenarian Study (NECS), we sought to characterize the serum proteome of 77 centenarians, 82 centenarians' offspring, and 65 age-matched controls of the offspring (mean ages: 105, 80, and 79 years). We identified 1312 proteins that significantly differ between centenarians and their offspring and controls (FDR < 1%), and two different protein signatures that predict longer survival in centenarians and in younger people. By comparing the centenarian signature with 2 independent proteomic studies of aging, we replicated the association of 484 proteins of aging and we identified two serum protein signatures that are specific of extreme old age. The data suggest that centenarians acquire similar aging signatures as seen in younger cohorts that have short survival periods, suggesting that they do not escape normal aging markers, but rather acquire them much later than usual. For example, centenarian signatures are significantly enriched for senescence-associated secretory phenotypes, consistent with those seen with younger aged individuals, and from this finding, we provide a new list of serum proteins that can be used to measure cellular senescence. Protein co-expression network analysis suggests that a small number of biological drivers may regulate aging and extreme longevity, and that changes in gene regulation may be important to reach extreme old age. This centenarian study thus provides additional signatures that can be used to measure aging and provides specific circulating biomarkers of healthy aging and longevity, suggesting potential mechanisms that could help prolong health and support longevity.
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http://dx.doi.org/10.1111/acel.13290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884029PMC
February 2021

Contextualized Protein-Protein Interactions.

Patterns (N Y) 2021 Jan 20;2(1):100153. Epub 2020 Nov 20.

Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA.

Protein-protein interaction (PPI) databases are an important bioinformatics resource, yet existing literature-curated databases usually represent cell-type-agnostic interactions, which is at variance with our understanding that protein dynamics are context specific and highly dependent on their environment. Here, we provide a resource derived through data mining to infer disease- and tissue-relevant interactions by annotating existing PPI databases with cell-contextual information extracted from reporting studies. This resource is applicable to the reconstruction and analysis of disease-centric molecular interaction networks. We have made the data and method publicly available and plan to release scheduled updates in the future. We expect these resources to be of interest to a wide audience of researchers in the life sciences.
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http://dx.doi.org/10.1016/j.patter.2020.100153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815950PMC
January 2021

Loss of G-Protein Pathway Suppressor 2 Promotes Tumor Growth Through Activation of AKT Signaling.

Front Cell Dev Biol 2020 7;8:608044. Epub 2021 Jan 7.

Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States.

G Protein Suppressor 2 (GPS2) is a multifunctional protein that exerts important roles in inflammation and metabolism in adipose, liver, and immune cells. GPS2 has recently been identified as a significantly mutated gene in breast cancer and other malignancies and proposed to work as a putative tumor suppressor. However, molecular mechanisms by which GPS2 prevents cancer development and/or progression are largely unknown. Here, we have profiled the phenotypic changes induced by GPS2 depletion in MDA-MB-231 triple negative breast cancer cells and investigated the underlying molecular mechanisms. We found that GPS2-deleted MDA-MB-231 cells exhibited increased proliferative, migratory, and invasive properties , and conferred greater tumor burden in an orthotopic xenograft mouse model. Transcriptomic, proteomic and phospho-proteomic profiling of GPS2-deleted MBA-MB-231 revealed a network of altered signals that relate to cell growth and PI3K/AKT signaling. Overlay of GPS2-regulated gene expression with MDA-MB-231 cells modified to express constitutively active AKT showed significant overlap, suggesting that sustained AKT activation is associated with loss of GPS2. Accordingly, we demonstrate that the pro-oncogenic phenotypes associated with GPS2 deletion are rescued by pharmacological inhibition of AKT with MK2206. Collectively, these observations confirm a tumor suppressor role for GPS2 and reveal that loss of GPS2 promotes breast cancer cell proliferation and tumor growth through uncontrolled activation of AKT signaling. Moreover, our study points to GPS2 as a potential biomarker for a subclass of breast cancers that would be responsive to PI3K-class inhibitor drugs.
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http://dx.doi.org/10.3389/fcell.2020.608044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817781PMC
January 2021

How the AHR Became Important in Cancer: The Role of Chronically Active AHR in Cancer Aggression.

Int J Mol Sci 2020 Dec 31;22(1). Epub 2020 Dec 31.

Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA.

For decades, the aryl hydrocarbon receptor (AHR) was studied for its role in environmental chemical toxicity i.e., as a quirk of nature and a mediator of unintended consequences of human pollution. During that period, it was not certain that the AHR had a "normal" physiological function. However, the ongoing accumulation of data from an ever-expanding variety of studies on cancer, cancer immunity, autoimmunity, organ development, and other areas bears witness to a staggering array of AHR-controlled normal and pathological activities. The objective of this review is to discuss how the AHR has gone from a likely contributor to genotoxic environmental carcinogen-induced cancer to a master regulator of malignant cell progression and cancer aggression. Particular focus is placed on the association between AHR activity and poor cancer outcomes, feedback loops that control chronic AHR activity in cancer, and the role of chronically active AHR in driving cancer cell invasion, migration, cancer stem cell characteristics, and survival.
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http://dx.doi.org/10.3390/ijms22010387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7795223PMC
December 2020

Naturally occurring hotspot cancer mutations in Gα promote oncogenic signaling.

J Biol Chem 2020 12 27;295(49):16897-16904. Epub 2020 Oct 27.

Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA. Electronic address:

Heterotrimeric G-proteins are signaling switches broadly divided into four families based on the sequence and functional similarity of their Gα subunits: G, G, G, and G Artificial mutations that activate Gα subunits of each of these families have long been known to induce oncogenic transformation in experimental systems. With the advent of next-generation sequencing, activating hotspot mutations in G, G, or G proteins have also been identified in patient tumor samples. In contrast, patient tumor-associated G mutations characterized to date lead to inactivation rather than activation. By using bioinformatic pathway analysis and signaling assays, here we identified cancer-associated hotspot mutations in Arg-200 of Gα (encoded by ) as potent activators of oncogenic signaling. First, we found that components of a G-dependent signaling cascade that culminates in activation of the Hippo pathway effectors YAP and TAZ is frequently altered in bladder cancer. Up-regulation of this signaling cascade correlates with increased YAP/TAZ activation transcriptional signatures in this cancer type. Among the G pathway alterations were mutations in Arg-200 of Gα, which we validated to promote YAP/TAZ-dependent (TEAD) and MRTF-A/B-dependent (SRE.L) transcriptional activity. We further showed that this mechanism relies on the same RhoGEF-RhoGTPase cascade components that are up-regulated in bladder cancers. Moreover, Gα Arg-200 mutants induced oncogenic transformation as determined by focus formation assays. In summary, our findings on Gα mutants establish that naturally occurring hotspot mutations in Gα subunits of any of the four families of heterotrimeric G-proteins are putative cancer drivers.
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http://dx.doi.org/10.1074/jbc.AC120.014698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864081PMC
December 2020

β-Catenin/CBP inhibition alters epidermal growth factor receptor fucosylation status in oral squamous cell carcinoma.

Mol Omics 2020 06 23;16(3):195-209. Epub 2020 Mar 23.

Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, rm 511, Boston, MA 02118, USA.

Epidermal growth factor receptor (EGFR) is a major driver of head and neck cancer, a devastating malignancy with a major sub-site in the oral cavity manifesting as oral squamous cell carcinoma (OSCC). EGFR is a glycoprotein receptor tyrosine kinase (RTK) whose activity is upregulated in >80% OSCC. Current anti-EGFR therapy relies on the use of cetuximab, a monoclonal antibody against EGFR, although it has had only a limited response in patients. Here, we uncover a novel mechanism regulating EGFR activity, identifying a role of the nuclear branch of the Wnt/β-catenin signaling pathway, the β-catenin/CBP axis, in control of post-translational modification of N-glycans on the EGFR. Genomic and structural analyses reveal that β-catenin/CBP signaling represses fucosylation on the antennae of N-linked glycans on EGFR. By employing nUPLC-MS/MS, we determined that malignant human OSCC cells harbor EGFR with a paucity of N-glycan antennary fucosylation, while indolent cells display higher levels of fucosylation at sites N420 and N579. Additionally, treatment with either ICG-001 or E7386, which are both small molecule inhibitors of β-catenin/CBP signaling, leads to increased transcriptional expression of fucosyltransferases FUT2 and FUT3, with a concomitant increase in EGFR N-glycan antennary fucosylation. In order to discover which fucosylated glycan epitopes are involved in the observed effect, we performed in-depth characterization of multiply-fucosylated N-glycans via tandem mass spectrometry analysis of the EGFR tryptic glycopeptides. Data are available via ProteomeXchange with identifier PXD017060. We propose that β-catenin/CBP signaling promotes EGFR oncogenic activity in OSCC by inhibiting its N-glycan antennary fucosylation through transcriptional repression of FUT2 and FUT3.
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http://dx.doi.org/10.1039/d0mo00009dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7299767PMC
June 2020

Yap suppresses T-cell function and infiltration in the tumor microenvironment.

PLoS Biol 2020 01 13;18(1):e3000591. Epub 2020 Jan 13.

Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America.

A major challenge for cancer immunotherapy is sustaining T-cell activation and recruitment in immunosuppressive solid tumors. Here, we report that the levels of the Hippo pathway effector Yes-associated protein (Yap) are sharply induced upon the activation of cluster of differentiation 4 (CD4)-positive and cluster of differentiation 8 (CD8)-positive T cells and that Yap functions as an immunosuppressive factor and inhibitor of effector differentiation. Loss of Yap in T cells results in enhanced T-cell activation, differentiation, and function, which translates in vivo to an improved ability for T cells to infiltrate and repress tumors. Gene expression analyses of tumor-infiltrating T cells following Yap deletion implicates Yap as a mediator of global T-cell responses in the tumor microenvironment and as a negative regulator of T-cell tumor infiltration and patient survival in diverse human cancers. Collectively, our results indicate that Yap plays critical roles in T-cell biology and suggest that Yap inhibition improves T-cell responses in cancer.
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http://dx.doi.org/10.1371/journal.pbio.3000591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980695PMC
January 2020

Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis.

Sci Rep 2019 11 15;9(1):16904. Epub 2019 Nov 15.

Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA.

The emergence of large-scale multi-omics data warrants method development for data integration. Genomic studies from cancer patients have identified epigenetic and genetic regulators - such as methylation marks, somatic mutations, and somatic copy number alterations (SCNAs), among others - as predictive features of cancer outcome. However, identification of "driver genes" associated with a given alteration remains a challenge. To this end, we developed a computational tool, iEDGE, to model cis and trans effects of (epi-)DNA alterations and identify potential cis driver genes, where cis and trans genes denote those genes falling within and outside the genomic boundaries of a given (epi-)genetic alteration, respectively. iEDGE first identifies the cis and trans gene expression signatures associated with the presence/absence of a particular epi-DNA alteration across samples. It then applies tests of statistical mediation to determine the cis genes predictive of the trans gene expression. Finally, cis and trans effects are annotated by pathway enrichment analysis to gain insights into the underlying regulatory networks. We used iEDGE to perform integrative analysis of SCNAs and gene expression data from breast cancer and 18 additional cancer types included in The Cancer Genome Atlas (TCGA). Notably, cis gene drivers identified by iEDGE were found to be significantly enriched for known driver genes from multiple compendia of validated oncogenes and tumor suppressors, suggesting that the remainder are of equal importance. Furthermore, predicted drivers were enriched for functionally relevant cancer genes with amplification-driven dependencies, which are of potential prognostic and therapeutic value. All the analyses results are accessible at https://montilab.bu.edu/iEDGE. In summary, integrative analysis of SCNAs and gene expression using iEDGE successfully identified known cancer driver genes and putative cancer therapeutic targets across 19 cancer types in the TCGA. The proposed method can easily be applied to the integration of gene expression profiles with other epi-DNA assays in a variety of disease contexts.
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http://dx.doi.org/10.1038/s41598-019-52886-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858347PMC
November 2019

hypeR: an R package for geneset enrichment workflows.

Bioinformatics 2020 02;36(4):1307-1308

Bioinformatics Department, Boston University, Boston, MA 02118, USA.

Summary: Geneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in providing the flexibility to tackle the varied challenges researchers face in such analyses, particularly when analyzing many signatures across multiple experiments. We present a comprehensive R package for geneset enrichment workflows that offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting. hypeR is a one-stop solution to performing geneset enrichment for a wide audience and range of use cases.

Availability And Implementation: The most recent version of the package is available at https://github.com/montilab/hypeR.
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http://dx.doi.org/10.1093/bioinformatics/btz700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7998712PMC
February 2020

CXCR4 upregulation is an indicator of sensitivity to B-cell receptor/PI3K blockade and a potential resistance mechanism in B-cell receptor-dependent diffuse large B-cell lymphomas.

Haematologica 2020 05 30;105(5):1361-1368. Epub 2019 Aug 30.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA

B-cell receptor (BCR) signaling pathway components represent promising treatment targets in multiple B-cell malignancies including diffuse large B-cell lymphoma (DLBCL). In and model systems, a subset of DLBCLs depend upon BCR survival signals and respond to proximal BCR/phosphoinositide 3 kinase (PI3K) blockade. However, single-agent BCR pathway inhibitors have had more limited activity in patients with DLBCL, underscoring the need for indicators of sensitivity to BCR blockade and insights into potential resistance mechanisms. Here, we report highly significant transcriptional upregulation of C-X-C chemokine receptor 4 (CXCR4) in BCR-dependent DLBCL cell lines and primary tumors following chemical spleen tyrosine kinase (SYK) inhibition, molecular SYK depletion or chemical PI3K blockade. SYK or PI3K inhibition also selectively upregulated cell surface CXCR4 protein expression in BCR-dependent DLBCLs. CXCR4 expression was directly modulated by fork-head box O1 via the PI3K/protein kinase B/forkhead box O1 signaling axis. Following chemical SYK inhibition, all BCR-dependent DLBCLs exhibited significantly increased stromal cell-derived factor-1α (SDF-1α) induced chemotaxis, consistent with the role of CXCR4 signaling in B-cell migration. Select PI3K isoform inhibitors also augmented SDF-1α induced chemotaxis. These data define CXCR4 upregulation as an indicator of sensitivity to BCR/PI3K blockade and identify CXCR4 signaling as a potential resistance mechanism in BCR-dependent DLBCLs.
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http://dx.doi.org/10.3324/haematol.2019.216218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193488PMC
May 2020

A serum protein signature of APOE genotypes in centenarians.

Aging Cell 2019 12 5;18(6):e13023. Epub 2019 Aug 5.

Geriatrics Section, Department of Medicine, School of Medicine and Boston Medical Center, Boston University, Boston, MA.

The discovery of treatments to prevent or delay dementia and Alzheimer's disease is a priority. The gene APOE is associated with cognitive change and late-onset Alzheimer's disease, and epidemiological studies have provided strong evidence that the e allele of APOE has a neuroprotective effect, it is associated with increased longevity and an extended healthy lifespan in centenarians. In this study, we correlated APOE genotype data of 222 participants of the New England Centenarian Study, including 75 centenarians, 82 centenarian offspring, and 65 controls, comprising 55 carriers of APOE e , with aptamer-based serum proteomics (SomaLogic technology) of 4,785 human proteins corresponding to 4,137 genes. We discovered a signature of 16 proteins that associated with different APOE genotypes and replicated the signature in three independent studies. We also show that the protein signature tracks with gene expression profiles in brains of late-onset Alzheimer's disease versus healthy controls. Finally, we show that seven of these proteins correlate with cognitive function patterns in longitudinally collected data. This analysis in particular suggests that Baculoviral IAP repeat containing two (BIRC2) is a novel biomarker of neuroprotection that associates with the neuroprotective allele of APOE. Therefore, targeting APOE e molecularly may preserve cognitive function.
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http://dx.doi.org/10.1111/acel.13023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826130PMC
December 2019

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines.

Front Genet 2019 28;10:614. Epub 2019 Jun 28.

Bioinformatics Program, Boston University, Boston, MA, United States.

The advent of high-throughput sequencing technologies has led to the need for flexible and user-friendly data preprocessing platforms. The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow scripting language and Anaconda package manager to generate modular computational workflows. We have used Pipeliner to create several pipelines for sequencing data processing including bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, as well as digital gene expression data. This report highlights the design methodology behind Pipeliner that enables the development of highly flexible and reproducible pipelines that are easy to extend and maintain on multiple computing environments. We also provide a quick start user guide demonstrating how to setup and execute available pipelines with toy datasets.
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http://dx.doi.org/10.3389/fgene.2019.00614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609566PMC
June 2019

The Carcinogenome Project: In Vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity.

Environ Health Perspect 2019 04;127(4):47002

1 Computational Biomedicine, Boston University School of Medicine , Boston, Massachusetts, USA.

Background: Most chemicals in commerce have not been evaluated for their carcinogenic potential. The de facto gold-standard approach to carcinogen testing adopts the 2-y rodent bioassay, a time-consuming and costly procedure. High-throughput in vitro assays are a promising alternative for addressing the limitations in carcinogen screening.

Objectives: We developed a screening process for predicting chemical carcinogenicity and genotoxicity and characterizing modes of actions (MoAs) using in vitro gene expression assays.

Methods: We generated a large toxicogenomics resource comprising [Formula: see text] expression profiles corresponding to 330 chemicals profiled in HepG2 (human hepatocellular carcinoma cell line) at multiple doses and replicates. Predictive models of carcinogenicity and genotoxicity were built using a random forest classifier. Differential pathway enrichment analysis was performed to identify pathways associated with carcinogen exposure. Signatures of carcinogenicity and genotoxicity were compared with external sources, including Drugmatrix and the Connectivity Map.

Results: Among profiles with sufficient bioactivity, our classifiers achieved 72.2% Area Under the ROC Curve (AUC) for predicting carcinogenicity and 82.3% AUC for predicting genotoxicity. Chemical bioactivity, as measured by the strength and reproducibility of the transcriptional response, was not significantly associated with long-term carcinogenicity in doses up to [Formula: see text]. However, sufficient bioactivity was necessary for a chemical to be used for prediction of carcinogenicity. Pathway enrichment analysis revealed pathways consistent with known pathways that drive cancer, including DNA damage and repair. The data is available at https://clue.io/CRCGN_ABC , and a portal for query and visualization of the results is accessible at https://carcinogenome.org .

Discussion: We demonstrated an in vitro screening approach using gene expression profiling to predict carcinogenicity and infer MoAs of chemical perturbations. https://doi.org/10.1289/EHP3986.
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http://dx.doi.org/10.1289/EHP3986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785232PMC
April 2019

Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques.

Front Genet 2019 5;10:150. Epub 2019 Mar 5.

Bioinformatics Program, Boston University, Boston, MA, United States.

The need to reduce per sample cost of RNA-seq profiling for scalable data generation has led to the emergence of highly multiplexed RNA-seq. These technologies utilize barcoding of cDNA sequences in order to combine multiple samples into a single sequencing lane to be separated during data processing. In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq, microarrays, as well as another low-cost highly multiplexed technique known as 3' digital gene expression (3'DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3'DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from lung cancer mutation signatures.
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http://dx.doi.org/10.3389/fgene.2019.00150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411637PMC
March 2019

CaDrA: A Computational Framework for Performing Candidate Driver Analyses Using Genomic Features.

Front Genet 2019 19;10:121. Epub 2019 Feb 19.

Bioinformatics Program, Boston University, Boston, MA, United States.

The identification of genetic alteration combinations as drivers of a given phenotypic outcome, such as drug sensitivity, gene or protein expression, and pathway activity, is a challenging task that is essential to gaining new biological insights and to discovering therapeutic targets. Existing methods designed to predict complementary drivers of such outcomes lack analytical flexibility, including the support for joint analyses of multiple genomic alteration types, such as somatic mutations and copy number alterations, multiple scoring functions, and rigorous significance and reproducibility testing procedures. To address these limitations, we developed Candidate Driver Analysis or CaDrA, an integrative framework that implements a step-wise heuristic search approach to identify functionally relevant subsets of genomic features that, together, are maximally associated with a specific outcome of interest. We show CaDrA's overall high sensitivity and specificity for typically sized multi-omic datasets using simulated data, and demonstrate CaDrA's ability to identify known mutations linked with sensitivity of cancer cells to drug treatment using data from the Cancer Cell Line Encyclopedia (CCLE). We further apply CaDrA to identify novel regulators of oncogenic activity mediated by Hippo signaling pathway effectors YAP and TAZ in primary breast cancer tumors using data from The Cancer Genome Atlas (TCGA), which we functionally validate . Finally, we use pan-cancer TCGA protein expression data to show the high reproducibility of CaDrA's search procedure. Collectively, this work demonstrates the utility of our framework for supporting the fast querying of large, publicly available multi-omics datasets, including but not limited to TCGA and CCLE, for potential drivers of a given target profile of interest.
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http://dx.doi.org/10.3389/fgene.2019.00121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390206PMC
February 2019

PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects.

Bioinformatics 2019 09;35(17):3046-3054

Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.

Motivation: Over the last decade, more diverse populations have been included in genome-wide association studies. If a genetic variant has a varying effect on a phenotype in different populations, genome-wide association studies applied to a dataset as a whole may not pinpoint such differences. It is especially important to be able to identify population-specific effects of genetic variants in studies that would eventually lead to development of diagnostic tests or drug discovery.

Results: In this paper, we propose PopCluster: an algorithm to automatically discover subsets of individuals in which the genetic effects of a variant are statistically different. PopCluster provides a simple framework to directly analyze genotype data without prior knowledge of subjects' ethnicities. PopCluster combines logistic regression modeling, principal component analysis, hierarchical clustering and a recursive bottom-up tree parsing procedure. The evaluation of PopCluster suggests that the algorithm has a stable low false positive rate (∼4%) and high true positive rate (>80%) in simulations with large differences in allele frequencies between cases and controls. Application of PopCluster to data from genetic studies of longevity discovers ethnicity-dependent heterogeneity in the association of rs3764814 (USP42) with the phenotype.

Availability And Implementation: PopCluster was implemented using the R programming language, PLINK and Eigensoft software, and can be found at the following GitHub repository: https://github.com/gurinovich/PopCluster with instructions on its installation and usage.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btz017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735784PMC
September 2019

Functional and genomic analyses reveal therapeutic potential of targeting β-catenin/CBP activity in head and neck cancer.

Genome Med 2018 07 20;10(1):54. Epub 2018 Jul 20.

Department of Molecular and Cell Biology, Goldman School of Dental Medicine, Boston University School of Medicine, 72 East Concord Street, E4, Boston, MA, 02118, USA.

Background: Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy characterized by tumor heterogeneity, locoregional metastases, and resistance to existing treatments. Although a number of genomic and molecular alterations associated with HNSCC have been identified, they have had limited impact on the clinical management of this disease. To date, few targeted therapies are available for HNSCC, and only a small fraction of patients have benefited from these treatments. A frequent feature of HNSCC is the inappropriate activation of β-catenin that has been implicated in cell survival and in the maintenance and expansion of stem cell-like populations, thought to be the underlying cause of tumor recurrence and resistance to treatment. However, the therapeutic value of targeting β-catenin activity in HNSCC has not been explored.

Methods: We utilized a combination of computational and experimental profiling approaches to examine the effects of blocking the interaction between β-catenin and cAMP-responsive element binding (CREB)-binding protein (CBP) using the small molecule inhibitor ICG-001. We generated and annotated in vitro treatment gene expression signatures of HNSCC cells, derived from human oral squamous cell carcinomas (OSCCs), using microarrays. We validated the anti-tumorigenic activity of ICG-001 in vivo using SCC-derived tumor xenografts in murine models, as well as embryonic zebrafish-based screens of sorted stem cell-like subpopulations. Additionally, ICG-001-inhibition signatures were overlaid with RNA-sequencing data from The Cancer Genome Atlas (TCGA) for human OSCCs to evaluate its association with tumor progression and prognosis.

Results: ICG-001 inhibited HNSCC cell proliferation and tumor growth in cellular and murine models, respectively, while promoting intercellular adhesion and loss of invasive phenotypes. Furthermore, ICG-001 preferentially targeted the ability of subpopulations of stem-like cells to establish metastatic tumors in zebrafish. Significantly, interrogation of the ICG-001 inhibition-associated gene expression signature in the TCGA OSCC human cohort indicated that the targeted β-catenin/CBP transcriptional activity tracked with tumor status, advanced tumor grade, and poor overall patient survival.

Conclusions: Collectively, our results identify β-catenin/CBP interaction as a novel target for anti-HNSCC therapy and provide evidence that derivatives of ICG-001 with enhanced inhibitory activity may serve as an effective strategy to interfere with aggressive features of HNSCC.
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http://dx.doi.org/10.1186/s13073-018-0569-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053793PMC
July 2018

Tributyltin induces a transcriptional response without a brite adipocyte signature in adipocyte models.

Arch Toxicol 2018 09 19;92(9):2859-2874. Epub 2018 Jul 19.

Department of Environmental Health, Boston University School of Public Health, 715 Albany Street, R-405, Boston, MA, 02118, USA.

Tributyltin (TBT), a peroxisome proliferator-activated receptor γ (PPARγ)/retinoid X receptor (RXR) ligand and founding member of the environmental obesogen chemical class, induces adipocyte differentiation and suppresses bone formation. A growing number of environmental PPARγ ligands are being identified. However, the potential for environmental PPARγ ligands to induce adverse metabolic effects has been questioned because PPARγ is a therapeutic target in treatment of type II diabetes. We evaluated the molecular consequences of TBT exposure during bone marrow multipotent mesenchymal stromal cell (BM-MSC) differentiation in comparison to rosiglitazone, a therapeutic PPARγ ligand, and LG100268, a synthetic RXR ligand. Mouse primary BM-MSCs (female, C57BL/6J) undergoing bone differentiation were exposed to maximally efficacious and human relevant concentrations of rosiglitazone (100 nM), LG100268 (100 nM) or TBT (80 nM) for 4 days. Gene expression was assessed using microarrays, and in silico functional annotation was performed using pathway enrichment analysis approaches. Pathways related to osteogenesis were downregulated by all three ligands, while pathways related to adipogenesis were upregulated by rosiglitazone and TBT. However, pathways related to mitochondrial biogenesis and brown-in-white (brite) adipocyte differentiation were more significantly upregulated in rosiglitazone-treated than TBT-treated cells. The lack of induction of genes involved in adipocyte energy dissipation by TBT was confirmed by an independent gene expression analysis in BM-MSCs undergoing adipocyte differentiation and by analysis of a publically available 3T3 L1 data set. Furthermore, rosiglitazone, but not TBT, induced mitochondrial biogenesis and respiration. This study is the first to show that an environmental PPARγ ligand has a limited capacity to induce health-promoting activities of PPARγ.
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http://dx.doi.org/10.1007/s00204-018-2268-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6815880PMC
September 2018

Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes.

Nat Med 2018 Aug;24(8):1290-1291

Mayo Clinic, Rochester, MN, USA.

In the version of this article originally published, an asterisk was omitted from Fig. 1a. The asterisk has been added to the figure. Additionally, a "NOTCH2" label was erroneously included in Fig. 4a. The label has been removed. The errors have been corrected in the PDF and HTML versions of this article.
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http://dx.doi.org/10.1038/s41591-018-0097-4DOI Listing
August 2018

Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes.

Nat Med 2018 Aug;24(8):1292

Mayo Clinic, Rochester, MN, USA.

In the version of this article originally published, some text above the "Tri-nucleotide sequence motifs" label in Fig. 2a appeared incorrectly. The text was garbled and should have appeared as nucleotide codes.Additionally, the labels on the bars in Fig. 2c were not italicized in the original publication. These are gene symbols, and they should have been italicized.The colored labels above the graphs in Fig. 4b were also erroneously not italicized. These labels represent gene names and loci, and they should have been italicized.
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http://dx.doi.org/10.1038/s41591-018-0098-3DOI Listing
August 2018

Towards Resolving the Pro- and Anti-Tumor Effects of the Aryl Hydrocarbon Receptor.

Int J Mol Sci 2018 May 7;19(5). Epub 2018 May 7.

Department of Environmental Health, Boston University School of Public Health, 72 East Concord St., Boston, MA 02118, USA.

We have postulated that the aryl hydrocarbon receptor (AHR) drives the later, more lethal stages of some cancers when chronically activated by endogenous ligands. However, other studies have suggested that, under some circumstances, the AHR can oppose tumor aggression. Resolving this apparent contradiction is critical to the design of AHR-targeted cancer therapeutics. Molecular (siRNA, shRNA, AHR repressor, CRISPR-Cas9) and pharmacological (AHR inhibitors) approaches were used to confirm the hypothesis that AHR inhibition reduces human cancer cell invasion (irregular colony growth in 3D Matrigel cultures and Boyden chambers), migration (scratch wound assay) and metastasis (human cancer cell xenografts in zebrafish). Furthermore, these assays were used for a head-to-head comparison between AHR antagonists and agonists. AHR inhibition or knockdown/knockout consistently reduced human ER/PR/Her2 and inflammatory breast cancer cell invasion, migration, and metastasis. This was associated with a decrease in invasion-associated genes (e.g., , , Thrombospondin, ) and an increase in , previously associated with decreased tumor aggression. Paradoxically, AHR agonists (2,3,7,8-tetrachlorodibenzo--dioxin and/or 3,3′-diindolylmethane) similarly inhibited irregular colony formation in Matrigel and blocked metastasis in vivo but accelerated migration. These data demonstrate the complexity of modulating AHR activity in cancer while suggesting that AHR inhibitors, and, under some circumstances, AHR agonists, may be useful as cancer therapeutics.
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http://dx.doi.org/10.3390/ijms19051388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983651PMC
May 2018
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