Publications by authors named "Lianbo Yu"

118 Publications

A Novel Inflammatory Dendritic Cell That Is Abundant and Contiguous to T Cells in the Kidneys of Patients With Lupus Nephritis.

Front Immunol 2021 17;12:621039. Epub 2021 Feb 17.

Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, OH, United States.

The mechanisms that promote local inflammatory injury during lupus nephritis (LN) flare are largely unknown. Understanding the key immune cells that drive intrarenal inflammation will advance our knowledge of disease pathogenesis and inform the development of new therapeutics for LN management. In this study, we analyzed kidney biopsies from patients with proliferative LN and identified a novel inflammatory dendritic cell (infDC) population that is highly expressed in the LN kidney, but minimally present in healthy human kidneys. During an agnostic evaluation of immune transcript expression in the kidneys of patients with proliferative LN, the most abundantly overexpressed transcript from isolated glomeruli was , which encodes the Fc receptor gamma chain (FcRγ). To identify the cell types expressing FcRγ that infiltrate the kidney in LN, studies were done on kidney biopsies from patients with active LN using confocal immunofluorescence (IF) microscopy. This showed that FcRγ is abundantly present in the periglomerular (PG) region of the kidney and to a lesser extent in the tubulointerstitium (TI). Further investigation of the surface markers of these cells showed that they were FcRγ, MHC II, CD11c, CD163, CD5, DC-SIGN, CD64, CD14, CD16, SIRPα, CD206, CD68, CD123, CD3, and CD11b, suggesting the cells were infDCs. Quantification of the infDCs showed an average 10-fold higher level of infDCs in the LN kidney compared to the healthy kidneys. Importantly, IF identified CD3 T cells to be adjacent to these infDCs in the PG space of the LN kidney, whereas both cell types are minimally present in the healthy kidney. Thus, we have identified a previously undescribed DC in lupus kidneys that may interact with intrarenal T cells and play a role in the pathogenesis of kidney injury during LN flare.
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http://dx.doi.org/10.3389/fimmu.2021.621039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919935PMC
February 2021

Establishing a Case for Anti-complement Therapy in Membranous Nephropathy.

Kidney Int Rep 2021 Feb 13;6(2):484-492. Epub 2020 Dec 13.

Department of Medicine, Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.

Introduction: Membranous nephropathy (MN) is a common cause of adult nephrotic syndrome that progresses to end-stage kidney disease in up to 40% of cases. It is an autoimmune disease characterized by glomerular subepithelial deposits containing IgG. In experimental MN, these deposits activate complement and cause kidney damage. The role of complement in human MN is less clearly defined. To address this, the current study focused on the role of complement in 2 independent primary (p) MN cohorts.

Methods: Glomeruli were isolated by laser capture microdissection and analyzed by mass spectrometry, focusing on complement proteins, from kidney biopsy specimens from a pMN cohort (n = 11) and from normal controls (n = 5). Immunohistological staining of kidney biopsy specimens for complement proteins was also done. In a second pMN cohort (n = 13), urine levels of Ba, C5a, and C5b-9 (membrane attack complex [MAC]) were measured.

Results: Mass spectrometry identified 8 complement pathway components (C1q, C3, C4, C5, C6, C7, C8, and C9) and 5 complement regulators (complement receptor type 1 [CR1], factor H [FH], FH-related protein 2 [FHR2], vitronectin, and clusterin). All complement levels were significantly higher in the MN groups than in the control group, except the level of CR1, which was lower. All pMN biopsy specimens showed negative or trace staining for C1q, positive staining for C3 and C4, and positive staining for at least 1 component of the lectin pathway. Urine Ba, C5a, and MAC were present in pMN, and their levels correlated ( = 0.87,  = 0.89, and  = 0.97,  = .001 for each correlation).

Conclusion: Elevated glomerular levels of C3, C4, and components of MAC (C5b-9) and absent or decreased levels of the complement regulator CR1, along with increased levels of complement activation products in the urine, support the involvement of complement in the pathogenesis of MN. These data raise the possibility that anti-complement therapies may be effective in some forms of MN.
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http://dx.doi.org/10.1016/j.ekir.2020.11.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7879111PMC
February 2021

Paracardial fat remodeling affects systemic metabolism through alcohol dehydrogenase 1.

J Clin Invest 2021 Feb;131(4)

Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA.

The relationship between adiposity and metabolic health is well established. However, very little is known about the fat depot, known as paracardial fat (pCF), located superior to and surrounding the heart. Here, we show that pCF remodels with aging and a high-fat diet and that the size and function of this depot are controlled by alcohol dehydrogenase 1 (ADH1), an enzyme that oxidizes retinol into retinaldehyde. Elderly individuals and individuals with obesity have low ADH1 expression in pCF, and in mice, genetic ablation of Adh1 is sufficient to drive pCF accumulation, dysfunction, and global impairments in metabolic flexibility. Metabolomics analysis revealed that pCF controlled the levels of circulating metabolites affecting fatty acid biosynthesis. Also, surgical removal of the pCF depot was sufficient to rescue the impairments in cardiometabolic flexibility and fitness observed in Adh1-deficient mice. Furthermore, treatment with retinaldehyde prevented pCF remodeling in these animals. Mechanistically, we found that the ADH1/retinaldehyde pathway works by driving PGC-1α nuclear translocation and promoting mitochondrial fusion and biogenesis in the pCF depot. Together, these data demonstrate that pCF is a critical regulator of cardiometabolic fitness and that retinaldehyde and its generating enzyme ADH1 act as critical regulators of adipocyte remodeling in the pCF depot.
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http://dx.doi.org/10.1172/JCI141799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7880313PMC
February 2021

Characterization of Clonal Evolution in Microsatellite Unstable Metastatic Cancers through Multiregional Tumor Sequencing.

Mol Cancer Res 2021 Mar 23;19(3):465-474. Epub 2020 Nov 23.

Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.

Microsatellites are short, repetitive segments of DNA, which are dysregulated in mismatch repair-deficient (MMRd) tumors resulting in microsatellite instability (MSI). MSI has been identified in many human cancer types with varying incidence, and microsatellite instability-high (MSI-H) tumors often exhibit increased sensitivity to immune-enhancing therapies such as PD-1/PD-L1 inhibition. Next-generation sequencing (NGS) has permitted advancements in MSI detection, and recent computational advances have enabled characterization of tumor heterogeneity via NGS. However, the evolution and heterogeneity of microsatellite changes in MSI-positive tumors remains poorly described. We determined MSI status in 6 patients using our previously published algorithm, MANTIS, and inferred subclonal composition and phylogeny with Canopy and SuperFreq. We developed a simulated annealing-based method to characterize microsatellite length distributions in specific subclones and assessed the evolution of MSI in the context of tumor heterogeneity. We identified three to eight tumor subclones per patient, and each subclone exhibited MMRd-associated base substitution signatures. We noted that microsatellites tend to shorten over time, and that MMRd fosters heterogeneity by introducing novel mutations throughout the disease course. Some microsatellites are altered among all subclones in a patient, whereas other loci are only altered in particular subclones corresponding to subclonal phylogenetic relationships. Overall, our results indicate that MMRd is a substantial driver of heterogeneity, leading to both MSI and subclonal divergence. IMPLICATIONS: We leveraged subclonal inference to assess clonal evolution based on somatic mutations and microsatellites, which provides insight into MMRd as a dynamic mutagenic process in MSI-H malignancies.
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http://dx.doi.org/10.1158/1541-7786.MCR-19-0955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7939074PMC
March 2021

Characterizing the function of EPB41L4A in the predisposition to papillary thyroid carcinoma.

Sci Rep 2020 11 17;10(1):19984. Epub 2020 Nov 17.

Human Cancer Genetics Program and Department of Cancer Biology and Genetics, Comprehensive Cancer Center, College of Medicine, The Ohio State University Wexner Medical Center, 804 Biomedical Research Tower, 460 W 12th Ave., Columbus, OH, 43210, USA.

Papillary thyroid carcinoma (PTC) is the most common histotype of thyroid carcinoma. The heritability of PTC is high compared to other cancers, but its underlying causes are unknown. A recent genome-wide association study revealed the association of a variant at the 5q22 locus, rs73227498, with PTC predisposition. We report that rs17134155, a variant in high linkage disequilibrium with rs73227498, is located in an enhancer region downstream of coding transcripts of EPB41L4A. Rs17134155 showed significant enhancer activity in luciferase assays, and haplotypes containing the protective allele of this variant conferred a significantly lower risk of PTC. While the index SNP, rs73227498, acted as a significant cis-eQTL for expression of EPB41L4A, rs17134155 was a significant cis-sQTL for the alternative splicing of a non-coding transcript of EPB41L4A, called EPB41L4A-203. We also performed knockdown of EPB41L4A followed by microarray analysis. Some of the top differentially-expressed genes were represented among regulators of the WNT/β-catenin signaling pathway. Our results indicate that an enhancer region at 5q22 regulates the expression and splicing of EPB41L4A transcripts. We also provide evidence that EPB41L4A expression is involved in regulating growth and differentiation pathways, suggesting that decreased expression of EPB41L4A is a mechanism in the predisposition to PTC.
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http://dx.doi.org/10.1038/s41598-020-76606-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7672090PMC
November 2020

Digital Otoscopy Videos Versus Composite Images: A Reader Study to Compare the Accuracy of ENT Physicians.

Laryngoscope 2021 May 10;131(5):E1668-E1676. Epub 2020 Nov 10.

Department of Otolaryngology, Ohio State University, Columbus, Ohio, U.S.A.

Objectives/hypothesis: With the increasing emphasis on developing effective telemedicine approaches in Otolaryngology, this study explored whether a single composite image stitched from a digital otoscopy video provides acceptable diagnostic information to make an accurate diagnosis, as compared with that provided by the full video.

Study Design: Diagnostic survey analysis.

Methods: Five Ear, Nose, and Throat (ENT) physicians reviewed the same set of 78 digital otoscope eardrum videos from four eardrum conditions: normal, effusion, retraction, and tympanosclerosis, along with the composite images generated by a SelectStitch method that selectively uses video frames with computer-assisted selection, as well as a Stitch method that incorporates all the video frames. Participants provided a diagnosis for each item along with a rating of diagnostic confidence. Diagnostic accuracy for each pathology of SelectStitch was compared with accuracy when reviewing the entire video clip and when reviewing the Stitch image.

Results: There were no significant differences in diagnostic accuracy for physicians reviewing SelectStitch images and full video clips, but both provided better diagnostic accuracy than Stitch images. The inter-reader agreement was moderate.

Conclusions: Equal to using full video clips, composite images of eardrums generated by SelectStitch provided sufficient information for ENTs to make the correct diagnoses for most pathologies. These findings suggest that use of a composite eardrum image may be sufficient for telemedicine approaches to ear diagnosis, eliminating the need for storage and transmission of large video files, along with future applications for improved documentation in electronic medical record systems, patient/family counseling, and clinical training.

Level Of Evidence: 3 Laryngoscope, 131:E1668-E1676, 2021.
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http://dx.doi.org/10.1002/lary.29253DOI Listing
May 2021

Differentiating Staphylococcus infection-associated glomerulonephritis and primary IgA nephropathy: a mass spectrometry-based exploratory study.

Sci Rep 2020 10 14;10(1):17179. Epub 2020 Oct 14.

Division of Nephrology, Department of Internal Medicine, Ground Floor, The Ohio State University Wexner Medical Center, 395 West 12th Avenue, Columbus, OH, 43210, USA.

Staphylococcus infection-associated glomerulonephritis (SAGN) and primary IgA nephropathy (IgAN) are separate disease entities requiring different treatment approaches. However, overlapping histologic features may cause a diagnostic dilemma. An exploratory proteomic study to identify potential distinguishing biomarkers was performed on formalin fixed paraffin embedded kidney biopsy tissue, using mass spectrometry (HPLC-MS/MS) (n = 27) and immunohistochemistry (IHC) (n = 64), on four main diagnostic groups-SAGN, primary IgAN, acute tubular necrosis (ATN) and normal kidney (baseline transplant biopsies). Spectral counts modeled as a negative binomial distribution were used for statistical comparisons and in silico pathway analysis. Analysis of variance techniques were used to compare groups and the ROC curve to evaluate classification algorithms. The glomerular proteomes of SAGN and IgAN showed remarkable similarities, except for significantly higher levels of monocyte/macrophage proteins in SAGN-mainly lysozyme and S100A9. This finding was confirmed by IHC. In contrast, the tubulointerstitial proteomes were markedly different in IgAN and SAGN, with a lower abundance of metabolic pathway proteins and a higher abundance of extracellular matrix proteins in SAGN. The stress protein transglutaminase-2 (TGM2) was also significantly higher in SAGN. IHC of differentially-expressed glomerular and tubulointerstitial proteins can be used to help discriminate between SAGN and IgAN in ambiguous cases.
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http://dx.doi.org/10.1038/s41598-020-73847-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560901PMC
October 2020

Transcriptomics-Based Drug Repurposing Approach Identifies Novel Drugs against Sorafenib-Resistant Hepatocellular Carcinoma.

Cancers (Basel) 2020 Sep 23;12(10). Epub 2020 Sep 23.

Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.

Hepatocellular carcinoma (HCC) is frequently diagnosed in patients with late-stage disease who are ineligible for curative surgical therapies. The majority of patients become resistant to sorafenib, the only approved first-line therapy for advanced cancer, underscoring the need for newer, more effective drugs. The purpose of this study is to expedite identification of novel drugs against sorafenib resistant (SR)-HCC. We employed a transcriptomics-based drug repurposing method termed connectivity mapping using gene signatures from in vitro-derived SR Huh7 HCC cells. For proof of concept validation, we focused on drugs that were FDA-approved or under clinical investigation and prioritized two anti-neoplastic agents (dasatinib and fostamatinib) with targets associated with HCC. We also prospectively validated predicted gene expression changes in drug-treated SR Huh7 cells as well as identified and validated the targets of Fostamatinib in HCC. Dasatinib specifically reduced the viability of SR-HCC cells that correlated with up-regulated activity of SRC family kinases, its targets, in our SR-HCC model. However, fostamatinib was able to inhibit both parental and SR HCC cells in vitro and in xenograft models. Ingenuity pathway analysis of fostamatinib gene expression signature from LINCS predicted JAK/STAT, PI3K/AKT, ERK/MAPK pathways as potential targets of fostamatinib that were validated by Western blot analysis. Fostamatinib treatment reversed the expression of genes that were deregulated in SR HCC. We provide proof of concept evidence for the validity of this drug repurposing approach for SR-HCC with implications for personalized medicine.
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http://dx.doi.org/10.3390/cancers12102730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7598246PMC
September 2020

RNA-Seq Reproducibility Assessment of the Sequencing Quality Control Project.

Authors:
Lianbo Yu

Cancer Inform 2020 20;19:1176935120922498. Epub 2020 May 20.

Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.

With the widespread RNA-seq applications of different sequencing platforms in biomedical science research in recent years, a systematic evaluation of RNA-seq data quality is crucial and timely. The Sequencing Quality Control (SEQC) project is a large-scale community effort for assessing the performance of RNA-seq technology across different platforms and multiple laboratories, where reference RNA samples with multiple replicates were sequenced at 12 laboratories using 3 sequencing platforms. Different from the SEQC project, we performed an independent and comprehensive analysis of RNA-seq data of the SEQC project to assess sequencing reproducibility across platforms, sequencing sites, sample replicates, and FlowCells, respectively. With the employment of graphical tools and statistical models, our systemic analysis supports a distinctive conclusion that reproducibility across platforms and sequencing sites are not acceptable, whereas reproducibility across sample replicates and FlowCells are acceptable.
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http://dx.doi.org/10.1177/1176935120922498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241209PMC
May 2020

Power analysis for RNA-Seq differential expression studies using generalized linear mixed effects models.

BMC Bioinformatics 2020 May 19;21(1):198. Epub 2020 May 19.

Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, 1800 Cannon Dr., Columbus, 43210, OH, USA.

Background: Power analysis becomes an inevitable step in experimental design of current biomedical research. Complex designs allowing diverse correlation structures are commonly used in RNA-Seq experiments. However, the field currently lacks statistical methods to calculate sample size and estimate power for RNA-Seq differential expression studies using such designs. To fill the gap, simulation based methods have a great advantage by providing numerical solutions, since theoretical distributions of test statistics are typically unavailable for such designs.

Results: In this paper, we propose a novel simulation based procedure for power estimation of differential expression with the employment of generalized linear mixed effects models for correlated expression data. We also propose a new procedure for power estimation of differential expression with the use of a bivariate negative binomial distribution for paired designs. We compare the performance of both the likelihood ratio test and Wald test under a variety of simulation scenarios with the proposed procedures. The simulated distribution was used to estimate the null distribution of test statistics in order to achieve the desired false positive control and was compared to the asymptotic Chi-square distribution. In addition, we applied the procedure for paired designs to the TCGA breast cancer data set.

Conclusions: In summary, we provide a framework for power estimation of RNA-Seq differential expression under complex experimental designs. Simulation results demonstrate that both the proposed procedures properly control the false positive rate at the nominal level.
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http://dx.doi.org/10.1186/s12859-020-3541-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236949PMC
May 2020

Exploratory analysis of immune checkpoint receptor expression by circulating T cells and tumor specimens in patients receiving neo-adjuvant chemotherapy for operable breast cancer.

BMC Cancer 2020 May 19;20(1):445. Epub 2020 May 19.

The Ohio State University Comprehensive Cancer Center, The Ohio State University, 410 W 12th Avenue, Columbus, OH, 43210, USA.

Background: While combinations of immune checkpoint (ICP) inhibitors and neo-adjuvant chemotherapy (NAC) have begun testing in patients with breast cancer (BC), the effects of chemotherapy on ICP expression in circulating T cells and within the tumor microenvironment are still unclear. This information could help with the design of future clinical trials by permitting the selection of the most appropriate ICP inhibitors for incorporation into NAC.

Methods: Peripheral blood samples and/or tumor specimens before and after NAC were obtained from 24 women with operable BC. The expression of CTLA4, PD-1, Lag3, OX40, and Tim3 on circulating T lymphocytes before and at the end of NAC were measured using flow cytometry. Furthermore, using multi-color immunohistochemistry (IHC), the expression of immune checkpoint molecules by stromal tumor-infiltrating lymphocytes (TILs), CD8+ T cells, and tumor cells was determined before and after NAC. Differences in the percentage of CD4+ and CD8+ T cells expressing various checkpoint receptors were determined by a paired Student's t-test.

Results: This analysis showed decreased ICP expression by circulating CD4+ T cells after NAC, including significant decreases in CTLA4, Lag3, OX40, and PD-1 (all p values < 0.01). In comparison, circulating CD8+ T cells showed a significant increase in CTLA4, Lag3, and OX40 (all p values < 0.01). Within tumor samples, TILs, CD8+ T cells, and PD-L1/PD-1 expression decreased after NAC. Additionally, fewer tumor specimens were considered to be PD-L1/PD-1 positive post-NAC as compared to pre-NAC biopsy samples using a cutoff of 1% expression.

Conclusions: This work revealed that NAC treatment can substantially downregulate CD4+ and upregulate CD8+ T cell ICP expression as well as deplete the amount of TILs and CD8+ T cells found in breast tumor samples. These findings provide a starting point to study the biological significance of these changes in BC patients.

Trial Registration: NCT04022616.
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http://dx.doi.org/10.1186/s12885-020-06949-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236344PMC
May 2020

Association of Epigenetic Age and p16INK4a With Markers of T-Cell Composition in a Healthy Cohort.

J Gerontol A Biol Sci Med Sci 2020 11;75(12):2299-2303

Department of Psychiatry and Behavioral Health, Institute for Behavioral Medicine, College of Medicine, The Ohio State University, Columbus.

How the measurement of aging biomarkers in peripheral blood T-lymphocytes (PBTLs) is influenced by cell composition is unclear. Here, we collected peripheral blood and isolated CD3+ PBTLs from 117 healthy couples between the ages of 21 and 72. Each sample was profiled for Horvath epigenetic clock (DNAm), p16INK4a expression, cytomegalovirus (CMV) seropositivity and 74 mRNA markers of PBTL subtype, differentiation, immune checkpoints, and cytokine production. Correlations between individual aging biomarkers (DNAm or p16INK4a) and PBTL mRNAs were corrected for chronological age, sex, and couple. DNAm measurements correlated with CMV seropositivity as well as PBTL mRNAs indicative of effector function (CD8A, EOMES, TBX21, GZMB), poor proliferative capacity (KLRG1, CD57), differentiation (CD45RO, CD45RA), and immune checkpoints (PDCD1, TIGIT, LAG3, CD160, CD244). In contrast, only three PBTL mRNAs, CD28, CD244, and p14ARF, showed a significant association with p16INK4a. p16INK4a expression also showed a weaker association with immunosenescent PBTL subsets than DNAm in flow cytometry analyses. These data suggest that PBTL composition has a greater influence on DNAm than p16INK4a and link accelerated epigenetic aging to immunosenescent phenotypes.
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http://dx.doi.org/10.1093/gerona/glaa108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7662168PMC
November 2020

Variants in reveal distinct mechanisms for predisposition to papillary thyroid carcinoma.

J Med Genet 2020 08 12;57(8):519-527. Epub 2020 Feb 12.

Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA

Background: Papillary thyroid carcinoma (PTC) demonstrates high heritability and a low somatic mutation burden relative to other cancers. Therefore, the genetic risk predisposing to PTC is likely due to a combination of low penetrance variants. A recent genome-wide association study revealed the association of PTC with a missense variant, rs6793295, at 3q26 in a gene called Leucine Repeat Rich Containing 34 ().

Methods: We report the mechanisms of PTC risk at 3q26 using a combination of overexpression, mass spectroscopy, knockdown, transcriptome profiling, migration assays and genetic analysis.

Results: We observed differential binding of wild-type and missense LRRC34 to RANBP1. Overexpression of missense LRRC34 reduced RanGTP levels and increased apoptosis. We also identified a second linkage disequilibrium (LD) block upstream of containing regulatory variants with allele-specific expression. Transcriptome profiling of knockdown cells showed changes in genes involved with cellular movement. knockdown reduced the migration of thyroid cancer cell lines. Lastly, we assessed the relative contribution of PTC risk from each locus using haplotype analysis.

Conclusions: Our study demonstrates two separate mechanisms, one in G protein signalling and the other in transcriptional control, dictating PTC risk at 3q26 using both biochemical and genetic techniques.
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http://dx.doi.org/10.1136/jmedgenet-2019-106554DOI Listing
August 2020

Fully moderated t-statistic in linear modeling of mixed effects for differential expression analysis.

BMC Bioinformatics 2019 Dec 20;20(Suppl 24):675. Epub 2019 Dec 20.

Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, 1800 Cannon Dr., Columbus, 43210, OH, USA.

Background: Gene expression profiling experiments with few replicates lead to great variability in the estimates of gene variances. Toward this end, several moderated t-test methods have been developed to reduce this variability and to increase power for testing differential expression. Most of these moderated methods are based on linear models with fixed effects where residual variances are smoothed under a hierarchical Bayes framework. However, they are inadequate for designs with complex correlation structures, therefore application of moderated methods to linear models with mixed effects are needed for differential expression analysis.

Results: We demonstrated the implementation of the fully moderated t-statistic method for linear models with mixed effects, where both residual variances and variance estimates of random effects are smoothed under a hierarchical Bayes framework. We compared the proposed method with two current moderated methods and show that the proposed method can control the expected number of false positives at the nominal level, while the two current moderated methods fail.

Conclusions: We proposed an approach for testing differential expression under complex correlation structures while providing variance shrinkage. The proposed method is able to improve power by moderation and controls the expected number of false positives properly at the nominal level.
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http://dx.doi.org/10.1186/s12859-019-3248-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923909PMC
December 2019

Comparative studies of two generations of NanoString nCounter System.

PLoS One 2019 21;14(11):e0225505. Epub 2019 Nov 21.

Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America.

The NanoString nCounter System has been widely used in basic science and translational science research for the past decade. The System consists of two instruments: the PrepStation and the Digital Analyzer, and both have been continuously improved with evolving technologies. A great amount of research data have been generated at multiple research laboratories with the employment of different generations of the System. With the need of integrating multiple datasets, researchers are interested to know whether signals are comparable between different generations of the System. Toward this end, we designed a profiling study to compare performance of two generations of the NanoString nCounter System using a common set of biological samples. Using graphical tools and statistical models, we found that two different generations of NanoString nCounter System produced equivalent signals and signal deviations are in the range of random background noises for the medium-high expression levels.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225505PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874068PMC
March 2020

Ibrutinib Potentiates Antihepatocarcinogenic Efficacy of Sorafenib by Targeting EGFR in Tumor Cells and BTK in Immune Cells in the Stroma.

Mol Cancer Ther 2020 02 3;19(2):384-396. Epub 2019 Oct 3.

Department of Pathology, The Ohio State University, Columbus, Ohio.

Hepatocellular carcinoma (HCC), the most prevalent primary liver cancer, is a leading cause of cancer-related death worldwide because of rising incidence and limited therapy. Although treatment with sorafenib or lenvatinib is the standard of care in patients with advanced-stage HCC, the survival benefit from sorafenib is limited due to low response rate and drug resistance. Ibrutinib, an irreversible tyrosine kinase inhibitor (TKI) of the TEC (e.g., BTK) and ErbB (e.g., EGFR) families, is an approved treatment for B-cell malignancies. Here, we demonstrate that ibrutinib inhibits proliferation, spheroid formation, and clonogenic survival of HCC cells, including sorafenib-resistant cells. Mechanistically, ibrutinib inactivated EGFR and its downstream Akt and ERK signaling in HCC cells, and downregulated a set of critical genes involved in cell proliferation, migration, survival, and stemness, and upregulated genes promoting differentiation. Moreover, ibrutinib showed synergy with sorafenib or regorafenib, a sorafenib congener, by inducing apoptosis of HCC cells. , this TKI combination significantly inhibited HCC growth and prolonged survival of immune-deficient mice bearing human HCCLM3 xenograft tumors and immune-competent mice bearing orthotopic mouse Hepa tumors at a dose that did not exhibit systemic toxicity. In immune-competent mice, the ibrutinib-sorafenib combination reduced the numbers of BTK immune cells in the tumor microenvironment. Importantly, we found that the BTK immune cells were also enriched in the tumor microenvironment in a subset of primary human HCCs. Collectively, our findings implicate BTK signaling in hepatocarcinogenesis and support clinical trials of the sorafenib-ibrutinib combination for this deadly disease.
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http://dx.doi.org/10.1158/1535-7163.MCT-19-0135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007841PMC
February 2020

Rethinking Lupus Nephritis Classification on a Molecular Level.

J Clin Med 2019 Sep 23;8(10). Epub 2019 Sep 23.

Division of Nephrology, Department of Medicine, Toronto General Hospital, University Health Network, Toronto, ON M5G 2C4, Canada.

The International Society of Nephrology/Renal Pathology Society (ISN/RPS) lupus nephritis (LN) classification is under reconsideration, given challenges with inter-rater reliability and resultant inconsistent relationship with treatment response. Integration of molecular classifiers into histologic evaluation can improve diagnostic precision and identify therapeutic targets. This study described the relationship between histological and molecular phenotypes and clinical responses in LN. Renal compartmental mRNA abundance was measured in 54 biopsy specimens from LN patients and correlated to ISN/RPS classification and individual histologic lesions. A subset of transcripts was also evaluated in sequential biopsies of a separate longitudinal cohort of 36 patients with paired samples obtained at the time of flare and at follow up. Unsupervised clustering based on mRNA abundance did not demonstrate a relationship with the (ISN/RPS) classification, nor did univariate statistical analysis. Exploratory analyses suggested a correlation with individual histologic lesions. Glomerular FN1 (fibronectin), SPP1 (secreted phosphoprotein 1), and LGALS3 (galectin 3) abundance correlated with disease activity and changed following treatment. Exploratory analyses suggested relationships between specific transcripts and individual histologic lesions, with the important representation of interferon-regulated genes. Our findings suggested that the current LN classification could be refined by the inclusion of molecular descriptors. Combining molecular and pathologic kidney biopsy phenotypes may hold promise to better classify disease and identify actionable treatment targets and merits further exploration in larger cohorts.
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http://dx.doi.org/10.3390/jcm8101524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6832959PMC
September 2019

Assessment of temporal functional changes and miRNA profiling of human iPSC-derived cardiomyocytes.

Sci Rep 2019 Sep 12;9(1):13188. Epub 2019 Sep 12.

Department of Emergency Medicine, Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA.

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have been developed for cardiac cell transplantation studies more than a decade ago. In order to establish the hiPSC-CM-based platform as an autologous source for cardiac repair and drug toxicity, it is vital to understand the functionality of cardiomyocytes. Therefore, the goal of this study was to assess functional physiology, ultrastructural morphology, gene expression, and microRNA (miRNA) profiling at Wk-1, Wk-2 & Wk-4 in hiPSC-CMs in vitro. Functional assessment of hiPSC-CMs was determined by multielectrode array (MEA), Ca cycling and particle image velocimetry (PIV). Results demonstrated that Wk-4 cardiomyocytes showed enhanced synchronization and maturation as compared to Wk-1 & Wk-2. Furthermore, ultrastructural morphology of Wk-4 cardiomyocytes closely mimicked the non-failing (NF) adult human heart. Additionally, modulation of cardiac genes, cell cycle genes, and pluripotency markers were analyzed by real-time PCR and compared with NF human heart. Increasing expression of fatty acid oxidation enzymes at Wk-4 supported the switching to lipid metabolism. Differential regulation of 12 miRNAs was observed in Wk-1 vs Wk-4 cardiomyocytes. Overall, this study demonstrated that Wk-4 hiPSC-CMs showed improved functional, metabolic and ultrastructural maturation, which could play a crucial role in optimizing timing for cell transplantation studies and drug screening.
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http://dx.doi.org/10.1038/s41598-019-49653-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742647PMC
September 2019

Tumor heterogeneity and acquired drug resistance in FGFR2-fusion-positive cholangiocarcinoma through rapid research autopsy.

Cold Spring Harb Mol Case Stud 2019 08 1;5(4). Epub 2019 Aug 1.

Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.

Cholangiocarcinoma is a highly aggressive and lethal malignancy, with limited treatment options available. Recently, FGFR inhibitors have been developed and utilized in FGFR-mutant cholangiocarcinoma; however, resistance often develops and the genomic determinants of resistance are not fully characterized. We completed whole-exome sequencing (WES) of 11 unique tumor samples obtained from a rapid research autopsy on a patient with FGFR-fusion-positive cholangiocarcinoma who initially responded to the pan-FGFR inhibitor, INCB054828. In vitro studies were carried out to characterize the novel FGFR alteration and secondary mutation identified. Multisite WES and analysis of tumor heterogeneity through subclonal inference identified four genetically distinct cancer cell populations, two of which were only observed after treatment. Additionally, WES revealed an N549H mutation hypothesized to confer resistance to the FGFR inhibitor INCB054828 in a single tumor sample. This hypothesis was corroborated with in vitro cell-based studies in which cells expressing fusion were sensitive to INCB054828 (IC value of 10.16 nM), whereas cells with the addition of the N549H mutation were resistant to INCB054828 (IC value of 1527.57 nM). Furthermore, the N549H secondary mutation displayed cross-resistance to other selective FGFR inhibitors, but remained sensitive to the nonselective inhibitor, ponatinib. Rapid research autopsy has the potential to provide unprecedented insights into the clonal evolution of cancer throughout the course of the disease. In this study, we demonstrate the emergence of a drug resistance mutation and characterize the evolution of tumor subclones within a cholangiocarcinoma disease course.
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http://dx.doi.org/10.1101/mcs.a004002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6672025PMC
August 2019

An IL-15-based superagonist ALT-803 enhances the NK cell response to cetuximab-treated squamous cell carcinoma of the head and neck.

Cancer Immunol Immunother 2019 Aug 23;68(8):1379-1389. Epub 2019 Jul 23.

Department of Surgery, The Ohio State University, Columbus, OH, USA.

Squamous cell carcinoma of the head and neck (SCCHN) is the sixth most common cancer worldwide and epidermal growth factor receptor (EGFR) is overexpressed in greater than 90% of patient tumors. Cetuximab is a monoclonal antibody that binds to EGFR and can activate immune cells, such as natural killer (NK) cells, that express receptors for the Fc (constant region) of immunoglobulin G. IL-15 (interleukin-15) is a critical factor for the development, proliferation and activation of effector NK cells. A novel IL-15 compound known as ALT-803 that consists of genetically modified IL-15 plus the IL-15 receptor alpha protein (IL15Rα) fused to the Fc portion of IgG1 has recently been developed. We hypothesized that treatment with ALT-803 would increase NK cell-mediated cytotoxicity of cetuximab-coated head and neck squamous cells. CD56 NK cells from normal healthy donors were treated overnight with ALT-803 and tested for their ability to lyse cetuximab-coated tumor cells. Cytotoxicity was greater following NK cell ALT-803 activation, as compared to controls. ALT-803-treated NK cells secreted significantly higher levels of IFN-γ than control conditions. Additionally, NK cells showed increased levels of phospho-ERK and phospho-STAT5 when co-cultured with cetuximab-coated tumors and ALT-803. Administration of both cetuximab and ALT-803 to mice harboring Cal27 SCCHN tumors resulted in significantly decreased tumor volume when compared to controls and compared to single-agent treatment alone. Overall, the present data suggest that cetuximab treatment in combination with ALT-803 in patients with EGFR-positive SCCHN may result in significant NK cell activation and have important anti-tumor activity.
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http://dx.doi.org/10.1007/s00262-019-02372-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7032639PMC
August 2019

Eμ-TCL1xMyc: A Novel Mouse Model for Concurrent CLL and B-Cell Lymphoma.

Clin Cancer Res 2019 10 11;25(20):6260-6273. Epub 2019 Jul 11.

Division of Hematology, The Ohio State University, Columbus, Ohio.

Purpose: Aberrant Myc expression is a major factor in the pathogenesis of aggressive lymphoma, and these lymphomas, while clinically heterogeneous, often are resistant to currently available treatments and have poor survival. Myc expression can also be seen in aggressive lymphomas that are observed in the context of CLL, and we sought to develop a mouse model that could be used to study therapeutic strategies for aggressive lymphoma in the context of CLL.

Experimental Design: We crossed the Eμ-TCL1 mouse model with the Eμ-Myc mouse model to investigate the clinical phenotype associated with B-cell-restricted expression of these oncogenes. The resulting malignancy was then extensively characterized, from both a clinical and biologic perspective.

Results: Eμ-TCL1xMyc mice uniformly developed highly aggressive lymphoid disease with histologically, immunophenotypically, and molecularly distinct concurrent CLL and B-cell lymphoma, leading to a significantly reduced lifespan. Injection of cells from diseased Eμ-TCL1xMyc into WT mice established a disease similar to that in the double-transgenic mice. Both Eμ-TCL1xMyc mice and mice with disease after adoptive transfer failed to respond to ibrutinib. Effective and durable disease control was, however, observed by selective inhibition of nuclear export protein exportin-1 (XPO1) using a compound currently in clinical development for relapsed/refractory malignancies, including CLL and lymphoma.

Conclusions: The Eμ-TCL1xMyc mouse is a new preclinical tool for testing experimental drugs for aggressive B-cell lymphoma, including in the context of CLL.
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http://dx.doi.org/10.1158/1078-0432.CCR-19-0273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6801062PMC
October 2019

A Microfluidic Chip Enables Isolation of Exosomes and Establishment of Their Protein Profiles and Associated Signaling Pathways in Ovarian Cancer.

Cancer Res 2019 07 16;79(13):3503-3513. Epub 2019 May 16.

Division of Gynecologic Oncology, Department of Obstetrics/Gynecology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio.

Because of limits on specificity and purity to allow for in-depth protein profiling, a standardized method for exosome isolation has yet to be established. In this study, we describe a novel, in-house microfluidic-based device to isolate exosomes from culture media and patient samples. This technology overcomes contamination issues because sample separation is based on the expression of highly specific surface markers CD63 and EpCAM. Mass spectrometry revealed over 25 exosome proteins that are differentially expressed in high-grade serous ovarian cancer (HGSOC) cell lines compared with normal cells-ovarian surface epithelia cells and fallopian tube secretory epithelial cells (FTSEC). Top exosome proteins were identified on the basis of their fold change and statistical significance between groups. Ingenuity pathway analysis identified STAT3 and HGF as top regulator proteins. We further validated exosome proteins of interest (pSTAT3, HGF, and IL6) in HGSOC samples of origin-based cell lines (OVCAR-8, FTSEC) and in early-stage HGSOC patient serum exosome samples using LC/MS-MS and proximity extension assay. Our microfluidic device will allow us to make new discoveries for exosome-based biomarkers for the early detection of HGSOC and will contribute to the development of new targeted therapies based on signaling pathways that are unique to HGSOC, both of which could improve the outcome for women with HGSOC. SIGNIFICANCE: A unique platform utilizing a microfluidic device enables the discovery of new exosome-based biomarkers in ovarian cancer.
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http://dx.doi.org/10.1158/0008-5472.CAN-18-3538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200082PMC
July 2019

Increased breast cancer risk in women with neurofibromatosis type 1: a meta-analysis and systematic review of the literature.

Hered Cancer Clin Pract 2019 25;17:12. Epub 2019 Mar 25.

1Division of Surgical Oncology, Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210 USA.

Background: Neurofibromatosis type 1 (NF1) is a cancer predisposing syndrome. Studies suggest that women < 50 years old (y.o.) with NF1 have an increased breast cancer (BC) incidence and BC associated mortality. However, this has not been widely recognized secondary to small study populations.

Methods: A systematic literature review was conducted through database searches for BC and NF1: 3456 articles identified, 166 reviewed, 58 used for descriptive analysis and 4 utilized for meta-analysis. Fisher's exact tests, Kaplan-Meier curves and random-effects meta-analysis models were used for analysis.

Results: Two hundred eighty-six cases of NF1 and female BC were identified with a median age of 46 years at diagnosis; 53% were <  50. Peak age of BC diagnosis was between 34 to 44 years. Women < 50 y.o. presented with more advanced disease vs. those ≥50 (56% vs. 22% stage III-IV, respectively;  = 0.005). Median survival for the entire cohort was 5 years vs. the reported median BC survival of over 20 years in the general population using the SEER database. Median age at BC death was 48.5 years; 64% of deceased patients were <  50. Meta-analysis of a total of 4178 women with NF1 revealed a BC standardized incidence ratio (SIR) of 3.07 (95%CI 2.16-4.38) for women with NF1 vs. the general population. Women < 50 y.o. demonstrated a higher SIR of 5.08 (95%CI 3.77-6.81) compared to 1.92 (95%CI 1.40-2.63) if ≥50 y.o.

Conclusions: This systematic literature review and meta-analysis suggests that women with NF1 <  50 y.o. have a five-fold increased risk of BC, present with more advanced disease, and may have an increased BC related mortality. Increased awareness and implementation of recent National Comprehensive Cancer Network early BC screening guidelines for this high-risk patient population is essential. Additional evaluation on the influence of gene mutations identified in patients undergoing hereditary cancer genetic testing on breast cancer risk in individuals without clinical evidence of NF1 is needed.
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http://dx.doi.org/10.1186/s13053-019-0110-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434896PMC
March 2019

Nontuberculous mycobacterium M. avium infection predisposes aged mice to cardiac abnormalities and inflammation.

Aging Cell 2019 06 4;18(3):e12926. Epub 2019 Mar 4.

Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio.

Biological aging dynamically alters normal immune and cardiac function, favoring the production of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) and increased instances of cardiac distress. Cardiac failure is the primary reason for hospitalization of the elderly (65+ years). The elderly are also increasingly susceptible to developing chronic bacterial infections due to aging associated immune abnormalities. Since bacterial infections compound the rates of cardiac failure in the elderly, and this phenomenon is not entirely understood, the interplay between the immune system and cardiovascular function in the elderly is of great interest. Using Mycobacterium avium, an opportunistic pathogen, we investigated the effect of mycobacteria on cardiac function in aged mice. Young (2-3 months) and old (18-20 months) C57BL/6 mice were intranasally infected with M. avium strain 104, and we compared the bacterial burden, immune status, cardiac electrical activity, pathology, and function of infected mice against uninfected age-matched controls. Herein, we show that biological aging may predispose old mice infected with M. avium to mycobacterial dissemination into the heart tissue and this leads to cardiac dysfunction. M. avium infected old mice had significant dysrhythmia, cardiac hypertrophy, increased recruitment of CD45 leukocytes, cardiac fibrosis, and increased expression of inflammatory genes in isolated heart tissue. This is the first study to report the effect of mycobacteria on cardiac function in an aged model. Our findings are critical to understanding how nontuberculous mycobacterium (NTM) and other mycobacterial infections contribute to cardiac dysfunction in the elderly population.
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http://dx.doi.org/10.1111/acel.12926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6516181PMC
June 2019

Genomic characterization of metastatic ultra-hypermutated interdigitating dendritic cell sarcoma through rapid research autopsy.

Oncotarget 2019 Jan 8;10(3):277-288. Epub 2019 Jan 8.

Department of Internal Medicine, Division of Medical Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA.

Interdigitating dendritic cell sarcoma (IDCS) is an extremely rare cancer of dendritic cell origin that lacks a standardized treatment approach. Here, we performed genomic characterization of metastatic IDCS through whole exome sequencing (WES) of tumor tissues procured from a patient who underwent research autopsy. WES was also performed on a treatment-naïve tumor biopsy sample obtained from prior surgical resection. Our analyses revealed ultra-hypermutation, defined as >100 mutations per megabase, in this patient's cancer, which was further characterized by the presence of three distinct mutational signatures including UV radiation and APOBEC signatures. To characterize clonal heterogeneity, we used the bioinformatics tool Canopy to leverage single nucleotide and copy number variants to catalog six subclones across various metastatic tumors. Truncal alterations, defined as being present in all clonal tumor cell populations, in this patient's cancer include point mutations in and and amplifications of and , which are likely driver mutations. In summary, we have performed genomic characterization evaluating tumor mutational burden (TMB) and heterogeneity in a patient with metastatic IDCS. Despite ultra-hypermutation, this patient's cancer was not responsive to treatment with PD-1 inhibition. Our results underscore the importance of characterizing clonal heterogeneity in TMB-high cancers.
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http://dx.doi.org/10.18632/oncotarget.26352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349455PMC
January 2019

Metabolic fingerprinting for diagnosis of fibromyalgia and other rheumatologic disorders.

J Biol Chem 2019 02 6;294(7):2555-2568. Epub 2018 Dec 6.

the Department of Food Science and Technology, and.

Diagnosis and treatment of fibromyalgia (FM) remains a challenge owing to the lack of reliable biomarkers. Our objective was to develop a rapid biomarker-based method for diagnosing FM by using vibrational spectroscopy to differentiate patients with FM from those with rheumatoid arthritis (RA), osteoarthritis (OA), or systemic lupus erythematosus (SLE) and to identify metabolites associated with these differences. Blood samples were collected from patients with a diagnosis of FM ( = 50), RA ( = 29), OA ( = 19), or SLE ( = 23). Bloodspot samples were prepared, and spectra collected with portable FT-IR and FT-Raman microspectroscopy and subjected to metabolomics analysis by ultra-HPLC (uHPLC), coupled to a photodiode array (PDA) and tandem MS/MS. Unique IR and Raman spectral signatures were identified by pattern recognition analysis and clustered all study participants into classes (FM, RA, and SLE) with no misclassifications ( < 0.05, and interclass distances > 2.5). Furthermore, the spectra correlated ( = 0.95 and 0.83 for IR and Raman, respectively) with FM pain severity measured with fibromyalgia impact questionnaire revised version (FIQR) assessments. Protein backbones and pyridine-carboxylic acids dominated this discrimination and might serve as biomarkers for syndromes such as FM. uHPLC-PDA-MS/MS provided insights into metabolites significantly differing among the disease groups, not only in molecular / and / values but also in UV-visible chromatograms. We conclude that vibrational spectroscopy may provide a reliable diagnostic test for differentiating FM from other disorders and for establishing serologic biomarkers of FM-associated pain.
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http://dx.doi.org/10.1074/jbc.RA118.005816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378985PMC
February 2019

Disruption of stromal hedgehog signaling initiates RNF5-mediated proteasomal degradation of PTEN and accelerates pancreatic tumor growth.

Life Sci Alliance 2018 Oct 26;1(5):e201800190. Epub 2018 Oct 26.

Hollings Cancer Center and Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC, USA.

The contribution of the tumor microenvironment to pancreatic ductal adenocarcinoma (PDAC) development is currently unclear. We therefore examined the consequences of disrupting paracrine Hedgehog (HH) signaling in PDAC stroma. Herein, we show that ablation of the key HH signaling gene () in stromal fibroblasts led to increased proliferation of pancreatic tumor cells. Furthermore, deletion resulted in proteasomal degradation of the tumor suppressor PTEN and activation of oncogenic protein kinase B (AKT) in fibroblasts. An unbiased proteomic screen identified RNF5 as a novel E3 ubiquitin ligase responsible for degradation of phosphatase and tensin homolog (PTEN) in -null fibroblasts. () knockdown or pharmacological inhibition of glycogen synthase kinase 3β (GSKβ), the kinase that marks PTEN for ubiquitination, rescued PTEN levels and reversed the oncogenic phenotype, identifying a new node of PTEN regulation. In PDAC patients, low stromal PTEN correlated with reduced overall survival. Mechanistically, PTEN loss decreased hydraulic permeability of the extracellular matrix, which was reversed by hyaluronidase treatment. These results define non-cell autonomous tumor-promoting mechanisms activated by disruption of the HH/PTEN axis and identifies new targets for restoring stromal tumor-suppressive functions.
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http://dx.doi.org/10.26508/lsa.201800190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238420PMC
October 2018

Transcriptional targeting of oncogene addiction in medullary thyroid cancer.

JCI Insight 2018 08 23;3(16). Epub 2018 Aug 23.

Division of Endocrinology, Diabetes, and Metabolism, The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA.

Metastatic medullary thyroid cancer (MTC) is incurable and FDA-approved kinase inhibitors that include oncogenic RET as a target do not result in complete responses. Association studies of human MTCs and murine models suggest that the CDK/RB pathway may be an alternative target. The objective of this study was to determine if CDKs represent therapeutic targets for MTC and to define mechanisms of activity. Using human MTC cells that are either sensitive or resistant to vandetanib, we demonstrate that palbociclib (CDK4/6 inhibitor) is not cytotoxic to MTC cells but that they are highly sensitive to dinaciclib (CDK1/2/5/9 inhibitor) accompanied by reduced CDK9 and RET protein and mRNA levels. CDK9 protein was highly expressed in 83 of 83 human MTCs and array-comparative genomic hybridization had copy number gain in 11 of 30 tumors. RNA sequencing demonstrated that RNA polymerase II-dependent transcription was markedly reduced by dinaciclib. The CDK7 inhibitor THZ1 also demonstrated high potency and reduced RET and CDK9 levels. ChIP-sequencing using H3K27Ac antibody identified a superenhancer in intron 1 of RET. Finally, combined inhibition of dinaciclib with a RET kinase inhibitor was synergistic. In summary, we have identified what we believe is a novel mechanism of RET transcription regulation that potentially can be exploited to improve RET therapeutic targeting.
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http://dx.doi.org/10.1172/jci.insight.122225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6141185PMC
August 2018

Stromal PTEN determines mammary epithelial response to radiotherapy.

Nat Commun 2018 07 17;9(1):2783. Epub 2018 Jul 17.

Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA.

The importance of the tumor-associated stroma in cancer progression is clear. However, it remains uncertain whether early events in the stroma are capable of initiating breast tumorigenesis. Here, we show that in the mammary glands of non-tumor bearing mice, stromal-specific phosphatase and tensin homolog (Pten) deletion invokes radiation-induced genomic instability in neighboring epithelium. In these animals, a single dose of whole-body radiation causes focal mammary lobuloalveolar hyperplasia through paracrine epidermal growth factor receptor (EGFR) activation, and EGFR inhibition abrogates these cellular changes. By analyzing human tissue, we discover that stromal PTEN is lost in a subset of normal breast samples obtained from reduction mammoplasty, and is predictive of recurrence in breast cancer patients. Combined, these data indicate that diagnostic or therapeutic chest radiation may predispose patients with decreased stromal PTEN expression to secondary breast cancer, and that prophylactic EGFR inhibition may reduce this risk.
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http://dx.doi.org/10.1038/s41467-018-05266-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050339PMC
July 2018