1
|
Colloca L, Mocci E, Wang Y, Massalee R, Chen S, White J, Johnson K, Patron Fidalgo GM, Wilson GM, Goldman D, Dorsey SG. Transcriptomic Profiles Associated with Experimental Placebo Effects in Chronic Pain. Clin Pharmacol Ther 2024. [PMID: 38711244 DOI: 10.1002/cpt.3286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
Gene expression networks associated with placebo effects are understudied; in this study, we identified transcriptomic profiles associated with placebo responsivity. Participants suffering from chronic pain underwent a verbal suggestion and conditioning paradigm with individually tailored thermal painful stimulations to elicit conditioned placebo effects. Participants reported pain intensity on a visual analog scale (VAS) anchored from zero = no pain to 100 = maximum imaginable pain. RNA was extracted from venous blood and RNA sequencing and validation tests were performed to identify differentially expressed genes (DEGs) associated with placebo effects, controlling for sex and level of pain. Unbiased enrichment analyses were performed to identify biological processes associated with placebo effects. Of the 10,700 protein-coding genes that passed quality control filters, 667 were found to be associated with placebo effects (FDR <0.05). Most genes (97%) upregulated were associated with larger placebo effects. The 17 top transcriptome-wide significant genes were further validated via RT-qPCR in an independent cohort of chronic pain participants. Six of them (CCDC85B, FBXL15, HAGH, PI3, SELENOM, and TNFRSF4) showed positive and significant (P < 0.05) correlation with placebo effects in the cohort. The overall DEGs were highly enriched in regulation of expression of SLITs and ROBOs (R-HSA-9010553, FDR = 1.26e-33), metabolism of RNA (R-HSA-8953854, FDR = 1.34e-30), Huntington's disease (hsa05016, FDR = 9.84e-31), and ribosome biogenesis (GO:0042254, FDR = 2.67e-15); alternations in these pathways might jeopardize the proneness to elicit placebo effects. Future studies are needed to replicate this finding and better understand the unique molecular dynamics of people who are more or less affected by pain and placebo.
Collapse
Affiliation(s)
- Luana Colloca
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Department of Anesthesiology and Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, USA
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, Maryland, USA
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Evelina Mocci
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, Maryland, USA
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Yang Wang
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, Maryland, USA
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Rachel Massalee
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Shuo Chen
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Jewel White
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Placebo Beyond Opinions Center, School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Kesha Johnson
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Gloria M Patron Fidalgo
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism (NIAAA), NIH, Rockville, Maryland, USA
| | - Susan G Dorsey
- Department of Pain and Translational Symptom Science, School of Nursing, University of Maryland, Baltimore, Maryland, USA
- Department of Anesthesiology and Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland, USA
- Center to Advance Chronic Pain Research, University of Maryland, Baltimore, Maryland, USA
| |
Collapse
|
2
|
Gudra D, Valdovska A, Jonkus D, Galina D, Kairisa D, Ustinova M, Viksne K, Fridmanis D, Kalnina I. Genomic Characterization and Initial Insight into Mastitis-Associated SNP Profiles of Local Latvian Bos taurus Breeds. Animals (Basel) 2023; 13:2776. [PMID: 37685039 PMCID: PMC10487150 DOI: 10.3390/ani13172776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Latvia has two local Bos taurus breeds-Latvian Brown (LBG) and Latvian Blue (LZG)-characterized by a good adaptation to the local climate, longevity, and high fat and protein contents in milk. Since these are desired traits in the dairy industry, this study investigated the genetic background of the LBG and LZG breeds and identified the genetic factors associated with mastitis. Blood and semen samples were acquired, and whole genome sequencing was then performed to acquire a genomic sequence with at least 35× or 10× coverage. The heterozygosity, nucleotide diversity, and LD analysis indicated that LBG and LZG cows have similar levels of genetic diversity compared to those of other breeds. An analysis of the population structure revealed that each breed clustered together, but the overall differentiation between the breeds was small. The highest genetic variance was observed in the LZG breed compared with the LBG breed. Our results show that SNP rs721295390 is associated with mastitis in the LBG breed, and SNPs rs383806754, chr29:43998719CG>C, and rs462030680 are associated with mastitis in the LZG breed. This study shows that local Latvian LBG and LZG breeds have a pronounced genetic differentiation, with each one suggesting its own mastitis-associated SNP profile.
Collapse
Affiliation(s)
- Dita Gudra
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
| | - Anda Valdovska
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
| | - Daina Jonkus
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia (D.K.)
| | - Daiga Galina
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
| | - Daina Kairisa
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia (D.K.)
| | - Maija Ustinova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
| | - Kristine Viksne
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia
| | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
| | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
| |
Collapse
|
3
|
Takahashi S, Takagane K, Itoh G, Kuriyama S, Umakoshi M, Goto A, Yanagihara K, Yashiro M, Iijima K, Tanaka M. CCDC85A is regulated by miR-224-3p and augments cancer cell resistance to endoplasmic reticulum stress. Front Oncol 2023; 13:1196546. [PMID: 37534255 PMCID: PMC10391547 DOI: 10.3389/fonc.2023.1196546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/29/2023] [Indexed: 08/04/2023] Open
Abstract
MicroRNAs (miRNAs) play pivotal roles in the tumor microenvironment. Here, we analyzed miRNAs in tumor stromal fibroblasts. Expression of miR-224-3p in cancer-associated fibroblasts (CAF) from scirrhous gastric cancer patients was lower than in normal fibroblasts (NF). Introduction of a miR-224-3p mimic attenuated migration and invasion of CAF. Coiled-coil domain containing 85A (CCDC85A), whose function in tumors is not understood, was the target gene of miR-224-3p. Immunohistological analysis revealed that CCDC85A is expressed to varying degrees by cancer cells and CAFs in gastric and pancreatic carcinomas. Downregulation of CCDC85A in cancer cells revealed that these cells are vulnerable to endoplasmic reticulum (ER) stress induced by thapsigargin or tunicamycin, which were ameliorated after addback of CCDC85A. Injection of NF-derived exosomes containing miR-224-3p into the xenograft tumor increased tumor shrinkage by cisplatin treatment. Mechanistically, CCDC85A associated with the molecular chaperone GRP78 and GRP94, thereby inhibiting association of these negative regulators of the unfolded protein response (UPR), leading to sustained activation of PERK and downstream eIF2〈 and ATF4 upon ER stress. These data suggest a novel miR-224-3p-mediated function for CCDC85A: protection from ER stress and cisplatin resistance.
Collapse
Affiliation(s)
- So Takahashi
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
- Department of Gastroenterology, Akita University Graduate School of Medicine, Akita, Japan
| | - Kurara Takagane
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Go Itoh
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Sei Kuriyama
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| | - Michinobu Umakoshi
- Department of Cellular and Organ Pathology, Akita University Graduate School of Medicine, Akita, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Akita University Graduate School of Medicine, Akita, Japan
| | - Kazuyoshi Yanagihara
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Masakazu Yashiro
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Katsunori Iijima
- Department of Gastroenterology, Akita University Graduate School of Medicine, Akita, Japan
| | - Masamitsu Tanaka
- Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan
| |
Collapse
|
4
|
Sokol L, Cuypers A, Truong ACK, Bouché A, Brepoels K, Souffreau J, Rohlenova K, Vinckier S, Schoonjans L, Eelen G, Dewerchin M, de Rooij LPMH, Carmeliet P. Prioritization and functional validation of target genes from single-cell transcriptomics studies. Commun Biol 2023; 6:648. [PMID: 37330599 PMCID: PMC10276815 DOI: 10.1038/s42003-023-05006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 06/01/2023] [Indexed: 06/19/2023] Open
Abstract
Translation of academic results into clinical practice is a formidable unmet medical need. Single-cell RNA-sequencing (scRNA-seq) studies generate long descriptive ranks of markers with predicted biological function, but without functional validation, it remains challenging to know which markers truly exert the putative function. Given the lengthy/costly nature of validation studies, gene prioritization is required to select candidates. We address these issues by studying tip endothelial cell (EC) marker genes because of their importance for angiogenesis. Here, by tailoring Guidelines On Target Assessment for Innovative Therapeutics, we in silico prioritize previously unreported/poorly described, high-ranking tip EC markers. Notably, functional validation reveals that four of six candidates behave as tip EC genes. We even discover a tip EC function for a gene lacking in-depth functional annotation. Thus, validating prioritized genes from scRNA-seq studies offers opportunities for identifying targets to be considered for possible translation, but not all top-ranked scRNA-seq markers exert the predicted function.
Collapse
Affiliation(s)
- Liliana Sokol
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Anne Cuypers
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Anh-Co K Truong
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Ann Bouché
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Katleen Brepoels
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Joris Souffreau
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Katerina Rohlenova
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Prague-West, Czech Republic
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Laura P M H de Rooij
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology (CCB), VIB and Department of Oncology, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark.
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
5
|
Priyanka PP, Yenugu S. Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology. Reprod Sci 2021; 28:2725-2734. [PMID: 33942254 DOI: 10.1007/s43032-021-00595-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/22/2021] [Indexed: 01/10/2023]
Abstract
The coiled-coil domain-containing (CCDC) proteins have been implicated in a variety of physiological and pathological processes. Their functional roles vary from their interaction with molecular components of signaling pathways to determining the physiological functions at the cellular and organ level. Thus, they govern important functions like gametogenesis, embryonic development, hematopoiesis, angiogenesis, and ciliary development. Further, they are implicated in the pathogenesis of a large number of cancers. Polymorphisms in CCDC genes are associated with the risk of lifetime diseases. Because of their role in many biological processes, they have been extensively studied. This review concisely presents the functional role of CCDC proteins that have been studied in the last decade. Studies on CCDC proteins continue to be an active area of investigation because of their indispensable functions. However, there is ample opportunity to further understand the involvement of CCDC proteins in many more functions. It is anticipated that basing on the available literature, the functional role of CCDC proteins will be explored much further.
Collapse
Affiliation(s)
| | - Suresh Yenugu
- Department of Animal Biology, University of Hyderabad, Hyderabad, 500046, India.
| |
Collapse
|
6
|
Phillips CA, Reading BJ, Livingston M, Livingston K, Ashwell CM. Evaluation via Supervised Machine Learning of the Broiler Pectoralis Major and Liver Transcriptome in Association With the Muscle Myopathy Wooden Breast. Front Physiol 2020; 11:101. [PMID: 32158398 PMCID: PMC7052112 DOI: 10.3389/fphys.2020.00101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/27/2020] [Indexed: 01/07/2023] Open
Abstract
The muscle myopathy wooden breast (WB) has recently appeared in broiler production and has a negative impact on meat quality. WB is described as hard/firm consistency found within the pectoralis major (PM). In the present study, we use machine learning from our PM and liver transcriptome dataset to capture the complex relationships that are not typically revealed by traditional statistical methods. Gene expression data was evaluated between the PM and liver of birds with WB and those that were normal. Two separate machine learning algorithms were performed to analyze the data set including the sequential minimal optimization (SMO) of support vector machines (SVMs) and Multilayer Perceptron (MLP) Artificial Neural Network (ANN). Machine learning algorithms were compared to identify genes within a gene expression data set of approximately 16,000 genes for both liver and PM, which can be correctly classified from birds with or without WB. The performance of both machine learning algorithms SMO and MLP was determined using percent correct classification during the cross-validations. By evaluating the WB transcriptome datasets by 5× cross-validation using ANNs, the expression of nine genes ranked based on Shannon Entropy (Information Gain) from PM were able to correctly classify if the individual bird was normal or exhibited WB 100% of the time. These top nine genes were all protein coding and potential biomarkers. When PM gene expression data were evaluated between normal birds and those with WB using SVMs they were correctly classified 95% of the time using 450 of the top genes sorted ranked based on Shannon Entropy (Information Gain) as a preprocessing step. When evaluating the 450 attributes that were 95% correctly classified using SVMs through Ingenuity Pathway Analysis (IPA) there was an overlap in top genes identified through MLP. This analysis allowed the identification of critical transcriptional responses for the first time in both liver and muscle during the onset of WB. The information provided has revealed many molecules and pathways making up a complex molecular mechanism involved with the progression of wooden breast and suggests that the etiology of the myopathy is not limited to activity in the muscle alone, but is an altered systemic pathology.
Collapse
Affiliation(s)
- Chelsea A. Phillips
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States
| | - Benjamin J. Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Matthew Livingston
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States
| | - Kimberly Livingston
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States
| | - Chris M. Ashwell
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
7
|
Krishnamachary B, Subramaniam D, Dandawate P, Ponnurangam S, Srinivasan P, Ramamoorthy P, Umar S, Thomas SM, Dhar A, Septer S, Weir SJ, Attard T, Anant S. Targeting transcription factor TCF4 by γ-Mangostin, a natural xanthone. Oncotarget 2019; 10:5576-5591. [PMID: 31608135 PMCID: PMC6771460 DOI: 10.18632/oncotarget.27159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/17/2019] [Indexed: 01/29/2023] Open
Abstract
Given that colon cancer is the third most common cancer in incidence and cause of death in the United States, and current treatment modalities are insufficient, there is a need to develop novel agents. Towards this, here we focus on γ-Mangostin, a bioactive compound present in the Mangosteen (Garcinia mangostana) fruit. γ-Mangostin suppressed proliferation and colony formation, and induced cell cycle arrest and apoptosis of colon cancer cell lines. Further, γ-Mangostin inhibited colonosphere formation. Molecular docking and CETSA (Cellular thermal shift assay) binding assays demonstrated that γ-Mangostin interacts with transcription factor TCF4 (T-Cell Factor 4) at the β-catenin binding domain with the binding energy of -5.5 Kcal/mol. Moreover, γ-Mangostin treatment decreased TCF4 expression and reduced TCF reporter activity. The compound also suppressed the expression of Wnt signaling target proteins cyclin D1 and c-Myc, and stem cell markers such as LGR5, DCLK1 and CD44. To determine the effect of γ-Mangostin on tumor growth in vivo, we administered nude mice harboring HCT116 tumor xenografts with 5 mg/Kg of γ-Mangostin intraperitoneally for 21 days. γ-Mangostin treatment significantly suppressed tumor growth, with notably lowered tumor volume and weight. In addition, western blot analysis revealed a significant decrease in the expression of TCF4 and its downstream targets such as cyclin D1 and c-Myc. Together, these data suggest that γ-Mangostin inhibits colon cancer growth through targeting TCF4. γ-Mangostin may be a potential therapeutic agent for colon cancer.
Collapse
Affiliation(s)
- Balaji Krishnamachary
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Prasad Dandawate
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sivapriya Ponnurangam
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Prabhu Ramamoorthy
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Shahid Umar
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sufi Mary Thomas
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Animesh Dhar
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Seth Septer
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Colorado, Aurora, CO, USA
| | - Scott J Weir
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Thomas Attard
- Department of Pediatrics, Division of Gastroenterology, Children's Mercy Hospital, Kansas City, KS, USA
| | - Shrikant Anant
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
8
|
Miller SJ, Glatzer JC, Hsieh YC, Rothstein JD. Cortical astroglia undergo transcriptomic dysregulation in the G93A SOD1 ALS mouse model. J Neurogenet 2018; 32:322-335. [PMID: 30398075 PMCID: PMC6444185 DOI: 10.1080/01677063.2018.1513508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 08/06/2018] [Indexed: 12/13/2022]
Abstract
Astroglia are the most abundant glia cell in the central nervous system, playing essential roles in maintaining homeostasis. Key functions of astroglia include, but are not limited to, neurotransmitter recycling, ion buffering, immune modulation, neurotrophin secretion, neuronal synaptogenesis and elimination, and blood-brain barrier maintenance. In neurological diseases, it is well appreciated that astroglia play crucial roles in the disease pathogenesis. In amyotrophic lateral sclerosis (ALS), a motor neuron degenerative disease, astroglia in the spinal cord and cortex downregulate essential transporters, among other proteins, that exacerbate disease progression. Spinal cord astroglia undergo dramatic transcriptome dysregulation. However, in the cortex, it has not been well studied what effects glia, especially astroglia, have on upper motor neurons in the pathology of ALS. To begin to shed light on the involvement and dysregulation that astroglia undergo in ALS, we isolated pure grey-matter cortical astroglia and subjected them to microarray analysis. We uncovered a vast number of genes that show dysregulation at end-stage in the ALS mouse model, G93A SOD1. Many of these genes play essential roles in ion homeostasis and the Wnt-signaling pathway. Several of these dysregulated genes are common in ALS spinal cord astroglia, while many of them are unique. This database serves as an approach for understanding the significance of dysfunctional genes and pathways in cortical astroglia in the context of motor neuron disease, as well as determining regional astroglia heterogeneity, and providing insight into ALS pathogenesis.
Collapse
Affiliation(s)
- Sean J. Miller
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Cellular and Molecular Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
| | - Jenna C. Glatzer
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Cellular and Molecular Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
| | - Yi-chun Hsieh
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
| | - Jeffrey D. Rothstein
- Dept. of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
- Cellular and Molecular Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205
- The Brain Science Institute, Johns Hopkins University, Baltimore, MD 21205
- Dept. of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205
| |
Collapse
|
9
|
Feng Y, Gao Y, Yu J, Jiang G, Zhang X, Lin X, Han Q, Rong X, Xu H, Li Q, Qiu X, Wang E. CCDC85B promotes non-small cell lung cancer cell proliferation and invasion. Mol Carcinog 2018; 58:126-134. [PMID: 30242906 DOI: 10.1002/mc.22914] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
Coiled-coil domain containing 85 B (CCDC85B) is involved in diverse biological processes; however, its expression patterns and functions in human cancers are yet unknown. The present study demonstrated that the expression of CCDC85B in the cytoplasm of the non-small cell lung cancer (NSCLC) tumor cells was significantly higher compared to adjacent normal lung tissues (P < 0.05). Furthermore, CCDC85B expression correlated with advanced TNM stage (P = 0.004) and positive regional lymph node metastasis (P = 0.009) of NSCLC. In addition, in A549 and H1299 lung cancer cell lines, the overexpression of CCDC85B promoted cell proliferation and invasion, while siRNA-mediated CCDC85B knockdown exhibited opposite effects. CCDC85B promoted AKT and GSK3β phosphorylation and upregulated the levels of active β-catenin, Wnt targets c-myc, cyclin D1, and MMP7. Besides, the CCDC85B-induced upregulation of phosphorylated GSK3β and active β-catenin was rescued following the treatment with PI3 K inhibitor, LY294002. In conclusion, CCDC85B was associated with NSCLC progression as it promoted the proliferation and invasion of lung cancer cells through activated AKT/GSK3β/β-catenin oncogenic signaling pathway. Therefore, CCDC85B might serve as a novel target for NSCLC treatment.
Collapse
Affiliation(s)
- Yangyang Feng
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yue Gao
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Juanhan Yu
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Guiyang Jiang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xiupeng Zhang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xuyong Lin
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Qiang Han
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xuezhu Rong
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Hongtao Xu
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Qingchang Li
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xueshan Qiu
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Enhua Wang
- Department of Pathology, First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| |
Collapse
|
10
|
Chakraborty S, Ghosh Z. A systemic insight into astrocytoma biology across different grades. J Cell Physiol 2018; 234:4243-4255. [DOI: 10.1002/jcp.27193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/17/2018] [Indexed: 01/05/2023]
Affiliation(s)
| | - Zhumur Ghosh
- Bioinformatics Centre, Bose Institute Kolkata India
| |
Collapse
|
11
|
Gladitz J, Klink B, Seifert M. Network-based analysis of oligodendrogliomas predicts novel cancer gene candidates within the region of the 1p/19q co-deletion. Acta Neuropathol Commun 2018; 6:49. [PMID: 29890994 PMCID: PMC5996550 DOI: 10.1186/s40478-018-0544-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/08/2018] [Indexed: 01/17/2023] Open
Abstract
Oligodendrogliomas are primary human brain tumors with a characteristic 1p/19q co-deletion of important prognostic relevance, but little is known about the pathology of this chromosomal mutation. We developed a network-based approach to identify novel cancer gene candidates in the region of the 1p/19q co-deletion. Gene regulatory networks were learned from gene expression and copy number data of 178 oligodendrogliomas and further used to quantify putative impacts of differentially expressed genes of the 1p/19q region on cancer-relevant pathways. We predicted 8 genes with strong impact on signaling pathways and 14 genes with strong impact on metabolic pathways widespread across the region of the 1p/19 co-deletion. Many of these candidates (e.g. ELTD1, SDHB, SEPW1, SLC17A7, SZRD1, THAP3, ZBTB17) are likely to push, whereas others (e.g. CAP1, HBXIP, KLK6, PARK7, PTAFR) might counteract oligodendroglioma development. For example, ELTD1, a functionally validated glioblastoma oncogene located on 1p, was overexpressed. Further, the known glioblastoma tumor suppressor SLC17A7 located on 19q was underexpressed. Moreover, known epigenetic alterations triggered by mutated SDHB in paragangliomas suggest that underexpressed SDHB in oligodendrogliomas may support and possibly enhance the epigenetic reprogramming induced by the IDH-mutation. We further analyzed rarely observed deletions and duplications of chromosomal arms within oligodendroglioma subcohorts identifying putative oncogenes and tumor suppressors that possibly influence the development of oligodendroglioma subgroups. Our in-depth computational study contributes to a better understanding of the pathology of the 1p/19q co-deletion and other chromosomal arm mutations. This might open opportunities for functional validations and new therapeutic strategies.
Collapse
|
12
|
Kuan PF, Waszczuk MA, Kotov R, Clouston S, Yang X, Singh PK, Glenn ST, Cortes Gomez E, Wang J, Bromet E, Luft BJ. Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study. Transl Psychiatry 2017; 7:1297. [PMID: 29249826 PMCID: PMC5802695 DOI: 10.1038/s41398-017-0050-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/11/2022] Open
Abstract
The gene expression approach has provided promising insights into the pathophysiology of posttraumatic stress disorder (PTSD). However, few studies used hypothesis-free transcriptome-wide approach to comprehensively understand gene expression underpinning PTSD. A transcriptome-wide expression study using RNA sequencing of whole blood was conducted in 324 World Trade Center responders (201 with never, 81 current, 42 past PTSD). Samples from current and never PTSD reponders were randomly split to form discovery (N = 195) and replication (N = 87) cohorts. Differentially expressed genes were used in pathway analysis and to create a polygenic expression score. There were 448 differentially expressed genes in the discovery cohort, of which 99 remained significant in the replication cohort, including FKBP5, which was found to be up-regulated in current PTSD regardless of the genotypes. Several enriched biological pathways were found, including glucocorticoid receptor signaling and immunity-related pathways, but these pathways did not survive FDR correction. The polygenic expression score computed by aggregating 30 differentially expressed genes using the elastic net algorithm achieved sensitivity/specificity of 0.917/0.508, respectively for identifying current PTSD in the replication cohort. Polygenic scores were similar in current and past PTSD, with both groups scoring higher than trauma-exposed controls without any history of PTSD. Together with the pathway analysis results, these findings point to HPA-axis and immune dysregulation as key biological processes underpinning PTSD. A novel polygenic expression aggregate that differentiates PTSD patients from trauma-exposed controls might be a useful screening tool for research and clinical practice, if replicated in other populations.
Collapse
Affiliation(s)
- Pei-Fen Kuan
- 0000 0001 2216 9681grid.36425.36Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | | | - Roman Kotov
- Department of Psychiatry, Stony Book University, Stony Brook, NY, USA
| | - Sean Clouston
- Department of Family and Preventive Medicine, Stony Book University, Stony Brook, NY, USA
| | - Xiaohua Yang
- 0000 0001 2181 8635grid.240614.5Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Prashant K. Singh
- 0000 0001 2181 8635grid.240614.5Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Sean T. Glenn
- 0000 0001 2181 8635grid.240614.5Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Eduardo Cortes Gomez
- 0000 0001 2181 8635grid.240614.5Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Jianmin Wang
- 0000 0001 2181 8635grid.240614.5Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Evelyn Bromet
- Department of Psychiatry, Stony Book University, Stony Brook, NY, USA
| | - Benjamin J. Luft
- 0000 0001 2216 9681grid.36425.36Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| |
Collapse
|
13
|
Ohara A, Takahashi Y, Kondo M, Okuda Y, Takeda S, Kushida M, Kobayashi K, Sumida K, Yamada T. Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice. Toxicol Res (Camb) 2017; 6:795-813. [PMID: 30090543 PMCID: PMC6062386 DOI: 10.1039/c7tx00163k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/23/2017] [Indexed: 12/12/2022] Open
Abstract
Phenobarbital (PB) is a nongenotoxic hepatocellular carcinogen in rodents. PB induces hepatocellular tumors by activating the constitutive androstane receptor (CAR). Some previous research has suggested the possible involvement of epigenetic regulation in PB-promoted hepatocellular tumorigenesis, but the details of its molecular mechanism are not fully understood. In the present study, comprehensive analyses of DNA methylation, hydroxymethylation and gene expression using microarrays were performed in mouse hepatocellular adenomas induced by a single 90 mg kg-1 intraperitoneal injection dose of diethylnitrosamine (DEN) followed by 500 ppm PB in the diet for 27 weeks. DNA modification and expression of hundreds of genes are coordinately altered in PB-induced mouse hepatocellular adenomas. Of these, gene network analysis showed alterations of CAR signaling and tumor development-related genes. Pathway enrichment analysis revealed that differentially methylated or hydroxymethylated genes belong mainly to pathways involved in development, immune response and cancer cells in contrast to differentially expressed genes belonging primarily to the cell cycle. Furthermore, overlap was evaluated between the genes with altered expression levels with 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) alterations in mouse hepatocellular adenoma induced by DEN/PB and the genes with altered expression levels in the liver of CD-1 mice or humanized chimeric mice treated with PB for 7 days. With the integration of transcriptomic and epigenetic approaches, we detected candidate genes responsible for early key events of PB-promoted mouse hepatocellular tumorigenesis. Interestingly, these genes did not overlap with genes altered by the PB treatment of humanized chimeric mice, thus suggesting a species difference between the effects of PB in mouse and human hepatocytes.
Collapse
Affiliation(s)
- Ayako Ohara
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Yasuhiko Takahashi
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Miwa Kondo
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Yu Okuda
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Shuji Takeda
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Masahiko Kushida
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Kentaro Kobayashi
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Kayo Sumida
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| | - Tomoya Yamada
- Environmental Health Science Laboratory , Sumitomo Chemical Co. , Ltd. , 1-98 , 3-Chome , Kasugade-Naka , Konohana-ku , Osaka 554-8558 , Japan . ; ; Tel: +81-66466-5322
| |
Collapse
|
14
|
The HSA21 gene EURL/C21ORF91 controls neurogenesis within the cerebral cortex and is implicated in the pathogenesis of Down Syndrome. Sci Rep 2016; 6:29514. [PMID: 27404227 PMCID: PMC4941730 DOI: 10.1038/srep29514] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/17/2016] [Indexed: 11/08/2022] Open
Abstract
Copy number variations to chromosome 21 (HSA21) cause intellectual disability and Down Syndrome, but our understanding of the HSA21 genetic factors which contribute to fetal brain development remains incomplete. Here, we focussed on the neurodevelopmental functions for EURL (also known as C21ORF91, Refseq Gene ID:54149), a protein-coding gene at the centromeric boundary of the Down Syndrome Critical Region (DSCR) of HSA21. We report that EURL is expressed during human and mouse cerebral cortex development, and we report that alterations to EURL mRNA levels within the human brain underlie Down Syndrome. Our gene perturbation studies in mice demonstrate that disruptions to Eurl impair progenitor proliferation and neuronal differentiation. Also, we find that disruptions to Eurl impair the long-term positioning and dendritic spine densities of cortical projection neurons. We provide evidence that EURL interacts with the coiled-coil domain-containing protein CCDC85B so as to modulate β-catenin levels in cells. Further, we utilised a fluorescent reporter (8xTOPFLASHd2EGFP) to demonstrate that disruptions to Eurl alter β-catenin signalling in vitro as well as in vivo. Together, these studies highlight EURL as an important new player in neuronal development that is likely to impact on the neuropathogenesis of HSA21-related disorders including Down Syndrome.
Collapse
|
15
|
Zhang FY, Hu Y, Que ZY, Wang P, Liu YH, Wang ZH, Xue YX. Shikonin Inhibits the Migration and Invasion of Human Glioblastoma Cells by Targeting Phosphorylated β-Catenin and Phosphorylated PI3K/Akt: A Potential Mechanism for the Anti-Glioma Efficacy of a Traditional Chinese Herbal Medicine. Int J Mol Sci 2015; 16:23823-48. [PMID: 26473829 PMCID: PMC4632727 DOI: 10.3390/ijms161023823] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/20/2015] [Accepted: 09/16/2015] [Indexed: 12/26/2022] Open
Abstract
Shikonin is an anthraquinone derivative extracted from the root of lithospermum. Shikonin is traditionally used in the treatment of inflammatory and infectious diseases such as hepatitis. Shikonin also inhibits proliferation and induces apoptosis in various tumors. However, the effect of shikonin on gliomas has not been fully elucidated. In the present study, we aimed to investigate the effects of shikonin on the migration and invasion of human glioblastoma cells as well as the underlying mechanisms. U87 and U251 human glioblastoma cells were treated with shikonin at 2.5, 5, and 7.5 μmol/L and cell viability, migration and invasiveness were assessed with CCK8, scratch wound healing, in vitro Transwell migration, and invasion assays. The expression and activity of matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9) and the expression of phosphorylated β-catenin (p-β-catenin) and phosphorylated PI3K/Akt were also checked. Results showed that shikonin significantly inhibited the cell proliferation, migration, invasion, and expression of MMP-2 and MMP-9 in U87 and U251 cells. The expression of p-β-catenin showed contrary trends in two cell lines. It was significantly inhibited in U87 cells and promoted in U251 cells. Results in this work indicated that shikonin displayed an inhibitory effect on the migration and invasion of glioma cells by inhibiting the expression and activity of MMP-2 and -9. In addition, shikonin also inhibited the expression of p-PI3K and p-Akt to attenuate cell migration and invasion and MMP-2 and MMP-9 expression in both cell lines, which could be reversed by the PI3K/Akt pathway agonist, insulin-like growth factor-1 (IGF-1).
Collapse
Affiliation(s)
- Feng-Ying Zhang
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, China.
- Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, China.
| | - Yi Hu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Zhong-You Que
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Ping Wang
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, China.
- Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, China.
| | - Yun-Hui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Zhen-Hua Wang
- Department of Physiology, College of Basic Medicine, China Medical University, Shenyang 110122, China.
| | - Yi-Xue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110122, China.
- Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110122, China.
| |
Collapse
|
16
|
Expression profiling reveals genes involved in the regulation of wool follicle bulb regression and regeneration in sheep. Int J Mol Sci 2015; 16:9152-66. [PMID: 25915029 PMCID: PMC4463583 DOI: 10.3390/ijms16059152] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 01/04/2023] Open
Abstract
Wool is an important material in textile manufacturing. In order to investigate the intrinsic factors that regulate wool follicle cycling and wool fiber properties, Illumina sequencing was performed on wool follicle bulb samples from the middle anagen, catagen and late telogen/early anagen phases. In total, 13,898 genes were identified. KRTs and KRTAPs are the most highly expressed gene families in wool follicle bulb. In addition, 438 and 203 genes were identified to be differentially expressed in wool follicle bulb samples from the middle anagen phase compared to the catagen phase and the samples from the catagen phase compared to the late telogen/early anagen phase, respectively. Finally, our data revealed that two groups of genes presenting distinct expression patterns during the phase transformation may have important roles for wool follicle bulb regression and regeneration. In conclusion, our results demonstrated the gene expression patterns in the wool follicle bulb and add new data towards an understanding of the mechanisms involved in wool fiber growth in sheep.
Collapse
|
17
|
Markham NO, Doll CA, Dohn MR, Miller RK, Yu H, Coffey RJ, McCrea PD, Gamse JT, Reynolds AB. DIPA-family coiled-coils bind conserved isoform-specific head domain of p120-catenin family: potential roles in hydrocephalus and heterotopia. Mol Biol Cell 2014; 25:2592-603. [PMID: 25009281 PMCID: PMC4148249 DOI: 10.1091/mbc.e13-08-0492] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Isoform-specific expression of p120 affects cell motility and migration during development and tumor progression. The DIPA coiled-coil protein is a novel binding partner to the conserved isoform 1–specific head domain of p120 family members. Zebrafish data suggest that DIPA is mechanistically linked to p120 isoform–specific function in development. p120-catenin (p120) modulates adherens junction (AJ) dynamics by controlling the stability of classical cadherins. Among all p120 isoforms, p120-3A and p120-1A are the most prevalent. Both stabilize cadherins, but p120-3A is preferred in epithelia, whereas p120-1A takes precedence in neurons, fibroblasts, and macrophages. During epithelial-to-mesenchymal transition, E- to N-cadherin switching coincides with p120-3A to -1A alternative splicing. These isoforms differ by a 101–amino acid “head domain” comprising the p120-1A N-terminus. Although its exact role is unknown, the head domain likely mediates developmental and cancer-associated events linked to p120-1A expression (e.g., motility, invasion, metastasis). Here we identified delta-interacting protein A (DIPA) as the first head domain–specific binding partner and candidate mediator of isoform 1A activity. DIPA colocalizes with AJs in a p120-1A- but not 3A-dependent manner. Moreover, all DIPA family members (Ccdc85a, Ccdc85b/DIPA, and Ccdc85c) interact reciprocally with p120 family members (p120, δ-catenin, p0071, and ARVCF), suggesting significant functional overlap. During zebrafish neural tube development, both knockdown and overexpression of DIPA phenocopy N-cadherin mutations, an effect bearing functional ties to a reported mouse hydrocephalus phenotype associated with Ccdc85c. These studies identify a novel, highly conserved interaction between two protein families that may participate either individually or collectively in N-cadherin–mediated development.
Collapse
Affiliation(s)
- Nicholas O Markham
- Vanderbilt-Ingram Cancer Center, Cancer Biology Department, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Caleb A Doll
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
| | - Michael R Dohn
- Vanderbilt-Ingram Cancer Center, Cancer Biology Department, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Rachel K Miller
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Huapeng Yu
- Vanderbilt-Ingram Cancer Center, Cancer Biology Department, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Robert J Coffey
- Epithelial Biology Center, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232
| | - Pierre D McCrea
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Joshua T Gamse
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
| | - Albert B Reynolds
- Vanderbilt-Ingram Cancer Center, Cancer Biology Department, Vanderbilt University Medical Center, Nashville, TN 37232
| |
Collapse
|
18
|
Markham NO, Cooper T, Goff M, Gribben EM, Carnahan RH, Reynolds AB. Monoclonal antibodies to DIPA: a novel binding partner of p120-catenin isoform 1. Hybridoma (Larchmt) 2012; 31:246-54. [PMID: 22894777 DOI: 10.1089/hyb.2012.0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The coiled-coil domain-containing delta-interacting protein A (DIPA) is a transcription factor implicated in developmental regulation. DIPA is the first protein discovered to selectively interact with the p120-catenin (p120) isoform 1, an alternatively spliced form of p120 expressed preferentially in mesenchymal cells. Although a small fraction of p120 can be observed in the nucleus under certain circumstances, the vast majority of it associates with classical cadherins at adherens junctions. We observed for the first time that a discrete fraction of DIPA exists at cell-cell junctions, in addition to its predominantly nuclear localization. Thus, the p120-DIPA interaction may regulate cell signaling and/or transcriptional events, as has been described previously for β-catenin and the LEF/TCF transcription factor family. To facilitate further study of DIPA and to determine the physiological relevance of its interaction with p120, we have generated and characterized a panel of five DIPA-specific monoclonal antibodies (MAbs) that function in immunoblotting, immunoprecipitation, and immunofluorescence assays.
Collapse
Affiliation(s)
- Nicholas O Markham
- Department of Cancer Biology, Vanderbilt University Medical Center, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | | | | | | | | | | |
Collapse
|