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Sekulovski N, Wettstein JC, Carleton AE, Juga LN, Taniguchi LE, Ma X, Rao S, Schmidt JK, Golos TG, Lin CW, Taniguchi K. Temporally resolved early BMP-driven transcriptional cascade during human amnion specification. bioRxiv 2024:2023.06.19.545574. [PMID: 38496419 PMCID: PMC10942271 DOI: 10.1101/2023.06.19.545574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Amniogenesis, a process critical for continuation of healthy pregnancy, is triggered in a collection of pluripotent epiblast cells as the human embryo implants. Previous studies have established that BMP signaling is a major driver of this lineage specifying process, but the downstream BMP-dependent transcriptional networks that lead to successful amniogenesis remain to be identified. This is, in part, due to the current lack of a robust and reproducible model system that enables mechanistic investigations exclusively into amniogenesis. Here, we developed an improved model of early amnion specification, using a human pluripotent stem cell-based platform in which the activation of BMP signaling is controlled and synchronous. Uniform amniogenesis is seen within 48 hours after BMP activation, and the resulting cells share transcriptomic characteristics with amnion cells of a gastrulating human embryo. Using detailed time-course transcriptomic analyses, we established a previously uncharacterized BMP-dependent amniotic transcriptional cascade, and identified markers that represent five distinct stages of amnion fate specification; the expression of selected markers was validated in early post-implantation macaque embryos. Moreover, a cohort of factors that could potentially control specific stages of amniogenesis was identified, including the transcription factor TFAP2A. Functionally, we determined that, once amniogenesis is triggered by the BMP pathway, TFAP2A controls the progression of amniogenesis. This work presents a temporally resolved transcriptomic resource for several previously uncharacterized amniogenesis states and demonstrates a critical intermediate role for TFAP2A during amnion fate specification.
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Affiliation(s)
- Nikola Sekulovski
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jenna C. Wettstein
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Amber E. Carleton
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Lauren N. Juga
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Linnea E. Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Xiaolong Ma
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Versiti Blood Research Institute, Milwaukee, WI 53226 USA
| | - Jenna K. Schmidt
- Wisconsin National Primate Research Center (WNPRC), Madison, WI, USA
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center (WNPRC), Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin - Madison School of Medicine and Public Health, Madison, WI USA
- Department of Comparative Biosciences, University of Wisconsin - Madison School of Veterinary Medicine, Madison, WI, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kenichiro Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Wang T, Lin CW. Using a centered general linear model for detection of interactions among biomarkers. Stat Methods Med Res 2024; 33:414-432. [PMID: 38320800 DOI: 10.1177/09622802231224639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The dummy variable based general linear model (gLM) is commonly used to model categorical factors and their interactions. However, the main factors and their interactions in a general linear model are often correlated even when the factors are independently distributed. Alternatively, the classical two-way factorial analysis of variance (ANOVA) model can avoid the correlation between the main factors and their interactions when the main factors are independent. But the ANOVA model is hardly applicable to a regular linear regression model especially in the presence of other covariates due to constraints on its model parameters. In this study, a centered general linear model (cgLM) is proposed for modeling interactions between categorical factors based on their centered dummy variables. We show that the cgLM can avoid the correlation between the main factors and their interactions as the ANOVA model when the main factors are independent. Meanwhile, similar to gLM, it can be used in regular regression and fitted conveniently using the standard least square approach by choosing appropriate baselines to avoid constraints on its model parameters. The potential advantage of cgLM over gLM for detection of interactions in model building procedures is also illustrated and compared via a simulation study. Finally, the cgLM is applied to a postmortem brain gene expression data set.
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Affiliation(s)
- Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
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Jing X, Jia S, Teng M, Day BW, Afolayan AJ, Jarzembowski JA, Lin CW, Hessner MJ, Pritchard KA, Naylor S, Konduri GG, Teng RJ. Cellular Senescence Contributes to the Progression of Hyperoxic Bronchopulmonary Dysplasia. Am J Respir Cell Mol Biol 2024; 70:94-109. [PMID: 37874230 DOI: 10.1165/rcmb.2023-0038oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023] Open
Abstract
Oxidative stress, inflammation, and endoplasmic reticulum (ER) stress sequentially occur in bronchopulmonary dysplasia (BPD), and all result in DNA damage. When DNA damage becomes irreparable, tumor suppressors increase, followed by apoptosis or senescence. Although cellular senescence contributes to wound healing, its persistence inhibits growth. Therefore, we hypothesized that cellular senescence contributes to BPD progression. Human autopsy lungs were obtained. Sprague-Dawley rat pups exposed to 95% oxygen between Postnatal Day 1 (P1) and P10 were used as the BPD phenotype. N-acetyl-lysyltyrosylcysteine-amide (KYC), tauroursodeoxycholic acid (TUDCA), and Foxo4 dri were administered intraperitoneally to mitigate myeloperoxidase oxidant generation, ER stress, and cellular senescence, respectively. Lungs were examined by histology, transcriptomics, and immunoblotting. Cellular senescence increased in rat and human BPD lungs, as evidenced by increased oxidative DNA damage, tumor suppressors, GL-13 stain, and inflammatory cytokines with decreased cell proliferation and lamin B expression. Cellular senescence-related transcripts in BPD rat lungs were enriched at P10 and P21. Single-cell RNA sequencing showed increased cellular senescence in several cell types, including type 2 alveolar cells. In addition, Foxo4-p53 binding increased in BPD rat lungs. Daily TUDCA or KYC, administered intraperitoneally, effectively decreased cellular senescence, improved alveolar complexity, and partially maintained the numbers of type 2 alveolar cells. Foxo4 dri administered at P4, P6, P8, and P10 led to outcomes similar to TUDCA and KYC. Our data suggest that cellular senescence plays an essential role in BPD after initial inducement by hyperoxia. Reducing myeloperoxidase toxic oxidant production, ER stress, and attenuating cellular senescence are potential therapeutic strategies for halting BPD progression.
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Affiliation(s)
- Xigang Jing
- Department of Pediatrics
- Children's Research Institute
| | - Shuang Jia
- Department of Pediatrics
- Children's Research Institute
| | - Maggie Teng
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri; and
| | | | | | | | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Equity, and
| | | | - Kirkwood A Pritchard
- Children's Research Institute
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
- ReNeuroGen LLC, Milwaukee, Wisconsin
| | | | | | - Ru-Jeng Teng
- Department of Pediatrics
- Children's Research Institute
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Alvarez-Argote S, Paddock SJ, Flinn MA, Moreno CW, Knas MC, Almeida VA, Buday SL, Bakhshian Nik A, Patterson M, Chen YG, Lin CW, O’Meara CC. IL-13 promotes functional recovery after myocardial infarction via direct signaling to macrophages. JCI Insight 2024; 9:e172702. [PMID: 38051583 PMCID: PMC10906228 DOI: 10.1172/jci.insight.172702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023] Open
Abstract
There is great interest in identifying signaling pathways that promote cardiac repair after myocardial infarction (MI). Prior studies suggest a beneficial role for IL-13 signaling in neonatal heart regeneration; however, the cell types mediating cardiac regeneration and the extent of IL-13 signaling in the adult heart after injury are unknown. We identified an abundant source of IL-13 and the related cytokine, IL-4, in neonatal cardiac type 2 innate lymphoid cells, but this phenomenon declined precipitously in adult hearts. Moreover, IL-13 receptor deletion in macrophages impaired cardiac function and resulted in larger scars early after neonatal MI. By using a combination of recombinant IL-13 administration and cell-specific IL-13 receptor genetic deletion models, we found that IL-13 signaling specifically to macrophages mediated cardiac functional recovery after MI in adult mice. Single transcriptomics revealed a subpopulation of cardiac macrophages in response to IL-13 administration. These IL-13-induced macrophages were highly efferocytotic and were identified by high IL-1R2 expression. Collectively, we elucidated a strongly proreparative role for IL-13 signaling directly to macrophages following cardiac injury. While this pathway is active in proregenerative neonatal stages, reactivation of macrophage IL-13 signaling is required to promote cardiac functional recovery in adults.
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Affiliation(s)
| | | | | | | | | | | | - Sydney L. Buday
- Department of Physiology
- Cardiovascular Research Center
- Department of Cell Biology, Neurobiology, and Anatomy
| | | | - Michaela Patterson
- Cardiovascular Research Center
- Department of Cell Biology, Neurobiology, and Anatomy
| | - Yi-Guang Chen
- Department of Pediatrics
- Department of Microbiology and Immunology, and
| | - Chien-Wei Lin
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Lin HJ, Chen CH, Su MW, Lin CW, Cheng YW, Tang SC, Jeng JS. Modifiable vascular risk factors contribute to stroke in 1080 NOTCH3 R544C carriers in Taiwan Biobank. Int J Stroke 2024; 19:105-113. [PMID: 37485895 DOI: 10.1177/17474930231191991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
BACKGROUND AND AIM Previous studies have suggested cardiovascular risk factors increase the risk of not only common sporadic stroke but also of stroke in patients with monogenic stroke disorders including CADASIL. We investigated the effects of the NOTCH3 Arg544Cys (R544C) variant and associated vascular risk factors on stroke in the Taiwanese population. METHODS This study was conducted using data from the Taiwan Biobank, consisting of at least 130,000 Han Chinese participants. The genotype was derived from customized genome-wide arrays for 650,000 to 750,000 single-nucleotide polymorphisms (SNPs). Individuals with NOTCH3 R544C were subsequently matched with noncarriers based on the propensity score at a 1:10 ratio by demographic and cardiovascular risk factors. The odds ratio (OR) for stroke or other phenotypes in NOTCH3 R544C carriers and matched noncarriers was then calculated. Univariate and multivariate regression analyses were performed on cardiovascular risk factors in NOTCH3 R544C carriers with and without stroke. The polygenic risk score (PRS) model, adopted from the UK Biobank, was then applied to evaluate the role of NOTCH3 R544C in stroke. RESULTS From the 114,282 participants with both genotype and questionnaire results, 1080 (0.95%) harbored the pathogenic NOTCH3 R544C variant. When compared to the matched controls (n = 10,800), the carriers presented with a history of stroke (OR: 2.52, 95% confidence interval (CI) (1.45, 4.37)), dementia (OR: 30.1, 95% CI (3.13, 289.43)), and sibling history of stroke (OR: 2.48, 95% CI (1.85, 3.34)) phenotypes. The risk of stroke increased with every 10-year increase in age (p = 0.006, Cochran-Mantel-Haenszel test). Among NOTCH3 R544C carriers, 16 (1.3%) of the 1080 carriers with a stroke history were older, male, and more likely to have hypertension, diabetes, dyslipidemia, and a family history of stroke. In the stepwise multivariate analysis, hypertension (OR: 11.28, 95% CI (3.54, 43.3)) and diabetes mellitus (OR: 4.10, 95% CI (1.31, 12.4)) were independently associated with stroke. Harboring the NOTCH3 R544C variant in the Taiwan Biobank is comparable with a 6.74 standard deviations increase in individual's polygenic risk score for stroke. CONCLUSION While the NOTCH3 R544C variant alone increased the risk of stroke, modifiable vascular risk factors also played a role in the occurrence of stroke in Taiwanese community-dwelling individuals carrying the NOTCH3 variant.
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Affiliation(s)
- Hung-Jen Lin
- Department of Medical Education, National Taiwan University Hospital, Taipei
| | - Chih-Hao Chen
- Department of Neurology, National Taiwan University Hospital, Taipei
| | - Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei
| | - Chien-Wei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei
| | - Yu-Wen Cheng
- Department of Neurology, National Taiwan University Hospital, Taipei
| | - Sung-Chun Tang
- Department of Neurology, National Taiwan University Hospital, Taipei
| | - Jiann-Shing Jeng
- Department of Neurology, National Taiwan University Hospital, Taipei
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Kasmani MY, Topchyan P, Brown AK, Brown RJ, Wu X, Chen Y, Khatun A, Alson D, Wu Y, Burns R, Lin CW, Kudek MR, Sun J, Cui W. A spatial sequencing atlas of age-induced changes in the lung during influenza infection. Nat Commun 2023; 14:6597. [PMID: 37852965 PMCID: PMC10584893 DOI: 10.1038/s41467-023-42021-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/26/2023] [Indexed: 10/20/2023] Open
Abstract
Influenza virus infection causes increased morbidity and mortality in the elderly. Aging impairs the immune response to influenza, both intrinsically and because of altered interactions with endothelial and pulmonary epithelial cells. To characterize these changes, we performed single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and bulk RNA sequencing (bulk RNA-seq) on lung tissue from young and aged female mice at days 0, 3, and 9 post-influenza infection. Our analyses identified dozens of key genes differentially expressed in kinetic, age-dependent, and cell type-specific manners. Aged immune cells exhibited altered inflammatory, memory, and chemotactic profiles. Aged endothelial cells demonstrated characteristics of reduced vascular wound healing and a prothrombotic state. Spatial transcriptomics identified novel profibrotic and antifibrotic markers expressed by epithelial and non-epithelial cells, highlighting the complex networks that promote fibrosis in aged lungs. Bulk RNA-seq generated a timeline of global transcriptional activity, showing increased expression of genes involved in inflammation and coagulation in aged lungs. Our work provides an atlas of high-throughput sequencing methodologies that can be used to investigate age-related changes in the response to influenza virus, identify novel cell-cell interactions for further study, and ultimately uncover potential therapeutic targets to improve health outcomes in the elderly following influenza infection.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Paytsar Topchyan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Ryan J Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Xiaopeng Wu
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Yao Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Donia Alson
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yue Wu
- Carter Immunology Center, University of Virginia, Charlottesville, VA, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Chien-Wei Lin
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Matthew R Kudek
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Pathology, Northwestern University, Chicago, IL, 60611, USA.
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Lin TC, Chu CN, Chiou YR, Tsai WN, Liao XP, Su MH, Lin CW, Liang JA. Designing Patient-Centered Health Education Materials for Radiation Dermatitis in Breast Cancer Patients: A Pilot Study and Single-Center Clinical Trial. Int J Radiat Oncol Biol Phys 2023; 117:e408. [PMID: 37785354 DOI: 10.1016/j.ijrobp.2023.06.1549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) For breast cancer patients receiving radiotherapy (RT), radiation dermatitis is the most commonly experienced discomfort. However, patients usually do not participate in the design of health education materials regarding radiation dermatitis. We designed a pilot study to investigate the unmet need of breast cancer patients who would be receiving RT at our department and created a patient-centered educational video. We initiated a single-arm clinical trial to evaluate the effectiveness of the video in improving patient and their family's knowledge of radiation dermatitis, alleviating their anxiety, and helping patients improve self-care skills during RT course. MATERIALS/METHODS The pilot study was executed in a radiation oncology department of a tertiary medical center in Taiwan. We designed a questionnaire to explore new breast cancer patients' idea of a comprehensive pre-RT health education. Enrolled patients would fill out an electronic questionnaire during their first visit at our outpatient clinic. They were asked to select at most two of the following items they considered most important for pre-RT health education: (1) The mechanism behind RT; (2) Self-care skills for irradiated skin; (3) Activities to be avoided during RT course; (4) The toxicity grading of radiation dermatitis. Given the above information, we created a 4-minute video set in a clinical scenario of a patient receiving pre-RT health education from a nurse. A single-arm clinical trial (IRB approval number: CMUH111-REC2-121) is currently recruiting. The video was launched on YouTube (Link: https://youtu.be/O1uTXpS_ed0) to give patients easy access to the video. Enrolled patients would complete Skindex-16 survey (translated into Chinese) at 3 timepoints: during their first visit at our clinic, in the middle of RT course, and at the first post-RT follow-up visit. Cronbach's alpha test was applied to determine the internal consistency of the questionnaires. RESULTS The pilot study included 19 patients with an average age of 46.6 (range: 34 to 69) years old. All patients' primary language was Chinese Mandarin. Most patients (84%) received at least secondary education. We found by surprise that RTOG skin toxicity grading was considered very important for most patients (79%), while less than half (42%) found the mechanism behind RT important. The internal validity of the Chinese version of Skindex-16 was good (Cronbach's alpha score = 0.87). For the recruiting trial, we have enrolled 10 patients and planned to close the trial upon enrolling 50 participants. The study result should be available before August 2023. CONCLUSION We suggest to actively involve patients in designing health education materials for patient-centered care. Toxicity grading of radiation dermatitis should be included in pre-RT health education for breast cancer patients. Whether the educational video helps reduce patients' anxiety and the incidence of severe radiation dermatitis will soon be answered by our ongoing clinical trial.
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Affiliation(s)
- T C Lin
- Division of Radiation Oncology, Department of Oncology, China Medical University Hospital, Taichung, Taichung, Taiwan
| | - C N Chu
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Y R Chiou
- China Medical University Hospital, Taiwan, Taichung, Taiwan
| | - W N Tsai
- China Medical University Hospital, Taichung, Taiwan
| | - X P Liao
- China Medical University Hospital, Taichung, Taiwan
| | - M H Su
- China Medical University Hospital, Taichung, Taiwan
| | - C W Lin
- China Medical University Hospital, Taichung, Taiwan
| | - J A Liang
- China Medical University Hospital, Taichung, Taiwan
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Li SS, Chen JJ, Su MW, Lin CW, Chen CC, Wang YH, Liu CC, Tsai YC, Hsieh TJ, Wu MT, Wu CF. Sex-specific interactive effect of melamine and DEHP on a marker of early kidney damage in Taiwanese adults: A national population-based study from the Taiwan Biobank. Ecotoxicol Environ Saf 2023; 263:115208. [PMID: 37413945 DOI: 10.1016/j.ecoenv.2023.115208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023]
Abstract
Taiwan had the high incidence of chronic kidney disease (CKD) worldwide. Our objective was to examine associations between daily exposure of phthalates and melamine, two common nephrotoxins, and kidney damage risk in a well-established nationwide cohort. Study subjects were from Taiwan Biobank (TWB) with existing data of questionnaire and biochemical examinations. Average daily intake (ADI) levels of melamine and seven parental phthalates, including DEHP (di-2-ethylhexylphthalate), DiBP (Dibutyl phthalate), DnBP (Di-n-butyl phthalate), BBzP (Butyl benzyl phthalate), DEP (Diethyl phthalate), and DMP (Dimethyl phthalate) were estimated using a creatinine excretion-based model from urine melamine and 10 phthalate metabolites. Urine microalbumin to creatinine ratio (ACR) was used to represent for the outcome of kidney damage. Two statistical strategies were used: First, a weighted quantile sum (WQS) regression model to select the most important exposure variables of ADI levels of phthalates and melamine associated with ACR; Second, to examine effects of those most important exposure variables on ACR in multivariable linear regression models. In total, 1153 eligible adults were left for analyses. Of them, 591 (51.3%) and 562 (48.7%) were men and women, respectively, with a median age of 49 years old. By WQS, a significant and positive association was found between ADI of melamine and phthalates and ACR (β = 0.14, p = 0.002). ADI levels of melamine had the highest weight (0.57), followed by DEHP (0.13). Next, examining the two most important exposures in association with ACR, we found that the higher the melamine and DEHP intakes, the higher the ACR levels were found. An interaction effect was also found between melamine and DEHP intakes on urine ACR (p = 0.015). This result was more prominent in men (p = 0.008) than in women (p = 0.651). Environmental co-exposure of melamine and DEHP can potentially affect ACR in the community-dwelling Taiwanese adult population.
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Affiliation(s)
- Sih-Syuan Li
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Jia-Jen Chen
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Ming-Wei Su
- Taiwan Biobank, Academia Sinica, Taipei, Taiwan.
| | | | - Chu-Chih Chen
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Taiwan.
| | - Yin-Han Wang
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Taiwan.
| | - Chia-Chu Liu
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Yi-Chun Tsai
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Tusty-Jiuan Hsieh
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Ming-Tsang Wu
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Ph.D. Program in Environmental and Occupational Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Public Health, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Chia-Fang Wu
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; International Master Program of Translational Medicine, National United University, Miaoli, Taiwan.
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9
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Ciecko AE, Wang Y, Harleston S, Drewek A, Serreze DV, Geurts AM, Lin CW, Chen YG. Heterogeneity of Islet-Infiltrating IL-21+ CD4 T Cells in a Mouse Model of Type 1 Diabetes. J Immunol 2023; 210:935-946. [PMID: 36762954 PMCID: PMC10483376 DOI: 10.4049/jimmunol.2200712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/29/2023] [Indexed: 02/11/2023]
Abstract
IL-21 is essential for type 1 diabetes (T1D) development in the NOD mouse model. IL-21-expressing CD4 T cells are present in pancreatic islets where they contribute to T1D progression. However, little is known about their phenotype and differentiation states. To fill this gap, we generated, to our knowledge, a novel IL-21 reporter NOD strain to further characterize IL-21+ CD4 T cells in T1D. IL-21+ CD4 T cells accumulate in pancreatic islets and recognize β cell Ags. Single-cell RNA sequencing revealed that CD4 T effector cells in islets actively express IL-21 and they are highly diabetogenic despite expressing multiple inhibitory molecules, including PD-1 and LAG3. Islet IL-21+ CD4 T cells segregate into four phenotypically and transcriptionally distinct differentiation states, that is, less differentiated early effectors, T follicular helper (Tfh)-like cells, and two Th1 subsets. Trajectory analysis predicts that early effectors differentiate into both Tfh-like and terminal Th1 cells. We further demonstrated that intrinsic IL-27 signaling controls the differentiation of islet IL-21+ CD4 T cells, contributing to their helper function. Collectively, our study reveals the heterogeneity of islet-infiltrating IL-21+ CD4 T cells and indicates that both Tfh-like and Th1 subsets produce IL-21 throughout their differentiation process, highlighting the important sources of IL-21 in T1D pathogenesis.
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Affiliation(s)
- Ashley E. Ciecko
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
- The Max McGee Research Center for Juvenile Diabetes, Children’s Research Institute of Children’s Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yu Wang
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Stephanie Harleston
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
- The Max McGee Research Center for Juvenile Diabetes, Children’s Research Institute of Children’s Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Amber Drewek
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
- The Max McGee Research Center for Juvenile Diabetes, Children’s Research Institute of Children’s Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - David V. Serreze
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Aron M. Geurts
- Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | - Yi-Guang Chen
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
- The Max McGee Research Center for Juvenile Diabetes, Children’s Research Institute of Children’s Hospital of Wisconsin, Milwaukee, WI, 53226, USA
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10
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Zenga J, Atkinson S, Yen T, Massey B, Stadler M, Bruening J, Peppard W, Reuben M, Hayward M, Mesich B, Buchan B, Ledeboer N, Sanchez JL, Fraser R, Lin CW, Holtz ML, Awan M, Wong SJ, Puram SV, Salzman N. A phase 2 trial of a topical antiseptic bundle in head and neck cancer surgery: Effects on surgical site infection and the oral microbiome. EBioMedicine 2022; 81:104099. [PMID: 35671624 PMCID: PMC9168040 DOI: 10.1016/j.ebiom.2022.104099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
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11
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Dong A, Pan X, Lin CW, Huang YW, Krause H, Pan P, Baim A, Thomas MJ, Chen X, Yu J, Michaelis L, Liu P, Wang LS, Atallah E. A Pilot Clinical Study to Investigate the Hypomethylating Properties of Freeze-dried Black Raspberries in Patients with Myelodysplastic Syndrome or Myeloproliferative Neoplasm. J Cancer Prev 2022; 27:129-138. [PMID: 35864858 PMCID: PMC9271408 DOI: 10.15430/jcp.2022.27.2.129] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022] Open
Abstract
Myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are bone marrow disorders characterized by cytopenias and progression to acute myeloid leukemia. Hypomethylating agents (HMAs) are Food and Drug Administration-approved therapies for MDS and MDS/MPN patients. HMAs have improved patients’ survival and quality of life when compared with other therapies. Although HMAs are effective in MDS and MDS/MPN patients, they are associated with significant toxicities that place a large burden on patients. Our goal is to develop a safer and more effective HMA from natural products. We previously reported that black raspberries (BRBs) have hypomethylating effects in the colon, blood, spleen, and bone marrow of mice. In addition, BRBs exert hypomethylating effects in patients with colorectal cancer and familial adenomatous polyposis. In the current study, we conducted a pilot clinical trial to evaluate the hypomethylating effects of BRBs in patients with low-risk MDS or MDS/MPN. Peripheral blood mononuclear cells (PBMCs) were isolated before and after three months of BRB intervention. CD45+ cells were isolated from PBMCs for methylation analysis using a reduced-representation bisulfite sequencing assay. Each patient served as their own matched control, with their measurements assessed before intervention providing a baseline for post-intervention results. Clinically, our data showed that BRBs were well-tolerated with no side effects. When methylation data was combined, BRBs significantly affected methylation levels of 477 promoter regions. Pathway analysis suggests that BRB-induced intragenic hypomethylation drives leukocyte differentiation. A randomized, placebo-controlled clinical trial of BRB use in low-risk MDS or MDS/MPN patients is warranted.
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Affiliation(s)
- Athena Dong
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Xiaoqing Pan
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hayden Krause
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pan Pan
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Arielle Baim
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael J Thomas
- Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Xiao Chen
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, Comprehensive Cancer Center, City of Hope National Medical Center, Duarte, CA, USA
| | - Laura Michaelis
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pengyuan Liu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ehab Atallah
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
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12
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Fang S, Wu J, Reho JJ, Lu KT, Brozoski DT, Kumar G, Werthman AM, Silva SD, Muskus Veitia PC, Wackman KK, Mathison AJ, Teng BQ, Lin CW, Quelle FW, Sigmund CD. RhoBTB1 reverses established arterial stiffness in angiotensin-II hypertension by promoting actin depolymerization. JCI Insight 2022; 7:158043. [PMID: 35358093 PMCID: PMC9090250 DOI: 10.1172/jci.insight.158043] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/30/2022] [Indexed: 11/17/2022] Open
Abstract
Arterial stiffness predicts cardiovascular disease and all-cause mortality, but its treatment remains challenging. Mice treated with angiotensin II (Ang II) develop hypertension, arterial stiffness, vascular dysfunction, and a downregulation of Rho-related BTB domain–containing protein 1 (RhoBTB1) in the vasculature. RhoBTB1 is associated with blood pressure regulation, but its function is poorly understood. We tested the hypothesis that restoring RhoBTB1 can attenuate arterial stiffness, hypertension, and vascular dysfunction in Ang II–treated mice. Genetic complementation of RhoBTB1 in the vasculature was achieved using mice expressing a tamoxifen-inducible, smooth muscle–specific RhoBTB1 transgene. RhoBTB1 restoration efficiently and rapidly alleviated arterial stiffness but not hypertension or vascular dysfunction. Mechanistic studies revealed that RhoBTB1 had no substantial effect on several classical arterial stiffness contributors, such as collagen deposition, elastin content, and vascular smooth muscle remodeling. Instead, Ang II increased actin polymerization in the aorta, which was reversed by RhoBTB1. Changes in the levels of 2 regulators of actin polymerization, cofilin and vasodilator-stimulated phosphoprotein, in response to RhoBTB1 were consistent with an actin depolymerization mechanism. Our study reveals an important function of RhoBTB1, demonstrates its vital role in antagonizing established arterial stiffness, and further supports a functional and mechanistic separation among hypertension, vascular dysfunction, and arterial stiffness.
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Affiliation(s)
- Shi Fang
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Jing Wu
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - John J Reho
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Ko-Ting Lu
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Daniel T Brozoski
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Gaurav Kumar
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Alec M Werthman
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Sebastiao Donato Silva
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Patricia C Muskus Veitia
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Kelsey K Wackman
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
| | - Angela J Mathison
- Department of Surgery and the Genomic Sciences and Precision Medicine Cente, Medical College of Wisconsin, Milwawkee, United States of America
| | - Bi Qing Teng
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, United States of America
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, United States of America
| | - Frederick W Quelle
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, United States of America
| | - Curt D Sigmund
- Department of Physiology and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, United States of America
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13
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Dong A, Lin CW, Echeveste CE, Huang YW, Oshima K, Yearsley M, Chen X, Yu J, Wang LS. Protocatechuic Acid, a Gut Bacterial Metabolite of Black Raspberries, Inhibits Adenoma Development and Alters Gut Microbiome Profiles in Apc Min/+ Mice. J Cancer Prev 2022; 27:50-57. [PMID: 35419306 PMCID: PMC8984655 DOI: 10.15430/jcp.2022.27.1.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 11/06/2022] Open
Abstract
Administration of black raspberries (BRBs) and their anthocyanin metabolites, including protocatechuic acid (PCA), has been demonstrated to exert chemopreventive effects against colorectal cancer through alteration of innate immune cell trafficking, modulation of metabolic and inflammatory pathways, etc. Previous research has shown that the gut microbiome is important in the effectiveness of chemoprevention of colorectal cancer. This study aimed to assess the potency of PCA versus BRB dietary administration for colorectal cancer prevention using an Apc Min/+ mouse model and determine how bacterial profiles change in response to PCA and BRBs. A control AIN-76A diet supplemented with 5% BRBs, 500 ppm PCA, or 1,000 ppm PCA was administered to Apc Min/+ mice. Changes in incidence, polyp number, and polyp size regarding adenomas of the small intestine and colon were assessed after completion of the diet regimen. There were significant decreases in adenoma development by dietary administration of PCA and BRBs in the small intestine and the 5% BRB-supplemented diet in the colon. Pro-inflammatory bacterial profiles were replaced with anti-inflammatory bacteria in all treatments, with the greatest effects in the 5% BRB and 500 ppm PCA-supplemented diets accompanied by decreased COX-2 and prostaglandin E2 levels in colonic mucosa. We further showed that 500 ppm PCA, but not 1,000 ppm PCA, increased IFN-γ and SMAD4 levels in primary cultured human natural killer cells. These results suggest that both BRBs and a lower dose PCA can benefit colorectal cancer patients by inhibiting the growth and proliferation of adenomas and promoting a more favorable gut microbiome condition.
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Affiliation(s)
- Athena Dong
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, WI, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, WI, USA
| | - Carla Elena Echeveste
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, WI, USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kiyoko Oshima
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Xiao Chen
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, WI, USA
| | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, WI, USA
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14
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Su MW, Chang CK, Lin CW, Chu HW, Tsai TN, Su WC, Chen YC, Chang TK, Huang CW, Tsai HL, Wu CC, Chou HC, Shiu BH, Wang JY. Genomic and Metabolomic Landscape of Right-Sided and Left-Sided Colorectal Cancer: Potential Preventive Biomarkers. Cells 2022; 11:cells11030527. [PMID: 35159336 PMCID: PMC8834628 DOI: 10.3390/cells11030527] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/27/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. The incidence and mortality rates of CRC are significantly higher in Taiwan than in other developed countries. Genes involved in CRC tumorigenesis differ depending on whether the tumor occurs on the left or right side of the colon, and genomic analysis is a keystone in the study and treatment of CRC subtypes. However, few studies have focused on the genetic landscape of Taiwanese patients with CRC. This study comprehensively analyzed the genomes of 141 Taiwanese patients with CRC through whole-exome sequencing. Significant genomic differences related to the site of CRC development were observed. Blood metabolomic profiling and polygenic risk score analysis were performed to identify potential biomarkers for the early identification and prevention of CRC in the Taiwanese population. Our findings provide vital clues for establishing population-specific treatments and health policies for CRC prevention in Taiwan.
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Affiliation(s)
- Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Chien-Wei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (M.-W.S.); (C.-K.C.); (C.-W.L.); ho (H.-W.C.)
| | - Tsen-Ni Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
| | - Wei-Chih Su
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yen-Cheng Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tsung-Kun Chang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
| | - Ching-Wen Huang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chang-Chieh Wu
- Department of Surgery, Tri-Service General Hospital Keelung Branch, National Defense Medical Center, Keelung 20042, Taiwan;
| | - Huang-Chi Chou
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan; (H.-C.C.); (B.-H.S.)
- Division of Colon and Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Bei-Hao Shiu
- School of Medicine, Chung Shan Medical University, Taichung 402306, Taiwan; (H.-C.C.); (B.-H.S.)
- Division of Colon and Rectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung 402306, Taiwan
| | - Jaw-Yuan Wang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (T.-N.T.); (W.-C.S.); (Y.-C.C.); (T.-K.C.); (C.-W.H.); (H.-L.T.)
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung 900, Taiwan
- Correspondence: & ; Tel.: +886-7-312-2805
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15
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Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics 2022; 220:6516514. [PMID: 35380657 PMCID: PMC8982048 DOI: 10.1093/genetics/iyac005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html.
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Affiliation(s)
- Mahima Vedi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S Nalabolu
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew J Hoffman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Morgan L Hill
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ketaki Thorat
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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16
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Abstract
Despite the growing recognition of a host genetic effect on shaping gut microbiota composition, the genetic determinants of oral microbiota remain largely unexplored, especially in the context of oral diseases. Here, we performed a microbiome genome-wide association study in 2 independent cohorts of patients with oral squamous cell carcinoma (OSCC, n = 144 and 67) and an additional group of noncancer individuals (n = 104). Besides oral bacterial dysbiosis and signatures observed in OSCC, associations of 3 loci with the abundance of genus-level taxa and 4 loci with β diversity measures were detected (q < 0.05) at the discovery stage. The most significant hit (rs10906082 with the genus Lachnoanaerobaculum, P = 3.55 × 10-9 at discovery stage) was replicated in a second OSCC cohort. Moreover, the other 2 taxonomical associations, rs10973953 with the genus Kingella (P = 1.38 × 10-9) and rs4721629 with the genus Parvimonas (P = 3.53 × 10-8), were suggestive in the meta-analysis combining 2 OSCC cohorts. Further pathway analysis revealed that these loci were enriched for genes in regulation of oncogenic and angiogenic responses, implicating a genetic anchor to the oral microbiome in estimation of casual relationships with OSCC. Our findings delineate the role of host genotypes in influencing the structure of oral microbial communities.
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Affiliation(s)
- S F Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - C W Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - C Y Chuang
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Otolaryngology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Y C Lee
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - W H Chung
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan.,Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - H C Lai
- Department of Medical Biotechnology and Laboratory Science, and Microbiota Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Central Research Laboratory, XiaMen Chang Gung Hospital, XiaMen, China
| | - L C Chang
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - S C Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan.,Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.,Central Research Laboratory, XiaMen Chang Gung Hospital, XiaMen, China
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17
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Ciecko AE, Schauder DM, Foda B, Petrova G, Kasmani MY, Burns R, Lin CW, Drobyski WR, Cui W, Chen YG. Self-Renewing Islet TCF1 + CD8 T Cells Undergo IL-27-Controlled Differentiation to Become TCF1 - Terminal Effectors during the Progression of Type 1 Diabetes. J Immunol 2021; 207:1990-2004. [PMID: 34507949 DOI: 10.4049/jimmunol.2100362] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 11/19/2022]
Abstract
In type 1 diabetes (T1D) autoreactive CD8 T cells infiltrate pancreatic islets and destroy insulin-producing β cells. Progression to T1D onset is a chronic process, which suggests that the effector activity of β-cell autoreactive CD8 T cells needs to be maintained throughout the course of disease development. The mechanism that sustains diabetogenic CD8 T cell effectors during the course of T1D progression has not been completely defined. Here we used single-cell RNA sequencing to gain further insight into the phenotypic complexity of islet-infiltrating CD8 T cells in NOD mice. We identified two functionally distinct subsets of activated CD8 T cells, CD44highTCF1+CXCR6- and CD44highTCF1-CXCR6+, in islets of prediabetic NOD mice. Compared with CD44highTCF1+CXCR6- CD8 T cells, the CD44highTCF1-CXCR6+ subset expressed higher levels of inhibitory and cytotoxic molecules and was more prone to apoptosis. Adoptive cell transfer experiments revealed that CD44highTCF1+CXCR6- CD8 T cells, through continuous generation of the CD44highTCF1-CXCR6+ subset, were more capable than the latter population to promote insulitis and the development of T1D. We further showed that direct IL-27 signaling in CD8 T cells promoted the generation of terminal effectors from the CD44highTCF1+CXCR6- population. These results indicate that islet CD44highTCF1+CXCR6- CD8 T cells are a progenitor-like subset with self-renewing capacity, and, under an IL-27-controlled mechanism, they differentiate into the CD44highTCF1-CXCR6+ terminal effector population. Our study provides new insight into the sustainability of the CD8 T cell response in the pathogenesis of T1D.
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Affiliation(s)
- Ashley E Ciecko
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - David M Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | - Bardees Foda
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI.,Department of Molecular Genetics and Enzymology, National Research Center, Dokki, Egypt
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | | | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Society, Medical College of Wisconsin, Milwaukee, WI; and
| | - William R Drobyski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI; .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI
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18
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Huang YW, Mo YY, Echeveste CE, Oshima K, Zhang J, Yearsley M, Lin CW, Yu J, Liu P, Du M, Sun C, Xiao J, Wang LS. Black raspberries attenuate colonic adenoma development in Apc Min mice: Relationship to hypomethylation of promoters and gene bodies. Food Front 2021; 1:234-242. [PMID: 34557678 PMCID: PMC8457619 DOI: 10.1002/fft2.45] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Recent studies have suggested that in addition to promoter region, DNA methylation in intragenic and intergenic regions also changes during physiological processes and disease. The current study showed that feeding of black raspberries (BRBs) to ApcMin mice suppressed colon and intestinal tumors. MBDCap-seq suggested that dietary BRBs hypomethylated promoter, intragenic, and intergenic regions. Annotation of those regions highlighted genes in pathways involved in immune regulation, inflammatory signaling, production of nitric oxide and reactive oxygen species, and progression of colorectal cancer. BRB phytochemicals (e.g., ellagic acid, anthocyanins, oligosaccharides) and their gut bacterial metabolites (e.g., urolithin, protocatechuic acid, short-chain fatty acids) inhibited DNMT1 and DNMT3B activities in a cell-free assay. Our results suggest that BRBs’ hypomethylating activities result from the combined effects of multiple BRB phytochemicals and their gut bacterial metabolites. Because similar substances are found in many plant products, our results with BRBs might also apply to commonly consumed fruits and vegetables.
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Affiliation(s)
- Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yue Yang Mo
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Carla Elena Echeveste
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kiyoko Oshima
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Jianying Zhang
- Division of Biostatistics, Department of Science of Informatics, City of Hope National Medical Center and Beckman Research Institute, Duarte, California
| | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, California
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Sir Run Run Shaw Hospital and Institute of Translational MedicineZhejiang University, Zhejiang, China
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, China
| | - Chongde Sun
- Laboratory of Fruit Quality Biology / Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology / The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, China
| | - Jianbo Xiao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical SciencesUniversity of Macau, Taipa, Macau, China
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
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19
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Li L, Long F, Lin CW, Ma M, Hu G, Zhang Y. [Controversy and prospect of transanal total mesorectal excision]. Zhonghua Wei Chang Wai Ke Za Zhi 2021; 24:727-734. [PMID: 34412192 DOI: 10.3760/cma.j.cn.441530-20200929-00545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As a novel surgical technique, taTME has developed rapidly in recent years. TaTME inevitably attracts some skepticism on safety, efficacy, and indication. First, the controversies over taTME are mainly reflected on the safety and effectiveness of taTME. On one hand, the increase of surgical complications, such as urethral injury, CO2 embolism, anastomotic leakage and pelvic infection, has raised concerns about the safety of taTME. Second, the poor quality of taTME specimens, the increased local recurrence rate and the impaired anal function after taTME, also make people question the effectiveness of taTME. Third, there are more or less controversies in the selection of taTME cases, surgical procedures and cost-effectiveness. However, it can not be denied that taTME has a promising future in view of both surgical theory and clinical practice. Furthermore, taTME is a relatively safe and effective supplementary surgical procedure, especially for patients with low rectal cancer. We should attach more importance to structured training for beginners and conduct high-quality clinical studies in the future development of taTME in China, so as to ensure the safe implementation of taTME and obtain high-level evidence-based medicine evidence, and then standardize the clinical practice of taTME.
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Affiliation(s)
- L Li
- Department of Gastrointestinal Surgery, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - F Long
- Department of Gastrointestinal Surgery, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - C W Lin
- Department of Gastrointestinal Surgery, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - M Ma
- Department of Gastrointestinal Surgery, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - G Hu
- Department of Gastrointestinal Surgery, the Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Y Zhang
- Department of Gastrointestinal Surgery, the Third Xiangya Hospital, Central South University, Changsha 410013, China
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20
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Lin CW, Chang LC, Ma T, Oh H, French B, Puralewski R, Mathews F, Fang Y, Lewis DA, Kennedy JL, Mueller D, Marshe VS, Jaffe A, Chen Q, Ursini G, Weinberger D, Newman AB, Lenze EJ, Nikolova YS, Tseng GC, Sibille E. Older molecular brain age in severe mental illness. Mol Psychiatry 2021; 26:3646-3656. [PMID: 32632206 PMCID: PMC7785531 DOI: 10.1038/s41380-020-0834-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 06/03/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022]
Abstract
Psychiatric disorders are associated with accelerated aging and enhanced risk for neurodegenerative disorders. Brain aging is associated with molecular, cellular, and structural changes that are robust on the group level, yet show substantial inter-individual variability. Here we assessed deviations in gene expression from normal age-dependent trajectories, and tested their validity as predictors of risk for major mental illnesses and neurodegenerative disorders. We performed large-scale gene expression and genotype analyses in postmortem samples of two frontal cortical brain regions from 214 control subjects aged 20-90 years. Individual estimates of "molecular age" were derived from age-dependent genes, identified by robust regression analysis. Deviation from chronological age was defined as "delta age". Genetic variants associated with deviations from normal gene expression patterns were identified by expression quantitative trait loci (cis-eQTL) of age-dependent genes or genome-wide association study (GWAS) on delta age, combined into distinct polygenic risk scores (PRScis-eQTL and PRSGWAS), and tested for predicting brain disorders or pathology in independent postmortem expression datasets and clinical cohorts. In these validation datasets, molecular ages, defined by 68 and 76 age-related genes for two brain regions respectively, were positively correlated with chronological ages (r = 0.88/0.91), elevated in bipolar disorder (BP) and schizophrenia (SCZ), and unchanged in major depressive disorder (MDD). Exploratory analyses in independent clinical datasets show that PRSs were associated with SCZ and MDD diagnostics, and with cognition in SCZ and pathology in Alzheimer's disease (AD). These results suggest that older molecular brain aging is a common feature of severe mental illnesses and neurodegeneration.
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Affiliation(s)
- Chien-Wei Lin
- Department of Biostatistics, Graduate school of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Lun-Ching Chang
- Department of Biostatistics, Graduate school of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Tianzhou Ma
- Department of Biostatistics, Graduate school of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD, 20742, USA
| | - Hyunjung Oh
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15312, USA
- Campbell Family Mental Health Research Institute of CAMH, Department of Psychiatry, University of Toronto, Toronto, M5T1R8, ON, Canada
| | - Beverly French
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15312, USA
| | - Rachel Puralewski
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15312, USA
| | - Fasil Mathews
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15312, USA
| | - Yusi Fang
- Department of Biostatistics, Graduate school of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15312, USA
| | - James L Kennedy
- Campbell Family Mental Health Research Institute of CAMH, Department of Psychiatry, University of Toronto, Toronto, M5T1R8, ON, Canada
| | - Daniel Mueller
- Campbell Family Mental Health Research Institute of CAMH, Department of Psychiatry, University of Toronto, Toronto, M5T1R8, ON, Canada
| | - Victoria S Marshe
- Campbell Family Mental Health Research Institute of CAMH, Department of Psychiatry, University of Toronto, Toronto, M5T1R8, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Andrew Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Daniel Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Anne B Newman
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eric J Lenze
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Yuliya S Nikolova
- Campbell Family Mental Health Research Institute of CAMH, Department of Psychiatry, University of Toronto, Toronto, M5T1R8, ON, Canada
| | - George C Tseng
- Department of Biostatistics, Graduate school of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Etienne Sibille
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15312, USA.
- Campbell Family Mental Health Research Institute of CAMH, Department of Psychiatry, University of Toronto, Toronto, M5T1R8, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, M5T1R8, ON, Canada.
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21
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Juang JMJ, Lu TP, Su MW, Lin CW, Yang JH, Chu HW, Chen CH, Hsiao YW, Lee CY, Chiang LM, Yu QY, Hsiao CK, Chen CYJ, Wu PE, Pai CH, Chuang EY, Shen CY. Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine. J Adv Res 2021; 30:147-158. [PMID: 34026292 PMCID: PMC8132201 DOI: 10.1016/j.jare.2020.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Introduction A population-specific genomic reference is important for research and clinical practice, yet it remains unavailable for Han Chinese (HC) in Taiwan. Objectives We report the first whole genome sequencing (WGS) database of HC (1000 Taiwanese genome (1KTW-WGS)) and demonstrate several applications to cardiovascular medicine. Methods Whole genomes of 997 HC were sequenced to at least 30X depth. A total of 20,117 relatively healthy HC individuals were genotyped using a customized Axiom GWAS array. We performed a genome-wide genotype imputation technique using IMPUTE2. Results We identified 26.7 million single-nucleotide variants (SNVs) and 4.2 million insertions-deletions. Of the SNVs, 16.1% were novel relative to dbSNP (build 152), and 34.2% were novel relative to gnomAD. A total of 18,450 healthy HC individuals were genotyped using a customized Genome-Wide Association Study (GWAS) array. We identified hypertension-associated variants and developed a hypertension prediction model based on the correlation between the WGS data and GWAS data (combined clinical and genetic models, AUC 0.887), and also identified 3 novel hyperlipidemia-associated variants. Each individual carried an average of 16.42 (SD = 3.72) disease-causing variants. Additionally, we established an online SCN5A (an important cardiac gene) database that can be used to explore racial differences. Finally, pharmacogenetics studies identified HC population-specific SNVs in genes (CYP2C9 and VKORC1) involved in drug metabolism and blood clotting. Conclusion This research demonstrates the benefits of constructing a population-specific genomic reference database for precision medicine.
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Affiliation(s)
- Jyh-Ming Jimmy Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Tzu-Pin Lu
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | | | | | - Jenn-Hwai Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
| | | | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
| | - Yi-Wen Hsiao
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Yueh Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Mei Chiang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Qi-You Yu
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chuhsing Kate Hsiao
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Ching-Yu Julius Chen
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Pei-Ei Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
| | | | - Eric Y. Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Yang Shen
- Taiwan Biobank, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
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22
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Wang S, Lin CW, Carleton AE, Cortez CL, Johnson C, Taniguchi LE, Sekulovski N, Townshend RF, Basrur V, Nesvizhskii AI, Zou P, Fu J, Gumucio DL, Duncan MC, Taniguchi K. Spatially resolved cell polarity proteomics of a human epiblast model. Sci Adv 2021; 7:7/17/eabd8407. [PMID: 33893097 PMCID: PMC8064645 DOI: 10.1126/sciadv.abd8407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/05/2021] [Indexed: 05/08/2023]
Abstract
Critical early steps in human embryonic development include polarization of the inner cell mass, followed by formation of an expanded lumen that will become the epiblast cavity. Recently described three-dimensional (3D) human pluripotent stem cell-derived cyst (hPSC-cyst) structures can replicate these processes. To gain mechanistic insights into the poorly understood machinery involved in epiblast cavity formation, we interrogated the proteomes of apical and basolateral membrane territories in 3D human hPSC-cysts. APEX2-based proximity bioinylation, followed by quantitative mass spectrometry, revealed a variety of proteins without previous annotation to specific membrane subdomains. Functional experiments validated the requirement for several apically enriched proteins in cyst morphogenesis. In particular, we found a key role for the AP-1 clathrin adaptor complex in expanding the apical membrane domains during lumen establishment. These findings highlight the robust power of this proximity labeling approach for discovering novel regulators of epithelial morphogenesis in 3D stem cell-based models.
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Affiliation(s)
- Sicong Wang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Amber E Carleton
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chari L Cortez
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Linnea E Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nikola Sekulovski
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ryan F Townshend
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deborah L Gumucio
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Kenichiro Taniguchi
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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23
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Huang YW, Lin CW, Pan P, Echeveste CE, Dong A, Oshima K, Yearsley M, Yu J, Wang LS. Dysregulated Free Fatty Acid Receptor 2 Exacerbates Colonic Adenoma Formation in Apc Min/+ Mice: Relation to Metabolism and Gut Microbiota Composition. J Cancer Prev 2021; 26:32-40. [PMID: 33842404 PMCID: PMC8020170 DOI: 10.15430/jcp.2021.26.1.32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Free fatty acid receptor 2 (FFAR2) has been reported as a tumor suppressor in colon cancer development. The current study investigated the effects of FFAR2 signaling on energy metabolism and gut microbiota profiling in a colorectal cancer mouse model (Apc Min/+ ). Ffar2 deficiency promoted colonic polyp development and enhanced fatty acid oxidation and bile acid metabolism. Gut microbiome sequencing analysis showed distinct clustering among wild-type, Apc Min/+ , and Apc Min/+ -Ffar2 -/- mice. The relative abundance of Flavobacteriaceae and Verrucomicrobiaceae was significantly increased in the Apc Min/+ -Ffar2 -/- mice compared to the Apc Min/+ mice. In addition, knocking-down FFAR2 in the human colon cancer cell lines (SW480 and HT29) resulted in increased expression of several key enzymes in fatty acid oxidation, such as carnitine palmitoyltransferase 2, acyl-CoA dehydrogenase, long-chain acyl-CoA dehydrogenase, C-2 to C-3 short chain, and hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase, alpha subunit. Collectively, these results demonstrated that Ffar2 deficiency significantly altered profiles of fatty acid metabolites and gut microbiome, which might promote colorectal cancer development.
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Affiliation(s)
- Yi-Wen Huang
- Department of Obstetrics & Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pan Pan
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Carla Elena Echeveste
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Athena Dong
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kiyoko Oshima
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, Comprehensive Cancer Center, City of Hope National Medical Center, Duarte, CA, USA
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
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24
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Khatun A, Kasmani MY, Zander R, Schauder DM, Snook JP, Shen J, Wu X, Burns R, Chen YG, Lin CW, Williams MA, Cui W. Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire. J Exp Med 2021; 218:e20200650. [PMID: 33201171 PMCID: PMC7676493 DOI: 10.1084/jem.20200650] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/24/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Tracking how individual naive T cells from a natural TCR repertoire clonally expand, differentiate, and make lineage choices in response to an infection has not previously been possible. Here, using single-cell sequencing technology to identify clones by their unique TCR sequences, we were able to trace the clonal expansion, differentiation trajectory, and lineage commitment of individual virus-specific CD4 T cells during an acute lymphocytic choriomeningitis virus (LCMV) infection. Notably, we found previously unappreciated clonal diversity and cellular heterogeneity among virus-specific helper T cells. Interestingly, although most naive CD4 T cells gave rise to multiple lineages at the clonal level, ∼28% of naive cells exhibited a preferred lineage choice toward either Th1 or TFH cells. Mechanistically, we found that TCR structure, in particular the CDR3 motif of the TCR α chain, skewed lineage decisions toward the TFH cell fate.
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Affiliation(s)
- Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Moujtaba Y. Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Ryan Zander
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - David M. Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Jeremy P. Snook
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Jian Shen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Xiaopeng Wu
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
- Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI
| | - Chien-Wei Lin
- Institute for Health and Equity, Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | - Matthew A. Williams
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
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25
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Li Y, Zeng X, Lin CW, Tseng GC. Simultaneous estimation of cluster number and feature sparsity in high-dimensional cluster analysis. Biometrics 2021; 78:574-585. [PMID: 33621349 DOI: 10.1111/biom.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
Estimating the number of clusters (K) is a critical and often difficult task in cluster analysis. Many methods have been proposed to estimate K, including some top performers using resampling approach. When performing cluster analysis in high-dimensional data, simultaneous clustering and feature selection is needed for improved interpretation and performance. To our knowledge, little has been studied for simultaneous estimation of K and feature sparsity parameter in a high-dimensional exploratory cluster analysis. In this paper, we propose a resampling method to bridge this gap and evaluate its performance under the sparse K-means clustering framework. The proposed target function balances between sensitivity and specificity of clustering evaluation of pairwise subjects from clustering of full and subsampled data. Through extensive simulations, the method performs among the best over classical methods in estimating K in low-dimensional data. For high-dimensional simulation data, it also shows superior performance to simultaneously estimate K and feature sparsity parameter. Finally, we evaluated the methods in four microarray, two RNA-seq, one SNP, and two nonomics datasets. The proposed method achieves better clustering accuracy with fewer selected predictive genes in almost all real applications.
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Affiliation(s)
- Yujia Li
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Xiangrui Zeng
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Wauwatosa, Wisconsin
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
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26
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Xin G, Chen Y, Topchyan P, Kasmani MY, Burns R, Volberding PJ, Wu X, Cohn A, Chen Y, Lin CW, Ho PC, Silverstein R, Dwinell MB, Cui W. Targeting PIM1-Mediated Metabolism in Myeloid Suppressor Cells to Treat Cancer. Cancer Immunol Res 2021; 9:454-469. [PMID: 33579728 DOI: 10.1158/2326-6066.cir-20-0433] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 12/24/2022]
Abstract
There is a strong correlation between myeloid-derived suppressor cells (MDSC) and resistance to immune checkpoint blockade (ICB), but the detailed mechanisms underlying this correlation are largely unknown. Using single-cell RNA sequencing analysis in a bilateral tumor model, we found that immunosuppressive myeloid cells with characteristics of fatty acid oxidative metabolism dominate the immune-cell landscape in ICB-resistant subjects. In addition, we uncovered a previously underappreciated role of a serine/threonine kinase, PIM1, in regulating lipid oxidative metabolism via PPARγ-mediated activities. Enforced PPARγ expression sufficiently rescued metabolic and functional defects of Pim1 -/- MDSCs. Consistent with this, pharmacologic inhibition of PIM kinase by AZD1208 treatment significantly disrupted the myeloid cell-mediated immunosuppressive microenvironment and unleashed CD8+ T-cell-mediated antitumor immunity, which enhanced PD-L1 blockade in preclinical cancer models. PIM kinase inhibition also sensitized nonresponders to PD-L1 blockade by selectively targeting suppressive myeloid cells. Overall, we have identified PIM1 as a metabolic modulator in MDSCs that is associated with ICB resistance and can be therapeutically targeted to overcome ICB resistance.
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Affiliation(s)
- Gang Xin
- Versiti Blood Research Institute, Milwaukee, Wisconsin. .,Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, Ohio.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Yao Chen
- Versiti Blood Research Institute, Milwaukee, Wisconsin.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Paytsar Topchyan
- Versiti Blood Research Institute, Milwaukee, Wisconsin.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Moujtaba Y Kasmani
- Versiti Blood Research Institute, Milwaukee, Wisconsin.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert Burns
- Versiti Blood Research Institute, Milwaukee, Wisconsin
| | - Peter J Volberding
- Versiti Blood Research Institute, Milwaukee, Wisconsin.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Xiaopeng Wu
- Versiti Blood Research Institute, Milwaukee, Wisconsin
| | - Alexandra Cohn
- Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yiliang Chen
- Versiti Blood Research Institute, Milwaukee, Wisconsin
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Roy Silverstein
- Versiti Blood Research Institute, Milwaukee, Wisconsin.,Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael B Dwinell
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Center for Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Weiguo Cui
- Versiti Blood Research Institute, Milwaukee, Wisconsin. .,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin
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27
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Huang YW, Lin CW, Pan P, Shan T, Echeveste CE, Mo YY, Wang HT, Aldakkak M, Tsai S, Oshima K, Yearsley M, Xiao J, Cao H, Sun C, Du M, Bai W, Yu J, Wang LS. Black Raspberries Suppress Colorectal Cancer by Enhancing Smad4 Expression in Colonic Epithelium and Natural Killer Cells. Front Immunol 2020; 11:570683. [PMID: 33424832 PMCID: PMC7793748 DOI: 10.3389/fimmu.2020.570683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/19/2020] [Indexed: 02/05/2023] Open
Abstract
Innate immune cells in the tumor microenvironment have been proposed to control the transition from benign to malignant stages. In many cancers, increased infiltration of natural killer (NK) cells associates with good prognosis. Although the mechanisms that enable NK cells to restrain colorectal cancer (CRC) are unclear, the current study suggests the involvement of Smad4. We found suppressed Smad4 expression in circulating NK cells of untreated metastatic CRC patients. Moreover, NK cell-specific Smad4 deletion promoted colon adenomas in DSS-treated ApcMin/+ mice and adenocarcinomas in AOM/DSS-treated mice. Other studies have shown that Smad4 loss or weak expression in colonic epithelium associates with poor survival in CRC patients. Therefore, targeting Smad4 in both colonic epithelium and NK cells could provide an excellent opportunity to manage CRC. Toward this end, we showed that dietary intervention with black raspberries (BRBs) increased Smad4 expression in colonic epithelium in patients with FAP or CRC and in the two CRC mouse models. Also, benzoate metabolites of BRBs, such as hippurate, upregulated Smad4 and Gzmb expression that might enhance the cytotoxicity of primary human NK cells. Of note, increased levels of hippurate is a metabolomic marker of a healthy gut microbiota in humans, and hippurate also has antitumor effects. In conclusion, our study suggests a new mechanism for the action of benzoate metabolites derived from plant-based foods. This mechanism could be exploited clinically to upregulate Smad4 in colonic epithelium and NK cells, thereby delaying CRC progression.
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Affiliation(s)
- Yi-Wen Huang
- Department of Obstetrics & Gynecology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Pan Pan
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tianjiao Shan
- Department of Obstetrics & Gynecology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Carla Elena Echeveste
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Yue Yang Mo
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Hsin-Tzu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Mohammed Aldakkak
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Susan Tsai
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Kiyoko Oshima
- Department of Pathology, Johns Hopkins University, Baltimore, MD, United States
| | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Jianbo Xiao
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macau, Macau
| | - Hui Cao
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macau, Macau
| | - Chongde Sun
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, China
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, China
| | - Weibin Bai
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangzhou, China
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, Comprehensive Cancer Center, City of Hope National Medical Center, Duarte, CA, United States
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
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28
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Gartz M, Lin CW, Sussman MA, Lawlor MW, Strande JL. Duchenne muscular dystrophy (DMD) cardiomyocyte-secreted exosomes promote the pathogenesis of DMD-associated cardiomyopathy. Dis Model Mech 2020; 13:13/11/dmm045559. [PMID: 33188007 PMCID: PMC7673361 DOI: 10.1242/dmm.045559] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/08/2020] [Indexed: 12/20/2022] Open
Abstract
Cardiomyopathy is a leading cause of early mortality in Duchenne muscular dystrophy (DMD). There is a need to gain a better understanding of the molecular pathogenesis for the development effective therapies. Exosomes (exo) are secreted vesicles and exert effects via their RNA, lipid and protein cargo. The role of exosomes in disease pathology is unknown. Exosomes derived from stem cells have demonstrated cardioprotection in the murine DMD heart. However, it is unknown how the disease status of the donor cell type influences exosome function. Here, we sought to determine the phenotypic responses of DMD cardiomyocytes (DMD-iCMs) after long-term exposure to DMD cardiac exosomes (DMD-exo). DMD-iCMs were vulnerable to stress, evidenced by production of reactive oxygen species, the mitochondrial membrane potential and cell death levels. Long-term exposure to non-affected exosomes (N-exo) was protective. By contrast, long-term exposure to DMD-exo was not protective, and the response to stress improved with inhibition of DMD-exo secretion in vitro and in vivo The microRNA (miR) cargo, but not exosome surface peptides, was implicated in the pathological effects of DMD-exo. Exosomal surface profiling revealed N-exo peptides associated with PI3K-Akt signaling. Transcriptomic profiling identified unique changes with exposure to either N- or DMD-exo. Furthermore, DMD-exo miR cargo regulated injurious pathways, including p53 and TGF-beta. The findings reveal changes in exosomal cargo between healthy and diseased states, resulting in adverse outcomes. Here, DMD-exo contained miR changes, which promoted the vulnerability of DMD-iCMs to stress. Identification of these molecular changes in exosome cargo and effectual phenotypes might shed new light on processes underlying DMD cardiomyopathy.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Melanie Gartz
- Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mark A Sussman
- San Diego Heart Institute and Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Michael W Lawlor
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer L Strande
- Cardiovascular Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA .,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Medicine, Cardiovascular Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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29
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Huang YW, Pan P, Echeveste CE, Wang HT, Oshima K, Lin CW, Yearsley M, Xiao J, Chen J, Sun C, Yu J, Wang LS. Transplanting fecal material from wild-type mice fed black raspberries alters the immune system of recipient mice. Food Front 2020; 1:253-259. [PMID: 34308364 PMCID: PMC8301209 DOI: 10.1002/fft2.34] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
By constantly stimulating intestinal immunity, gut microbes play important regulatory roles, and their possible involvement in human physical and mental disorders beyond intestinal diseases suggests the importance of maintaining homeostasis in the gut microbiota. Both transplantation of fecal microbiota and dietary interventions have been shown to restore microbial homeostasis in recipients. In the current study with wild-type mice, we combined these two approaches to determine if transplanting fecal material from mice fed black raspberries (BRB, 5%) altered recipients' immune system. The donors received a control or 5% BRB diet, and fecal transplantation was performed every other day 15 times into recipients fed control diet. Afterward, we used flow cytometry to analyze populations of CD3+ T, CD4+ T, CD8+ T cells, and NK cells among bone marrow cells, splenocytes, and peripheral blood mononuclear cells (PBMCs) collected from the recipients. We found that BRB-fecal material that contained both fecal microbiota and their metabolites increased NK cell populations among bone marrow cells, splenocytes, and PBMCs, and raised levels of CD8+ T cells in splenocytes. Our findings suggest that fecal transplantation can modulate the immune system and might therefore be valuable for managing a range of physical and mental disorders.
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Affiliation(s)
- Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Wauwatosa, Wisconsin
| | - Pan Pan
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Wauwatosa, Wisconsin
| | - Carla Elena Echeveste
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Wauwatosa, Wisconsin
| | - Hsin-Tzu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Wauwatosa, Wisconsin
| | - Kiyoko Oshima
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Wauwatosa, Wisconsin
| | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Jianbo Xiao
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macau, China
| | - Jiebiao Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, China
| | - Chongde Sun
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou, China
| | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute, Duarte, California
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Wauwatosa, Wisconsin
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30
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Zeng X, Zong W, Lin CW, Fang Z, Ma T, Lewis DA, Enwright JF, Tseng GC. Comparative Pathway Integrator: A Framework of Meta-Analytic Integration of Multiple Transcriptomic Studies for Consensual and Differential Pathway Analysis. Genes (Basel) 2020; 11:genes11060696. [PMID: 32599927 PMCID: PMC7348908 DOI: 10.3390/genes11060696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 11/16/2022] Open
Abstract
Pathway enrichment analysis provides a knowledge-driven approach to interpret differentially expressed genes associated with disease status. Many tools have been developed to analyze a single study. However, when multiple studies of different conditions are jointly analyzed, novel integrative tools are needed. In addition, pathway redundancy introduced by combining multiple public pathway databases hinders interpretation and knowledge discovery. We present a meta-analytic integration tool, Comparative Pathway Integrator (CPI), to address these issues using adaptively weighted Fisher’s method to discover consensual and differential enrichment patterns, a tight clustering algorithm to reduce pathway redundancy, and a text mining algorithm to assist interpretation of the pathway clusters. We applied CPI to jointly analyze six psychiatric disorder transcriptomic studies to demonstrate its effectiveness, and found functions confirmed by previous biological studies as well as novel enrichment patterns. CPI’s R package is accessible online on Github metaOmics/MetaPath.
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Affiliation(s)
- Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Wei Zong
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15260, USA; (W.Z.); (Z.F.)
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Wauwatosa, WI 53226, USA;
| | - Zhou Fang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15260, USA; (W.Z.); (Z.F.)
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20742, USA;
| | - David A. Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15260, USA; (D.A.L.); (J.F.E.)
| | - John F. Enwright
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15260, USA; (D.A.L.); (J.F.E.)
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15260, USA; (W.Z.); (Z.F.)
- Correspondence:
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31
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Ma T, Huo Z, Kuo A, Zhu L, Fang Z, Zeng X, Lin CW, Liu S, Wang L, Liu P, Rahman T, Chang LC, Kim S, Li J, Park Y, Song C, Oesterreich S, Sibille E, Tseng GC. MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis. Bioinformatics 2020; 35:1597-1599. [PMID: 30304367 DOI: 10.1093/bioinformatics/bty825] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 01/09/2023] Open
Abstract
SUMMARY The rapid advances of omics technologies have generated abundant genomic data in public repositories and effective analytical approaches are critical to fully decipher biological knowledge inside these data. Meta-analysis combines multiple studies of a related hypothesis to improve statistical power, accuracy and reproducibility beyond individual study analysis. To date, many transcriptomic meta-analysis methods have been developed, yet few thoughtful guidelines exist. Here, we introduce a comprehensive analytical pipeline and browser-based software suite, called MetaOmics, to meta-analyze multiple transcriptomic studies for various biological purposes, including quality control, differential expression analysis, pathway enrichment analysis, differential co-expression network analysis, prediction, clustering and dimension reduction. The pipeline includes many public as well as >10 in-house transcriptomic meta-analytic methods with data-driven and biological-aim-driven strategies, hands-on protocols, an intuitive user interface and step-by-step instructions. AVAILABILITY AND IMPLEMENTATION MetaOmics is freely available at https://github.com/metaOmics/metaOmics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tianzhou Ma
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Anche Kuo
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Li Zhu
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhou Fang
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiangrui Zeng
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lin Wang
- School of Statistics, Capital University of Economics and Business, China
| | - Peng Liu
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Tanbin Rahman
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Lun-Ching Chang
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Sunghwan Kim
- Department of Statistics, Keimyung University, Korea
| | - Jia Li
- Henry Ford Health System, USA
| | - Yongseok Park
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA
| | - Chi Song
- Division of Biostatistics, Ohio State University, Columbus, OH, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Etienne Sibille
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - George C Tseng
- Department of Biostatistics, Graduate School of Public Health University of Pittsburgh, Pittsburgh, PA, USA
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32
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Pan P, Zhu Z, Oshima K, Aldakkak M, Tsai S, Huang YW, Dong W, Zhang J, Lin CW, Wang Y, Yearsley M, Yu J, Wang LS. Black raspberries suppress pancreatic cancer through modulation of NKp46 +, CD8 +, and CD11b + immune cells. Food Front 2020; 1:70-82. [PMID: 32368735 DOI: 10.1002/fft2.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a fatal disease with a low survival rate (9%). Epidemiologic studies show that healthy dietary patterns enriched of fruits and vegetables lower the risk of PDAC. We previously showed that supplementing black raspberries (BRBs) to patients with colorectal cancer increased tumor-infiltrating NK cells and their cytotoxicity. We aimed to determine whether BRBs combat PDAC by modulating cancer immunity. NOD.SCID mice lacking T and B cells were injected with human Panc-1-Luc cells orthotopically, and immunocompetent Kras LSL.G12D/+ -Trp53 LSL.R172H/+ -Pdx-1-Cre mice were fed BRBs. Peripheral blood mononuclear cells (PBMCs) from PDAC patients were treated with butyrate, a microbial metabolite of BRBs. The absence of T and B cells did not dampen BRBs' anti-tumor effects in the NOD.SCID mice. In the Kras LSL.G12D/+ -Trp53 LSL.R172H/+ -Pdx-1-Cre mice, BRBs significantly prolonged survival (189 days versus 154 days). In both models, BRBs decreased tumor-infiltrating CD11b+ cells and the expression of IL-1β, sEH, and Ki67. BRBs also increased tumor-infiltrating NKp46+ cells and the expression of CD107a, a functional marker of cytolytic NK and CD8+ T cells. In Kras LSL.G12D/+ -Trp53 LSL.R172H/+ -Pdx-1-Cre mice, tumor infiltration of CD8+ T cells was increased by BRBs. Further using the PBMCs from PDAC patients, we show that butyrate decreased the population of myeloid-derived suppressor cells (MDSCs). Butyrate also reversed CD11b+ cell-mediated suppression on CD8+ T cells. Interestingly, there is a negative association between MDSC changes and patients' survival, suggesting that the more decrease in MDSC population induced by butyrate treatment, the longer the patient had survived. Our study suggests the immune-modulating potentials of BRBs in PDAC.
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Affiliation(s)
- Pan Pan
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin
| | - Zheng Zhu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute
| | | | | | - Susan Tsai
- Department of Surgery, Medical College of Wisconsin
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin
| | - Wenjuan Dong
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute
| | - Jianying Zhang
- Division of Biostatistics, Department of Science of Informatics, City of Hope National Medical Center and Beckman Research Institute
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin
| | - Youwei Wang
- The James Cancer Hospital, The Ohio State University
| | | | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center and Beckman Research Institute
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin
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33
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Wu PK, Hong SK, Chen W, Becker AE, Gundry RL, Lin CW, Shao H, Gestwicki JE, Park JI. Mortalin (HSPA9) facilitates BRAF-mutant tumor cell survival by suppressing ANT3-mediated mitochondrial membrane permeability. Sci Signal 2020; 13:13/622/eaay1478. [PMID: 32156782 DOI: 10.1126/scisignal.aay1478] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mortalin [also known as heat shock protein family A (HSP70) member 9 (HSPA9) or glucose-regulated protein 75 (GRP75)] is a mitochondrial molecular chaperone that is often up-regulated and mislocalized in tumors with abnormal activation of the kinases MEK and ERK. Here, we found that mortalin depletion was selectively lethal to tumor and immortalized normal cells expressing the mutant kinase B-RafV600E or the chimeric protein ΔRaf-1:ER and that MEK-ERK-sensitive regulation of the peptide-binding domain in mortalin was critical to cell survival or death. Proteomics screening identified adenine nucleotide translocase 3 (ANT3) as a previously unknown mortalin substrate and cell survival/death effector. Mechanistically, increased MEK-ERK signaling activity and mortalin function converged opposingly on the regulation of mitochondrial permeability. Specifically, whereas MEK-ERK activity increased mitochondrial permeability by promoting the interaction between ANT3 and the peptidyl-prolyl isomerase cyclophilin D (CypD), mortalin decreased mitochondrial permeability by inhibiting this interaction. Hence, mortalin depletion increased mitochondrial permeability in MEK-ERK-deregulated cells to an extent that triggered cell death. HSP70 inhibitor derivatives that effectively inhibited mortalin suppressed the proliferation of B-RafV600E tumor cells in culture and in vivo, including their B-Raf inhibitor-resistant progenies. These findings suggest that targeting mortalin has potential as a selective therapeutic strategy in B-Raf-mutant or MEK-ERK-driven tumors.
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Affiliation(s)
- Pui-Kei Wu
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Seung-Keun Hong
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wenjing Chen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andrew E Becker
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hao Shao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jong-In Park
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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Su MW, Chang CK, Lin CW, Ling SJ, Hsiung CN, Chu HW, Wu PE, Shen CY. Blood multiomics reveal insights into population clusters with low prevalence of diabetes, dyslipidemia and hypertension. PLoS One 2020; 15:e0229922. [PMID: 32134946 PMCID: PMC7058291 DOI: 10.1371/journal.pone.0229922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/18/2020] [Indexed: 12/04/2022] Open
Abstract
Diabetes, dyslipidemia and hypertension are important metabolic diseases that impose a great burden on many populations worldwide. However, certain population strata have reduced prevalence for all three diseases, but the underlying mechanisms are poorly understood. We sought to identify the phenotypic, genomic and metabolomic characteristics of the low-prevalence population to gain insights into possible innate non-susceptibility against metabolic diseases. We performed k-means cluster analysis of 16,792 subjects using anthropometric and clinical biochemistry data collected by the Taiwan Biobank. Nuclear magnetic resonance spectra-based metabolome analysis was carried out for 217 subjects with normal body mass index, good exercise habits and healthy lifestyles. We found that the gene APOA5 was significantly associated with reduced prevalence of disease, and lesser associations included the genes HIF1A, LIMA1, LPL, MLXIPL, and TRPC4. Blood plasma of subjects belonging to the low disease prevalence cluster exhibited lowered levels of the GlycA inflammation marker, very low-density lipoprotein and low-density lipoprotein cholesterol, triglycerides, valine and leucine compared to controls. Literature mining revealed that these genes and metabolites are biochemically linked, with the linkage between lipoprotein metabolism and inflammation being particularly prominent. The combination of phenomic, genomic and metabolomic analysis may also be applied towards the study of metabolic disease prevalence in other populations.
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Affiliation(s)
- Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chien-Wei Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shiu-Jie Ling
- Wego Private Bilingual Senior High School, Taipei, Taiwan
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Ei Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- College of Public Health, China Medical University, Taichung, Taiwan
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Hsiung CN, Chang YC, Lin CW, Chang CW, Chou WC, Chu HW, Su MW, Wu PE, Shen CY. The Causal Relationship of Circulating Triglyceride and Glycated Hemoglobin: A Mendelian Randomization Study. J Clin Endocrinol Metab 2020; 105:5648095. [PMID: 31784746 DOI: 10.1210/clinem/dgz243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022]
Abstract
CONTEXT The association between circulating triglyceride (TG) and glycated hemoglobin A1c (HbA1c), a biomarker for type 2 diabetes, has been widely addressed, but the causal direction of the relationship is still ambiguous. OBJECTIVE To confirm the causal relationship between TG and HbA1c by using bidirectional and 2-step Mendelian randomization (MR) approaches. METHODS We carried out a bidirectional MR approach using the summarized results from the public database to examine any potential causal effects between serum TG and HbA1c in 16 000 individuals of the Taiwan Biobank cohort. We used the MR estimate and the MR inverse variance-weighted method to reveal that relationship between TG and HbA1c. To further determine whether the DNA methylation at specific sequences mediate the causal pathway between TG and HbA1c, using the 2-step MR approach. RESULTS We identified that a single-unit increase in TG measured via log transformation of mg/dL data was associated with a significant increase of 10 units of HbA1c (95% CI = 1.05-18.95, P = 0.029). In contrast, the genetic determinants of HbA1c do not contribute to the amount of circulating TG (beta = 1.75, 95% CI = -11.50 to 14.90). Sensitivity analyses, included the weighted-median approach and MR-Egger regression, were performed to confirm no pleiotropic effect among these instrumental variables. Furthermore, we identified the genetic variant, rs1823200, is associated with both methylation of the CpG site adjacent to CADPS gene and HbA1c level. CONCLUSION Our study suggests that higher circulating TG can have an affect on genomic methylation status, ultimately causing elevated level of circulating HbA1c.
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Affiliation(s)
- Chia-Ni Hsiung
- Institute of Bioinformatics and Structure Biology, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Cheng Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | | | | | - Wen-Cheng Chou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hou-Wei Chu
- Taiwan Biobank, Academia Sinica, Taipei, Taiwan
| | - Ming-Wei Su
- Taiwan Biobank, Academia Sinica, Taipei, Taiwan
| | - Pei-Ei Wu
- Taiwan Biobank, Academia Sinica, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- College of Public Health, China Medical University, Taichung, Taiwan
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36
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Liu P, Lin CW, Park Y, Tseng G. MethylSeqDesign: a framework for Methyl-Seq genome-wide power calculation and study design issues. Biostatistics 2019; 22:35-50. [PMID: 31107532 DOI: 10.1093/biostatistics/kxz016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 02/20/2019] [Accepted: 03/04/2019] [Indexed: 01/07/2023] Open
Abstract
Bisulfite DNA methylation sequencing (Methyl-Seq) becomes one of the most important technologies to study methylation level difference at a genome-wide scale. Due to the complexity and large scale of methyl-Seq data, power calculation and study design method have not been developed. Here, we propose a "MethylSeqDesign" framework for power calculation and study design of Methyl-Seq experiments by utilizing information from pilot data. Differential methylation analysis is based on a beta-binomial model. Power calculation is achieved using mixture model fitting of p-values from pilot data and a parametric bootstrap procedure. To circumvent the issue of existing tens of millions of methylation sites, we focus on the inference of pre-specified targeted regions. The performance of the method was evaluated with simulations. Two real examples are analyzed to illustrate our method. An R package "MethylSeqDesign" to implement this method is publicly available.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, USA
| | - Yongseok Park
- Department of Biostatistics, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, 130 De Soto Street, Pittsburgh, PA 15261, USA
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37
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Ciecko AE, Schauder DM, Foda BM, Lin CW, Cui W, Chen YG. Single-cell transcriptome analysis reveals diverse islet-infiltrating T cell subsets and a role for BATF in promoting the diabetogenic activity of CD8 T cells. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.115.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
T cells infiltrate pancreatic islets and directly mediate the destruction of insulin-producing β cells during the development of type 1 diabetes (T1D). However, islet-infiltrating T cell differentiation states and functional diversity have not been completely defined. We used unbiased single-cell RNA sequencing analyses to define the phenotypic complexity of islet-infiltrating T cells in non-obese diabetic (NOD) mice. In the CD4 T cell compartment, we identified naïve, memory, and regulatory T cells, as well as multiple Il21 expressing effector subsets positive for markers indicative of Th1 and Tfh cells. In the CD8 T cell compartment, we identified naïve cells and two activated subsets defined by Slamf6 or Cxcr6 expression, respectively resembling the self-renewing progenitor cells and terminally differentiated effectors found during chronic lymphocytic choriomeningitis virus (LCMV) infection. Single-cell regulatory network inference and clustering (SCENIC) analysis revealed that regulon activity of several transcription factors with known roles in effector CD8 T cell function including Batf were turned on in the Slamf6+ and Cxcr6+ cells. Previous studies have shown that IL-21 induced BATF expression in CD8 T cells is critical to sustain their effector function against chronic LCMV infection. Similarly, we found lower BATF expression in activated islet CD8 T cells from NOD. Il21+/− compared to NOD mice. We further demonstrated that overexpression of BATF in β cell autoreactive CD8 T cells eliminated their need for IL-21 to cause T1D. Our results reveal phenotypically diverse and novel islet-infiltrating T cell subsets and suggest a model in which the IL-21-BATF pathway is critical for the diabetogenic activity of CD8 T cells.
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Affiliation(s)
| | | | | | | | - Weiguo Cui
- 1Medical College of Wisconsin
- 2Blood Research Institute
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38
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Lin CW, Liao SG, Liu P, Park YS, Lee MLT, Tseng GC. RNASeqDesign: A framework for RNA-Seq genome-wide power calculation and study design issues. J R Stat Soc Ser C Appl Stat 2018; 68:683-704. [PMID: 33692596 DOI: 10.1111/rssc.12330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Massively parallel sequencing (a.k.a. next-generation sequencing, NGS) technology has emerged as a powerful tool in characterizing genomic profiles. Among many NGS applications, RNA sequencing (RNA-Seq) has gradually become a standard tool for global transcriptomic monitoring. Although the cost of NGS experiments has dropped constantly, the high sequencing cost and bioinformatic complexity are still obstacles for many biomedical projects. Unlike earlier fluorescence-based technologies such as microarray, modelling of NGS data should consider discrete count data. In addition to sample size, sequencing depth also directly relates to the experimental cost. Consequently, given total budget and pre-specified unit experimental cost, the study design issue in RNA-Seq is conceptually a more complex multi-dimensional constrained optimization problem rather than one-dimensional sample size calculation in traditional hypothesis setting. In this paper, we propose a statistical framework, namely "RNASeqDesign", to utilize pilot data for power calculation and study design of RNA-Seq experiments. The approach is based on mixture model fitting of p-value distribution from pilot data and a parametric bootstrap procedure based on approximated Wald test statistics to infer genome-wide power for optimal sample size and sequencing depth. We further illustrate five practical study design tasks for practitioners. We perform simulations and three real applications to evaluate the performance and compare to existing methods.
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Affiliation(s)
- Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Serena G Liao
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261
| | - Yong Seok Park
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261
| | - Mei-Ling Ting Lee
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20742
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261
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Chowdhury TA, Koceja C, Eisa-Beygi S, Kleinstiver BP, Kumar SN, Lin CW, Li K, Prabhudesai S, Joung JK, Ramchandran R. Temporal and Spatial Post-Transcriptional Regulation of Zebrafish tie1 mRNA by Long Noncoding RNA During Brain Vascular Assembly. Arterioscler Thromb Vasc Biol 2018; 38:1562-1575. [PMID: 29724820 PMCID: PMC6023729 DOI: 10.1161/atvbaha.118.310848] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 04/19/2018] [Indexed: 12/14/2022]
Abstract
Supplemental Digital Content is available in the text. Objective— Tie1 (tyrosine kinase containing immunoglobulin and epidermal growth factor homology 1), an endothelial and hematopoietic cell–specific receptor tyrosine kinase, is an important regulator of angiogenesis and critical for maintaining vascular integrity. The post-transcriptional regulation of tie1 mRNA expression is not understood, but it might partly explain Tie1’s differential expression pattern in endothelium. Following up on our previous work that identified natural antisense transcripts from the tie1 locus—tie1 antisense (tie1AS), which regulates tie1 mRNA levels in zebrafish—we attempted to identify the mechanism of this regulation. Approach and Results— Through in vitro and in vivo ribonucleoprotein binding studies, we demonstrated that tie1AS long noncoding RNA interacts with an RNA binding protein—embryonic lethal and abnormal vision Drosophila-like 1 (Elavl1)—that regulates tie1 mRNA levels. When we disrupted the interaction between tie1AS and Elavl1 by using constitutively active antisense morpholino oligonucleotides or photoactivatable morpholino oligonucleotides, tie1 mRNA levels increased between 26 and 31 hours post-fertilization, particularly in the head. This increase correlated with dilation of primordial midbrain channels, smaller eyes, and reduced ventricular space. We also observed these phenotypes when we used CRISPR (clustered regularly interspaced short palindromic repeats)–mediated CRISPRi (CRISPR-mediated interference) to knock down tie1AS. Treatment of the morpholino oligonucleotide–injected embryos with a small molecule that decreased tie1 mRNA levels rescued all 3 abnormal phenotypes. Conclusions— We identified a novel mode of temporal and spatial post-transcriptional regulation of tie1 mRNA. It involves long noncoding RNA, tie1AS, and Elavl1 (an interactor of tie1AS).
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Affiliation(s)
| | - Chris Koceja
- From the Division of Neonatology, Department of Pediatrics (C.K., K.L., S.P., R.R.)
| | | | - Benjamin P Kleinstiver
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown (B.P.K., J.K.J.).,Department of Pathology, Harvard Medical School, Boston, MA (B.P.K., J.K.J.)
| | | | - Chien-Wei Lin
- Division of Biostatistics (C.-W.L.), Developmental Vascular Biology Program, Children's Research Institute, Medical College of Wisconsin, Milwaukee
| | - Keguo Li
- From the Division of Neonatology, Department of Pediatrics (C.K., K.L., S.P., R.R.).,Obstetrics and Gynecology (T.A.C., K.L., R.R.)
| | | | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown (B.P.K., J.K.J.).,Department of Pathology, Harvard Medical School, Boston, MA (B.P.K., J.K.J.)
| | - Ramani Ramchandran
- From the Division of Neonatology, Department of Pediatrics (C.K., K.L., S.P., R.R.) .,Obstetrics and Gynecology (T.A.C., K.L., R.R.)
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40
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Fang WY, Lin CW, Wang BF, Feng SG. [Effect of paraquat on the expression of a disintegrin and metalloproteinase-17 in A549 cells]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2018; 36:12-17. [PMID: 29495171 DOI: 10.3760/cma.j.issn.1001-9391.2018.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: Construct a paraquat (PQ) cell fibrosis model in vitro, observe the effect of PQ on the expression of a disintegrin and metalloproteinase-17 (ADAM17) in A549 cells, and explore the role of ADAM17 in the pulmonary fibrosis induced by PQ poisoning. Methods: A549 cells are divided into normal control group, different concentration of PQ groups, CCK-8 is used to detect cell viability, screening concentration and time of PQ, cell morphology is observed under microscope; Enzyme-linked immunosorbent assay (ELISA) detectes fibrosis markers of collagen type I (Col I) and fibronectin (FN) expression. Establishment of cell model of fibrosis; distribution by immunocytochemical detection of ADAM17 in A549 cells, Reverse transcription-polymerase chain reaction and Western blot are used to detect the expression of ADAM17 mRNA and protein. Results: 1. With the increase of PQ concentration and the prolongation of the action time, the activity of A549 cells decreased (P< 0.05) , which is dose-dependent and time dependent. 2.The normal A549 cells fusion is paving stone growth and arranged more closely. After PQ induction, the cell arrangement was loose, the intercellular connection became loose, and some cells dissolved and died. 3.ELISA showed that with the increase of PQ concentration, the expression of Col I and FN increased (P<0.05) , and Col I and FN expression gradually increased with the prolongation of PQ time (P<0.05) , and the fibroblast model is successfully established. 4. Immunocytochemistry showes that ADAM17 is expressed in the cytoplasm of A549 cells. 5. RT-PCR and Western blot showed that the expression of ADAM17 mRNA and protein increased significantly with the increase of PQ concentration (P<0.05) , which is most obvious at PQ 200 μmol/L. With the prolonged action of PQ, the expression level of ADAM17 mRNA and protein also increased significantly (P<0.05) , and reached the peak in 24 h. Conclusion: PQ can induce morphological changes of alveolar epithelial cells, cause cell damage, and successfully establish a cell fibrosis model, which has a dose and time dependence on the toxicity of A549 cells. ADAM17 is overexpressed in the A549 cells induced by PQ and may be involved in the process of pulmonary fibrosis induced by paraquat.
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Affiliation(s)
- W Y Fang
- Graduate School of Luzhou Southwest Medical University, Luzhou 646000, China
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41
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Diniz BS, Reynolds CF, Sibille E, Lin CW, Tseng G, Lotrich F, Aizenstein HJ, Butters MA. Enhanced Molecular Aging in Late-Life Depression: the Senescent-Associated Secretory Phenotype. Am J Geriatr Psychiatry 2017; 25:64-72. [PMID: 27856124 PMCID: PMC5164865 DOI: 10.1016/j.jagp.2016.08.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/27/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVE This study aims to investigate whether a systemic molecular pattern associated with aging (senescent-associated secretory phenotype [SASP]) is elevated in adults with late-life depression (LLD), compared with never-depressed elderly comparison participants. DESIGN Cross-sectional study. PARTICIPANTS We included 111 older adults (80 with LLD and 31 comparison participants) in this study. MEASUREMENT A panel of 22 SASP-related proteins was extracted from a previous multiplex protein panel performed in these participants. We conducted a principal component analysis to create the SASP index based on individual weights of each of protein. RESULTS Participants with LLD showed a significantly increased SASP index compared with comparison participants, after controlling for age, depressive symptoms, medical comorbidity (CIRS-G) scores, sex, and cognitive performance (F(1,98) = 7.3, p = 0.008). Correlation analyses revealed that the SASP index was positively correlated with age (r = 0.2, p = 0.03) and CIRS score (r = 0.27, p = 0.005), and negatively correlated with information processing speed (r = -0.34, p = 0.001), executive function (r = -0.27, p = 0.004) and global cognitive performance (r = -0.28, p = 0.007). CONCLUSIONS To the best of our knowledge, this is the first study to show that a set of proteins (i.e., SASP index) primarily associated with cellular aging is abnormally regulated and elevated in LLD. These results suggest that individuals with LLD display enhanced aging-related molecular patterns that are associated with higher medical comorbidity and worse cognitive function. Finally, we provide a set of proteins that can serve as potential therapeutic targets and biomarkers to monitor the effects of therapeutic or preventative interventions in LLD.
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Affiliation(s)
- Breno Satler Diniz
- Department of Psychiatry & Behavioral Sciences, University of Texas Health Science Center at Houston, Houston, TX.
| | - Charles F Reynolds
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Etienne Sibille
- Departments of Psychiatry and of Pharmacology and Toxicology, Campbell Family Mental Health Research Institute of CAMH, University of Toronto, Toronto, Ontario, Canada
| | - Chien-Wei Lin
- Department of Statistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA
| | - George Tseng
- Department of Statistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA
| | - Francis Lotrich
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Howard J Aizenstein
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Meryl A Butters
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Lin CY, Huang HY, Lu PN, Lin CW, Lu KM, Tsai HJ. Ras-Related Nuclear Protein is required for late developmental stages of retinal cells in zebrafish eyes. Int J Dev Biol 2016; 59:435-42. [PMID: 26864484 DOI: 10.1387/ijdb.150310ht] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Ras-related nuclear protein (Ran) is involved in cell division by regulating nucleocytoplasmic transport and modulating the assembly of tubulin. However, its function in embryonic development is unclear. We used zebrafish to study the roles of Ran in eye development. The ran transcripts were restrictedly expressed in head and eyes after the pharyngula stage. The microphthalmos, in which no ordered layers with differentiated retinal cells were detected, was observed in the ran-deficient embryos. They exhibited faster decline cyclinD1-expressed cells, suggesting that cell cycle regulation in retinae was defective. The apoptotic signals in the retinae of ran-deficient embryos remained low at early (24 hpf) stage. Early eye field specification markers, rx1 and pax6, were only slightly affected, and markers for establishing axon migration, fgf8 and pax2, were normally expressed, suggesting Ran is not required in the early stages of eye development. However, the early optic nerve differentiation marker p57kip2 was not expressed at middle (48 hpf) and late (72 hpf) stages. We also observed a decrease in the retinal neuron proteins HuC and Neurolin. The proneural gene ath5, which first determines the cell fate of the developing ganglion cell layer, was undetectable. Furthermore, we found that Ran was associated with ADP-ribosylation factor-like protein 6-interacting protein 1 (Arl6ip1), which plays a role in retinal development, suggesting that Ran associates with Arl6ip1 to regulate retinal development. Therefore, while the effects of Ran are minimal during early specification of the eye field, Ran is required for proliferation and differentiation of retinal cells at later developmental stages.
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Affiliation(s)
- Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
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Diniz BS, Lin CW, Sibille E, Tseng G, Lotrich F, Aizenstein HJ, Reynolds CF, Butters MA. Circulating biosignatures of late-life depression (LLD): Towards a comprehensive, data-driven approach to understanding LLD pathophysiology. J Psychiatr Res 2016; 82:1-7. [PMID: 27447786 PMCID: PMC9344393 DOI: 10.1016/j.jpsychires.2016.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 11/30/2022]
Abstract
There is scarce information about the pathophysiological processes underlying Late-Life Depression (LLD). We aimed to determine the neurobiological abnormalities related to LLD through a multi-modal biomarker approach combining a large, unbiased peripheral proteomic panel and structural brain imaging. We examined data from 44 LLD and 31 control participants. Plasma proteomic analysis was performed using a multiplex immunoassay. We evaluated the differential protein expression between groups with random intercept models. We carried out enrichment pathway analyses (EPA) to uncover biological pathways and processes related to LLD. Machine learning analysis was applied to the combined dataset to determine the accuracy with which specific proteins could correctly discriminate LLD versus control participants. Sixty-one proteins were differentially expressed in LLD (p < 0.05 and FDR < 0.01). EPA showed that these proteins were related to abnormal immune-inflammatory control, cell survival and proliferation, proteostasis control, lipid metabolism, intracellular signaling. Machine learning analysis showed that a panel of three proteins (C-peptide, FABP-liver, ApoA-IV) discriminated LLD and control participants with 100% accuracy. The plasma proteomic profile in LLD revealed dysregulation in biological processes essential to the maintenance of homeostasis at cellular and systemic levels. These abnormalities increase brain and systemic allostatic load leading to the downstream negative outcomes of LLD, including increased risk of medical comorbidities and dementia. The peripheral biosignature of LLD has predictive power and may suggest novel putative therapeutic targets for prevention, treatment, and neuroprotection in LLD.
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Affiliation(s)
- Breno Satler Diniz
- Department of Psychiatry & Behavioral Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Chien-Wei Lin
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Etienne Sibille
- Campbell Family Mental Health Research Institute of CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Francis Lotrich
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Howard J. Aizenstein
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Charles F. Reynolds
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Meryl A. Butters
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Corresponding author. 3811 O’Hara Street, Pittsburgh, PA, 15213, USA. (M.A. Butters)
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Belzeaux R, Lin CW, Ding Y, Bergon A, Ibrahim EC, Turecki G, Tseng G, Sibille E. Predisposition to treatment response in major depressive episode: A peripheral blood gene coexpression network analysis. J Psychiatr Res 2016; 81:119-26. [PMID: 27438688 DOI: 10.1016/j.jpsychires.2016.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/12/2016] [Accepted: 07/06/2016] [Indexed: 12/28/2022]
Abstract
Antidepressant efficacy is insufficient, unpredictable and poorly understood in major depressive episode (MDE). Gene expression studies allow for the identification of significantly dysregulated genes but can limit the exploration of biological pathways. In the present study, we proposed a gene coexpression analysis to investigate biological pathways associated with treatment response predisposition and their regulation by microRNAs (miRNAs) in peripheral blood samples of MDE and healthy control subjects. We used a discovery cohort that included 34 MDE patients that were given 12-week treatment with citalopram and 33 healthy controls. Two replication cohorts with similar design were also analyzed. Expression-based gene network was built to define clusters of highly correlated sets of genes, called modules. Association between each module's first principal component of the expression data and clinical improvement was tested in the three cohorts. We conducted gene ontology analysis and miRNA prediction based on the module gene list. Nine of the 59 modules from the gene coexpression network were associated with clinical improvement. The association was partially replicated in other cohorts. Gene ontology analysis demonstrated that 4 modules were associated with cytokine production, acute inflammatory response or IL-8 functions. Finally, we found 414 miRNAs that may regulate one or several modules associated with clinical improvement. By contrast, only 12 miRNAs were predicted to specifically regulate modules unrelated to clinical improvement. Our gene coexpression analysis underlines the importance of inflammation-related pathways and the involvement of a large miRNA program as biological processes predisposing associated with antidepressant response.
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Affiliation(s)
- Raoul Belzeaux
- McGill Group for Suicide Studies, Department of Psychiatry, McGill University, Douglas Mental Health University Institute, Montreal, QC, Canada; Fondation FondaMental, Créteil, France; CRN2M-UMR7286, Aix-Marseille Université, CNRS, Marseille, France.
| | - Chien-Wei Lin
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - El Chérif Ibrahim
- Fondation FondaMental, Créteil, France; CRN2M-UMR7286, Aix-Marseille Université, CNRS, Marseille, France
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Department of Psychiatry, McGill University, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Etienne Sibille
- Campbell Family Mental Health Research Institute of CAMH, Departments of Psychiatry and of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
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Grubisha MJ, Lin CW, Tseng GC, Penzes P, Sibille E, Sweet RA. Age-dependent increase in Kalirin-9 and Kalirin-12 transcripts in human orbitofrontal cortex. Eur J Neurosci 2016; 44:2483-2492. [PMID: 27471199 DOI: 10.1111/ejn.13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022]
Abstract
KALRN (KAL) is a Rho GEF that is highly involved in regulation of the actin cytoskeleton within dendrites. There are several isoforms of the protein that arise from differential splicing of KALRN's 66 exons. KAL isoforms have different functions in development. For example, overexpression of the KAL9 and KAL12 isoforms induce dendritic elongation in early development. However, in mature neurons KAL9 overexpression reduces dendritic length, a phenotype also observed in normal human ageing. We therefore hypothesized that KAL9 would have increased expression with age, and undertook to evaluate the expression of individual KALRN exons throughout the adult lifespan. Postmortem human brain grey matter from Brodmann's area (BA) 11 and BA47 derived from a cohort of 209 individuals without psychiatric or neurodegenerative disease, ranging in age from 16 to 91 years, were analysed for KALRN expression by Affymetrix exon array. Analysis of the exon array data in an isoform-specific manner, as well as confirmatory isoform-specific qPCR studies, indicated that the longer KAL9 and KAL12 isoforms demonstrated a statistically significant, but modest, increase with age. The small magnitude of the age effect suggests that inter-individual factors other than age likely contribute to a higher degree to KAL9 and KAL12 expression. In contrast to KAL9 and KAL12, global KALRN expression did not increase with age. Our work suggests that global measures of KALRN gene expression may be misleading and future studies should focus on isoform-specific quantification.
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Affiliation(s)
- Melanie J Grubisha
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Chien-Wei Lin
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Penzes
- Departments of Physiology and Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Etienne Sibille
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, USA.,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA.,Departments of Psychiatry, Pharmacology and Toxicology, Campbell Family Mental Health Research Institute of CAMH, University of Toronto, Toronto, ON, Canada
| | - Robert A Sweet
- Departments of Psychiatry and Neurology, University of Pittsburgh School of Medicine, Biomedical Science Tower, Rm W-1645, 3811 O'Hara Street, Pittsburgh, PA, 15213-2593, USA. .,Mental Illness Research, Education, and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA.
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Affiliation(s)
- Yu-Jen Liang
- Graduate
Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
- Institute
of Statistical Science, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ting Lin
- Institute
of Statistical Science, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Wei Chen
- Institute
of Statistical Science, Academia Sinica, Taipei 115, Taiwan
| | - Chien-Wei Lin
- Institute
of Statistical Science, Academia Sinica, Taipei 115, Taiwan
| | - Kun-Mao Chao
- Graduate
Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
- Department
of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Wen-Harn Pan
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Chou Yang
- Institute
of Statistical Science, Academia Sinica, Taipei 115, Taiwan
- Institute
of Public Health, National Yang Ming University, Taipei 11221, Taiwan
- Department
of Statistics, National Cheng Kung University, Tainan 701, Taiwan
- Institute
of Statistics, National Tsing Hua University, Hsinchu 30013, Taiwan
- School
of Public Health, National Defense Medical Center, Taipei 114, Taiwan
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Kim S, Lin CW, Tseng GC. MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis. Bioinformatics 2016; 32:1966-73. [PMID: 27153719 DOI: 10.1093/bioinformatics/btw115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION Supervised machine learning is widely applied to transcriptomic data to predict disease diagnosis, prognosis or survival. Robust and interpretable classifiers with high accuracy are usually favored for their clinical and translational potential. The top scoring pair (TSP) algorithm is an example that applies a simple rank-based algorithm to identify rank-altered gene pairs for classifier construction. Although many classification methods perform well in cross-validation of single expression profile, the performance usually greatly reduces in cross-study validation (i.e. the prediction model is established in the training study and applied to an independent test study) for all machine learning methods, including TSP. The failure of cross-study validation has largely diminished the potential translational and clinical values of the models. The purpose of this article is to develop a meta-analytic top scoring pair (MetaKTSP) framework that combines multiple transcriptomic studies and generates a robust prediction model applicable to independent test studies. RESULTS We proposed two frameworks, by averaging TSP scores or by combining P-values from individual studies, to select the top gene pairs for model construction. We applied the proposed methods in simulated data sets and three large-scale real applications in breast cancer, idiopathic pulmonary fibrosis and pan-cancer methylation. The result showed superior performance of cross-study validation accuracy and biomarker selection for the new meta-analytic framework. In conclusion, combining multiple omics data sets in the public domain increases robustness and accuracy of the classification model that will ultimately improve disease understanding and clinical treatment decisions to benefit patients. AVAILABILITY AND IMPLEMENTATION An R package MetaKTSP is available online. (http://tsenglab.biostat.pitt.edu/software.htm). CONTACT ctseng@pitt.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- SungHwan Kim
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA Department of Statistics, Korea University, Seoul, South Korea
| | - Chien-Wei Lin
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA Department of Computational and Systems Biology Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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McKinney BC, Lin CW, Oh H, Tseng GC, Lewis DA, Sibille E. Hypermethylation of BDNF and SST Genes in the Orbital Frontal Cortex of Older Individuals: A Putative Mechanism for Declining Gene Expression with Age. Neuropsychopharmacology 2015; 40:2604-13. [PMID: 25881116 PMCID: PMC4569950 DOI: 10.1038/npp.2015.107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/20/2015] [Accepted: 04/08/2015] [Indexed: 12/29/2022]
Abstract
Expression of brain-derived neurotrophic factor (BDNF) and somatostatin (SST) mRNAs in the brain decreases progressively and robustly with age, and lower BDNF and SST expression in the brain has been observed in many brain disorders. BDNF is known to regulate SST expression; however, the mechanisms underlying decreased expression of both genes are not understood. DNA methylation (DNAm) is an attractive candidate mechanism. To investigate the contribution of DNAm to the age-related decline in BDNF and SST expression, the Illumina Infinium HumanMethylation450 Beadchip Array was used to quantify DNAm of BDNF (26 CpG loci) and SST (9 CpG loci) in the orbital frontal cortices of postmortem brains from 22 younger (age <42 years) and 22 older individuals (age >60 years) with known age-dependent BDNF and SST expression differences. Relative to the younger individuals, 10 of the 26 CpG loci in BDNF and 8 of the 9 CpG loci in SST were significantly hypermethylated in the older individuals. DNAm in BDNF exons/promoters I, II, and IV negatively correlated with BDNF expression (r=-0.37, p<0.05; r=-0.40, p<0.05; r=-0.24, p=0.07), and DNAm in SST 5' UTR and first exon/intron negatively correlated with SST expression (r=-0.48, p<0.01; r=-0.63, p<0.001), respectively. An expanded set of BDNF- and GABA-related genes exhibited similar age-related changes in DNAm and correlation with gene expression. These results suggest that DNAm may be a proximal mechanism for decreased expression of BDNF, SST, and other BDNF- and GABA-related genes with brain aging and, by extension, for brain disorders in which their expression is decreased.
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Affiliation(s)
- Brandon C McKinney
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Chien-Wei Lin
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyunjung Oh
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Etienne Sibille
- Department of Psychiatry, University of Pittsburgh Medical School, Pittsburgh, PA, USA,Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA,Campbell Family Mental Health Research Institute of CAMH, Departments of Psychiatry, Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada,Centre for Addiction and Mental Health (CAMH), 250 College Street, Room 134, Toronto, ON M5T 1R8, Canada, Tel: +1 416 535 8501, ext 36571, E-mail:
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Nikolova YS, Iruku SP, Lin CW, Conley ED, Puralewski R, French B, Hariri AR, Sibille E. FRAS1-related extracellular matrix 3 (FREM3) single-nucleotide polymorphism effects on gene expression, amygdala reactivity and perceptual processing speed: An accelerated aging pathway of depression risk. Front Psychol 2015; 6:1377. [PMID: 26441752 PMCID: PMC4584966 DOI: 10.3389/fpsyg.2015.01377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/27/2015] [Indexed: 12/24/2022] Open
Abstract
The A allele of the FRAS1-related extracellular matrix protein 3 (FREM3) rs7676614 single nucleotide polymorphism (SNP) was linked to major depressive disorder (MDD) in an early genome-wide association study (GWAS), and to symptoms of psychomotor retardation in a follow-up investigation. In line with significant overlap between age- and depression-related molecular pathways, parallel work has shown that FREM3 expression in postmortem human brain decreases with age. Here, we probe the effect of rs7676614 on amygdala reactivity and perceptual processing speed, both of which are altered in depression and aging. Amygdala reactivity was assessed using a face-matching BOLD fMRI paradigm in 365 Caucasian participants in the Duke Neurogenetics Study (DNS) (192 women, mean age 19.7 ± 1.2). Perceptual processing speed was indexed by reaction times in the same task and the Trail Making Test (TMT). The effect of rs7676614 on FREM3 mRNA brain expression levels was probed in a postmortem cohort of 169 Caucasian individuals (44 women, mean age 50.8 ± 14.9). The A allele of rs7676614 was associated with blunted amygdala reactivity to faces, slower reaction times in the face-matching condition (p < 0.04), as well as marginally slower performance on TMT Part B (p = 0.056). In the postmortem cohort, the T allele of rs6537170 (proxy for the rs7676614 A allele), was associated with trend-level reductions in gene expression in Brodmann areas 11 and 47 (p = 0.066), reminiscent of patterns characteristic of older age. The low-expressing allele of another FREM3 SNP (rs1391187) was similarly associated with reduced amygdala reactivity and slower TMT Part B speed, in addition to reduced BA47 activity and extraversion (p < 0.05). Together, these results suggest common genetic variation associated with reduced FREM3 expression may confer risk for a subtype of depression characterized by reduced reactivity to environmental stimuli and slower perceptual processing speed, possibly suggestive of accelerated aging.
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Affiliation(s)
- Yuliya S Nikolova
- Campbell Family Mental Health Research Institute of CAMH Toronto, ON, Canada
| | - Swetha P Iruku
- Laboratory of NeuroGenetics, Department of Psychology & Neuroscience, Duke University Durham, NC, USA
| | - Chien-Wei Lin
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh Pittsburgh, PA, USA
| | | | - Rachel Puralewski
- Department of Psychiatry, University of Pittsburgh Pittsburgh, PA, USA
| | - Beverly French
- Department of Psychiatry, University of Pittsburgh Pittsburgh, PA, USA
| | - Ahmad R Hariri
- Laboratory of NeuroGenetics, Department of Psychology & Neuroscience, Duke University Durham, NC, USA
| | - Etienne Sibille
- Campbell Family Mental Health Research Institute of CAMH Toronto, ON, Canada ; Department of Psychiatry, University of Pittsburgh Pittsburgh, PA, USA ; Department of Psychiatry, Department of Pharmacology and Toxicology, University of Toronto Toronto, ON, Canada
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Lin WT, Chang CH, Cheng CY, Chen MC, Wen YR, Lin CT, Lin CW. Effects of low amplitude pulsed radiofrequency stimulation with different waveform in rats for neuropathic pain. Annu Int Conf IEEE Eng Med Biol Soc 2015; 2013:3590-3. [PMID: 24110506 DOI: 10.1109/embc.2013.6610319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Pulsed-radiofrequency (PRF) electrical stimulation has been widely used for chronic pain treatment. It has been demonstrated with advantages of low temperature over traditional continuous radiofrequency (CRF) lesions with higher amplitude and mono polar electrode to treat pain in clinics (frequency 500 KHz, Pulse duration 20 msec, Amplitude 45 V, Treatment 2 min). We compare the effects of different pulse waveforms and PRF parameters (Pulse duration 25 ms, Treatment duration 5 min, low amplitude of 2.5/1.25 V) with a miniature bi-polar electrode on Dorsal root ganglion (DRG). The pain relief effect due to PRF is evaluated by using Von Frey method for the pain threshold index based on behavior response to mechanical stimulus of various strengths. Experimental results of Von Frey Score show that the sinusoidal group has higher responses than the square wave one. Both fast and secondary expressed proteins of c-fos and pp38 are measured from spinal cord tissue sectioning slides to characterize the pain associated inflammatory responses and their responses due to PRF stimulation.
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