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Wang YW, Wang L, Yuan SJ, Zhang Y, Zhang X, Zhou LT. Postoperative Cognitive Dysfunction and Alzheimer’s Disease: A Transcriptome-Based Comparison of Animal Models. Front Aging Neurosci 2022; 14:900350. [PMID: 35837480 PMCID: PMC9273890 DOI: 10.3389/fnagi.2022.900350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/08/2022] [Indexed: 12/02/2022] Open
Abstract
Background Postoperative cognitive dysfunction (POCD) is a common complication characterized by a significant cognitive decline. Increasing evidence suggests an association between the pathogenesis of POCD and Alzheimer’s disease (AD). However, a comprehensive understanding of their relationships is still lacking. Methods First, related databases were obtained from GEO, ArrayExpress, CNGB, and DDBJ repositories. De novo analysis was performed on the raw data using a uniform bioinformatics workflow. Then, macro- and micro-level comparisons were conducted between the transcriptomic changes associated with AD and POCD. Lastly, POCD was induced in male C57BL/6j mice and the hippocampal expression levels of mRNAs of interest were verified by PCR and compared to those in AD congenic models. Results There was a very weak correlation in the fold-changes in protein-coding transcripts between AD and POCD. Overall pathway-level comparison suggested that AD and POCD are two disease entities. Consistently, in the classical AD pathway, the mitochondrial complex and tubulin mRNAs were downregulated in both the POCD hippocampus and cortex. POCD and AD hippocampi might share the same pathways, such as tryptophan metabolism, but undergo different pathological changes in phagosome and transferrin endocytosis pathways. The core cluster in the hippocampal network was mainly enriched in mitosis-related pathways. The hippocampal expression levels of genes of interest detected by PCR showed good consistency with those generated by high throughput platforms. Conclusion POCD and AD are associated with different transcriptomic changes despite their similar clinical manifestations. This study provides a valuable resource for identifying biomarkers and therapeutic targets for POCD.
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Affiliation(s)
- Yi-Wei Wang
- Department of Anesthesiology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Liang Wang
- Department of Internal Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Sheng-Jie Yuan
- Department of Anesthesiology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Yuan Zhang
- Department of Internal Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Xin Zhang
- Department of Anesthesiology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University School of Medicine, Durham, NC, United States
- Xin Zhang,
| | - Le-Ting Zhou
- Department of Internal Medicine, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
- *Correspondence: Le-Ting Zhou,
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Mattioli K, Oliveros W, Gerhardinger C, Andergassen D, Maass PG, Rinn JL, Melé M. Cis and trans effects differentially contribute to the evolution of promoters and enhancers. Genome Biol 2020; 21:210. [PMID: 32819422 PMCID: PMC7439725 DOI: 10.1186/s13059-020-02110-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants located on the same DNA molecule as the target gene, trans effects are due to genetic variants that affect diffusible elements. Previous studies have mostly assessed the impact of cis and trans effects at the gene level. However, how cis and trans effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we use massively parallel reporter assays to directly measure the transcriptional outputs of thousands of individual regulatory elements in embryonic stem cells and measure cis and trans effects between human and mouse. RESULTS Our approach reveals that cis effects are widespread across transcribed regulatory elements, and the strongest cis effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we find that trans effects are rare but stronger in enhancers than promoters and are associated with a subset of transcription factors that are differentially expressed between human and mouse. While we find that cis-trans compensation is common within promoters, we do not see evidence of widespread cis-trans compensation at enhancers. Cis-trans compensation is inversely correlated with enhancer redundancy, suggesting that such compensation may often occur across multiple enhancers. CONCLUSIONS Our results highlight differences in the mode of evolution between promoters and enhancers in complex mammalian genomes and indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.
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Affiliation(s)
- Kaia Mattioli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel Andergassen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Philipp G Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - John L Rinn
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, CO, 80301, USA
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain.
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Knapp DW, Dhawan D, Ramos-Vara JA, Ratliff TL, Cresswell GM, Utturkar S, Sommer BC, Fulkerson CM, Hahn NM. Naturally-Occurring Invasive Urothelial Carcinoma in Dogs, a Unique Model to Drive Advances in Managing Muscle Invasive Bladder Cancer in Humans. Front Oncol 2020; 9:1493. [PMID: 32039002 PMCID: PMC6985458 DOI: 10.3389/fonc.2019.01493] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
There is a great need to improve the outlook for people facing urinary bladder cancer, especially for patients with invasive urothelial carcinoma (InvUC) which is lethal in 50% of cases. Improved outcomes for patients with InvUC could come from advances on several fronts including emerging immunotherapies, targeted therapies, and new drug combinations; selection of patients most likely to respond to a given treatment based on molecular subtypes, immune signatures, and other characteristics; and prevention, early detection, and early intervention. Progress on all of these fronts will require clinically relevant animal models for translational research. The animal model(s) should possess key features that drive success or failure of cancer drugs in humans including tumor heterogeneity, genetic-epigenetic crosstalk, immune cell responsiveness, invasive and metastatic behavior, and molecular subtypes (e.g., luminal, basal). Experimental animal models, while essential in bladder cancer research, do not possess these collective features to accurately predict outcomes in humans. These key features, however, are present in naturally-occurring InvUC in pet dogs. Canine InvUC closely mimics muscle-invasive bladder cancer in humans in cellular and molecular features, molecular subtypes, immune response patterns, biological behavior (sites and frequency of metastasis), and response to therapy. Thus, dogs can offer a highly relevant animal model to complement other models in research for new therapies for bladder cancer. Clinical treatment trials in pet dogs with InvUC are considered a win-win-win scenario; the individual dog benefits from effective treatment, the results are expected to help other dogs, and the findings are expected to translate to better treatment outcomes in humans. In addition, the high breed-associated risk for InvUC in dogs (e.g., 20-fold increased risk in Scottish Terriers) offers an unparalleled opportunity to test new strategies in primary prevention, early detection, and early intervention. This review will provide an overview of canine InvUC, summarize the similarities (and differences) between canine and human InvUC, and provide evidence for the expanding value of this canine model in bladder cancer research.
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Affiliation(s)
- Deborah W Knapp
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, United States.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Deepika Dhawan
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, United States
| | - José A Ramos-Vara
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States.,Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Timothy L Ratliff
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States.,Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Gregory M Cresswell
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Sagar Utturkar
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Breann C Sommer
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, United States
| | - Christopher M Fulkerson
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, United States.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Noah M Hahn
- Department of Oncology and Urology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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