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Wu S, Li F, Mo K, Huang H, Yu Y, Huang Y, Liu J, Li M, Tan J, Lin Z, Han Z, Wang L, Ouyang H. IGF2BP2 Maintains Retinal Pigment Epithelium Homeostasis by Stabilizing PAX6 and OTX2. Invest Ophthalmol Vis Sci 2024; 65:17. [PMID: 38861275 PMCID: PMC11174093 DOI: 10.1167/iovs.65.6.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/15/2024] [Indexed: 06/12/2024] Open
Abstract
Purpose N6-methyladenosine (m6A) methylation is a chemical modification that occurs on RNA molecules, where the hydrogen atom of adenine (A) nucleotides is replaced by a methyl group, forming N6-methyladenosine. This modification is a dynamic and reversible process that plays a crucial role in regulating various biological processes, including RNA stability, transport, translation, and degradation. Currently, there is a lack of research on the role of m6A modifications in maintaining the characteristics of RPE cells. m6A readers play a crucial role in executing the functions of m6A modifications, which prompted our investigation into their regulatory roles in the RPE. Methods Phagocytosis assays, immunofluorescence staining, flow cytometry experiments, β-galactosidase staining, and RNA sequencing (RNA-seq) were conducted to assess the functional and cellular characteristics changes in retinal pigment epithelium (RPE) cells following short-hairpin RNA-mediated knockdown of insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). RNA-seq and ultraviolet crosslinking immunoprecipitation with high-throughput sequencing (HITS-CLIP) were employed to identify the target genes regulated by IGF2BP2. adeno-associated virus (AAV) subretinal injection was performed in 6- to 8-week-old C57 mice to reduce IGF2BP2 expression in the RPE, and the impact of IGF2BP2 knockdown on mouse visual function was assessed using immunofluorescence, quantitative real-time PCR, optical coherence tomography, and electroretinography. Results IGF2BP2 was found to have a pronounced effect on RPE phagocytosis. Subsequent in-depth exploration revealed that IGF2BP2 modulates the mRNA stability of PAX6 and OTX2, and the loss of IGF2BP2 induces inflammatory and aging phenotypes in RPE cells. IGF2BP2 knockdown impaired RPE function, leading to retinal dysfunction in vivo. Conclusions Our data suggest a crucial role of IGF2BP2 as an m6A reader in maintaining RPE homeostasis by regulating the stability of PAX6 and OTX2, making it a potential target for preventing the occurrence of retinal diseases related to RPE malfunction.
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Affiliation(s)
- Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Fuxi Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Yankun Yu
- Department of Pathology, The First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, China
| | - Ying Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Zesong Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Zhuo Han
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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Khullar S, Huang X, Ramesh R, Svaren J, Wang D. NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.25.563769. [PMID: 37961577 PMCID: PMC10634989 DOI: 10.1101/2023.10.25.563769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Transcription factor (TF) coordination plays a key role in target gene (TG) regulation via protein-protein interactions (PPIs) and DNA co-binding to regulatory elements. Single-cell technologies facilitate gene expression measurement for individual cells and cell-type identification, yet the connection between TF coordination and TG regulation of various cell types remains unclear. To address this, we have developed a novel computational approach, Network Regression Embeddings (NetREm), to reveal cell-type TF-TF coordination activities for TG regulation. NetREm leverages network-constrained regularization using prior knowledge of direct and/or indirect PPIs among TFs to analyze single-cell gene expression data. We test NetREm by simulation data and benchmark its performance in 4 real-world applications that have gold standard TF-TG networks available: mouse (mESCs) and simulated human (hESCs) embryonic stem (ESCs), human hematopoietic stem (HSCs), and mouse dendritic (mDCs) cells. Further, we use NetREm to prioritize valid novel TF-TF coordination links in human Peripheral Blood Mononuclear cell (PBMC) sub-types. We apply NetREm to analyze various cell types in both central (CNS) and peripheral (PNS) nerve system (NS) (e.g. neuronal, glial, Schwann cells (SCs)) as well as in Alzheimers disease (AD). Our findings uncover cell-type coordinating TFs and identify new TF-TG candidate links. We validate our top predictions using Cut&Run and knockout loss-of-function expression data in rat/mouse models and compare results with additional functional genomic data, including expression quantitative trait loci (eQTL) and Genome-Wide Association Studies (GWAS) to link genetic variants (single nucleotide polymorphisms (SNPs)) to TF coordination.
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Parivesh A, Délot E, Reyes A, Ryan J, Bhattacharya S, Harley V, Vilain E. Reprograming skin fibroblasts into Sertoli cells: a patient-specific tool to understand effects of genetic variants on gonadal development. Biol Sex Differ 2024; 15:24. [PMID: 38520033 PMCID: PMC10958866 DOI: 10.1186/s13293-024-00599-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 02/22/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Disorders/differences of sex development (DSD) are congenital conditions in which the development of chromosomal, gonadal, or anatomical sex is atypical. With overlapping phenotypes and multiple genes involved, poor diagnostic yields are achieved for many of these conditions. The current DSD diagnostic regimen can be augmented by investigating transcriptome/proteome in vivo, but it is hampered by the unavailability of affected gonadal tissue at the relevant developmental stage. We try to mitigate this limitation by reprogramming readily available skin tissue-derived dermal fibroblasts into Sertoli cells (SC), which could then be deployed for different diagnostic strategies. SCs form the target cell type of choice because they act like an organizing center of embryonic gonadal development and many DSD arise when these developmental processes go awry. METHODS We employed a computational predictive algorithm for cell conversions called Mogrify to predict the transcription factors (TFs) required for direct reprogramming of human dermal fibroblasts into SCs. We established trans-differentiation culture conditions where stable transgenic expression of these TFs was achieved in 46, XY adult dermal fibroblasts using lentiviral vectors. The resulting Sertoli like cells (SLCs) were validated for SC phenotype using several approaches. RESULTS SLCs exhibited Sertoli-like morphological and cellular properties as revealed by morphometry and xCelligence cell behavior assays. They also showed Sertoli-specific expression of molecular markers such as SOX9, PTGDS, BMP4, or DMRT1 as revealed by IF imaging, RNAseq and qPCR. The SLC transcriptome shared about two thirds of its differentially expressed genes with a human adult SC transcriptome and expressed markers typical of embryonic SCs. Notably, SLCs lacked expression of most markers of other gonadal cell types such as Leydig, germ, peritubular myoid or granulosa cells. CONCLUSIONS The trans-differentiation method was applied to a variety of commercially available 46, XY fibroblasts derived from patients with DSD and to a 46, XX cell line. The DSD SLCs displayed altered levels of trans-differentiation in comparison to normal 46, XY-derived SLCs, thus showcasing the robustness of this new trans-differentiation model. Future applications could include using the SLCs to improve definitive diagnosis of DSD in patients with variants of unknown significance.
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Affiliation(s)
- Abhinav Parivesh
- Center for Genetic Medicine Research, Children's National Hospital, Washington D.C., 20010, USA
| | - Emmanuèle Délot
- Center for Genetic Medicine Research, Children's National Hospital, Washington D.C., 20010, USA
| | - Alejandra Reyes
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, VIC, 3168, Australia
| | - Janelle Ryan
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, VIC, 3168, Australia
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Hospital, Washington D.C., 20010, USA
| | - Vincent Harley
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, VIC, 3168, Australia
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, CA, USA.
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Wytock TP, Motter AE. Cell reprogramming design by transfer learning of functional transcriptional networks. Proc Natl Acad Sci U S A 2024; 121:e2312942121. [PMID: 38437548 PMCID: PMC10945810 DOI: 10.1073/pnas.2312942121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/26/2024] [Indexed: 03/06/2024] Open
Abstract
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to reprogram cells. The main challenges to seizing this opportunity are the incomplete knowledge of the cellular network and the combinatorial explosion of possible interventions, both of which are insurmountable by experiments. To address these challenges, we develop a transfer learning approach to control cell behavior that is pre-trained on transcriptomic data associated with human cell fates, thereby generating a model of the network dynamics that can be transferred to specific reprogramming goals. The approach combines transcriptional responses to gene perturbations to minimize the difference between a given pair of initial and target transcriptional states. We demonstrate our approach's versatility by applying it to a microarray dataset comprising >9,000 microarrays across 54 cell types and 227 unique perturbations, and an RNASeq dataset consisting of >10,000 sequencing runs across 36 cell types and 138 perturbations. Our approach reproduces known reprogramming protocols with an AUROC of 0.91 while innovating over existing methods by pre-training an adaptable model that can be tailored to specific reprogramming transitions. We show that the number of gene perturbations required to steer from one fate to another increases with decreasing developmental relatedness and that fewer genes are needed to progress along developmental paths than to regress. These findings establish a proof-of-concept for our approach to computationally design control strategies and provide insights into how gene regulatory networks govern phenotype.
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Affiliation(s)
- Thomas P. Wytock
- Department of Physics and Astronomy, Northwestern University, Evanston, IL60208
- Center for Network Dynamics, Northwestern University, Evanston, IL60208
| | - Adilson E. Motter
- Department of Physics and Astronomy, Northwestern University, Evanston, IL60208
- Center for Network Dynamics, Northwestern University, Evanston, IL60208
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL60208
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL60208
- National Institute for Theory and Mathematics in Biology, Evanston, IL60208
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5
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Wytock TP, Motter AE. Cell reprogramming design by transfer learning of functional transcriptional networks. ARXIV 2024:arXiv:2403.04837v1. [PMID: 38495570 PMCID: PMC10942484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to reprogram cell behavior. The main challenges to seizing this opportunity are the incomplete knowledge of the cellular network and the combinatorial explosion of possible interventions, both of which are insurmountable by experiments. To address these challenges, we develop a transfer learning approach to control cell behavior that is pre-trained on transcriptomic data associated with human cell fates to generate a model of the functional network dynamics that can be transferred to specific reprogramming goals. The approach additively combines transcriptional responses to gene perturbations (single-gene knockdowns and overexpressions) to minimize the transcriptional difference between a given pair of initial and target states. We demonstrate the flexibility of our approach by applying it to a microarray dataset comprising over 9,000 microarrays across 54 cell types and 227 unique perturbations, and an RNASeq dataset consisting of over 10,000 sequencing runs across 36 cell types and 138 perturbations. Our approach reproduces known reprogramming protocols with an average AUROC of 0.91 while innovating over existing methods by pre-training an adaptable model that can be tailored to specific reprogramming transitions. We show that the number of gene perturbations required to steer from one fate to another increases as the developmental relatedness decreases. We also show that fewer genes are needed to progress along developmental paths than to regress. Together, these findings establish a proof-of-concept for our approach to computationally design control strategies and demonstrate their ability to provide insights into the dynamics of gene regulatory networks.
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Affiliation(s)
- Thomas P Wytock
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Center for Network Dynamics, Northwestern University, Evanston, Illinois 60208, USA
| | - Adilson E Motter
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Center for Network Dynamics, Northwestern University, Evanston, Illinois 60208, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois 60208, USA
- National Institute for Theory and Mathematics in Biology, Evanston, Illinois 60208, USA
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Ren L, Ma W, Wang Y. SpecLoop predicts cell type-specific chromatin loop via transcription factor cooperation. Comput Biol Med 2024; 171:108182. [PMID: 38422958 DOI: 10.1016/j.compbiomed.2024.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/18/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Cell-type-Specific Chromatin Loops (CSCLs) are crucial for gene regulation and cell fate determination. However, the mechanisms governing their establishment remain elusive. Here, we present SpecLoop, a network regularization-based machine learning framework, to investigate the role of transcription factors (TFs) cooperation in CSCL formation. SpecLoop integrates multi-omics data, including gene expression, chromatin accessibility, sequence, protein-protein interaction, and TF binding motif data, to predict CSCLs and identify TF cooperations. Using high resolution Hi-C data as the gold standard, SpecLoop accurately predicts CSCL in GM12878, IMR90, HeLa-S3, K562, HUVEC, HMEC, and NHEK seven cell types, with the AUROC values ranging from 0.8645 to 0.9852 and AUPR values ranging from 0.8654 to 0.9734. Notably SpecLoop demonstrates improved accuracy in predicting long-distance CSCLs and identifies TF complexes with strong predictive ability. Our study systematically explores the TFs and TF pairs associated with CSCL through effective integration of diverse omics data. SpecLoop is freely available at https://github.com/AMSSwanglab/SpecLoop.
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Affiliation(s)
- Lixin Ren
- Department of Applied Mathematics, School of Mathematics and Physics, University of Science and Technology Beijing, 100083, Beijing, China.
| | - Wanbiao Ma
- Department of Applied Mathematics, School of Mathematics and Physics, University of Science and Technology Beijing, 100083, Beijing, China.
| | - Yong Wang
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 330106, China.
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7
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Barvaux S, Okawa S, Del Sol A. SinCMat: A single-cell-based method for predicting functional maturation transcription factors. Stem Cell Reports 2024; 19:270-284. [PMID: 38215756 PMCID: PMC10874865 DOI: 10.1016/j.stemcr.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
A major goal of regenerative medicine is to generate tissue-specific mature and functional cells. However, current cell engineering protocols are still unable to systematically produce fully mature functional cells. While existing computational approaches aim at predicting transcription factors (TFs) for cell differentiation/reprogramming, no method currently exists that specifically considers functional cell maturation processes. To address this challenge, here, we develop SinCMat, a single-cell RNA sequencing (RNA-seq)-based computational method for predicting cell maturation TFs. Based on a model of cell maturation, SinCMat identifies pairs of identity TFs and signal-dependent TFs that co-target genes driving functional maturation. A large-scale application of SinCMat to the Mouse Cell Atlas and Tabula Sapiens accurately recapitulates known maturation TFs and predicts novel candidates. We expect SinCMat to be an important resource, complementary to preexisting computational methods, for studies aiming at producing functionally mature cells.
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Affiliation(s)
- Sybille Barvaux
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg; University of Pittsburgh School of Medicine, Vascular Medicine Institute, Department of Computational and Systems Biology, McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, 4367 Esch-Belval Esch-sur-Alzette, Luxembourg; CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
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Hamano M, Nakamura T, Ito R, Shimada Y, Iwata M, Takeshita JI, Eguchi R, Yamanishi Y. DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion. Bioinformatics 2024; 40:btae048. [PMID: 38273708 PMCID: PMC10868337 DOI: 10.1093/bioinformatics/btae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
MOTIVATION Direct reprogramming (DR) is a process that directly converts somatic cells to target cells. Although DR via small molecules is safer than using transcription factors (TFs) in terms of avoidance of tumorigenic risk, the determination of DR-inducing small molecules is challenging. RESULTS Here we present a novel in silico method, DIRECTEUR, to predict small molecules that replace TFs for DR. We extracted DR-characteristic genes using transcriptome profiles of cells in which DR was induced by TFs, and performed a variant of simulated annealing to explore small molecule combinations with similar gene expression patterns with DR-inducing TFs. We applied DIRECTEUR to predicting combinations of small molecules that convert fibroblasts into neurons or cardiomyocytes, and were able to reproduce experimentally verified and functionally related molecules inducing the corresponding conversions. The proposed method is expected to be useful for practical applications in regenerative medicine. AVAILABILITY AND IMPLEMENTATION The code and data are available at the following link: https://github.com/HamanoLaboratory/DIRECTEUR.git.
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Affiliation(s)
- Momoko Hamano
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Toru Nakamura
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Ryoku Ito
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Yuki Shimada
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Jun-ichi Takeshita
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8569, Japan
| | - Ryohei Eguchi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
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Shao F, Van Otterloo E, Cao H. Computational identification of key transcription factors for embryonic and postnatal Sox2+ dental epithelial stem cell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573158. [PMID: 38187542 PMCID: PMC10769342 DOI: 10.1101/2023.12.22.573158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
While many reptiles can replace their tooth throughout life, human loss the tooth replacement capability after formation of the permanent teeth. It was thought that the difference in tooth regeneration capability depends on the persistence of a specialized dental epithelial structure, the dental lamina that contains dental epithelial stem cells (DESC). Currently, we know very little about DESC such as what genes are expressed or its chromatin accessibility profile. Multiple markers of DESC have been proposed such as Sox2 and Lgr5 . Few single cell RNA-seq experiments have been performed previously, but no obvious DESC cluster was identified in these scRNA-seq datasets, possible due to that the expression level of DESC markers such as Sox2 and Lgr5 is too low or the percentage of DESC is too low in whole tooth. We utilize a mouse line Sox2-GFP to enrich Sox2+ DESC and use Smart-Seq2 protocol and ATAC-seq protocol to generate transcriptome profile and chromatin accessibility profile of P2 Sox2+ DESC. Additionally, we generate transcriptome profile and chromatin accessibility profile of E11.5 Sox2+ dental lamina cells. With transcriptome profile and chromatin accessibility profile, we systematically identify potential key transcription factors for E11.5 Sox2+ cells and P2 Sox2+ cells. We identified transcription factors including Pitx2, Id3, Pitx1, Tbx1, Trp63, Nkx2-3, Grhl3, Dlx2, Runx1, Nfix, Zfp536 , etc potentially formed the core transcriptional regulatory networks of Sox2+ DESC in both embryonic and postnatal stages.
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Wang P, Wen X, Li H, Lang P, Li S, Lei Y, Shu H, Gao L, Zhao D, Zeng J. Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON. Nat Commun 2023; 14:8459. [PMID: 38123534 PMCID: PMC10733330 DOI: 10.1038/s41467-023-44103-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Single-cell technologies enable the dynamic analyses of cell fate mapping. However, capturing the gene regulatory relationships and identifying the driver factors that control cell fate decisions are still challenging. We present CEFCON, a network-based framework that first uses a graph neural network with attention mechanism to infer a cell-lineage-specific gene regulatory network (GRN) from single-cell RNA-sequencing data, and then models cell fate dynamics through network control theory to identify driver regulators and the associated gene modules, revealing their critical biological processes related to cell states. Extensive benchmarking tests consistently demonstrated the superiority of CEFCON in GRN construction, driver regulator identification, and gene module identification over baseline methods. When applied to the mouse hematopoietic stem cell differentiation data, CEFCON successfully identified driver regulators for three developmental lineages, which offered useful insights into their differentiation from a network control perspective. Overall, CEFCON provides a valuable tool for studying the underlying mechanisms of cell fate decisions from single-cell RNA-seq data.
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Affiliation(s)
- Peizhuo Wang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Xiao Wen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
| | - Han Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Yipin Lei
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Hantao Shu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, 710071, Xi'an, Shaanxi Province, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China.
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Hecker D, Lauber M, Behjati Ardakani F, Ashrafiyan S, Manz Q, Kersting J, Hoffmann M, Schulz MH, List M. Computational tools for inferring transcription factor activity. Proteomics 2023; 23:e2200462. [PMID: 37706624 DOI: 10.1002/pmic.202200462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Abstract
Transcription factors (TFs) are essential players in orchestrating the regulatory landscape in cells. Still, their exact modes of action and dependencies on other regulatory aspects remain elusive. Since TFs act cell type-specific and each TF has its own characteristics, untangling their regulatory interactions from an experimental point of view is laborious and convoluted. Thus, there is an ongoing development of computational tools that estimate transcription factor activity (TFA) from a variety of data modalities, either based on a mapping of TFs to their putative target genes or in a genome-wide, gene-unspecific fashion. These tools can help to gain insights into TF regulation and to prioritize candidates for experimental validation. We want to give an overview of available computational tools that estimate TFA, illustrate examples of their application, debate common result validation strategies, and discuss assumptions and concomitant limitations.
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Affiliation(s)
- Dennis Hecker
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Michael Lauber
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Fatemeh Behjati Ardakani
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Shamim Ashrafiyan
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Quirin Manz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Johannes Kersting
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- GeneSurge GmbH, München, Germany
| | - Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcel H Schulz
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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12
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Dubois‐Chevalier J, Gheeraert C, Berthier A, Boulet C, Dubois V, Guille L, Fourcot M, Marot G, Gauthier K, Dubuquoy L, Staels B, Lefebvre P, Eeckhoute J. An extended transcription factor regulatory network controls hepatocyte identity. EMBO Rep 2023; 24:e57020. [PMID: 37424431 PMCID: PMC10481658 DOI: 10.15252/embr.202357020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023] Open
Abstract
Cell identity is specified by a core transcriptional regulatory circuitry (CoRC), typically limited to a small set of interconnected cell-specific transcription factors (TFs). By mining global hepatic TF regulons, we reveal a more complex organization of the transcriptional regulatory network controlling hepatocyte identity. We show that tight functional interconnections controlling hepatocyte identity extend to non-cell-specific TFs beyond the CoRC, which we call hepatocyte identity (Hep-ID)CONNECT TFs. Besides controlling identity effector genes, Hep-IDCONNECT TFs also engage in reciprocal transcriptional regulation with TFs of the CoRC. In homeostatic basal conditions, this translates into Hep-IDCONNECT TFs being involved in fine tuning CoRC TF expression including their rhythmic expression patterns. Moreover, a role for Hep-IDCONNECT TFs in the control of hepatocyte identity is revealed in dedifferentiated hepatocytes where Hep-IDCONNECT TFs are able to reset CoRC TF expression. This is observed upon activation of NR1H3 or THRB in hepatocarcinoma or in hepatocytes subjected to inflammation-induced loss of identity. Our study establishes that hepatocyte identity is controlled by an extended array of TFs beyond the CoRC.
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Affiliation(s)
| | - Céline Gheeraert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Clémence Boulet
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Vanessa Dubois
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
- Basic and Translational Endocrinology (BaTE), Department of Basic and Applied Medical SciencesGhent UniversityGhentBelgium
| | - Loïc Guille
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Marie Fourcot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 – UAR 2014 – PLBSLilleFrance
| | - Guillemette Marot
- Univ. Lille, Inria, CHU Lille, ULR 2694 – METRICS: Évaluation des technologies de santé et des pratiques médicalesLilleFrance
| | - Karine Gauthier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, INRAE USC 1370, École Normale Supérieure de LyonLyonFrance
| | - Laurent Dubuquoy
- Univ. Lille, Inserm, CHU Lille, U1286 – INFINITE – Institute for Translational Research in InflammationLilleFrance
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011‐EGIDLilleFrance
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13
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Fang YM, Chen WC, Zheng WJ, Yang YS, Zhang Y, Chen XL, Pei MQ, Lin S, He HF. A cutting-edge strategy for spinal cord injury treatment: resident cellular transdifferentiation. Front Cell Neurosci 2023; 17:1237641. [PMID: 37711511 PMCID: PMC10498389 DOI: 10.3389/fncel.2023.1237641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Spinal cord injury causes varying degrees of motor and sensory function loss. However, there are no effective treatments for spinal cord repair following an injury. Moreover, significant preclinical advances in bioengineering and regenerative medicine have not yet been translated into effective clinical therapies. The spinal cord's poor regenerative capacity makes repairing damaged and lost neurons a critical treatment step. Reprogramming-based neuronal transdifferentiation has recently shown great potential in repair and plasticity, as it can convert mature somatic cells into functional neurons for spinal cord injury repair in vitro and in vivo, effectively halting the progression of spinal cord injury and promoting functional improvement. However, the mechanisms of the neuronal transdifferentiation and the induced neuronal subtypes are not yet well understood. This review analyzes the mechanisms of resident cellular transdifferentiation based on a review of the relevant recent literature, describes different molecular approaches to obtain different neuronal subtypes, discusses the current challenges and improvement methods, and provides new ideas for exploring therapeutic approaches for spinal cord injury.
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Affiliation(s)
- Yu-Ming Fang
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Wei-Can Chen
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Wan-Jing Zheng
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Yu-Shen Yang
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Yan Zhang
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Xin-Li Chen
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Meng-Qin Pei
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Neuroendocrinology Group, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - He-Fan He
- Department of Anaesthesiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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14
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Wang M, Chen Q, Wang S, Xie H, Liu J, Huang R, Xiang Y, Jiang Y, Tian D, Bian E. Super-enhancers complexes zoom in transcription in cancer. J Exp Clin Cancer Res 2023; 42:183. [PMID: 37501079 PMCID: PMC10375641 DOI: 10.1186/s13046-023-02763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Super-enhancers (SEs) consist of multiple typical enhancers enriched at high density with transcription factors, histone-modifying enzymes and cofactors. Oncogenic SEs promote tumorigenesis and malignancy by altering protein-coding gene expression and noncoding regulatory element function. Therefore, they play central roles in the treatment of cancer. Here, we review the structural characteristics, organization, identification, and functions of SEs and the underlying molecular mechanism by which SEs drive oncogenic transcription in tumor cells. We then summarize abnormal SE complexes, SE-driven coding genes, and noncoding RNAs involved in tumor development. In summary, we believe that SEs show great potential as biomarkers and therapeutic targets.
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Affiliation(s)
- MengTing Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - QingYang Chen
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - ShuJie Wang
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - RuiXiang Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YuFei Xiang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YanYi Jiang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
| | - DaSheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
| | - ErBao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
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15
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Arts JA, Laberthonnière C, Lima Cunha D, Zhou H. Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease. Cells 2023; 12:1808. [PMID: 37443842 PMCID: PMC10340756 DOI: 10.3390/cells12131808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease.
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Affiliation(s)
- Julian A. Arts
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Camille Laberthonnière
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Dulce Lima Cunha
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
| | - Huiqing Zhou
- Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands; (J.A.A.)
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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16
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Pan X, Ma Z, Sun X, Li H, Zhang T, Zhao C, Wang N, Heller R, Hung Wong W, Wang W, Jiang Y, Wang Y. CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:632-648. [PMID: 36494035 PMCID: PMC10787174 DOI: 10.1016/j.gpb.2022.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 11/12/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The genetic information coded in DNA leads to trait innovation via a gene regulatory network (GRN) in development. Here, we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) to investigate the ruminant multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we defined toolkit transcription factors (TTFs) and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development. Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules. Notably, 6 TTFs (OTX1, SOX21, HOXC8, SOX2, TP63, and PPARG), as well as 16 active-RSCNEs, functionally distinguished the rumen from the esophagus. Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.
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Affiliation(s)
- Xiangyu Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Department of Medical Research, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Zhaoxia Ma
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinqi Sun
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Tingting Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chen Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Yong Wang
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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17
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Yuan Y, Kong W, Liu XM, Shi GH. Gene Therapy Activates Retinal Pigment Epithelium Cell Proliferation for Age-related Macular Degeneration in a Mouse Model. Curr Med Sci 2023; 43:384-392. [PMID: 36944806 DOI: 10.1007/s11596-022-2684-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/21/2022] [Indexed: 03/23/2023]
Abstract
OBJECTIVE Age-related macular degeneration (AMD) is a degenerative retinal disease. The degeneration or death of retinal pigment epithelium (RPE) cells is implicated in the pathogenesis of AMD. This study aimed to activate the proliferation of RPE cells in vivo by using an adeno-associated virus (AAV) vector encoding β-catenin to treat AMD in a mouse model. METHODS Mice were intravitreally injected with AAV2/8-Y733F-VMD2-β-catenin for 2 or 4 weeks, and β-catenin expression was measured using immunofluorescence staining, real-time quantitative reverse transcription polymerase chain reaction (PCR), and Western blotting. The function of β-catenin was determined using retinal flat mounts and laser-induced damage models. Finally, the safety of AAV2/8-Y733F-VMD2-β-catenin was evaluated by multiple intravitreal injections. RESULTS AAV2/8-Y733F-VMD2-β-catenin induced the expression of β-catenin in RPE cells. It activated the proliferation of RPE cells and increased cyclin D1 expression. It was beneficial to the recovery of laser-induced damage by activating the proliferation of RPE cells. Furthermore, it could induce apoptosis of RPE cells by increasing the expression of Trp53, Bax and caspase3 while decreasing the expression of Bcl-2. CONCLUSION AAV2/8-Y733F-VMD2-β-catenin increased β-catenin expression in RPE cells, activated RPE cell proliferation, and helped mice heal from laser-induced eye injury. Furthermore, it could induce the apoptosis of RPE cells. Therefore, it may be a safe approach for AMD treatment.
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Affiliation(s)
- Yun Yuan
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215000, China.
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215000, China.
| | - Wen Kong
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215000, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215000, China
| | - Xiao-Mei Liu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215000, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215000, China
| | - Guo-Hua Shi
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou, 215000, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, 215000, China
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18
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Merhi M, Ahmad F, Taib N, Inchakalody V, Uddin S, Shablak A, Dermime S. The complex network of transcription factors, immune checkpoint inhibitors and stemness features in colorectal cancer: A recent update. Semin Cancer Biol 2023; 89:1-17. [PMID: 36621515 DOI: 10.1016/j.semcancer.2023.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Cancer immunity is regulated by several mechanisms that include co-stimulatory and/or co-inhibitory molecules known as immune checkpoints expressed by the immune cells. In colorectal cancer (CRC), CTLA-4, LAG3, TIM-3 and PD-1 are the major co-inhibitory checkpoints involved in tumor development and progression. On the other hand, the deregulation of transcription factors and cancer stem cells activity plays a major role in the development of drug resistance and in the spread of metastatic disease in CRC. In this review, we describe how the modulation of such transcription factors affects the response of CRC to therapies. We also focus on the role of cancer stem cells in tumor metastasis and chemoresistance and discuss both preclinical and clinical approaches for targeting stem cells to prevent their tumorigenic effect. Finally, we provide an update on the clinical applications of immune checkpoint inhibitors in CRC and discuss the regulatory effects of transcription factors on the expression of the immune inhibitory checkpoints with specific focus on the PD-1 and PD-L1 molecules.
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Affiliation(s)
- Maysaloun Merhi
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Fareed Ahmad
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Inchakalody
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Alaaeldin Shablak
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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19
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Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 2023; 14:346. [PMID: 36681680 PMCID: PMC9867739 DOI: 10.1038/s41467-023-35833-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-seq, ATAC-Seq, RNA-seq, and SNP arrays. We integrate 153 individual data sets from 42 patients and nominate 50 histology-specific master transcription factors (MTF) to define RCC histologic subtypes, including EPAS1 and ETS-1 in ccRCC, HNF1B in pRCC, and FOXI1 in chRCC. We confirm histology-specific MTFs via immunohistochemistry including a ccRCC-specific TF, BHLHE41. FOXI1 overexpression with knock-down of EPAS1 in the 786-O ccRCC cell line induces transcriptional upregulation of chRCC-specific genes, TFCP2L1, ATP6V0D2, KIT, and INSRR, implicating FOXI1 as a MTF for chRCC. Integrating RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data reveals that risk-variants are significantly enriched in allelically-imbalanced peaks. This epigenomic atlas in primary human samples provides a resource for future investigation.
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Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan C Baca
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elio Adib
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Talal El Zarif
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - David A Braun
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Heng Du
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michel Alchoueiry
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sayed G Matar
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Andres Acosta
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yue Hou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacob E Berchuck
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elizabeth Henske
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Toni K Choueiri
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
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20
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Cohen-Gulkar M, David A, Messika-Gold N, Eshel M, Ovadia S, Zuk-Bar N, Idelson M, Cohen-Tayar Y, Reubinoff B, Ziv T, Shamay M, Elkon R, Ashery-Padan R. The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration. PLoS Biol 2023; 21:e3001924. [PMID: 36649236 PMCID: PMC9844853 DOI: 10.1371/journal.pbio.3001924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/16/2022] [Indexed: 01/18/2023] Open
Abstract
Tissue-specific transcription factors (TFs) control the transcriptome through an association with noncoding regulatory regions (cistromes). Identifying the combination of TFs that dictate specific cell fate, their specific cistromes and examining their involvement in complex human traits remain a major challenge. Here, we focus on the retinal pigmented epithelium (RPE), an essential lineage for retinal development and function and the primary tissue affected in age-related macular degeneration (AMD), a leading cause of blindness. By combining mechanistic findings in stem-cell-derived human RPE, in vivo functional studies in mice and global transcriptomic and proteomic analyses, we revealed that the key developmental TFs LHX2 and OTX2 function together in transcriptional module containing LDB1 and SWI/SNF (BAF) to regulate the RPE transcriptome. Importantly, the intersection between the identified LHX2-OTX2 cistrome with published expression quantitative trait loci, ATAC-seq data from human RPE, and AMD genome-wide association study (GWAS) data, followed by functional validation using a reporter assay, revealed a causal genetic variant that affects AMD risk by altering TRPM1 expression in the RPE through modulation of LHX2 transcriptional activity on its promoter. Taken together, the reported cistrome of LHX2 and OTX2, the identified downstream genes and interacting co-factors reveal the RPE transcription module and uncover a causal regulatory risk single-nucleotide polymorphism (SNP) in the multifactorial common blinding disease AMD.
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Affiliation(s)
- Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Ahuvit David
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Naama Messika-Gold
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Mai Eshel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Shai Ovadia
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Nitay Zuk-Bar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Maria Idelson
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and Department of Gynecology, Jerusalem, Israel
| | - Yamit Cohen-Tayar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Benjamin Reubinoff
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy and Department of Gynecology, Jerusalem, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Meir Shamay
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RE); (RAP)
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RE); (RAP)
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21
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A single cell-based computational platform to identify chemical compounds targeting desired sets of transcription factors for cellular conversion. Stem Cell Reports 2023; 18:131-144. [PMID: 36400030 PMCID: PMC9859931 DOI: 10.1016/j.stemcr.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
Cellular conversion can be induced by perturbing a handful of key transcription factors (TFs). Replacement of direct manipulation of key TFs with chemical compounds offers a less laborious and safer strategy to drive cellular conversion for regenerative medicine. Nevertheless, identifying optimal chemical compounds currently requires large-scale screening of chemical libraries, which is resource intensive. Existing computational methods aim at predicting cell conversion TFs, but there are no methods for identifying chemical compounds targeting these TFs. Here, we develop a single cell-based platform (SiPer) to systematically prioritize chemical compounds targeting desired TFs to guide cellular conversions. SiPer integrates a large compendium of chemical perturbations on non-cancer cells with a network model and predicted known and novel chemical compounds in diverse cell conversion examples. Importantly, we applied SiPer to develop a highly efficient protocol for human hepatic maturation. Overall, SiPer provides a valuable resource to efficiently identify chemical compounds for cell conversion.
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22
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Reprogramming cell fates towards novel cancer immunotherapies. Curr Opin Pharmacol 2022; 67:102312. [PMID: 36335715 DOI: 10.1016/j.coph.2022.102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/18/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Recent advances in our understanding of host immune and cancer cells interactions have made immunotherapy a prominent choice in cancer treatment. Despite such promise, cell-based immunotherapies remain inapplicable to many patients due to severe limitations in the availability and quality of immune cells isolated from donors. Reprogramming technologies that facilitate the engineering of cell types of interest, are emerging as a putative solution to such challenges. Here we focus on the recent progress being made in reprogramming technologies with respect to the immune system and their potential for clinical applications.
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23
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Heuts BMH, Arza-Apalategi S, Frölich S, Bergevoet SM, van den Oever SN, van Heeringen SJ, van der Reijden BA, Martens JHA. Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework. Sci Rep 2022; 12:18656. [PMID: 36333382 PMCID: PMC9636203 DOI: 10.1038/s41598-022-21148-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022] Open
Abstract
Advanced computational methods exploit gene expression and epigenetic datasets to predict gene regulatory networks controlled by transcription factors (TFs). These methods have identified cell fate determining TFs but require large amounts of reference data and experimental expertise. Here, we present an easy to use network-based computational framework that exploits enhancers defined by bidirectional transcription, using as sole input CAGE sequencing data to correctly predict TFs key to various human cell types. Next, we applied this Analysis Algorithm for Networks Specified by Enhancers based on CAGE (ANANSE-CAGE) to predict TFs driving red and white blood cell development, and THP-1 leukemia cell immortalization. Further, we predicted TFs that are differentially important to either cell line- or primary- associated MLL-AF9-driven gene programs, and in primary MLL-AF9 acute leukemia. Our approach identified experimentally validated as well as thus far unexplored TFs in these processes. ANANSE-CAGE will be useful to identify transcription factors that are key to any cell fate change using only CAGE-seq data as input.
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Affiliation(s)
- B. M. H. Heuts
- grid.5590.90000000122931605Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - S. Arza-Apalategi
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - S. Frölich
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - S. M. Bergevoet
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - S. N. van den Oever
- grid.5590.90000000122931605Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - S. J. van Heeringen
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - B. A. van der Reijden
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - J. H. A. Martens
- grid.5590.90000000122931605Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, 6525 GA Nijmegen, The Netherlands
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24
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Lin P, Zhang G, Peng R, Zhao M, Li H. Increased expression of bone/cartilage-associated genes and core transcription factors in keloids by RNA sequencing. Exp Dermatol 2022; 31:1586-1596. [PMID: 35730251 DOI: 10.1111/exd.14630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/01/2022] [Accepted: 06/19/2022] [Indexed: 02/05/2023]
Abstract
Fibroblasts in keloids undergo cell identity transition with altered transcriptional characteristics. However, the core transcription factors driving this cellular reprogramming remain largely unknown. Here, we report the results of transcriptional profiling from 48 keloid and 24 control dermal tissues. We identified 1187 upregulated differentially expressed genes (foldchange > 2, false discovery rate < 0.05) in keloids, which were mainly enriched in extracellular matrix organization and bone/cartilage development, with significantly increased expression of bone/cartilage-associated collagens (COL5A1, COL10A1, and COL11A1) and glycoproteins (ACAN, COMP, and SPARC). Deconvolution analysis also revealed significantly increased composition of osteoblasts in keloid dermis. A total of 92 upregulated transcription factors were screened out from differentially expressed genes and mainly enriched in transcription process and skeleton development. Additional sequencing of six keloid individuals with multiple regions and intersection further narrow the list with 10 transcription factors. Finally, AEBP1, CREB3L1, RUNX2, and ZNF469 have been identified as candidate core regulators in promoting the gaining of bone/cartilage-like characteristics in keloids. RNA-sequencing of full-skin keloids consolidated the existence of these four transcription factors. Immunohistochemistry was employed to verify the expression of AEBP1, CREB3L1, RUNX2, and ZNF469 in keloid fibroblasts. In conclusion, we bioinformatically discovered the increased expression of bone/cartilage-associated genes and candidate core transcription factors in keloids. Our findings promise to provide molecular clues to develop novel therapeutic modalities against skin fibrosis.
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Affiliation(s)
- Pingping Lin
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Guohong Zhang
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Rui Peng
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Mingming Zhao
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Hang Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
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25
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Tian H, Chen Z, Zhu X, Ou Q, Wang Z, Wu B, Xu JY, Jin C, Gao F, Wang J, Zhang J, Zhang J, Lu L, Xu GT. Induced retinal pigment epithelial cells with anti-epithelial-to-mesenchymal transition ability delay retinal degeneration. iScience 2022; 25:105050. [PMID: 36185374 PMCID: PMC9519511 DOI: 10.1016/j.isci.2022.105050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/12/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
The hostile microenvironment of the retina in patients with age-related macular degeneration (AMD) may trigger epithelial-to-mesenchymal transition (EMT) of grafted retinal pigment epithelial (RPE) cells, thus attenuating the therapeutic outcome. Here, we transformed human dedifferentiated induced pluripotent stem cell-derived RPE (iPSC-RPE) cells into induced RPE (iRPE) cells using a cocktail of four transcription factors (TFs)—CRX, MITF-A, NR2E1, and C-MYC. These critical TFs maintained the epithelial property of iRPE cells by regulating the expression of bmp7, forkhead box f2, lin7a, and pard6b, and conferred resistance to TGF-β-induced EMT in iRPE cells by targeting ppm1a. The iRPE cells with Tet-on system-regulated c-myc expression exhibited EMT resistance and better therapeutic function compared with iPSC-RPE cells in rat AMD model. Our study demonstrates that endowing RPE cells with anti-EMT property avoids the risk of EMT after cells are grafted into the subretinal space, and it may provide a suitable candidate for AMD treatment. CRX, MITF-A, NR2E1, and C-MYC transform De-iPSC-RPE cells into iRPE cells iRPE cells have resistance to TGF-β-induced EMT BMP7, FOXF2, LIN7A, PARD6B, and PPM1A mediate the functions of TFs in iRPE cells iRPE cells have better retinal protective function than iPSC-RPE cells
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26
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Zhu X, Chen Z, Wang L, Ou Q, Feng Z, Xiao H, Shen Q, Li Y, Jin C, Xu JY, Gao F, Wang J, Zhang J, Zhang J, Xu Z, Xu GT, Lu L, Tian H. Direct conversion of human umbilical cord mesenchymal stem cells into retinal pigment epithelial cells for treatment of retinal degeneration. Cell Death Dis 2022; 13:785. [PMID: 36096985 PMCID: PMC9468174 DOI: 10.1038/s41419-022-05199-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 01/21/2023]
Abstract
Age-related macular degeneration (AMD) is a major vision-threatening disease. Although mesenchymal stem cells (MSCs) exhibit beneficial neural protective effects, their limited differentiation capacity in vivo attenuates their therapeutic function. Therefore, the differentiation of MSCs into retinal pigment epithelial (RPE) cells in vitro and their subsequent transplantation into the subretinal space is expected to improve the outcome of cell therapy. Here, we transdifferentiated human umbilical cord MSCs (hUCMSCs) into induced RPE (iRPE) cells using a cocktail of five transcription factors (TFs): CRX, NR2E1, C-MYC, LHX2, and SIX6. iRPE cells exhibited RPE specific properties, including phagocytic ability, epithelial polarity, and gene expression profile. In addition, high expression of PTPN13 in iRPE cells endows them with an epithelial-to-mesenchymal transition (EMT)-resistant capacity through dephosphorylating syntenin1, and subsequently promoting the internalization and degradation of transforming growth factor-β receptors. After grafting into the subretinal space of the sodium iodate-induced rat AMD model, iRPE cells demonstrated a better therapeutic function than hUCMSCs. These results suggest that hUCMSC-derived iRPE cells may be promising candidates to reverse AMD pathophysiology.
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Affiliation(s)
- Xiaoman Zhu
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Zhiyang Chen
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Li Wang
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Qingjian Ou
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Zhong Feng
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Honglei Xiao
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Qi Shen
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Yingao Li
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Caixia Jin
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Jing-Ying Xu
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Furong Gao
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Juan Wang
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Jingfa Zhang
- grid.16821.3c0000 0004 0368 8293Department of Ophthalmology, Shanghai General Hospital (Shanghai First People’s Hospital), Shanghai Jiao Tong University, Shanghai, 200080 China
| | - Jieping Zhang
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China ,Department of Physiology and Pharmacology, TUSM, Shanghai, 200092 China
| | - Zhiguo Xu
- Huzhou college, Zhejiang, 313000 China
| | - Guo-Tong Xu
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China ,Department of Physiology and Pharmacology, TUSM, Shanghai, 200092 China ,grid.24516.340000000123704535The collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200092 China
| | - Lixia Lu
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
| | - Haibin Tian
- grid.24516.340000000123704535Department of Ophthalmology of Tongji Hospital and Laboratory of Clinical and Visual Sciences of Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200065 China
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27
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Tercan B, Aguilar B, Huang S, Dougherty ER, Shmulevich I. Probabilistic boolean networks predict transcription factor targets to induce transdifferentiation. iScience 2022; 25:104951. [PMID: 36093045 PMCID: PMC9460527 DOI: 10.1016/j.isci.2022.104951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 06/28/2022] [Accepted: 08/09/2022] [Indexed: 12/02/2022] Open
Abstract
We developed a computational approach to find the best intervention to achieve transcription factor (TF) mediated transdifferentiation. We construct probabilistic Boolean networks (PBNs) from single-cell RNA sequencing data of two different cell states to model hematopoietic transcription factors cross-talk. This was achieved by a “sampled network” approach, which enabled us to construct large networks. The interventions to induce transdifferentiation consisted of permanently activating or deactivating each of the TFs and determining the probability mass transfer of steady-state probabilities from the departure to the destination cell type or state. Our findings support the common assumption that TFs that are differentially expressed between the two cell types are the best intervention points to achieve transdifferentiation. TFs whose interventions are found to transdifferentiate progenitor B cells into monocytes include EBF1 down-regulation, CEBPB up-regulation, TCF3 down-regulation, and STAT3 up-regulation. Differentially expressed transcription factors are the best for transdifferentiation Probabilistic Boolean networks (PBNs) are used to model transdifferentiation using the scRNAseq data at one time point A new approach works for a large number of network nodes
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Affiliation(s)
| | | | - Sui Huang
- Institute for Systems Biology, Seattle, WA, USA
| | - Edward R. Dougherty
- Texas A&M University Department of Electrical & Computer Engineering, College Station, TX, USA
| | - Ilya Shmulevich
- Institute for Systems Biology, Seattle, WA, USA
- Corresponding author
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28
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Hammelman J, Patel T, Closser M, Wichterle H, Gifford D. Ranking reprogramming factors for cell differentiation. Nat Methods 2022; 19:812-822. [PMID: 35710610 PMCID: PMC10460539 DOI: 10.1038/s41592-022-01522-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2022] [Indexed: 12/16/2022]
Abstract
Transcription factor over-expression is a proven method for reprogramming cells to a desired cell type for regenerative medicine and therapeutic discovery. However, a general method for the identification of reprogramming factors to create an arbitrary cell type is an open problem. Here we examine the success rate of methods and data for differentiation by testing the ability of nine computational methods (CellNet, GarNet, EBseq, AME, DREME, HOMER, KMAC, diffTF and DeepAccess) to discover and rank candidate factors for eight target cell types with known reprogramming solutions. We compare methods that use gene expression, biological networks and chromatin accessibility data, and comprehensively test parameter and preprocessing of input data to optimize performance. We find the best factor identification methods can identify an average of 50-60% of reprogramming factors within the top ten candidates, and methods that use chromatin accessibility perform the best. Among the chromatin accessibility methods, complex methods DeepAccess and diffTF have higher correlation with the ranked significance of transcription factor candidates within reprogramming protocols for differentiation. We provide evidence that AME and diffTF are optimal methods for transcription factor recovery that will allow for systematic prioritization of transcription factor candidates to aid in the design of new reprogramming protocols.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, MIT, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Tulsi Patel
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael Closser
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - David Gifford
- Computational and Systems Biology, MIT, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
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Lu Y, Feng Z, Zhang S, Wang Y. Annotating regulatory elements by heterogeneous network embedding. Bioinformatics 2022; 38:2899-2911. [PMID: 35561169 PMCID: PMC9326849 DOI: 10.1093/bioinformatics/btac185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/05/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Regulatory elements (REs), such as enhancers and promoters, are known as regulatory sequences functional in a heterogeneous regulatory network to control gene expression by recruiting transcription regulators and carrying genetic variants in a context specific way. Annotating those REs relies on costly and labor-intensive next-generation sequencing and RNA-guided editing technologies in many cellular contexts. RESULTS We propose a systematic Gene Ontology Annotation method for Regulatory Elements (RE-GOA) by leveraging the powerful word embedding in natural language processing. We first assemble a heterogeneous network by integrating context specific regulations, protein-protein interactions and gene ontology (GO) terms. Then we perform network embedding and associate regulatory elements with GO terms by assessing their similarity in a low dimensional vector space. With three applications, we show that RE-GOA outperforms existing methods in annotating TFs' binding sites from ChIP-seq data, in functional enrichment analysis of differentially accessible peaks from ATAC-seq data, and in revealing genetic correlation among phenotypes from their GWAS summary statistics data. AVAILABILITY AND IMPLEMENTATION The source code and the systematic RE annotation for human and mouse are available at https://github.com/AMSSwanglab/RE-GOA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yurun Lu
- CEMS, NCMIS, HCMS, MADIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanying Feng
- CEMS, NCMIS, HCMS, MADIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Songmao Zhang
- CEMS, NCMIS, HCMS, MADIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Yong Wang
- To whom correspondence should be addressed. or
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Eguchi R, Hamano M, Iwata M, Nakamura T, Oki S, Yamanishi Y. TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach. Bioinformatics 2022; 38:2839-2846. [PMID: 35561200 DOI: 10.1093/bioinformatics/btac209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Direct reprogramming involves the direct conversion of fully differentiated mature cell types into various other cell types while bypassing an intermediate pluripotent state (e.g. induced pluripotent stem cells). Cell differentiation by direct reprogramming is determined by two types of transcription factors (TFs): pioneer factors (PFs) and cooperative TFs. PFs have the distinct ability to open chromatin aggregations, assemble a collective of cooperative TFs and activate gene expression. The experimental determination of two types of TFs is extremely difficult and costly. RESULTS In this study, we developed a novel computational method, TRANSDIRE (TRANS-omics-based approach for DIrect REprogramming), to predict the TFs that induce direct reprogramming in various human cell types using multiple omics data. In the algorithm, potential PFs were predicted based on low signal chromatin regions, and the cooperative TFs were predicted through a trans-omics analysis of genomic data (e.g. enhancers), transcriptome data (e.g. gene expression profiles in human cells), epigenome data (e.g. chromatin immunoprecipitation sequencing data) and interactome data. We applied the proposed methods to the reconstruction of TFs that induce direct reprogramming from fibroblasts to six other cell types: hepatocytes, cartilaginous cells, neurons, cardiomyocytes, pancreatic cells and Paneth cells. We demonstrated that the methods successfully predicted TFs for most cell conversions with high accuracy. Thus, the proposed methods are expected to be useful for various practical applications in regenerative medicine. AVAILABILITY AND IMPLEMENTATION The source code and data are available at the following website: http://figshare.com/s/b653781a5b9e6639972b. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ryohei Eguchi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Momoko Hamano
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Toru Nakamura
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka 820-8502, Japan
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Hörnblad A, Remeseiro S. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency. Cells 2022; 11:cells11091404. [PMID: 35563711 PMCID: PMC9105757 DOI: 10.3390/cells11091404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Genome architecture, epigenetics and enhancer function control the fate and identity of cells. Reprogramming to induced pluripotent stem cells (iPSCs) changes the transcriptional profile and chromatin landscape of the starting somatic cell to that of the pluripotent cell in a stepwise manner. Changes in the regulatory networks are tightly regulated during normal embryonic development to determine cell fate, and similarly need to function in cell fate control during reprogramming. Switching off the somatic program and turning on the pluripotent program involves a dynamic reorganization of the epigenetic landscape, enhancer function, chromatin accessibility and 3D chromatin topology. Within this context, we will review here the current knowledge on the processes that control the establishment and maintenance of pluripotency during somatic cell reprogramming.
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Affiliation(s)
- Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
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Johnson AO, Fowler SB, Webster CI, Brown AJ, James DC. Bioinformatic Design of Dendritic Cell-Specific Synthetic Promoters. ACS Synth Biol 2022; 11:1613-1626. [PMID: 35389220 PMCID: PMC9016764 DOI: 10.1021/acssynbio.2c00027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Next-generation DNA vectors for cancer
immunotherapies and vaccine
development require promoters eliciting predefined transcriptional
activities specific to target cell types, such as dendritic cells
(DCs), which underpin immune response. In this study, we describe
the de novo design of DC-specific synthetic promoters via in silico assembly of cis-transcription
factor response elements (TFREs) that harness the DC transcriptional
landscape. Using computational genome mining approaches, candidate
TFREs were identified within promoter sequences of highly expressed
DC-specific genes or those exhibiting an upregulated expression during
DC maturation. Individual TFREs were then screened in vitro in a target DC line and off-target cell lines derived from skeletal
muscle, fibroblast, epithelial, and endothelial cells using homotypic
(TFRE repeats in series) reporter constructs. Based on these data,
a library of heterotypic promoter assemblies varying in the TFRE composition,
copy number, and sequential arrangement was constructed and tested in vitro to identify DC-specific promoters. Analysis of
the transcriptional activity and specificity of these promoters unraveled
underlying design rules, primarily TFRE composition, which govern
the DC-specific synthetic promoter activity. Using these design rules,
a second library of exclusively DC-specific promoters exhibiting varied
transcriptional activities was generated. All DC-specific synthetic
promoter assemblies exhibited >5-fold activity in the target DC
line
relative to off-target cell lines, with transcriptional activities
ranging from 8 to 67% of the nonspecific human cytomegalovirus (hCMV-IE1)
promoter. We show that bioinformatic analysis of a mammalian cell
transcriptional landscape is an effective strategy for de
novo design of cell-type-specific synthetic promoters with
precisely controllable transcriptional activities.
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Affiliation(s)
- Abayomi O. Johnson
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
- SynGenSys Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K
| | - Susan B. Fowler
- Antibody Discovery and Protein Engineering, R&D, AstraZeneca, Cambridge CB21 6GH, U.K
| | - Carl I. Webster
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB21 6GH, U.K
| | - Adam J. Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
- SynGenSys Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K
| | - David C. James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
- SynGenSys Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K
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Maeda T, Mandai M, Sugita S, Kime C, Takahashi M. Strategies of pluripotent stem cell-based therapy for retinal degeneration: update and challenges. Trends Mol Med 2022; 28:388-404. [DOI: 10.1016/j.molmed.2022.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
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Zhang S, Postnikov Y, Lobanov A, Furusawa T, Deng T, Bustin M. H3K27ac nucleosomes facilitate HMGN localization at regulatory sites to modulate chromatin binding of transcription factors. Commun Biol 2022; 5:159. [PMID: 35197580 PMCID: PMC8866397 DOI: 10.1038/s42003-022-03099-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Nucleosomes containing acetylated H3K27 are a major epigenetic mark of active chromatin and identify cell-type specific chromatin regulatory regions which serve as binding sites for transcription factors. Here we show that the ubiquitous nucleosome binding proteins HMGN1 and HMGN2 bind preferentially to H3K27ac nucleosomes at cell-type specific chromatin regulatory regions. HMGNs bind directly to the acetylated nucleosome; the H3K27ac residue and linker DNA facilitate the preferential binding of HMGNs to the modified nucleosomes. Loss of HMGNs increases the levels of H3K27me3 and the histone H1 occupancy at enhancers and promoters and alters the interaction of transcription factors with chromatin. These experiments indicate that the H3K27ac epigenetic mark enhances the interaction of architectural protein with chromatin regulatory sites and identify determinants that facilitate the localization of HMGN proteins at regulatory sites to modulate cell-type specific gene expression.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Maryland, MD, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
- Cell Translation Laboratory, NCATS, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA.
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Woogeng IN, Kaczkowski B, Abugessaisa I, Hu H, Tachibana A, Sahara Y, Hon CC, Hasegawa A, Sakai N, Nishida M, Sanyal H, Sho J, Kajita K, Kasukawa T, Takasato M, Carninci P, Maeda A, Mandai M, Arner E, Takahashi M, Kime C. Inducing human retinal pigment epithelium-like cells from somatic tissue. Stem Cell Reports 2022; 17:289-306. [PMID: 35030321 PMCID: PMC8828536 DOI: 10.1016/j.stemcr.2021.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/23/2022] Open
Abstract
Regenerative medicine relies on basic research outcomes that are only practical when cost effective. The human eyeball requires the retinal pigment epithelium (RPE) to interface the neural retina and the choroid at large. Millions of people suffer from age-related macular degeneration (AMD), a blinding multifactor genetic disease among RPE degradation pathologies. Recently, autologous pluripotent stem-cell-derived RPE cells were prohibitively expensive due to time; therefore, we developed a faster reprogramming system. We stably induced RPE-like cells (iRPE) from human fibroblasts (Fibs) by conditional overexpression of both broad plasticity and lineage-specific transcription factors (TFs). iRPE cells displayed critical RPE benchmarks and significant in vivo integration in transplanted retinas. Herein, we detail the iRPE system with comprehensive single-cell RNA sequencing (scRNA-seq) profiling to interpret and characterize its best cells. We anticipate that our system may enable robust retinal cell induction for basic research and affordable autologous human RPE tissue for regenerative cell therapy. Human Fibs reprogrammed to stable RPE-like cells Reprogramming factors selected for pioneering, plasticity, lineage, and target cell Nicotinamide (NIC) and Chetomin (CTM) improved the reprogramming outcomes scRNA-seq analysis identifies high-quality subpopulation resembling model cells
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Affiliation(s)
| | | | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Haiming Hu
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | | | - Yoshiki Sahara
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Renal and Cardiovascular Research, New Drug Research Division, Otsuka Pharmaceutical Co. Ltd., Tokushima 771-0192, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Noriko Sakai
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | | | - Hashimita Sanyal
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Junki Sho
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Keisuke Kajita
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Minoru Takasato
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Human Technopole, Via Rita Levi Montalcini 1, Milan, Italy
| | - Akiko Maeda
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Michiko Mandai
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masayo Takahashi
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Cody Kime
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
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Ali M, Ribeiro MM, Del Sol A. Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Research. Methods Mol Biol 2022; 2471:83-109. [PMID: 35175592 DOI: 10.1007/978-1-0716-2193-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The large-scale development of high-throughput sequencing technologies has not only allowed the generation of reliable omics data related to various regulatory layers but also the development of novel computational models in the field of stem cell research. These computational approaches have enabled the disentangling of a complex interplay between these interrelated layers of regulation by interpreting large quantities of biomedical data in a systematic way. In the context of stem cell research, network modeling of complex gene-gene interactions has been successfully used for understanding the mechanisms underlying stem cell differentiation and cellular conversion. Notably, it has proven helpful for predicting cell-fate determinants and signaling molecules controlling such processes. This chapter will provide an overview of various computational approaches that rely on single-cell and/or bulk RNA sequencing data for elucidating the molecular underpinnings of cell subpopulation identities, lineage specification, and the process of cell-fate decisions. Furthermore, we discuss how these computational methods provide the right framework for computational modeling of biological systems in order to address long-standing challenges in the stem cell field by guiding experimental efforts in stem cell research and regenerative medicine.
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Affiliation(s)
- Muhammad Ali
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Mariana Messias Ribeiro
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
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Tran A, Yang P, Yang JYH, Ormerod J. OUP accepted manuscript. Brief Funct Genomics 2022; 21:270-279. [PMID: 35411370 PMCID: PMC9328023 DOI: 10.1093/bfgp/elac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
Abstract
Recent advances in direct cell reprogramming have made possible the conversion of one cell type to another cell type, offering a potential cell-based treatment to many major diseases. Despite much attention, substantial roadblocks remain including the inefficiency in the proportion of reprogrammed cells of current experiments, and the requirement of a significant amount of time and resources. To this end, several computational algorithms have been developed with the goal of guiding the hypotheses to be experimentally validated. These approaches can be broadly categorized into two main types: transcription factor identification methods which aim to identify candidate transcription factors for a desired cell conversion, and transcription factor perturbation methods which aim to simulate the effect of a transcription factor perturbation on a cell state. The transcription factor perturbation methods can be broken down into Boolean networks, dynamical systems and regression models. We summarize the contributions and limitations of each method and discuss the innovation that single cell technologies are bringing to these approaches and we provide a perspective on the future direction of this field.
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Affiliation(s)
- Andy Tran
- School of Mathematics and Statistics, The University of Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, NSW, Australia
| | | | | | - John Ormerod
- Corresponding author: John Ormerod, School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW 2006, Australia. Tel.: +61293515787; Fax: +61293514534; E-mail:
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Martinez-Ruíz GU, Morales-Sánchez A, Bhandoola A. Transcriptional and epigenetic regulation in thymic epithelial cells. Immunol Rev 2022; 305:43-58. [PMID: 34750841 PMCID: PMC8766885 DOI: 10.1111/imr.13034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/03/2023]
Abstract
The thymus is required for the development of both adaptive and innate-like T cell subsets. There is keen interest in manipulating thymic function for therapeutic purposes in circumstances of autoimmunity, immunodeficiency, and for purposes of immunotherapy. Within the thymus, thymic epithelial cells play essential roles in directing T cell development. Several transcription factors are known to be essential for thymic epithelial cell development and function, and a few transcription factors have been studied in considerable detail. However, the role of many other transcription factors is less well understood. Further, it is likely that roles exist for other transcription factors not yet known to be important in thymic epithelial cells. Recent progress in understanding of thymic epithelial cell heterogeneity has provided some new insight into transcriptional requirements in subtypes of thymic epithelial cells. However, it is unknown whether progenitors of thymic epithelial cells exist in the adult thymus, and consequently, developmental relationships linking putative precursors with differentiated cell types are poorly understood. While we do not presently possess a clear understanding of stage-specific requirements for transcription factors in thymic epithelial cells, new single-cell transcriptomic and epigenomic technologies should enable rapid progress in this field. Here, we review our current knowledge of transcription factors involved in the development, maintenance, and function of thymic epithelial cells, and the mechanisms by which they act.
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Affiliation(s)
- Gustavo Ulises Martinez-Ruíz
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Research Division, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
- Children’s Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Abigail Morales-Sánchez
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Children’s Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Reddy J, Fonseca MAS, Corona RI, Nameki R, Segato Dezem F, Klein IA, Chang H, Chaves-Moreira D, Afeyan LK, Malta TM, Lin X, Abbasi F, Font-Tello A, Sabedot T, Cejas P, Rodríguez-Malavé N, Seo JH, Lin DC, Matulonis U, Karlan BY, Gayther SA, Pasaniuc B, Gusev A, Noushmehr H, Long H, Freedman ML, Drapkin R, Young RA, Abraham BJ, Lawrenson K. Predicting master transcription factors from pan-cancer expression data. SCIENCE ADVANCES 2021; 7:eabf6123. [PMID: 34818047 PMCID: PMC8612691 DOI: 10.1126/sciadv.abf6123] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.
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Affiliation(s)
- Jessica Reddy
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Marcos A. S. Fonseca
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Rosario I. Corona
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robbin Nameki
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Felipe Segato Dezem
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Isaac A. Klein
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
| | - Heidi Chang
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | | | - Lena K. Afeyan
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of
Technology, Cambridge, MA, USA
| | | | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Forough Abbasi
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | | | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Norma Rodríguez-Malavé
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | - Ursula Matulonis
- Division of Gynecologic Oncology, Dana Farber
Cancer Institute, Boston, MA, USA
| | - Beth Y. Karlan
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Cancer Population Genetics, Jonsson Comprehensive
Cancer Center, David Geffen School of Medicine, University of California, Los
Angeles, Los Angeles, CA, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program,
University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School
of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine,
David Geffen School of Medicine, University of California, Los Angeles, Los
Angeles, CA, USA
- Department of Computational Medicine, David Geffen
School of Medicine, University of California, Los Angeles, Los Angeles, CA,
USA
| | - Alexander Gusev
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- McGraw/Patterson Center for Population Sciences,
Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge,
MA, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of
Pennsylvania, Philadelphia, PA, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, M.I.T., Cambridge, MA,
USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude
Children’s Research Hospital, Memphis, TN, USA
- Corresponding author.
(B.J.A.);
(K.L.)
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Corresponding author.
(B.J.A.);
(K.L.)
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40
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Wang J, Liu C, Chen Y, Wang W. Taiji-reprogram: a framework to uncover cell-type specific regulators and predict cellular reprogramming cocktails. NAR Genom Bioinform 2021; 3:lqab100. [PMID: 34761218 PMCID: PMC8573821 DOI: 10.1093/nargab/lqab100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 12/21/2022] Open
Abstract
Cellular reprogramming is a promising technology to develop disease models and cell-based therapies. Identification of the key regulators defining the cell type specificity is pivotal to devising reprogramming cocktails for successful cell conversion but remains a great challenge. Here, we present a systems biology approach called Taiji-reprogram to efficiently uncover transcription factor (TF) combinations for conversion between 154 diverse cell types or tissues. This method integrates the transcriptomic and epigenomic data to construct cell-type specific genetic networks and assess the global importance of TFs in the network. Comparative analysis across cell types revealed TFs that are specifically important in a particular cell type and often tightly associated with cell-type specific functions. A systematic search of TFs with differential importance in the source and target cell types uncovered TF combinations for desired cell conversion. We have shown that Taiji-reprogram outperformed the existing methods to better recover the TFs in the experimentally validated reprogramming cocktails. This work not only provides a comprehensive catalog of TFs defining cell specialization but also suggests TF combinations for direct cell conversion.
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Affiliation(s)
- Jun Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Cong Liu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Yue Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
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41
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Li B, Hon GC. Single-Cell Genomics: Catalyst for Cell Fate Engineering. Front Bioeng Biotechnol 2021; 9:748942. [PMID: 34733831 PMCID: PMC8558416 DOI: 10.3389/fbioe.2021.748942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
As we near a complete catalog of mammalian cell types, the capability to engineer specific cell types on demand would transform biomedical research and regenerative medicine. However, the current pace of discovering new cell types far outstrips our ability to engineer them. One attractive strategy for cellular engineering is direct reprogramming, where induction of specific transcription factor (TF) cocktails orchestrates cell state transitions. Here, we review the foundational studies of TF-mediated reprogramming in the context of a general framework for cell fate engineering, which consists of: discovering new reprogramming cocktails, assessing engineered cells, and revealing molecular mechanisms. Traditional bulk reprogramming methods established a strong foundation for TF-mediated reprogramming, but were limited by their small scale and difficulty resolving cellular heterogeneity. Recently, single-cell technologies have overcome these challenges to rapidly accelerate progress in cell fate engineering. In the next decade, we anticipate that these tools will enable unprecedented control of cell state.
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Affiliation(s)
- Boxun Li
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Gary C. Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, United States
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42
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Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A. Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell Syst 2021; 12:885-899.e8. [PMID: 34352221 PMCID: PMC8522198 DOI: 10.1016/j.cels.2021.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/27/2020] [Accepted: 07/09/2021] [Indexed: 02/07/2023]
Abstract
Identifying the particular transcription factors that maintain cell type in vitro is important for manipulating cell type. Identifying such transcription factors by their cell-type-specific expression or their involvement in developmental regulation has had limited success. We hypothesized that because cell type is often resilient to perturbations, the transcriptional response to perturbations would reveal identity-maintaining transcription factors. We developed perturbation panel profiling (P3) as a framework for perturbing cells across many conditions and measuring gene expression responsiveness transcriptome-wide. In human iPSC-derived cardiac myocytes, P3 showed that transcription factors important for cardiac myocyte differentiation and maintenance were among the most frequently upregulated (most responsive). We reasoned that one function of responsive genes may be to maintain cellular identity. We identified responsive transcription factors in fibroblasts using P3 and found that suppressing their expression led to enhanced reprogramming. We propose that responsiveness to perturbations is a property of transcription factors that help maintain cellular identity in vitro. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Ian A Mellis
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Genomics and Computational Biology Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hailey I Edelstein
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel Truitt
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yogesh Goyal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren E Beck
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Orsolya Symmons
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Margaret C Dunagin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Ricardo A Linares Saldana
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Parisha P Shah
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Arun Padmanabhan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wenli Yang
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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43
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Xu Q, Georgiou G, Frölich S, van der Sande M, Veenstra G, Zhou H, van Heeringen S. ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination. Nucleic Acids Res 2021; 49:7966-7985. [PMID: 34244796 PMCID: PMC8373078 DOI: 10.1093/nar/gkab598] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Proper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors. However, experimental elucidation of key transcription factors that drive cellular identity is currently often intractable. Here, we present ANANSE (ANalysis Algorithm for Networks Specified by Enhancers), a network-based method that exploits enhancer-encoded regulatory information to identify the key transcription factors in cell fate determination. As cell type-specific transcription factors predominantly bind to enhancers, we use regulatory networks based on enhancer properties to prioritize transcription factors. First, we predict genome-wide binding profiles of transcription factors in various cell types using enhancer activity and transcription factor binding motifs. Subsequently, applying these inferred binding profiles, we construct cell type-specific gene regulatory networks, and then predict key transcription factors controlling cell fate transitions using differential networks between cell types. This method outperforms existing approaches in correctly predicting major transcription factors previously identified to be sufficient for trans-differentiation. Finally, we apply ANANSE to define an atlas of key transcription factors in 18 normal human tissues. In conclusion, we present a ready-to-implement computational tool for efficient prediction of transcription factors in cell fate determination and to study transcription factor-mediated regulatory mechanisms. ANANSE is freely available at https://github.com/vanheeringen-lab/ANANSE.
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Affiliation(s)
- Quan Xu
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Georgios Georgiou
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Siebren Frölich
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Maarten van der Sande
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Huiqing Zhou
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
- Radboud University Medical Center, Department of Human Genetics, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
| | - Simon J van Heeringen
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6525GA Nijmegen, The Netherlands
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44
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Zou M, Duren Z, Yuan Q, Li H, Hutchins AP, Wong WH, Wang Y. MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting. Brief Bioinform 2021; 22:6309927. [PMID: 34180954 PMCID: PMC8575015 DOI: 10.1093/bib/bbab235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 11/14/2022] Open
Abstract
Multi-omics data allow us to select a small set of informative markers for the discrimination of specific cell types and study of cellular heterogeneity. However, it is often challenging to choose an optimal marker panel from the high-dimensional molecular profiles for a large amount of cell types. Here, we propose a method called Mixed Integer programming Model to Identify Cell type-specific marker panel (MIMIC). MIMIC maintains the hierarchical topology among different cell types and simultaneously maximizes the specificity of a fixed number of selected markers. MIMIC was benchmarked on the mouse ENCODE RNA-seq dataset, with 29 diverse tissues, for 43 surface markers (SMs) and 1345 transcription factors (TFs). MIMIC could select biologically meaningful markers and is robust for different accuracy criteria. It shows advantages over the standard single gene-based approaches and widely used dimensional reduction methods, such as multidimensional scaling and t-SNE, both in accuracy and in biological interpretation. Furthermore, the combination of SMs and TFs achieves better specificity than SMs or TFs alone. Applying MIMIC to a large collection of 641 RNA-seq samples covering 231 cell types identifies a panel of TFs and SMs that reveal the modularity of cell type association networks. Finally, the scalability of MIMIC is demonstrated by selecting enhancer markers from mouse ENCODE data. MIMIC is freely available at https://github.com/MengZou1/MIMIC.
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Affiliation(s)
- Meng Zou
- Department of Mathematics, Huazhong University of Science and Technology, Beijing 100190, China
| | - Zhana Duren
- Department of Genetics and Biochemistry, Clemson University, Beijing 100190, China
| | - Qiuyue Yuan
- Academy of Mathematics and Systems Science, CAS, Beijing 100190, China
| | - Henry Li
- Department of Health Research & Policy, Bio-X Program Stanford University, Beijing 100190, China
| | | | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program Stanford University, Beijing 100190, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, CAS, Beijing 100190, China
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45
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Lago S, Nadai M, Cernilogar FM, Kazerani M, Domíniguez Moreno H, Schotta G, Richter SN. Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome. Nat Commun 2021; 12:3885. [PMID: 34162892 PMCID: PMC8222265 DOI: 10.1038/s41467-021-24198-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
Cell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity. By G4-ChIP-seq/RNA-seq analysis on liposarcoma cells we confirmed that G4s in promoters are invariably associated with high transcription levels in open chromatin. Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different G4-folding state: high transcript levels consistently associated with G4-folding. Transcription factors AP-1 and SP1, whose binding sites were the most significantly represented in G4-folded sequences, coimmunoprecipitated with their G4-folded promoters. Thus, G4s and their associated transcription factors cooperate to determine cell-specific transcriptional programs, making G4s to strongly emerge as new epigenetic regulators of the transcription machinery.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Maryam Kazerani
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Helena Domíniguez Moreno
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy.
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46
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Deng CC, Hu YF, Zhu DH, Cheng Q, Gu JJ, Feng QL, Zhang LX, Xu YP, Wang D, Rong Z, Yang B. Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymal fibroblasts in human fibrotic skin diseases. Nat Commun 2021; 12:3709. [PMID: 34140509 PMCID: PMC8211847 DOI: 10.1038/s41467-021-24110-y] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Fibrotic skin disease represents a major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix. Fibroblasts are found to be heterogeneous in multiple fibrotic diseases, but fibroblast heterogeneity in fibrotic skin diseases is not well characterized. In this study, we explore fibroblast heterogeneity in keloid, a paradigm of fibrotic skin diseases, by using single-cell RNA-seq. Our results indicate that keloid fibroblasts can be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory. Interestingly, the percentage of mesenchymal fibroblast subpopulation is significantly increased in keloid compared to normal scar. Functional studies indicate that mesenchymal fibroblasts are crucial for collagen overexpression in keloid. Increased mesenchymal fibroblast subpopulation is also found in another fibrotic skin disease, scleroderma, suggesting this is a broad mechanism for skin fibrosis. These findings will help us better understand skin fibrotic pathogenesis, and provide potential targets for fibrotic disease therapies.
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Affiliation(s)
- Cheng-Cheng Deng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yong-Fei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ding-Heng Zhu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Qing Cheng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jing-Jing Gu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Qing-Lan Feng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Li-Xue Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Ying-Ping Xu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhili Rong
- Dermatology Hospital, Southern Medical University, Guangzhou, China.
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Guangzhou, China.
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China.
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47
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Almeida N, Chung MWH, Drudi EM, Engquist EN, Hamrud E, Isaacson A, Tsang VSK, Watt FM, Spagnoli FM. Employing core regulatory circuits to define cell identity. EMBO J 2021; 40:e106785. [PMID: 33934382 PMCID: PMC8126924 DOI: 10.15252/embj.2020106785] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
The interplay between extrinsic signaling and downstream gene networks controls the establishment of cell identity during development and its maintenance in adult life. Advances in next-generation sequencing and single-cell technologies have revealed additional layers of complexity in cell identity. Here, we review our current understanding of transcription factor (TF) networks as key determinants of cell identity. We discuss the concept of the core regulatory circuit as a set of TFs and interacting factors that together define the gene expression profile of the cell. We propose the core regulatory circuit as a comprehensive conceptual framework for defining cellular identity and discuss its connections to cell function in different contexts.
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Affiliation(s)
- Nathalia Almeida
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Matthew W H Chung
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Elena M Drudi
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Elise N Engquist
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Eva Hamrud
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Abigail Isaacson
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Victoria S K Tsang
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Francesca M Spagnoli
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
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48
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Feng Z, Duren Z, Xiong Z, Wang S, Liu F, Wong WH, Wang Y. hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context. Commun Biol 2021; 4:442. [PMID: 33824393 PMCID: PMC8024315 DOI: 10.1038/s42003-021-01970-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
Cranial Neural Crest Cells (CNCC) originate at the cephalic region from forebrain, midbrain and hindbrain, migrate into the developing craniofacial region, and subsequently differentiate into multiple cell types. The entire specification, delamination, migration, and differentiation process is highly regulated and abnormalities during this craniofacial development cause birth defects. To better understand the molecular networks underlying CNCC, we integrate paired gene expression & chromatin accessibility data and reconstruct the genome-wide human Regulatory network of CNCC (hReg-CNCC). Consensus optimization predicts high-quality regulations and reveals the architecture of upstream, core, and downstream transcription factors that are associated with functions of neural plate border, specification, and migration. hReg-CNCC allows us to annotate genetic variants of human facial GWAS and disease traits with associated cis-regulatory modules, transcription factors, and target genes. For example, we reveal the distal and combinatorial regulation of multiple SNPs to core TF ALX1 and associations to facial distances and cranial rare disease. In addition, hReg-CNCC connects the DNA sequence differences in evolution, such as ultra-conserved elements and human accelerated regions, with gene expression and phenotype. hReg-CNCC provides a valuable resource to interpret genetic variants as early as gastrulation during embryonic development. The network resources are available at https://github.com/AMSSwanglab/hReg-CNCC .
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Affiliation(s)
- Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China.,School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhana Duren
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA.,Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA, USA
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Sijia Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China.
| | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA, USA.
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China. .,School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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49
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Ng AHM, Khoshakhlagh P, Rojo Arias JE, Pasquini G, Wang K, Swiersy A, Shipman SL, Appleton E, Kiaee K, Kohman RE, Vernet A, Dysart M, Leeper K, Saylor W, Huang JY, Graveline A, Taipale J, Hill DE, Vidal M, Melero-Martin JM, Busskamp V, Church GM. A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol 2021; 39:510-519. [PMID: 33257861 PMCID: PMC7610615 DOI: 10.1038/s41587-020-0742-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 10/19/2020] [Indexed: 02/06/2023]
Abstract
Human pluripotent stem cells (hPSCs) offer an unprecedented opportunity to model diverse cell types and tissues. To enable systematic exploration of the programming landscape mediated by transcription factors (TFs), we present the Human TFome, a comprehensive library containing 1,564 TF genes and 1,732 TF splice isoforms. By screening the library in three hPSC lines, we discovered 290 TFs, including 241 that were previously unreported, that induce differentiation in 4 days without alteration of external soluble or biomechanical cues. We used four of the hits to program hPSCs into neurons, fibroblasts, oligodendrocytes and vascular endothelial-like cells that have molecular and functional similarity to primary cells. Our cell-autonomous approach enabled parallel programming of hPSCs into multiple cell types simultaneously. We also demonstrated orthogonal programming by including oligodendrocyte-inducible hPSCs with unmodified hPSCs to generate cerebral organoids, which expedited in situ myelination. Large-scale combinatorial screening of the Human TFome will complement other strategies for cell engineering based on developmental biology and computational systems biology.
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Affiliation(s)
- Alex H M Ng
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Parastoo Khoshakhlagh
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Jesus Eduardo Rojo Arias
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Giovanni Pasquini
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - Kai Wang
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Anka Swiersy
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - Seth L Shipman
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Evan Appleton
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Kiavash Kiaee
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- GC Therapeutics, Inc, Cambridge, MA, USA
| | - Richie E Kohman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Andyna Vernet
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Matthew Dysart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Kathleen Leeper
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Wren Saylor
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Jeremy Y Huang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Amanda Graveline
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - David E Hill
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marc Vidal
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Juan M Melero-Martin
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Volker Busskamp
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany.
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany.
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- GC Therapeutics, Inc, Cambridge, MA, USA.
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50
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Baca SC, Takeda DY, Seo JH, Hwang J, Ku SY, Arafeh R, Arnoff T, Agarwal S, Bell C, O'Connor E, Qiu X, Alaiwi SA, Corona RI, Fonseca MAS, Giambartolomei C, Cejas P, Lim K, He M, Sheahan A, Nassar A, Berchuck JE, Brown L, Nguyen HM, Coleman IM, Kaipainen A, De Sarkar N, Nelson PS, Morrissey C, Korthauer K, Pomerantz MM, Ellis L, Pasaniuc B, Lawrenson K, Kelly K, Zoubeidi A, Hahn WC, Beltran H, Long HW, Brown M, Corey E, Freedman ML. Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer. Nat Commun 2021; 12:1979. [PMID: 33785741 PMCID: PMC8010057 DOI: 10.1038/s41467-021-22139-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is the development of neuroendocrine prostate cancer (NEPC) after treatment of prostate adenocarcinoma (PRAD) with inhibitors of androgen signaling. NEPC is an aggressive variant of prostate cancer that aberrantly expresses genes characteristic of neuroendocrine (NE) tissues and no longer depends on androgens. Here, we investigate the epigenomic basis of this resistance mechanism by profiling histone modifications in NEPC and PRAD patient-derived xenografts (PDXs) using chromatin immunoprecipitation and sequencing (ChIP-seq). We identify a vast network of cis-regulatory elements (N~15,000) that are recurrently activated in NEPC. The FOXA1 transcription factor (TF), which pioneers androgen receptor (AR) chromatin binding in the prostate epithelium, is reprogrammed to NE-specific regulatory elements in NEPC. Despite loss of dependence upon AR, NEPC maintains FOXA1 expression and requires FOXA1 for proliferation and expression of NE lineage-defining genes. Ectopic expression of the NE lineage TFs ASCL1 and NKX2-1 in PRAD cells reprograms FOXA1 to bind to NE regulatory elements and induces enhancer activity as evidenced by histone modifications at these sites. Our data establish the importance of FOXA1 in NEPC and provide a principled approach to identifying cancer dependencies through epigenomic profiling.
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Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Y Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Justin Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sheng Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rand Arafeh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Taylor Arnoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Supreet Agarwal
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rosario I Corona
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcos A S Fonseca
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Istituto Italiano di Tecnologia, Genova, Italy
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anjali Sheahan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin Nassar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa M Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Arja Kaipainen
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Keegan Korthauer
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leigh Ellis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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