1
|
Rouleau M, Villeneuve L, Allain EP, McCabe-Leroux J, Tremblay S, Nguyen Van Long F, Uchil A, Joly-Beauparlant C, Droit A, Guillemette C. Non-canonical transcriptional regulation of the poor prognostic factor UGT2B17 in chronic lymphocytic leukemic and normal B cells. BMC Cancer 2024; 24:410. [PMID: 38566115 PMCID: PMC10985967 DOI: 10.1186/s12885-024-12143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND High expression of the glycosyltransferase UGT2B17 represents an independent adverse prognostic marker in chronic lymphocytic leukemia (CLL). It also constitutes a predictive marker for therapeutic response and a drug resistance mechanism. The key determinants driving expression of the UGT2B17 gene in normal and leukemic B-cells remain undefined. The UGT2B17 transcriptome is complex and is comprised of at least 10 alternative transcripts, identified by previous RNA-sequencing of liver and intestine. We hypothesized that the transcriptional program regulating UGT2B17 in B-lymphocytes is distinct from the canonical expression previously characterized in the liver. RESULTS RNA-sequencing and genomics data revealed a specific genomic landscape at the UGT2B17 locus in normal and leukemic B-cells. RNA-sequencing and quantitative PCR data indicated that the UGT2B17 enzyme is solely encoded by alternative transcripts expressed in CLL patient cells and not by the canonical transcript widely expressed in the liver and intestine. Chromatin accessible regions (ATAC-Seq) in CLL cells mapped with alternative promoters and non-coding exons, which may be derived from endogenous retrotransposon elements. By luciferase reporter assays, we identified key cis-regulatory STAT3, RELA and interferon regulatory factor (IRF) binding sequences driving the expression of UGT2B17 in lymphoblastoid and leukemic B-cells. Electrophoretic mobility shift assays and pharmacological inhibition demonstrated key roles for the CLL prosurvival transcription factors STAT3 and NF-κB in the leukemic expression of UGT2B17. CONCLUSIONS UGT2B17 expression in B-CLL is driven by key regulators of CLL progression. Our data suggest that a NF-κB/STAT3/IRF/UGT2B17 axis may represent a novel B-cell pathway promoting disease progression and drug resistance.
Collapse
Affiliation(s)
- Michèle Rouleau
- Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center - Université Laval (CRCHUQc- UL), Université Laval, Québec, QC, Canada
- Cancer research center of Université Laval, Québec, Canada
| | - Lyne Villeneuve
- Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center - Université Laval (CRCHUQc- UL), Université Laval, Québec, QC, Canada
- Cancer research center of Université Laval, Québec, Canada
| | - Eric P Allain
- Molecular Genetics Laboratory, Vitalité Health Network, Dr. Georges-L.-Dumont University Hospital Center, Moncton, NB, Canada
| | - Jules McCabe-Leroux
- Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center - Université Laval (CRCHUQc- UL), Université Laval, Québec, QC, Canada
- Cancer research center of Université Laval, Québec, Canada
| | - Sophie Tremblay
- Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center - Université Laval (CRCHUQc- UL), Université Laval, Québec, QC, Canada
- Cancer research center of Université Laval, Québec, Canada
| | - Flora Nguyen Van Long
- Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center - Université Laval (CRCHUQc- UL), Université Laval, Québec, QC, Canada
- Cancer research center of Université Laval, Québec, Canada
| | - Ashwini Uchil
- Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center - Université Laval (CRCHUQc- UL), Université Laval, Québec, QC, Canada
- Cancer research center of Université Laval, Québec, Canada
| | - Charles Joly-Beauparlant
- Cancer research center of Université Laval, Québec, Canada
- CRCHUQc-UL and Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Arnaud Droit
- Cancer research center of Université Laval, Québec, Canada
- CRCHUQc-UL and Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Chantal Guillemette
- Faculty of Pharmacy, Centre Hospitalier Universitaire de Québec Research Center - Université Laval (CRCHUQc- UL), Université Laval, Québec, QC, Canada.
- Cancer research center of Université Laval, Québec, Canada.
- Canada Research Chair in Pharmacogenomics, Faculty of Pharmacy, Université Laval, Québec, QC, Canada.
| |
Collapse
|
2
|
Lammers S, Barrera V, Brennecke P, Miller C, Yoon J, Balolong J, Anderson MS, Ho Sui S, Steinmetz LM, von Andrian UH, Rattay K. Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development. Front Immunol 2024; 14:1277365. [PMID: 38420512 PMCID: PMC10901246 DOI: 10.3389/fimmu.2023.1277365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/29/2023] [Indexed: 03/02/2024] Open
Abstract
Thymic epithelial cells are indispensable for T cell maturation and selection and the induction of central immune tolerance. The self-peptide repertoire expressed by medullary thymic epithelial cells is in part regulated by the transcriptional regulator Aire (Autoimmune regulator) and the transcription factor Fezf2. Due to the high complexity of mTEC maturation stages (i.e., post-Aire, Krt10+ mTECs, and Dclk1+ Tuft mTECs) and the heterogeneity in their gene expression profiles (i.e., mosaic expression patterns), it has been challenging to identify the additional factors complementing the transcriptional regulation. We aimed to identify the transcriptional regulators involved in the regulation of mTEC development and self-peptide expression in an unbiased and genome-wide manner. We used ATAC footprinting analysis as an indirect approach to identify transcription factors involved in the gene expression regulation in mTECs, which we validated by ChIP sequencing. This study identifies Fezf2 as a regulator of the recently described thymic Tuft cells (i.e., Tuft mTECs). Furthermore, we identify that transcriptional regulators of the ELF, ESE, ERF, and PEA3 subfamily of the ETS transcription factor family and members of the Krüppel-like family of transcription factors play a role in the transcriptional regulation of genes involved in late mTEC development and promiscuous gene expression.
Collapse
Affiliation(s)
- Sören Lammers
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Victor Barrera
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Philip Brennecke
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
| | - Corey Miller
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Joon Yoon
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Jared Balolong
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Shannan Ho Sui
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lars M. Steinmetz
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ulrich H. von Andrian
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Kristin Rattay
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- Pharmacological Institute, Biochemical Pharmacological Center, University of Marburg, Marburg, Germany
| |
Collapse
|
3
|
Maiques-Diaz A, Martin-Subero JI. Biological, prognostic, and therapeutic impact of the epigenome in CLL. Semin Hematol 2023:S0037-1963(23)00092-6. [PMID: 38151379 DOI: 10.1053/j.seminhematol.2023.11.005] [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: 11/06/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by widespread alterations in the genetic and epigenetic landscapes which seem to underlie the variable clinical manifestations observed in patients. Over the last decade, epigenomic studies have described the whole-genome maps of DNA methylation and chromatin features of CLL and normal B cells, identifying distinct epigenetic mechanisms operating in tumoral cells. DNA methylation analyses have identified that the CLL methylome contains imprints of the cell of origin, as well as of the proliferative history of the tumor cells, with both being strong independent prognostic predictors. Moreover, single-cell analysis revealed a higher degree of DNA methylation noise in CLL cells, which associates with transcriptional plasticity and disease aggressiveness. Integrative analysis of chromatin has uncovered chromatin signatures, as well as regulatory regions specifically active in each CLL subtype or in Richter transformed samples. Unique transcription factor (TF) binding motifs are overrepresented on those regions, suggesting that altered TF networks operate from disease initiation to progression as nongenetic factors mediating the oncogenic transcriptional profiles. Multiomics analysis has identified that response to treatment is modulated by an epigenetic imprint, and that treatments affect chromatin through the activity of particular set of TFs. Additionally, the epigenome is an axis of therapeutic vulnerability in CLL, as it can be targeted by inhibitors of histone modifying enzymes, that have shown promising preclinical results. Altogether, this review aims at summarizing the major findings derived from published literature to distill how altered epigenomic mechanisms contribute to CLL origin, evolution, clinical behavior, and response to treatment.
Collapse
Affiliation(s)
- Alba Maiques-Diaz
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-Subero
- Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.
| |
Collapse
|
4
|
Wang H, Sun H, Liang B, Zhang F, Yang F, Cui B, Ding L, Wang X, Wang R, Cai J, Tang Y, Rao J, Hu W, Zhao S, Wu W, Chen X, Wu K, Lai J, Xie Y, Li B, Tang J, Shen S, Liu Y. Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia. Nat Commun 2023; 14:6792. [PMID: 37880218 PMCID: PMC10600232 DOI: 10.1038/s41467-023-42565-z] [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: 03/03/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
For around half of the pediatric B-lineage acute lymphoblastic leukemia (B-ALL) patients, the molecular mechanism of relapse remains unclear. To fill this gap in knowledge, here we characterize the chromatin accessibility landscape in pediatric relapsed B-ALL. We observe rewired accessible chromatin regions (ACRs) associated with transcription dysregulation in leukemia cells as compared with normal B-cell progenitors. We show that over a quarter of the ACRs in B-ALL are in quiescent regions with high heterogeneity among B-ALLs. We identify subtype-specific and allele-imbalanced chromatin accessibility by integrating multi-omics data. By characterizing the differential ACRs between diagnosis and relapse in B-ALL, we identify alterations in chromatin accessibility during drug treatment. Further analysis of ACRs associated with relapse free survival leads to the identification of a subgroup of B-ALL which show early relapse. These data provide an advanced and integrative portrait of the importance of chromatin accessibility alterations in tumorigenesis and drug responses.
Collapse
Affiliation(s)
- Han Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huiying Sun
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bilin Liang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Zhang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Wang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ronghua Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaoyang Cai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjing Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianan Rao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Hu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuang Zhao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Wu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxiao Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kefei Wu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junchen Lai
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangyang Xie
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyan Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou, China.
| |
Collapse
|
5
|
Zhang D, Zhu Y, Ju Y, Zhang H, Zou X, She S, Zhu D, Guan Y. TEAD4 antagonizes cellular senescence by remodeling chromatin accessibility at enhancer regions. Cell Mol Life Sci 2023; 80:330. [PMID: 37856006 PMCID: PMC10587282 DOI: 10.1007/s00018-023-04980-9] [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: 05/10/2023] [Revised: 09/23/2023] [Accepted: 09/23/2023] [Indexed: 10/20/2023]
Abstract
Dramatic alterations in epigenetic landscapes are known to impact genome accessibility and transcription. Extensive evidence demonstrates that senescent cells undergo significant changes in chromatin structure; however, the mechanisms underlying the crosstalk between epigenetic parameters and gene expression profiles have not been fully elucidated. In the present study, we delineate the genome-wide redistribution of accessible chromatin regions that lead to broad transcriptome effects during senescence. We report that distinct senescence-activated accessibility regions (SAAs) are always distributed in H3K27ac-occupied enhancer regions, where they are responsible for elevated flanking senescence-associated secretory phenotype (SASP) expression and aberrant cellular signaling relevant to SASP secretion. Mechanistically, a single transcription factor, TEAD4, moves away from H3K27ac-labled SAAs to allow for prominent chromatin accessibility reconstruction during senescence. The enhanced SAAs signal driven by TEAD4 suppression subsequently induces a robust increase in the expression of adjacent SASP genes and the secretion of downstream factors, which contribute to the progression of senescence. Our findings illustrate a dynamic landscape of chromatin accessibility following senescence entry, and further reveal an insightful function for TEAD4 in regulating the broad chromatin state that modulates the overall transcriptional program of SASP genes.
Collapse
Affiliation(s)
- Donghui Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang, 524045, People's Republic of China
| | - Yanmei Zhu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang, 524045, People's Republic of China
| | - Yanmin Ju
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Hongyong Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang, 524045, People's Republic of China
| | - Xiaopeng Zou
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang, 524045, People's Republic of China
| | - Shangrong She
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Danping Zhu
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Yiting Guan
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang, 524045, People's Republic of China.
| |
Collapse
|
6
|
Piroeva KV, McDonald C, Xanthopoulos C, Fox C, Clarkson CT, Mallm JP, Vainshtein Y, Ruje L, Klett LC, Stilgenbauer S, Mertens D, Kostareli E, Rippe K, Teif VB. Nucleosome repositioning in chronic lymphocytic leukemia. Genome Res 2023; 33:1649-1661. [PMID: 37699659 PMCID: PMC10691546 DOI: 10.1101/gr.277298.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/07/2023] [Indexed: 09/14/2023]
Abstract
The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we conducted a genome-wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant changes of nucleosome positioning in CLL. Globally, the spacing between nucleosomes-the nucleosome repeat length (NRL)-is shortened in CLL. This effect is stronger in the more aggressive IGHV-unmutated CLL subtype than in the IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF as well as immune response-related transcription factors and delineated mechanisms of epigenetic deregulation. The principal component analysis of nucleosome occupancy in cancer-specific regions allowed the classification of samples between cancer subtypes and normal controls. Furthermore, patients could be better assigned to CLL subtypes according to differential nucleosome occupancy than based on DNA methylation or gene expression. Thus, nucleosome positioning constitutes a novel readout to dissect molecular mechanisms of disease progression and to stratify patients. Furthermore, we anticipate that the global nucleosome repositioning detected in our study, such as changes in the NRL, can be exploited for liquid biopsy applications based on cell-free DNA to stratify patients and monitor disease progression.
Collapse
Affiliation(s)
- Kristan V Piroeva
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Charlotte McDonald
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Charalampos Xanthopoulos
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom
| | - Chelsea Fox
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Christopher T Clarkson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Jan-Philipp Mallm
- German Cancer Research Center (DKFZ) Heidelberg, Single Cell Open Lab, 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Yevhen Vainshtein
- Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB, 70569 Stuttgart, Germany
| | - Luminita Ruje
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Lara C Klett
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Stephan Stilgenbauer
- Division of CLL, University Hospital Ulm, Department of Internal Medicine III, 89081 Ulm, Germany
| | - Daniel Mertens
- Division of CLL, University Hospital Ulm, Department of Internal Medicine III, 89081 Ulm, Germany
- German Cancer Research Center (DKFZ) Heidelberg, Cooperation Unit Mechanisms of Leukemogenesis, 69120 Heidelberg, Germany
| | - Efterpi Kostareli
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, United Kingdom;
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, 69120 Heidelberg, Germany;
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, 69120 Heidelberg, Germany
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom;
| |
Collapse
|
7
|
Zhang P, Wu H. IChrom-Deep: An Attention-Based Deep Learning Model for Identifying Chromatin Interactions. IEEE J Biomed Health Inform 2023; 27:4559-4568. [PMID: 37402191 DOI: 10.1109/jbhi.2023.3292299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Identification of chromatin interactions is crucial for advancing our knowledge of gene regulation. However, due to the limitations of high-throughput experimental techniques, there is an urgent need to develop computational methods for predicting chromatin interactions. In this study, we propose a novel attention-based deep learning model, termed IChrom-Deep, to identify chromatin interactions using sequence features and genomic features. The experimental results based on the datasets of three cell lines demonstrate that the IChrom-Deep achieves satisfactory performance and is superior to the previous methods. We also investigate the effect of DNA sequence and associated features and genomic features on chromatin interactions, and highlight the applicable scenarios of some features, such as sequence conservation and distance. Moreover, we identify a few genomic features that are extremely important across different cell lines, and IChrom-Deep achieves comparable performance with only these significant genomic features versus using all genomic features. It is believed that IChrom-Deep can serve as a useful tool for future studies that seek to identify chromatin interactions.
Collapse
|
8
|
Zhang D, Zhang C, Zhu Y, Xie H, Yue C, Li M, Wei W, Peng Y, Yin G, Guo Y, Guan Y. Recruitment of transcription factor ETS1 to activated accessible regions promotes the transcriptional program of cilia genes. Nucleic Acids Res 2023:gkad506. [PMID: 37326025 PMCID: PMC10359609 DOI: 10.1093/nar/gkad506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Defects in cilia genes, which are critical for cilia formation and function, can cause complicated ciliopathy syndromes involving multiple organs and tissues; however, the underlying regulatory mechanisms of the networks of cilia genes in ciliopathies remain enigmatic. Herein, we have uncovered the genome-wide redistribution of accessible chromatin regions and extensive alterations of expression of cilia genes during Ellis-van Creveld syndrome (EVC) ciliopathy pathogenesis. Mechanistically, the distinct EVC ciliopathy-activated accessible regions (CAAs) are shown to positively regulate robust changes in flanking cilia genes, which are a key requirement for cilia transcription in response to developmental signals. Moreover, a single transcription factor, ETS1, can be recruited to CAAs, leading to prominent chromatin accessibility reconstruction in EVC ciliopathy patients. In zebrafish, the collapse of CAAs driven by ets1 suppression subsequently causes defective cilia proteins, resulting in body curvature and pericardial oedema. Our results depict a dynamic landscape of chromatin accessibility in EVC ciliopathy patients, and uncover an insightful role for ETS1 in controlling the global transcriptional program of cilia genes by reprogramming the widespread chromatin state.
Collapse
Affiliation(s)
- Donghui Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Chong Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yanmei Zhu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Haixia Xie
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Caifeng Yue
- Precision Clinical Laboratory, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
- Department of Laboratory Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Mingfeng Li
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Wenlu Wei
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yu Peng
- Pediatric Intensive Care Unit Central, People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Guibin Yin
- Department of Orthopedics, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yunmiao Guo
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| | - Yiting Guan
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang 524045, PR China
| |
Collapse
|
9
|
Liu Z, Liang Q, Ren Y, Guo C, Ge X, Wang L, Cheng Q, Luo P, Zhang Y, Han X. Immunosenescence: molecular mechanisms and diseases. Signal Transduct Target Ther 2023; 8:200. [PMID: 37179335 PMCID: PMC10182360 DOI: 10.1038/s41392-023-01451-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Infection susceptibility, poor vaccination efficacy, age-related disease onset, and neoplasms are linked to innate and adaptive immune dysfunction that accompanies aging (known as immunosenescence). During aging, organisms tend to develop a characteristic inflammatory state that expresses high levels of pro-inflammatory markers, termed inflammaging. This chronic inflammation is a typical phenomenon linked to immunosenescence and it is considered the major risk factor for age-related diseases. Thymic involution, naïve/memory cell ratio imbalance, dysregulated metabolism, and epigenetic alterations are striking features of immunosenescence. Disturbed T-cell pools and chronic antigen stimulation mediate premature senescence of immune cells, and senescent immune cells develop a proinflammatory senescence-associated secretory phenotype that exacerbates inflammaging. Although the underlying molecular mechanisms remain to be addressed, it is well documented that senescent T cells and inflammaging might be major driving forces in immunosenescence. Potential counteractive measures will be discussed, including intervention of cellular senescence and metabolic-epigenetic axes to mitigate immunosenescence. In recent years, immunosenescence has attracted increasing attention for its role in tumor development. As a result of the limited participation of elderly patients, the impact of immunosenescence on cancer immunotherapy is unclear. Despite some surprising results from clinical trials and drugs, it is necessary to investigate the role of immunosenescence in cancer and other age-related diseases.
Collapse
Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Qimeng Liang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 4500052, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
| |
Collapse
|
10
|
Salma M, Andrieu-Soler C, Deleuze V, Soler E. High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies. Blood Cells Mol Dis 2023; 101:102745. [PMID: 37121019 DOI: 10.1016/j.bcmd.2023.102745] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
Genome-wide analysis of transcription factors and epigenomic features is instrumental to shed light on DNA-templated regulatory processes such as transcription, cellular differentiation or to monitor cellular responses to environmental cues. Two decades of technological developments have led to a rich set of approaches progressively pushing the limits of epigenetic profiling towards single cells. More recently, disruptive technologies using innovative biochemistry came into play. Assays such as CUT&RUN, CUT&Tag and variations thereof show considerable potential to survey multiple TFs or histone modifications in parallel from a single experiment and in native conditions. These are in the path to become the dominant assays for genome-wide analysis of TFs and chromatin modifications in bulk, single-cell, and spatial genomic applications. The principles together with pros and cons are discussed.
Collapse
Affiliation(s)
- Mohammad Salma
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Charlotte Andrieu-Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Virginie Deleuze
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France
| | - Eric Soler
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France; Université de Paris, Laboratory of Excellence GR-Ex, France.
| |
Collapse
|
11
|
Bhattacharyya S, Kollipara RK, Orquera-Tornakian G, Goetsch S, Zhang M, Perry C, Li B, Shelton JM, Bhakta M, Duan J, Xie Y, Xiao G, Evers BM, Hon GC, Kittler R, Munshi NV. Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm. J Clin Invest 2023; 133:e153635. [PMID: 36454649 PMCID: PMC9888383 DOI: 10.1172/jci153635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Comprehensive cis-regulatory landscapes are essential for accurate enhancer prediction and disease variant mapping. Although cis-regulatory element (CRE) resources exist for most tissues and organs, many rare - yet functionally important - cell types remain overlooked. Despite representing only a small fraction of the heart's cellular biomass, the cardiac conduction system (CCS) unfailingly coordinates every life-sustaining heartbeat. To globally profile the mouse CCS cis-regulatory landscape, we genetically tagged CCS component-specific nuclei for comprehensive assay for transposase-accessible chromatin-sequencing (ATAC-Seq) analysis. Thus, we established a global CCS-enriched CRE database, referred to as CCS-ATAC, as a key resource for studying CCS-wide and component-specific regulatory functions. Using transcription factor (TF) motifs to construct CCS component-specific gene regulatory networks (GRNs), we identified and independently confirmed several specific TF sub-networks. Highlighting the functional importance of CCS-ATAC, we also validated numerous CCS-enriched enhancer elements and suggested gene targets based on CCS single-cell RNA-Seq data. Furthermore, we leveraged CCS-ATAC to improve annotation of existing human variants related to cardiac rhythm and nominated a potential enhancer-target pair that was dysregulated by a specific SNP. Collectively, our results established a CCS-regulatory compendium, identified novel CCS enhancer elements, and illuminated potential functional associations between human genomic variants and CCS component-specific CREs.
Collapse
Affiliation(s)
| | | | | | - Sean Goetsch
- Department of Internal Medicine, Division of Cardiology
| | - Minzhe Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Cameron Perry
- Department of Internal Medicine, Division of Cardiology
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | | | - Minoti Bhakta
- Department of Internal Medicine, Division of Cardiology
| | - Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
- Department of Bioinformatics
| | - Bret M. Evers
- Department of Internal Medicine, Division of Cardiology
| | - Gary C. Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology
- Department of Bioinformatics
- Hamon Center for Regenerative Science and Medicine, and
| | - Ralf Kittler
- McDermott Center for Human Growth and Development
| | - Nikhil V. Munshi
- Department of Internal Medicine, Division of Cardiology
- McDermott Center for Human Growth and Development
- Hamon Center for Regenerative Science and Medicine, and
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
12
|
Kulis M, Martin-Subero JI. Integrative epigenomics in chronic lymphocytic leukaemia: Biological insights and clinical applications. Br J Haematol 2023; 200:280-290. [PMID: 36121003 DOI: 10.1111/bjh.18465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 01/21/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is not only characterised by driver genetic alterations but by extensive epigenetic changes. Over the last decade, epigenomic studies have described the DNA methylome, chromatin accessibility, histone modifications and the three-dimensional (3D) genome architecture of CLL. Beyond its regulatory role, the DNA methylome contains imprints of the cellular origin and proliferative history of CLL cells. These two aspects are strong independent prognostic factors. Integrative analyses of chromatin marks have uncovered novel regulatory elements and altered transcription factor networks as non-genetic means mediating gene deregulation in CLL. Additionally, CLL cells display a disease-specific pattern of 3D genome interactions. From the technological perspective, we are currently witnessing a transition from bulk omics to single-cell analyses. This review aims at summarising the major findings from the epigenomics field as well as providing a prospect of the present and future of single-cell analyses in CLL.
Collapse
Affiliation(s)
- Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| |
Collapse
|
13
|
Hing ZA, Walker JS, Whipp EC, Brinton L, Cannon M, Zhang P, Sher S, Cempre CB, Brown F, Smith PL, Agostinelli C, Pileri SA, Skinner JN, Williams K, Phillips H, Shaffer J, Beaver LP, Pan A, Shin K, Gregory CT, Ozer GH, Yilmaz SA, Harrington BK, Lehman AM, Yu L, Coppola V, Yan P, Scherle P, Wang M, Pitis P, Xu C, Vaddi K, Chen-Kiang S, Woyach J, Blachly JS, Alinari L, Yang Y, Byrd JC, Baiocchi RA, Blaser BW, Lapalombella R. Dysregulation of PRMT5 in chronic lymphocytic leukemia promotes progression with high risk of Richter's transformation. Nat Commun 2023; 14:97. [PMID: 36609611 PMCID: PMC9823097 DOI: 10.1038/s41467-022-35778-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 12/22/2022] [Indexed: 01/08/2023] Open
Abstract
Richter's Transformation (RT) is a poorly understood and fatal progression of chronic lymphocytic leukemia (CLL) manifesting histologically as diffuse large B-cell lymphoma. Protein arginine methyltransferase 5 (PRMT5) is implicated in lymphomagenesis, but its role in CLL or RT progression is unknown. We demonstrate herein that tumors uniformly overexpress PRMT5 in patients with progression to RT. Furthermore, mice with B-specific overexpression of hPRMT5 develop a B-lymphoid expansion with increased risk of death, and Eµ-PRMT5/TCL1 double transgenic mice develop a highly aggressive disease with transformation that histologically resembles RT; where large-scale transcriptional profiling identifies oncogenic pathways mediating PRMT5-driven disease progression. Lastly, we report the development of a SAM-competitive PRMT5 inhibitor, PRT382, with exclusive selectivity and optimal in vitro and in vivo activity compared to available PRMT5 inhibitors. Taken together, the discovery that PRMT5 drives oncogenic pathways promoting RT provides a compelling rationale for clinical investigation of PRMT5 inhibitors such as PRT382 in aggressive CLL/RT cases.
Collapse
Affiliation(s)
- Zachary A Hing
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Janek S Walker
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Ethan C Whipp
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Lindsey Brinton
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Matthew Cannon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Pu Zhang
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Steven Sher
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Casey B Cempre
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Fiona Brown
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Porsha L Smith
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Claudio Agostinelli
- Haematopathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Stefano A Pileri
- European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
- Department of Specialized, Experimental and Diagnostic Medicine, University of Bologna, Bologna, Italy
| | - Jordan N Skinner
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Katie Williams
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Hannah Phillips
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Jami Shaffer
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Larry P Beaver
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Alexander Pan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Kyle Shin
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Charles T Gregory
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Gulcin H Ozer
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Selen A Yilmaz
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Bonnie K Harrington
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Amy M Lehman
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Pearlly Yan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Min Wang
- Prelude Therapeutics, Wilmington, DE, USA
| | | | - Chaoyi Xu
- Prelude Therapeutics, Wilmington, DE, USA
| | - Kris Vaddi
- Prelude Therapeutics, Wilmington, DE, USA
| | - Selina Chen-Kiang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jennifer Woyach
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Yiping Yang
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Robert A Baiocchi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Bradley W Blaser
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Rosa Lapalombella
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
14
|
Xu X, Zhao Y, Ye H, Qi Y, Xu W, Ling Y, Yang S. Analysis of Data on Fludarabine, Cyclophosphamide, and Rituximab Chemoimmunotherapy for Chronic Lymphocytic Leukemia Shows High Patient Heterogeneity and the Need for More Consideration of Individualized Treatment. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7451395. [PMID: 36226246 PMCID: PMC9550475 DOI: 10.1155/2022/7451395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/11/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022]
Abstract
Methods Data from single-cell RNA sequencing (RNA-seq) of CLL patients were obtained from the Gene Expression Omnibus database. The R package was utilized to analyze the data, and the relation of results was predicted via the GeneMANIA website. The information of 7 samples covered three stages: observation stage, pretreatment by CIT with rituximab, fludarabine, and cyclophosphamide (pre-CIT), and post-CIT. The differentially expressed genes (DEGs) were identified, and functional enrichment analyses were performed. B cell subpopulations and pseudotime trajectories analysis was conducted. Results A total of 70,659 DEGs were identified. Each patient's DEGs presented their own characteristics, with low similarity. Therefore, it is difficult to identify potential hub genes. Similarly, pathway enrichment analysis showed significant tumor heterogeneity among CLL patients. Analysis of relapsed post-CIT compared to the observation stage suggested that the TP53 pathway should be taken seriously as it is closely related to treatment strategy and patient prognosis. Conclusions Tumor heterogeneity may be a more common manifestation of CLL. Individualized treatment should be considered for CLL. TP53 abnormality and its regulatory factors should still be the focus of CLL diagnosis and treatment.
Collapse
Affiliation(s)
- Xiaoli Xu
- Department of Hematology, First People's Hospital of Foshan, Foshan, China
| | - Ying Zhao
- Department of Hematology, First People's Hospital of Foshan, Foshan, China
| | - Haiyan Ye
- Department of Hematology, First People's Hospital of Foshan, Foshan, China
| | - Yonglei Qi
- Department of Hematology, First People's Hospital of Foshan, Foshan, China
| | - Wenning Xu
- Department of Hematology, First People's Hospital of Foshan, Foshan, China
| | - Yiwen Ling
- Department of Hematology, First People's Hospital of Foshan, Foshan, China
| | - Shaojiang Yang
- Department of Hematology, First People's Hospital of Foshan, Foshan, China
| |
Collapse
|
15
|
Zhao X, Peng T, Cao X, Hou Y, Li R, Han T, Fan Z, Zhao M, Chang Y, Chen H, Li C, Huang X. In vivo G-CSF treatment activates the GR-SOCS1 axis to suppress IFN-γ secretion by natural killer cells. Cell Rep 2022; 40:111342. [PMID: 36103837 DOI: 10.1016/j.celrep.2022.111342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 12/15/2022] Open
Abstract
Natural killer (NK) cells are lymphocytes that are involved in controlling tumors or microbial infections through the production of interferon gamma (IFN-γ). Granulocyte colony-stimulating factor (G-CSF) inhibits IFN-γ secretion by NK cells, but the mechanism underlying this effect remains unclear. Here, by comparing the multi-omics profiles of human NK cells before and after in vivo G-CSF treatment, we identify a pathway that is activated in response to G-CSF treatment, which suppresses IFN-γ secretion in NK cells. Specifically, glucocorticoid receptors (GRs) activated by G-CSF inhibit secretion of IFN-γ by promoting interactions between SOCS1 promoters and enhancers, as well as increasing the expression of SOCS1. Experiments in mice confirm that G-CSF treatment significantly downregulates IFN-γ secretion and upregulates GR and SOCS1 expression in NK cells. In addition, GR blockade by the antagonist RU486 significantly reverses the effects of G-CSF, demonstrating that GRs upregulate SOCS1 and inhibit the production of IFN-γ by NK cells.
Collapse
Affiliation(s)
- Xiangyu Zhao
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Ting Peng
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Xunhong Cao
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yingping Hou
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | - Ruifeng Li
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Tingting Han
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Zeying Fan
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Ming Zhao
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Yingjun Chang
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Hebin Chen
- Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Xiaojun Huang
- Peking University People's Hospital, National Clinical Research Center for Hematologic Disease, Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China.
| |
Collapse
|
16
|
Ramirez N, Posadas-Cantera S, Langer N, de Oteyza ACG, Proietti M, Keller B, Zhao F, Gernedl V, Pecoraro M, Eibel H, Warnatz K, Ballestar E, Geiger R, Bossen C, Grimbacher B. Multi-omics analysis of naïve B cells of patients harboring the C104R mutation in TACI. Front Immunol 2022; 13:938240. [PMID: 36072607 PMCID: PMC9443529 DOI: 10.3389/fimmu.2022.938240] [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: 05/07/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most prevalent form of symptomatic primary immunodeficiency in humans. The genetic cause of CVID is still unknown in about 70% of cases. Ten percent of CVID patients carry heterozygous mutations in the tumor necrosis factor receptor superfamily member 13B gene (TNFRSF13B), encoding TACI. Mutations in TNFRSF13B alone may not be sufficient for the development of CVID, as 1% of the healthy population carry these mutations. The common hypothesis is that TACI mutations are not fully penetrant and additional factors contribute to the development of CVID. To determine these additional factors, we investigated the perturbations of transcription factor (TF) binding and the transcriptome profiles in unstimulated and CD40L/IL21-stimulated naïve B cells from CVID patients harboring the C104R mutation in TNFRSF13B and compared them to their healthy relatives with the same mutation. In addition, the proteome of stimulated naïve B cells was investigated. For functional validation, intracellular protein concentrations were measured by flow cytometry. Our analysis revealed 8% less accessible chromatin in unstimulated naïve B cells and 25% less accessible chromatin in class-switched memory B cells from affected and unaffected TACI mutation carriers compared to healthy donors. The most enriched TF binding motifs in TACI mutation carriers involved members from the ETS, IRF, and NF-κB TF families. Validation experiments supported dysregulation of the NF-κB and MAPK pathways. In steady state, naïve B cells had increased cell death pathways and reduced cell metabolism pathways, while after stimulation, enhanced immune responses and decreased cell survival were detected. Using a multi-omics approach, our findings provide valuable insights into the impaired biology of naïve B cells from TACI mutation carriers.
Collapse
Affiliation(s)
- Neftali Ramirez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiencies, Medical Center – University Hospital Freiburg, Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Sara Posadas-Cantera
- Institute for Immunodeficiency, Center for Chronic Immunodeficiencies, Medical Center – University Hospital Freiburg, Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Niko Langer
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Andres Caballero Garcia de Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiencies, Medical Center – University Hospital Freiburg, Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Michele Proietti
- Institute for Immunodeficiency, Center for Chronic Immunodeficiencies, Medical Center – University Hospital Freiburg, Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Hannover Medical University, Hannover, Germany
- Resolving Infection Susceptibility (RESIST) – Cluster of Excellence 2155, Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Baerbel Keller
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Fangwen Zhao
- Medical Epigenomics & Genome Technology, Research Center for Molecular Medicine(CeMM) of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Gernedl
- Medical Epigenomics & Genome Technology, Research Center for Molecular Medicine(CeMM) of the Austrian Academy of Sciences, Vienna, Austria
| | - Matteo Pecoraro
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Hermann Eibel
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Oncology Research, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Claudia Bossen
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiencies, Medical Center – University Hospital Freiburg, Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
- Resolving Infection Susceptibility (RESIST) – Cluster of Excellence 2155, Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF) – German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs University, Freiburg, Germany
- *Correspondence: Bodo Grimbacher,
| |
Collapse
|
17
|
Bühler MM, Martin-Subero JI, Pan-Hammarström Q, Campo E, Rosenquist R. Towards precision medicine in lymphoid malignancies. J Intern Med 2022; 292:221-242. [PMID: 34875132 DOI: 10.1111/joim.13423] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Careful histopathologic examination remains the cornerstone in the diagnosis of the clinically and biologically heterogeneous group of lymphoid malignancies. However, recent advances in genomic and epigenomic characterization using high-throughput technologies have significantly improved our understanding of these tumors. Although no single genomic alteration is completely specific for a lymphoma entity, some alterations are highly recurrent in certain entities and thus can provide complementary diagnostic information when integrated in the hematopathological diagnostic workup. Moreover, other alterations may provide important information regarding the clinical course, that is, prognostic or risk-stratifying markers, or response to treatment, that is, predictive markers, which may allow tailoring of the patient's treatment based on (epi)genetic characteristics. In this review, we will focus on clinically relevant diagnostic, prognostic, and predictive biomarkers identified in more common types of B-cell malignancies, and discuss how diagnostic assays designed for comprehensive molecular profiling may pave the way for the implementation of precision diagnostics/medicine approaches. We will also discuss future directions in this rapidly evolving field, including the application of single-cell sequencing and other omics technologies, to decipher clonal dynamics and evolution in lymphoid malignancies.
Collapse
Affiliation(s)
- Marco M Bühler
- Department of Pathology and Molecular Pathology, University Hospital of Zurich, Zurich, Switzerland.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - José I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| |
Collapse
|
18
|
Bruch PM, Giles HA, Kolb C, Herbst SA, Becirovic T, Roider T, Lu J, Scheinost S, Wagner L, Huellein J, Berest I, Kriegsmann M, Kriegsmann K, Zgorzelski C, Dreger P, Zaugg JB, Müller-Tidow C, Zenz T, Huber W, Dietrich S. Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL. Mol Syst Biol 2022; 18:e10855. [PMID: 35959629 PMCID: PMC9372727 DOI: 10.15252/msb.202110855] [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: 12/06/2021] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
The tumour microenvironment and genetic alterations collectively influence drug efficacy in cancer, but current evidence is limited and systematic analyses are lacking. Using chronic lymphocytic leukaemia (CLL) as a model disease, we investigated the influence of 17 microenvironmental stimuli on 12 drugs in 192 genetically characterised patient samples. Based on microenvironmental response, we identified four subgroups with distinct clinical outcomes beyond known prognostic markers. Response to multiple microenvironmental stimuli was amplified in trisomy 12 samples. Trisomy 12 was associated with a distinct epigenetic signature. Bromodomain inhibition reversed this epigenetic profile and could be used to target microenvironmental signalling in trisomy 12 CLL. We quantified the impact of microenvironmental stimuli on drug response and their dependence on genetic alterations, identifying interleukin 4 (IL4) and Toll‐like receptor (TLR) stimulation as the strongest actuators of drug resistance. IL4 and TLR signalling activity was increased in CLL‐infiltrated lymph nodes compared with healthy samples. High IL4 activity correlated with faster disease progression. The publicly available dataset can facilitate the investigation of cell‐extrinsic mechanisms of drug resistance and disease progression.
Collapse
Affiliation(s)
- Peter-Martin Bruch
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Holly Ar Giles
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Sophie A Herbst
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tina Becirovic
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Tobias Roider
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany
| | - Junyan Lu
- EMBL Heidelberg, Heidelberg, Germany
| | - Sebastian Scheinost
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumour Diseases, Heidelberg, Germany
| | - Lena Wagner
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumour Diseases, Heidelberg, Germany
| | | | | | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | | | | | - Peter Dreger
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Judith B Zaugg
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Thorsten Zenz
- Department of Hematology, University of Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
19
|
Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00469-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
20
|
Sahinyan K, Blackburn DM, Simon MM, Lazure F, Kwan T, Bourque G, Soleimani VD. Application of ATAC-Seq for genome-wide analysis of the chromatin state at single myofiber resolution. eLife 2022; 11:72792. [PMID: 35188098 PMCID: PMC8901173 DOI: 10.7554/elife.72792] [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: 08/04/2021] [Accepted: 02/09/2022] [Indexed: 12/11/2022] Open
Abstract
Myofibers are the main components of skeletal muscle, which is the largest tissue in the body. Myofibers are highly adaptive and can be altered under different biological and disease conditions. Therefore, transcriptional and epigenetic studies on myofibers are crucial to discover how chromatin alterations occur in the skeletal muscle under different conditions. However, due to the heterogenous nature of skeletal muscle, studying myofibers in isolation proves to be a challenging task. Single-cell sequencing has permitted the study of the epigenome of isolated myonuclei. While this provides sequencing with high dimensionality, the sequencing depth is lacking, which makes comparisons between different biological conditions difficult. Here, we report the first implementation of single myofiber ATAC-Seq, which allows for the sequencing of an individual myofiber at a depth sufficient for peak calling and for comparative analysis of chromatin accessibility under various physiological and disease conditions. Application of this technique revealed significant differences in chromatin accessibility between resting and regenerating myofibers, as well as between myofibers from a mouse model of Duchenne Muscular Dystrophy (mdx) and wild-type (WT) counterparts. This technique can lead to a wide application in the identification of chromatin regulatory elements and epigenetic mechanisms in muscle fibers during development and in muscle-wasting diseases.
Collapse
Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Canada.,McGill Genome Centre, Montreal, Canada.,Canadian Centre for Computational Genomics, Montreal, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montreal, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| |
Collapse
|
21
|
Schmid KT, Höllbacher B, Cruceanu C, Böttcher A, Lickert H, Binder EB, Theis FJ, Heinig M. scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies. Nat Commun 2021; 12:6625. [PMID: 34785648 PMCID: PMC8595682 DOI: 10.1038/s41467-021-26779-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Single cell RNA-seq has revolutionized transcriptomics by providing cell type resolution for differential gene expression and expression quantitative trait loci (eQTL) analyses. However, efficient power analysis methods for single cell data and inter-individual comparisons are lacking. Here, we present scPower; a statistical framework for the design and power analysis of multi-sample single cell transcriptomic experiments. We modelled the relationship between sample size, the number of cells per individual, sequencing depth, and the power of detecting differentially expressed genes within cell types. We systematically evaluated these optimal parameter combinations for several single cell profiling platforms, and generated broad recommendations. In general, shallow sequencing of high numbers of cells leads to higher overall power than deep sequencing of fewer cells. The model, including priors, is implemented as an R package and is accessible as a web tool. scPower is a highly customizable tool that experimentalists can use to quickly compare a multitude of experimental designs and optimize for a limited budget.
Collapse
Affiliation(s)
- Katharina T Schmid
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Informatics, Technical University Munich, Munich, Germany
| | - Barbara Höllbacher
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Informatics, Technical University Munich, Munich, Germany
| | - Cristiana Cruceanu
- Department of Translational Research, Max Planck Institute for Psychiatry, Munich, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich, Munich, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- School of Medicine, Technical University of Munich, Munich, Germany
| | - Elisabeth B Binder
- Department of Translational Research, Max Planck Institute for Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Georgia, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technical University Munich, Munich, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
- Department of Informatics, Technical University Munich, Munich, Germany.
| |
Collapse
|
22
|
van der Kouwe E, Heller G, Czibere A, Pulikkan JA, Agreiter C, Castilla LH, Delwel R, Di Ruscio A, Ebralidze AK, Forte M, Grebien F, Heyes E, Kazianka L, Klinger J, Kornauth C, Le T, Lind K, Barbosa IAM, Pemovska T, Pichler A, Schmolke AS, Schweicker CM, Sill H, Sperr WR, Spittler A, Surapally S, Trinh BQ, Valent P, Vanura K, Welner RS, Zuber J, Tenen DG, Staber PB. Core-binding factor leukemia hijacks the T-cell-prone PU.1 antisense promoter. Blood 2021; 138:1345-1358. [PMID: 34010414 PMCID: PMC8525333 DOI: 10.1182/blood.2020008971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/09/2021] [Indexed: 11/20/2022] Open
Abstract
The blood system serves as a key model for cell differentiation and cancer. It is orchestrated by precise spatiotemporal expression of crucial transcription factors. One of the key master regulators in the hematopoietic systems is PU.1. Reduced levels of PU.1 are characteristic for human acute myeloid leukemia (AML) and are known to induce AML in mouse models. Here, we show that transcriptional downregulation of PU.1 is an active process involving an alternative promoter in intron 3 that is induced by RUNX transcription factors driving noncoding antisense transcription. Core-binding factor (CBF) fusions RUNX1-ETO and CBFβ-MYH11 in t(8;21) and inv(16) AML, respectively, activate the PU.1 antisense promoter that results in a shift from sense toward antisense transcription and myeloid differentiation blockade. In patients with CBF-AML, we found that an elevated antisense/sense transcript and promoter accessibility ratio represents a hallmark compared with normal karyotype AML or healthy CD34+ cells. Competitive interaction of an enhancer with the proximal or the antisense promoter forms a binary on/off switch for either myeloid or T-cell development. Leukemic CBF fusions thus use a physiological mechanism used by T cells to decrease sense transcription. Our study is the first example of a sense/antisense promoter competition as a crucial functional switch for gene expression perturbation by oncogenes. Hence, this disease mechanism reveals a previously unknown Achilles heel for future precise therapeutic targeting of oncogene-induced chromatin remodeling.
Collapse
Affiliation(s)
- E van der Kouwe
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - G Heller
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | | | | | - C Agreiter
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - L H Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - R Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Di Ruscio
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - A K Ebralidze
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
| | - M Forte
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - F Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - E Heyes
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L Kazianka
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - J Klinger
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - C Kornauth
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - T Le
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - K Lind
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - I A M Barbosa
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - T Pemovska
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A Pichler
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A-S Schmolke
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - C M Schweicker
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - H Sill
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - W R Sperr
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - A Spittler
- Core Facility Flow Cytometry and Surgical Research Laboratories, and
| | - S Surapally
- Versiti Blood Research Institute, Milwaukee, WI
| | - B Q Trinh
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
| | - P Valent
- Department of Medicine I, Division of Hematology and Hemostaseology, and
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - K Vanura
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| | - R S Welner
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL; and
| | - J Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - D G Tenen
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
- Cancer Science Institute, National University of Singapore, Singapore
| | - P B Staber
- Department of Medicine I, Division of Hematology and Hemostaseology, and
| |
Collapse
|
23
|
Long J, Long T, Li Y, Yuan P, Liu K, Li J, Cheng L. A Functional Polymorphism in Accessible Chromatin Region Confers Risk of Non-Small Cell Lung Cancer in Chinese Population. Front Oncol 2021; 11:698993. [PMID: 34552866 PMCID: PMC8450516 DOI: 10.3389/fonc.2021.698993] [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: 04/22/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
Background The disease-associated non-coding variants identified by genome-wide association studies (GWASs) were enriched in open chromatin regions (OCRs) and implicated in gene regulation. Genetic variants in OCRs thus may exert regulatory functions and contribute to non-small cell lung cancer (NSCLC) susceptibility. Objective To fine map potential functional variants in GWAS loci that contribute to NSCLC predisposition using chromatin accessibility and histone modification data and explore their functions by population study and biochemical experimental analyses. Methods We mapped the chromatin accessible regions of lung tissues using data of assay for transposase-accessible chromatin using sequencing (ATAC-seq) in The Cancer Genome Atlas (TCGA) and prioritized potential regulatory variants within lung cancer GWAS loci by aligning with histone signatures using data of chromatin immunoprecipitation assays followed by sequencing (ChIP-seq) in the Encyclopedia of DNA Elements (ENCODE). A two-stage case–control study with 1,830 cases and 2,001 controls was conducted to explore the associations between candidate variants and NSCLC risk in Chinese population. Bioinformatic annotations and biochemical experiments were performed to further reveal the potential functions of significant variants. Results Sixteen potential functional single-nucleotide polymorphisms (SNPs) were selected as candidates from bioinformatics analyses. Three variants out of the 16 candidate SNPs survived after genotyping in stage 1 case–control study, and only the results of SNP rs13064999 were successfully validated in the analyses of stage 2 case–control study. In combined analyses, rs13064999 was significantly associated with NSCLC risk [additive model; odds ratio (OR) = 1.17; 95%CI, 1.07–1.29; p = 0.001]. Functional annotations indicated its potential enhancer bioactivity, and dual-luciferase reporter assays revealed a significant increase in luciferase activity for the reconstructed plasmid with rs13064999 A allele, when compared to the one with wild-type G allele (pA549 < 0.001, pSK-MES-1 = 0.004). Further electrophoretic mobility shift assays (EMSA) and super-shift assays confirmed a stronger affinity of HP1γ for the binding motif containing SNP rs13064999 A allele. Conclusion These findings suggested that the functional variant rs13064999, identified by the integration of ATAC-seq and ChIP-seq data, contributes to the susceptibility of NSCLC by affecting HP1γ binding, while the exact biological mechanism awaits further exploration.
Collapse
Affiliation(s)
- Jieyi Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tingting Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peihong Yuan
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
24
|
Chromatin-based, in cis and in trans regulatory rewiring underpins distinct oncogenic transcriptomes in multiple myeloma. Nat Commun 2021; 12:5450. [PMID: 34521827 PMCID: PMC8440555 DOI: 10.1038/s41467-021-25704-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 08/17/2021] [Indexed: 11/09/2022] Open
Abstract
Multiple myeloma is a genetically heterogeneous cancer of the bone marrow plasma cells (PC). Distinct myeloma transcriptome profiles are primarily driven by myeloma initiating events (MIE) and converge into a mutually exclusive overexpression of the CCND1 and CCND2 oncogenes. Here, with reference to their normal counterparts, we find that myeloma PC enhanced chromatin accessibility combined with paired transcriptome profiling can classify MIE-defined genetic subgroups. Across and within different MM genetic subgroups, we ascribe regulation of genes and pathways critical for myeloma biology to unique or shared, developmentally activated or de novo formed candidate enhancers. Such enhancers co-opt recruitment of existing transcription factors, which although not transcriptionally deregulated per se, organise aberrant gene regulatory networks that help identify myeloma cell dependencies with prognostic impact. Finally, we identify and validate the critical super-enhancer that regulates ectopic expression of CCND2 in a subset of patients with MM and in chronic lymphocytic leukemia. Despite extensive genetic heterogeneity, nearly half of all multiple myeloma (MM) cases are driven by cyclin D2 (CCND2) over-expression. Here the authors dissect the chromatin landscape of MM to provide insights into the transcriptional regulatory landscape driving MM and divergent transcriptomes corresponding to different MM genetic subtypes.
Collapse
|
25
|
Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet 2021; 29:2761-2774. [PMID: 32744316 DOI: 10.1093/hmg/ddaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ~ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.
Collapse
Affiliation(s)
- Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
26
|
Cao F, Zhang Y, Cai Y, Animesh S, Zhang Y, Akincilar SC, Loh YP, Li X, Chng WJ, Tergaonkar V, Kwoh CK, Fullwood MJ. Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences. Genome Biol 2021; 22:226. [PMID: 34399797 PMCID: PMC8365954 DOI: 10.1186/s13059-021-02453-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 08/04/2021] [Indexed: 11/10/2022] Open
Abstract
Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chromatin interactions between open chromatin regions using only DNA sequences. ChINN predicts CTCF- and RNA polymerase II-associated and Hi-C chromatin interactions. ChINN shows good across-sample performances and captures various sequence features for chromatin interaction prediction. We apply ChINN to 6 chronic lymphocytic leukemia (CLL) patient samples and a published cohort of 84 CLL open chromatin samples. Our results demonstrate extensive heterogeneity in chromatin interactions among CLL patient samples.
Collapse
Affiliation(s)
- Fan Cao
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, Block N4, 50 Nanyang Avenue, Singapore, 639798 Singapore
| | - Yichao Cai
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Sambhavi Animesh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Semih Can Akincilar
- Institute of Molecular and Cell Biology, Agency for Science (IMCB), A*STAR (Agency for Science, Technology and Research,, Singapore, 138673 Singapore
| | - Yan Ping Loh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
| | - Xinya Li
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore, 119228 Singapore
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, NUH Zone B, Medical Centre, Singapore, 119074 Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology, Agency for Science (IMCB), A*STAR (Agency for Science, Technology and Research,, Singapore, 138673 Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117597 Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, Block N4, 50 Nanyang Avenue, Singapore, 639798 Singapore
| | - Melissa J. Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599 Singapore
- Institute of Molecular and Cell Biology, Agency for Science (IMCB), A*STAR (Agency for Science, Technology and Research,, Singapore, 138673 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| |
Collapse
|
27
|
CLL intraclonal fractions exhibit established and recently acquired patterns of DNA methylation. Blood Adv 2021; 4:893-905. [PMID: 32150608 DOI: 10.1182/bloodadvances.2019000817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
Intraclonal subpopulations of circulating chronic lymphocytic leukemia (CLL) cells with different proliferative histories and reciprocal surface expression of CXCR4 and CD5 have been observed in the peripheral blood of CLL patients and named proliferative (PF), intermediate (IF), and resting (RF) cellular fractions. Here, we found that these intraclonal circulating fractions share persistent DNA methylation signatures largely associated with the mutation status of the immunoglobulin heavy chain locus (IGHV) and their origins from distinct stages of differentiation of antigen-experienced B cells. Increased leukemic birth rate, however, showed a very limited impact on DNA methylation of circulating CLL fractions independent of IGHV mutation status. Additionally, DNA methylation heterogeneity increased as leukemic cells advanced from PF to RF in the peripheral blood. This frequently co-occurred with heterochromatin hypomethylation and hypermethylation of Polycomb-repressed regions in the PF, suggesting accumulation of longevity-associated epigenetic features in recently born cells. On the other hand, transcriptional differences between paired intraclonal fractions confirmed their proliferative experience and further supported a linear advancement from PF to RF in the peripheral blood. Several of these differentially expressed genes showed unique associations with clinical outcome not evident in the bulk clone, supporting the pathological and therapeutic relevance of studying intraclonal CLL fractions. We conclude that independent methylation and transcriptional landscapes reflect both preexisting cell-of-origin fingerprints and more recently acquired hallmarks associated with the life cycle of circulating CLL cells.
Collapse
|
28
|
Labreche K, Daniau M, Sud A, Law PJ, Royer-Perron L, Holroyd A, Broderick P, Went M, Benazra M, Ahle G, Soubeyran P, Taillandier L, Chinot OL, Casasnovas O, Bay JO, Jardin F, Oberic L, Fabbro M, Damaj G, Brion A, Mokhtari K, Philippe C, Sanson M, Houillier C, Soussain C, Hoang-Xuan K, Houlston RS, Alentorn A. A genome-wide association study identifies susceptibility loci for primary central nervous system lymphoma at 6p25.3 and 3p22.1: a LOC Network study. Neuro Oncol 2021; 21:1039-1048. [PMID: 31102405 DOI: 10.1093/neuonc/noz088] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Primary central nervous system lymphoma (PCNSL) is a rare form of extra-nodal non-Hodgkin lymphoma. PCNSL is a distinct subtype of non-Hodgkin lymphoma, with over 95% of tumors belonging to the diffuse large B-cell lymphoma (DLBCL) group. We have conducted a genome-wide association study (GWAS) on immunocompetent patients to address the possibility that common genetic variants influence the risk of developing PCNSL. METHODS We performed a meta-analysis of 2 new GWASs of PCNSL totaling 475 cases and 1134 controls of European ancestry. To increase genomic resolution, we imputed >10 million single nucleotide polymorphisms using the 1000 Genomes Project combined with UK10K as reference. In addition we performed a transcription factor binding disruption analysis and investigated the patterns of local chromatin by Capture Hi-C data. RESULTS We identified independent risk loci at 3p22.1 (rs41289586, ANO10, P = 2.17 × 10-8) and 6p25.3 near EXOC2 (rs116446171, P = 1.95 x 10-13). In contrast, the lack of an association between rs41289586 and DLBCL suggests distinct germline predisposition to PCNSL and DLBCL. We found looping chromatin interactions between noncoding regions at 6p25.3 (rs11646171) with the IRF4 promoter and at 8q24.21 (rs13254990) with the MYC promoter, both genes with strong relevance to B-cell tumorigenesis. CONCLUSION To our knowledge this is the first study providing insight into the genetic predisposition to PCNSL. Our findings represent an important step in defining the contribution of common genetic variation to the risk of developing PCNSL.
Collapse
Affiliation(s)
- Karim Labreche
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK.,(i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Mailys Daniau
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Amit Sud
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Louis Royer-Perron
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Amy Holroyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Molly Went
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Marion Benazra
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,ICM, iGenSeq Platform, Paris, France
| | - Guido Ahle
- Department of Neurology, Colmar Civil Hospitals, Colmar Cedex, France
| | - Pierre Soubeyran
- Department of Medical Oncology, Bergnoié Institute, Bordeaux, France.,Inserm Research Unit U1218, Bordeaux, France
| | - Luc Taillandier
- Neuro-oncology Department, Nancy University Hospital and The Center of Research in Automatic Control of Nancy, Joint Research Unit 7039, National Center for Scientific Research, SBS BEAM Department, Nancy University, Vandoeuvre-lès-Nancy, France
| | - Olivier L Chinot
- Department of Pathology and Neuropathology, Timone Hospital, Aix-Marseille University (AMU), Public Assistance-Hospitals of Marseille, Marseille, France.,AMU Research Center in Oncology Biology and Oncopharmacology, Marseille, France
| | | | - Jacques-Olivier Bay
- Department of Hematology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fabrice Jardin
- Department of Hematology, Henri Becquerel Cancer Center, Rouen, France and Inserm U1245, Henri Becquerel Cancer Center, Institute of Research and Innovation in Biomedicine, University of Normandy, Rouen, France
| | - Lucie Oberic
- Department of Hematology, University Cancer Institute of Toulouse-Oncopole, Toulouse, France
| | | | - Gandhi Damaj
- Department of Hematology, University Hospital of Caen, Caen, France
| | - Annie Brion
- Department of Hematology, Regional and University Hospitals Besançon, Besançon, France
| | - Karima Mokhtari
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Raymond Escourolle Department of Neuropathology, Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | | | - Marc Sanson
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France.,OncoNeuroTek, ICM, Paris, France
| | - Caroline Houillier
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France
| | - Carole Soussain
- Department of Hematology, René Huguenin Hospital, Curie Institute, Saint-Cloud, France
| | - Khê Hoang-Xuan
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Agusti Alentorn
- (i) National Institute of Health and Medical Research (Inserm) U 1127, Paris, France, (ii) National Center for Scientific Research, Joint Research Unit 7225, Paris, France, (iii) Brain and Spine Institute (ICM), Paris, France, and (iv) Sorbonne University, Pierre and Marie Curie University, Paris 6, Paris, France.,Neurology Service 2 (Mazarin), Public Assistance-Hospitals of Paris, Hospital Group of Pitié-Salpêtrière, Paris, France; Pierre and Marie Curie University, Paris 6, Paris, France
| | | |
Collapse
|
29
|
Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021; 1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
Abstract
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of the eukaryotic genome. As active regulatory DNA elements are generally 'accessible', the genome-wide profiling of chromatin accessibility can be used to identify candidate regulatory genomic regions in a tissue or cell type. Multiple biochemical methods have been developed to profile chromatin accessibility, both in bulk and at the single-cell level. Depending on the method, enzymatic cleavage, transposition or DNA methyltransferases are used, followed by high-throughput sequencing, providing a view of genome-wide chromatin accessibility. In this Primer, we discuss these biochemical methods, as well as bioinformatics tools for analysing and interpreting the generated data, and insights into the key regulators underlying developmental, evolutionary and disease processes. We outline standards for data quality, reproducibility and deposition used by the genomics community. Although chromatin accessibility profiling is invaluable to study gene regulation, alone it provides only a partial view of this complex process. Orthogonal assays facilitate the interpretation of accessible regions with respect to enhancer-promoter proximity, functional transcription factor binding and regulatory function. We envision that technological improvements including single-molecule, multi-omics and spatial methods will bring further insight into the secrets of genome regulation.
Collapse
Affiliation(s)
- Liesbeth Minnoye
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lixia Pan
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | | | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Stein Aerts
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| |
Collapse
|
30
|
Tanaka A, Ishitsuka Y, Ohta H, Fujimoto A, Yasunaga JI, Matsuoka M. Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells. PLoS Comput Biol 2020; 16:e1008422. [PMID: 33253153 PMCID: PMC7728210 DOI: 10.1371/journal.pcbi.1008422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/10/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards the genome as a string of 1s and 0s based on a set of peaks and calculates the Hamming distances between the strings. This algorithm with the systematically optimized set of peaks enables us to quantitatively evaluate differences between samples of hematopoietic cells and classify cell types, potentially leading to a better understanding of leukemia pathogenesis.
Collapse
Affiliation(s)
- Azusa Tanaka
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- * E-mail: (AT); (YI); (HO)
| | - Yasuhiro Ishitsuka
- Center for Science Adventure and Collaborative Research Advancement, Graduate School of Science, Kyoto University, Kyoto, Japan
- Department of Mathematics, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail: (AT); (YI); (HO)
| | - Hiroki Ohta
- Center for Science Adventure and Collaborative Research Advancement, Graduate School of Science, Kyoto University, Kyoto, Japan
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail: (AT); (YI); (HO)
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun-ichirou Yasunaga
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology, Rheumatology and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology, Rheumatology and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
31
|
Liu Q, Zaba LC, Satpathy AT, Longmire M, Zhang W, Li K, Granja J, Guo C, Lin J, Li R, Tolentino K, Kania G, Distler O, Fiorentino D, Chung L, Qu K, Chang HY. Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis. Nat Commun 2020; 11:5843. [PMID: 33203843 PMCID: PMC7672105 DOI: 10.1038/s41467-020-19702-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022] Open
Abstract
Systemic sclerosis (SSc) is a disease at the intersection of autoimmunity and fibrosis. However, the epigenetic regulation and the contributions of diverse cell types to SSc remain unclear. Here we survey, using ATAC-seq, the active DNA regulatory elements of eight types of primary cells in normal skin from healthy controls, as well as clinically affected and unaffected skin from SSc patients. We find that accessible DNA elements in skin-resident dendritic cells (DCs) exhibit the highest enrichment of SSc-associated single-nucleotide polymorphisms (SNPs) and predict the degrees of skin fibrosis in patients. DCs also have the greatest disease-associated changes in chromatin accessibility and the strongest alteration of cell-cell interactions in SSc lesions. Lastly, data from an independent cohort of patients with SSc confirm a significant increase of DCs in lesioned skin. Thus, the DCs epigenome links inherited susceptibility and clinically apparent fibrosis in SSc skin, and can be an important driver of SSc pathogenesis.
Collapse
Affiliation(s)
- Qian Liu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Lisa C Zaba
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Longmire
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Wen Zhang
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Kun Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jeffrey Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chuang Guo
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jun Lin
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gabriela Kania
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - David Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lorinda Chung
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
- CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230027, China.
- School of Data Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
32
|
Saint Fleur-Lominy S, Evensen NA, Bhatla T, Sethia G, Narang S, Choi JH, Ma X, Yang JJ, Kelly S, Raetz E, Harvey RC, Willman C, Loh ML, Hunger SP, Brown PA, Getz KM, Meydan C, Mason CE, Tsirigos A, Carroll WL. Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Its Role in Drug Resistance. Cancer Res 2020; 80:5189-5202. [PMID: 33067268 DOI: 10.1158/0008-5472.can-20-1145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022]
Abstract
Although B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy in children and while highly curable, it remains a leading cause of cancer-related mortality. The outgrowth of tumor subclones carrying mutations in genes responsible for resistance to therapy has led to a Darwinian model of clonal selection. Previous work has indicated that alterations in the epigenome might contribute to clonal selection, yet the extent to which the chromatin state is altered under the selective pressures of therapy is unknown. To address this, we performed chromatin immunoprecipitation, gene expression analysis, and enhanced reduced representation bisulfite sequencing on a cohort of paired diagnosis and relapse samples from individual patients who all but one relapsed within 36 months of initial diagnosis. The chromatin state at diagnosis varied widely among patients, while the majority of peaks remained stable between diagnosis and relapse. Yet a significant fraction was either lost or newly gained, with some patients showing few differences and others showing massive changes of the epigenetic state. Evolution of the epigenome was associated with pathways previously linked to therapy resistance as well as novel candidate pathways through alterations in pyrimidine biosynthesis and downregulation of polycomb repressive complex 2 targets. Three novel, relapse-specific superenhancers were shared by a majority of patients including one associated with S100A8, the top upregulated gene seen at relapse in childhood B-ALL. Overall, our results support a role of the epigenome in clonal evolution and uncover new candidate pathways associated with relapse. SIGNIFICANCE: This study suggests a major role for epigenetic mechanisms in driving clonal evolution in B-ALL and identifies novel pathways associated with drug resistance.
Collapse
Affiliation(s)
- Shella Saint Fleur-Lominy
- Perlmutter Cancer Center, NYU Langone Health, New York, New York.,Department of Medicine, NYU Langone Health, New York, New York
| | - Nikki A Evensen
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Teena Bhatla
- Department of Pediatrics, Children's Hospital of New Jersey at NBI, RWJBarnabas Health, Newark, New Jersey
| | - Gunjan Sethia
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Sonali Narang
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Jun H Choi
- Department of Medicine, NYU Langone Health, New York, New York
| | - Xiaotu Ma
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephen Kelly
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Elizabeth Raetz
- Perlmutter Cancer Center, NYU Langone Health, New York, New York.,Department of Pediatrics, NYU Health, New York, New York
| | - Richard C Harvey
- University of New Mexico Comprehensive Cancer Center, Department of Pathology, University of New Mexico School of Medicine and Health Sciences Center, Albuquerque, New Mexico
| | - Cheryl Willman
- University of New Mexico Comprehensive Cancer Center, Department of Pathology, University of New Mexico School of Medicine and Health Sciences Center, Albuquerque, New Mexico
| | - Mignon L Loh
- Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, California
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Patrick A Brown
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kylie M Getz
- Department of Physiology and Biophysics and Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics and Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Christopher E Mason
- Department of Physiology and Biophysics and Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Aristotelis Tsirigos
- Perlmutter Cancer Center, NYU Langone Health, New York, New York. .,Department of Pathology, NYU Langone Health, New York, New York
| | - William L Carroll
- Perlmutter Cancer Center, NYU Langone Health, New York, New York. .,Department of Pediatrics, NYU Health, New York, New York.,Department of Pathology, NYU Langone Health, New York, New York
| |
Collapse
|
33
|
Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17207386. [PMID: 33050454 PMCID: PMC7650680 DOI: 10.3390/ijerph17207386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 11/17/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by disruptions in social communication and behavioral flexibility. Both genetic and environmental factors contribute to ASD risk. Epidemiologic studies indicate that roadway vehicle exhaust and in utero exposure to diesel particulate matter (DPM) are associated with ASD. Using the Comparative Toxicogenomics Database (CTD), we identified genes connected to DPM exposure and ASD, extracted the known enhancers/promoters of the identified genes, and integrated this with Assay for Transposase Accessible Chromatin (ATAC-seq) data from DPM-exposed human neural progenitor cells. Enhancer/promoter elements with significantly different chromosome accessibility revealed enriched DNA sequence motifs with transcription factor binding sites for EGR1. Variant extraction for linkage disequilibrium blocks of these regions followed by analysis through Genome Wide Association Studies (GWAS) revealed multiple neurological trait associations including exploratory eye movement and brain volume measurement. This approach highlights the effects of pollution on the regulatory regions of genes implicated in ASD by genetic studies, indicating convergence of genetic and environmental factors on molecular networks that contribute to ASD. Integration of publicly available data from the CTD, cell culture exposure studies, and phenotypic genetics synergize extensive evidence of chemical exposures on gene regulation for altered brain development.
Collapse
|
34
|
Yu YR, Imrichova H, Wang H, Chao T, Xiao Z, Gao M, Rincon-Restrepo M, Franco F, Genolet R, Cheng WC, Jandus C, Coukos G, Jiang YF, Locasale JW, Zippelius A, Liu PS, Tang L, Bock C, Vannini N, Ho PC. Disturbed mitochondrial dynamics in CD8 + TILs reinforce T cell exhaustion. Nat Immunol 2020; 21:1540-1551. [PMID: 33020660 DOI: 10.1038/s41590-020-0793-3] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/24/2020] [Indexed: 12/19/2022]
Abstract
The metabolic challenges present in tumors attenuate the metabolic fitness and antitumor activity of tumor-infiltrating T lymphocytes (TILs). However, it remains unclear whether persistent metabolic insufficiency can imprint permanent T cell dysfunction. We found that TILs accumulated depolarized mitochondria as a result of decreased mitophagy activity and displayed functional, transcriptomic and epigenetic characteristics of terminally exhausted T cells. Mechanistically, reduced mitochondrial fitness in TILs was induced by the coordination of T cell receptor stimulation, microenvironmental stressors and PD-1 signaling. Enforced accumulation of depolarized mitochondria with pharmacological inhibitors induced epigenetic reprogramming toward terminal exhaustion, indicating that mitochondrial deregulation caused T cell exhaustion. Furthermore, supplementation with nicotinamide riboside enhanced T cell mitochondrial fitness and improved responsiveness to anti-PD-1 treatment. Together, our results reveal insights into how mitochondrial dynamics and quality orchestrate T cell antitumor responses and commitment to the exhaustion program.
Collapse
Affiliation(s)
- Yi-Ru Yu
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Haiping Wang
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Tung Chao
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Zhengtao Xiao
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Min Gao
- Institute of Bioengineering, Institute of Materials Science and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marcela Rincon-Restrepo
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Fabien Franco
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Raphael Genolet
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Wan-Chen Cheng
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Camilla Jandus
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - George Coukos
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Yi-Fan Jiang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Alfred Zippelius
- Department of Biomedicine, Laboratory Cancer Immunology, University Hospital and University of Basel, Basel, Switzerland.,Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Pu-Ste Liu
- Institute of Cellular and System Medicine, National Health Research Institute, Miaoli County, Taiwan
| | - Li Tang
- Institute of Bioengineering, Institute of Materials Science and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Nicola Vannini
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland. .,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland.
| |
Collapse
|
35
|
Rogerson C, Ogden S, Britton E, Ang Y, Sharrocks AD. Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma. eLife 2020; 9:e57189. [PMID: 32880368 PMCID: PMC7544504 DOI: 10.7554/elife.57189] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Oesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths. Barrett's oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the molecular events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin to directly regulate cell cycle genes specifically in OAC cells. This new KLF5 target gene programme has potential prognostic significance as high levels correlate with poorer patient survival. Thus, the repurposing of KLF5 for novel regulatory activity in OAC provides new insights into the mechanisms behind disease progression.
Collapse
Affiliation(s)
- Connor Rogerson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Edward Britton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Yeng Ang
- School of Medical Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- GI Science Centre, Salford Royal NHS FT, University of ManchesterSalfordUnited Kingdom
| | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| |
Collapse
|
36
|
Hao Shi, Yan KK, Ding L, Qian C, Chi H, Yu J. Network Approaches for Dissecting the Immune System. iScience 2020; 23:101354. [PMID: 32717640 PMCID: PMC7390880 DOI: 10.1016/j.isci.2020.101354] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/21/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
The immune system is a complex biological network composed of hierarchically organized genes, proteins, and cellular components that combat external pathogens and monitor the onset of internal disease. To meet and ultimately defeat these challenges, the immune system orchestrates an exquisitely complex interplay of numerous cells, often with highly specialized functions, in a tissue-specific manner. One of the major methodologies of systems immunology is to measure quantitatively the components and interaction levels in the immunologic networks to construct a computational network and predict the response of the components to perturbations. The recent advances in high-throughput sequencing techniques have provided us with a powerful approach to dissecting the complexity of the immune system. Here we summarize the latest progress in integrating omics data and network approaches to construct networks and to infer the underlying signaling and transcriptional landscape, as well as cell-cell communication, in the immune system, with a focus on hematopoiesis, adaptive immunity, and tumor immunology. Understanding the network regulation of immune cells has provided new insights into immune homeostasis and disease, with important therapeutic implications for inflammation, cancer, and other immune-mediated disorders.
Collapse
Affiliation(s)
- Hao Shi
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Koon-Kiu Yan
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chenxi Qian
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
37
|
Weichenhan D, Lipka DB, Lutsik P, Goyal A, Plass C. Epigenomic technologies for precision oncology. Semin Cancer Biol 2020; 84:60-68. [PMID: 32822861 DOI: 10.1016/j.semcancer.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Epigenetic patterns in a cell control the expression of genes and consequently determine the phenotype of a cell. Cancer cells possess altered epigenomes which include aberrant patterns of DNA methylation, histone tail modifications, nucleosome positioning and of the three-dimensional chromatin organization within a nucleus. These altered epigenetic patterns are potential useful biomarkers to detect cancer cells and to classify tumor types. In addition, the cancer epigenome dictates the response of a cancer cell to therapeutic intervention and, therefore its knowledge, will allow to predict response to different therapeutic approaches. Here we review the current state-of-the-art technologies that have been developed to decipher epigenetic patterns on the genomic level and discuss how these methods are potentially useful for precision oncology.
Collapse
Affiliation(s)
- Dieter Weichenhan
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg & German Cancer Research Center, Im Neuenheimer Feld 581, D-69120, Heidelberg, Germany; Faculty of Medicine, Medical Center, Otto-von-Guericke-University, Leipziger Straße 44, D-39120, Magdeburg, Germany.
| | - Pavlo Lutsik
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Ashish Goyal
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Christoph Plass
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| |
Collapse
|
38
|
Erarslan-Uysal B, Kunz JB, Rausch T, Richter-Pechańska P, van Belzen IA, Frismantas V, Bornhauser B, Ordoñez-Rueada D, Paulsen M, Benes V, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Loukanov T, Gorenflo M, Waszak SM, Bourquin JP, Muckenthaler MU, Korbel JO, Kulozik AE. Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors. EMBO Mol Med 2020; 12:e12104. [PMID: 32755029 PMCID: PMC7507092 DOI: 10.15252/emmm.202012104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 01/11/2023] Open
Abstract
We aimed at identifying the developmental stage at which leukemic cells of pediatric T-ALLs are arrested and at defining leukemogenic mechanisms based on ATAC-Seq. Chromatin accessibility maps of seven developmental stages of human healthy T cells revealed progressive chromatin condensation during T-cell maturation. Developmental stages were distinguished by 2,823 signature chromatin regions with 95% accuracy. Open chromatin surrounding SAE1 was identified to best distinguish thymic developmental stages suggesting a potential role of SUMOylation in T-cell development. Deconvolution using signature regions revealed that T-ALLs, including those with mature immunophenotypes, resemble the most immature populations, which was confirmed by TF-binding motif profiles. We integrated ATAC-Seq and RNA-Seq and found DAB1, a gene not related to leukemia previously, to be overexpressed, abnormally spliced and hyper-accessible in T-ALLs. DAB1-negative patients formed a distinct subgroup with particularly immature chromatin profiles and hyper-accessible binding sites for SPI1 (PU.1), a TF crucial for normal T-cell maturation. In conclusion, our analyses of chromatin accessibility and TF-binding motifs showed that pediatric T-ALL cells are most similar to immature thymic precursors, indicating an early developmental arrest.
Collapse
Affiliation(s)
- Büşra Erarslan-Uysal
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Tobias Rausch
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ianthe Aem van Belzen
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Viktoras Frismantas
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Diana Ordoñez-Rueada
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Malte Paulsen
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gabriele Escherich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kseniya Bakharevich
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Tsvetomir Loukanov
- Department of Cardiac Surgery, University of Heidelberg, Heidelberg, Germany
| | - Matthias Gorenflo
- Department of Pediatric Cardiology and Congenital Heart Diseases, University of Heidelberg, Heidelberg, Germany
| | - Sebastian M Waszak
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jan O Korbel
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ) Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| |
Collapse
|
39
|
Targeting Nuclear NOTCH2 by Gliotoxin Recovers a Tumor-Suppressor NOTCH3 Activity in CLL. Cells 2020; 9:cells9061484. [PMID: 32570839 PMCID: PMC7348714 DOI: 10.3390/cells9061484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/29/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
NOTCH signaling represents a promising therapeutic target in chronic lymphocytic leukemia (CLL). We compared the anti-neoplastic effects of the nuclear NOTCH2 inhibitor gliotoxin and the pan-NOTCH γ-secretase inhibitor RO4929097 in primary CLL cells with special emphasis on the individual roles of the different NOTCH receptors. Gliotoxin rapidly induced apoptosis in all CLL cases tested, whereas RO4929097 exerted a variable and delayed effect on CLL cell viability. Gliotoxin-induced apoptosis was associated with inhibition of the NOTCH2/FCER2 (CD23) axis together with concomitant upregulation of the NOTCH3/NR4A1 axis. In contrast, RO4929097 downregulated the NOTCH3/NR4A1 axis and counteracted the spontaneous and gliotoxin-induced apoptosis. On the cell surface, NOTCH3 and CD23 expression were mutually exclusive, suggesting that downregulation of NOTCH2 signaling is a prerequisite for NOTCH3 expression in CLL cells. ATAC-seq confirmed that gliotoxin targeted the canonical NOTCH signaling, as indicated by the loss of chromatin accessibility at the potential NOTCH/CSL site containing the gene regulatory elements. This was accompanied by a gain in accessibility at the NR4A1, NFκB, and ATF3 motifs close to the genes involved in B-cell activation, differentiation, and apoptosis. In summary, these data show that gliotoxin recovers a non-canonical tumor-suppressing NOTCH3 activity, indicating that nuclear NOTCH2 inhibitors might be beneficial compared to pan-NOTCH inhibitors in the treatment of CLL.
Collapse
|
40
|
Nadeu F, Diaz-Navarro A, Delgado J, Puente XS, Campo E. Genomic and Epigenomic Alterations in Chronic Lymphocytic Leukemia. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:149-177. [PMID: 31977296 DOI: 10.1146/annurev-pathmechdis-012419-032810] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chronic lymphocytic leukemia is a common disease in Western countries and has heterogeneous clinical behavior. The relevance of the genetic basis of the disease has come to the forefront recently, with genome-wide studies that have provided a comprehensive view of structural variants, somatic mutations, and different layers of epigenetic changes. The mutational landscape is characterized by relatively common copy number alterations, a few mutated genes occurring in 10-15% of cases, and a large number of genes mutated in a small number of cases. The epigenomic profile has revealed a marked reprogramming of regulatory regions in tumor cells compared with normal B cells. All of these alterations are differentially distributed in clinical and biological subsets of the disease, indicating that they may underlie the heterogeneous evolution of the disease. These global studies are revealing the molecular complexity of chronic lymphocytic leukemia and provide new perspectives that have helped to understand its pathogenic mechanisms and improve the clinical management of patients.
Collapse
Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; ,
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematology Department, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
| |
Collapse
|
41
|
Liu Y. Clinical implications of chromatin accessibility in human cancers. Oncotarget 2020; 11:1666-1678. [PMID: 32405341 PMCID: PMC7210018 DOI: 10.18632/oncotarget.27584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/03/2020] [Indexed: 01/19/2023] Open
Abstract
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) has not yet been widely used in cancer research. Clinical implications of chromatin accessibility assessed by ATAC-seq profiling in human cancers especially in a large patient cohort is largely unknown. In this study, we analyzed ATAC-seq data in 404 cancer patients from the Cancer Genome Atlas, representing the largest cancer patient cohort with ATAC-seq data, and correlated chromatin accessibility with patient demographics, tumor histology, molecular subtypes, and survival. Our results showed that chromatin accessibility varies from chromosome to chromosome, and is different in different genomic regions along the same chromosome. Chromatin accessibility especially on the X chromosome is strongly dependent on patient sex, but not much on patient age or tumor stage. Striking difference in chromatin accessibility is observed between lung adenocarcinoma and lung squamous cell carcinoma, the two most common histological subgroups in lung cancer. Furthermore, chromatin accessibility was different between basal and non-basal breast cancer. Finally, we identified prognostic peaks in the promoter regions that were significantly correlated with survival. In particular, we identified six peaks in the ESR1 gene promoter region in the ATAC-seq profiling and found that the peak about 247 bp away from the transcription start site was significantly associated with better survival. In conclusion, our study provides an alternative mechanism underlying tumor prognosis.
Collapse
Affiliation(s)
- Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
42
|
Tripodi IJ, Chowdhury M, Gruca M, Dowell RD. Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data. PLoS One 2020; 15:e0232332. [PMID: 32353042 PMCID: PMC7192442 DOI: 10.1371/journal.pone.0232332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/13/2020] [Indexed: 01/12/2023] Open
Abstract
The assay for transposase-accessible chromatin followed by sequencing (ATAC-seq) is an inexpensive protocol for measuring open chromatin regions. ATAC-seq is also relatively simple and requires fewer cells than many other high-throughput sequencing protocols. Therefore, it is tractable in numerous settings where other high throughput assays are challenging to impossible. Hence it is important to understand the limits of what can be inferred from ATAC-seq data. In this work, we leverage ATAC-seq to predict the presence of nascent transcription. Nascent transcription assays are the current gold standard for identifying regions of active transcription, including markers for functional transcription factor (TF) binding. We combine mapped short reads from ATAC-seq with the underlying peak sequence, to determine regions of active transcription genome-wide. We show that a hybrid signal/sequence representation classified using recurrent neural networks (RNNs) can identify these regions across different cell types.
Collapse
Affiliation(s)
- Ignacio J. Tripodi
- Computer Science, University of Colorado, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Murad Chowdhury
- Computer Science, University of Colorado, Boulder, Colorado, United States of America
| | - Margaret Gruca
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Robin D. Dowell
- Computer Science, University of Colorado, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
| |
Collapse
|
43
|
Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo ML, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens JHA. Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. Cell Rep 2020; 26:1059-1069.e6. [PMID: 30673601 PMCID: PMC6363099 DOI: 10.1016/j.celrep.2018.12.098] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Global investigation of histone marks in acute myeloid leukemia (AML) remains limited. Analyses of 38 AML samples through integrated transcriptional and chromatin mark analysis exposes 2 major subtypes. One subtype is dominated by patients with NPM1 mutations or MLL-fusion genes, shows activation of the regulatory pathways involving HOX-family genes as targets, and displays high self-renewal capacity and stemness. The second subtype is enriched for RUNX1 or spliceosome mutations, suggesting potential interplay between the 2 aberrations, and mainly depends on IRF family regulators. Cellular consequences in prognosis predict a relatively worse outcome for the first subtype. Our integrated profiling establishes a rich resource to probe AML subtypes on the basis of expression and chromatin data.
Collapse
MESH Headings
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin/pathology
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Humans
- Leukemia, Myeloid, Acute/classification
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mutation
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
Collapse
Affiliation(s)
- Guoqiang Yi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Albertus T J Wierenga
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands; Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Francesca Petraglia
- Dipartimento di Biochimica, Biofisica e Patologia generale, Università degli Studi della Campania "Luigi Vanvitelli," Vico L. De Crecchio 7, 80138 Napoli, Italy
| | - Pankaj Narang
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Eva M Janssen-Megens
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Amit Mandoli
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain
| | - Kim Berentsen
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bowon Kim
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Abhishek A Singh
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Koen H M Prange
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - André B Mulder
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Barcelona, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Jan Jacob Schuringa
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Lucia Altucci
- Dipartimento di Biochimica, Biofisica e Patologia generale, Università degli Studi della Campania "Luigi Vanvitelli," Vico L. De Crecchio 7, 80138 Napoli, Italy
| | - Edo Vellenga
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, the Netherlands.
| |
Collapse
|
44
|
Yan F, Powell DR, Curtis DJ, Wong NC. From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. Genome Biol 2020; 21:22. [PMID: 32014034 PMCID: PMC6996192 DOI: 10.1186/s13059-020-1929-3] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/08/2020] [Indexed: 12/16/2022] Open
Abstract
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis). We also review the reconstruction of transcriptional regulatory networks with multiomics data and highlight the current challenges of each step. Finally, we describe the potential of single-cell ATAC-seq and highlight the necessity of developing ATAC-seq specific analysis tools to obtain biologically meaningful insights.
Collapse
Affiliation(s)
- Feng Yan
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia
| | - David J Curtis
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.,Department of Clinical Haematology, Alfred Health, Melbourne, VIC, Australia
| | - Nicholas C Wong
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia.
| |
Collapse
|
45
|
Rendeiro AF, Krausgruber T, Fortelny N, Zhao F, Penz T, Farlik M, Schuster LC, Nemc A, Tasnády S, Réti M, Mátrai Z, Alpár D, Bödör C, Schmidl C, Bock C. Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL. Nat Commun 2020; 11:577. [PMID: 31996669 PMCID: PMC6989523 DOI: 10.1038/s41467-019-14081-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 12/11/2019] [Indexed: 01/10/2023] Open
Abstract
The Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for patients with chronic lymphocytic leukemia (CLL), despite extensive heterogeneity in this disease. To define the underlining regulatory dynamics, we analyze high-resolution time courses of ibrutinib treatment in patients with CLL, combining immune-phenotyping, single-cell transcriptome profiling, and chromatin mapping. We identify a consistent regulatory program starting with a sharp decrease of NF-κB binding in CLL cells, which is followed by reduced activity of lineage-defining transcription factors, erosion of CLL cell identity, and acquisition of a quiescence-like gene signature. We observe patient-to-patient variation in the speed of execution of this program, which we exploit to predict patient-specific dynamics in the response to ibrutinib based on the pre-treatment patient samples. In aggregate, our study describes time-dependent cellular, molecular, and regulatory effects for therapeutic inhibition of B cell receptor signaling in CLL, and it establishes a broadly applicable method for epigenome/transcriptome-based treatment monitoring. Ibrutinib, a Bruton tyrosine kinase inhibitor, provides effective treatment for chronic lymphocytic leukemia (CLL). Here, the authors describe time-dependent molecular changes to malignant cells and to the immune system in patients undergoing ibrutinib therapy, with can be used for therapy monitoring.
Collapse
Affiliation(s)
- André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fangwen Zhao
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Linda C Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Szabolcs Tasnády
- Department of Haematology and Stem Cell Transplantation, Central Hospital of Southern Pest, National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Marienn Réti
- Department of Haematology and Stem Cell Transplantation, Central Hospital of Southern Pest, National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Zoltán Mátrai
- Department of Haematology and Stem Cell Transplantation, Central Hospital of Southern Pest, National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | - Donát Alpár
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,MTA-SE Lendület Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Csaba Bödör
- MTA-SE Lendület Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria. .,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
46
|
Popova AA, Levkin PA. Precision Medicine in Oncology: In Vitro Drug Sensitivity and Resistance Test (DSRT) for Selection of Personalized Anticancer Therapy. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Anna A. Popova
- Karlsruhe Institute of TechnologyInstitute of Toxicology and Genetics Hermann‐von‐Helmholtz‐Platz 1 76344 Eggenstein‐Leopoldshafen Germany
| | - Pavel A. Levkin
- Karlsruhe Institute of TechnologyInstitute of Toxicology and Genetics Hermann‐von‐Helmholtz‐Platz 1 76344 Eggenstein‐Leopoldshafen Germany
- Karlsruhe Institute of TechnologyInstitute of Organic Chemistry Fritz‐Haber Weg 6 76131 Karlsruhe Germany
| |
Collapse
|
47
|
Korchynska S, Krassnitzer M, Malenczyk K, Prasad RB, Tretiakov EO, Rehman S, Cinquina V, Gernedl V, Farlik M, Petersen J, Hannes S, Schachenhofer J, Reisinger SN, Zambon A, Asplund O, Artner I, Keimpema E, Lubec G, Mulder J, Bock C, Pollak DD, Romanov RA, Pifl C, Groop L, Hökfelt TGM, Harkany T. Life-long impairment of glucose homeostasis upon prenatal exposure to psychostimulants. EMBO J 2020; 39:e100882. [PMID: 31750562 PMCID: PMC6939201 DOI: 10.15252/embj.2018100882] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/21/2022] Open
Abstract
Maternal drug abuse during pregnancy is a rapidly escalating societal problem. Psychostimulants, including amphetamine, cocaine, and methamphetamine, are amongst the illicit drugs most commonly consumed by pregnant women. Neuropharmacology concepts posit that psychostimulants affect monoamine signaling in the nervous system by their affinities to neurotransmitter reuptake and vesicular transporters to heighten neurotransmitter availability extracellularly. Exacerbated dopamine signaling is particularly considered as a key determinant of psychostimulant action. Much less is known about possible adverse effects of these drugs on peripheral organs, and if in utero exposure induces lifelong pathologies. Here, we addressed this question by combining human RNA-seq data with cellular and mouse models of neuroendocrine development. We show that episodic maternal exposure to psychostimulants during pregnancy coincident with the intrauterine specification of pancreatic β cells permanently impairs their ability of insulin production, leading to glucose intolerance in adult female but not male offspring. We link psychostimulant action specifically to serotonin signaling and implicate the sex-specific epigenetic reprogramming of serotonin-related gene regulatory networks upstream from the transcription factor Pet1/Fev as determinants of reduced insulin production.
Collapse
Affiliation(s)
- Solomiia Korchynska
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Maria Krassnitzer
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Katarzyna Malenczyk
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Rashmi B Prasad
- Department of Clinical Sciences, Diabetes and Endocrinology CRCSkåne University Hospital MalmöMalmöSweden
| | - Evgenii O Tretiakov
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Sabah Rehman
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Valentina Cinquina
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Victoria Gernedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Julian Petersen
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Sophia Hannes
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Julia Schachenhofer
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Sonali N Reisinger
- Department of Neurophysiology and NeuropharmacologyCenter for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Alice Zambon
- Department of Neurophysiology and NeuropharmacologyCenter for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Olof Asplund
- Department of Clinical Sciences, Diabetes and Endocrinology CRCSkåne University Hospital MalmöMalmöSweden
| | - Isabella Artner
- Stem Cell CenterLund UniversityLundSweden
- Endocrine Cell Differentiation and FunctionLund University Diabetes CenterLund UniversityMalmöSweden
| | - Erik Keimpema
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Gert Lubec
- Paracelsus Medical UniversitySalzburgAustria
| | - Jan Mulder
- Science for Life LaboratoryKarolinska InstitutetSolnaSweden
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Daniela D Pollak
- Department of Neurophysiology and NeuropharmacologyCenter for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Roman A Romanov
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Christian Pifl
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology CRCSkåne University Hospital MalmöMalmöSweden
- Institute for Molecular Medicine Finland (FIMM)Helsinki UniversityHelsinkiFinland
| | | | - Tibor Harkany
- Department of Molecular NeurosciencesCenter for Brain ResearchMedical University of ViennaViennaAustria
- Department of NeuroscienceKarolinska InstitutetSolnaSweden
| |
Collapse
|
48
|
Cinquina V, Calvigioni D, Farlik M, Halbritter F, Fife-Gernedl V, Shirran SL, Fuszard MA, Botting CH, Poullet P, Piscitelli F, Máté Z, Szabó G, Yanagawa Y, Kasper S, Di Marzo V, Mackie K, McBain CJ, Bock C, Keimpema E, Harkany T. Life-long epigenetic programming of cortical architecture by maternal 'Western' diet during pregnancy. Mol Psychiatry 2020; 25:22-36. [PMID: 31735910 DOI: 10.1038/s41380-019-0580-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 10/11/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023]
Abstract
The evolution of human diets led to preferences toward polyunsaturated fatty acid (PUFA) content with 'Western' diets enriched in ω-6 PUFAs. Mounting evidence points to ω-6 PUFA excess limiting metabolic and cognitive processes that define longevity in humans. When chosen during pregnancy, ω-6 PUFA-enriched 'Western' diets can reprogram maternal bodily metabolism with maternal nutrient supply precipitating the body-wide imprinting of molecular and cellular adaptations at the level of long-range intercellular signaling networks in the unborn fetus. Even though unfavorable neurological outcomes are amongst the most common complications of intrauterine ω-6 PUFA excess, cellular underpinnings of life-long modifications to brain architecture remain unknown. Here, we show that nutritional ω-6 PUFA-derived endocannabinoids desensitize CB1 cannabinoid receptors, thus inducing epigenetic repression of transcriptional regulatory networks controlling neuronal differentiation. We found that cortical neurons lose their positional identity and axonal selectivity when mouse fetuses are exposed to excess ω-6 PUFAs in utero. Conversion of ω-6 PUFAs into endocannabinoids disrupted the temporal precision of signaling at neuronal CB1 cannabinoid receptors, chiefly deregulating Stat3-dependent transcriptional cascades otherwise required to execute neuronal differentiation programs. Global proteomics identified the immunoglobulin family of cell adhesion molecules (IgCAMs) as direct substrates, with DNA methylation and chromatin accessibility profiling uncovering epigenetic reprogramming at >1400 sites in neurons after prolonged cannabinoid exposure. We found anxiety and depression-like behavioral traits to manifest in adult offspring, which is consistent with genetic models of reduced IgCAM expression, to suggest causality for cortical wiring defects. Overall, our data uncover a regulatory mechanism whose disruption by maternal food choices could limit an offspring's brain function for life.
Collapse
Affiliation(s)
- Valentina Cinquina
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Daniela Calvigioni
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Florian Halbritter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Fife-Gernedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sally L Shirran
- School of Chemistry, University of St. Andrews, St. Andrews, United Kingdom
| | - Matthew A Fuszard
- School of Chemistry, University of St. Andrews, St. Andrews, United Kingdom.,Faculty of Medicine, Martin-Luther University, Halle-Wittenberg, Halle, Germany
| | | | | | - Fabiana Piscitelli
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Pozzuoli, Italy
| | - Zoltán Máté
- Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gábor Szabó
- Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Yuchio Yanagawa
- Department of Genetic and Behavioral Neuroscience, Gunma University School of Medicine, Maebashi, Japan
| | - Siegfried Kasper
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Pozzuoli, Italy.,Canada Excellence Research Chair, Institut Universitaire de Cardiologie et de Pneumologie de Québec and Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Québec, QC, Canada
| | - Ken Mackie
- Department of Psychological & Brain Sciences, Indiana University, Bloomington, Indiana, USA
| | - Chris J McBain
- Program in Developmental Neuroscience, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, NIH, Bethesda, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Erik Keimpema
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria. .,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
49
|
Eckert C, Groeneveld-Krentz S, Kirschner-Schwabe R, Hagedorn N, Chen-Santel C, Bader P, Borkhardt A, Cario G, Escherich G, Panzer-Grümayer R, Astrahantseff K, Eggert A, Sramkova L, Attarbaschi A, Bourquin JP, Peters C, Henze G, von Stackelberg A. Improving Stratification for Children With Late Bone Marrow B-Cell Acute Lymphoblastic Leukemia Relapses With Refined Response Classification and Integration of Genetics. J Clin Oncol 2019; 37:3493-3506. [DOI: 10.1200/jco.19.01694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Minimal residual disease (MRD) helps to accurately assess when children with late bone marrow relapses of B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) will benefit from allogeneic hematopoietic stem-cell transplantation (allo-HSCT). More detailed dissection of MRD response heterogeneity and the specific genetic aberrations could improve current practice. PATIENTS AND METHODS MRD was assessed after induction treatment and at different times during relapse treatment until allo-HSCT (indicated in poor responders to induction; MRD ≥ 10−3) for patients being treated for late BCP-ALL bone marrow relapses (n = 413; median follow-up, 9.4 years) in the ALL-REZ BFM 2002 trial/registry (ClinicalTrials.gov identifier: NCT00114348 ). RESULTS Patients with both good (MRD < 10−3) and poor responses to induction treatment reached excellent event-free survival (EFS; 72% v 65%) and overall survival (OS; 82% v 74%). Patients with MRD of 10−2 or greater after induction had reduced EFS (56%), and their MRD persisted until allo-HSCT more frequently than it did in patients with MRD of 10−3 or greater to less than 10−2 ( P = .037). Patients with 25% or more leukemic blasts after induction (early nonresponders) had the poorest prognosis (EFS, 22%). Interestingly, patients with MRD of 10−3 or greater before allo-HSCT (late nonresponders) still had an EFS of 50% and OS of 63%, which in principle justifies allo-HSCT in these patients. From a panel of selected candidate genes, TP53 alterations (frequency, 8%) were the only genetic alteration with independent prognostic value in any MRD-based response subgroup. CONCLUSION After induction treatment, MRD-based treatment stratification resulted in excellent survival in patients with late relapsed BCP-ALL. Prognosis could be further improved in very poor responders by intensifying treatment directly after induction. TP53 alterations can be defined as a novel genetic high-risk marker in all MRD response groups in late relapsed BCP-ALL. Here we identified early and late nonresponders to be considered as events in future trials.
Collapse
Affiliation(s)
- Cornelia Eckert
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | - Renate Kirschner-Schwabe
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | | | - Peter Bader
- University Hospital Frankfurt, Frankfurt, Germany
| | | | - Gunnar Cario
- University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Angelika Eggert
- Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium, and German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | | - Günter Henze
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | | |
Collapse
|
50
|
Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Rep 2019; 29:3147-3159.e12. [DOI: 10.1016/j.celrep.2019.10.106] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 09/20/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022] Open
|