1
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Stephenson-Gussinye A, Rendón-Bautista LA, Ruiz-Medina BE, Blanco-Olais E, Pérez-Molina R, Marcial-Medina C, Chavarri-Guerra Y, Soto-Pérez-de-Celis E, Morales-Alfaro A, Esquivel-López A, Candanedo-González F, Gamboa-Domínguez A, Cortes-González R, Alfaro-Goldaracena A, Vázquez-Manjarrez SE, Grajales-Figueroa G, Astudillo-Romero B, Ruiz-Manriquez J, Poot-Hernández AC, Licona-Limón P, Furlan-Magaril M. Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis. Front Mol Biosci 2024; 11:1420308. [PMID: 39239354 PMCID: PMC11375512 DOI: 10.3389/fmolb.2024.1420308] [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: 04/19/2024] [Accepted: 07/16/2024] [Indexed: 09/07/2024] Open
Abstract
Molecular and cellular characterization of tumors is essential due to the complex and heterogeneous nature of cancer. In recent decades, many bioinformatic tools and experimental techniques have been developed to achieve personalized characterization of tumors. However, sample handling continues to be a major challenge as limitations such as prior treatments before sample acquisition, the amount of tissue obtained, transportation, or the inability to process fresh samples pose a hurdle for experimental strategies that require viable cell suspensions. Here, we present an optimized protocol that allows the recovery of highly viable cell suspensions from breast cancer primary tumor biopsies. Using these cell suspensions we have successfully characterized genome architecture through Hi-C. Also, we have evaluated single-cell gene expression and the tumor cellular microenvironment through single-cell RNAseq. Both technologies are key in the detailed and personalized molecular characterization of tumor samples. The protocol described here is a cost-effective alternative to obtain viable cell suspensions from biopsies simply and efficiently.
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Affiliation(s)
- Aura Stephenson-Gussinye
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Luis A Rendón-Bautista
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Blanca E Ruiz-Medina
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Eduardo Blanco-Olais
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Rosario Pérez-Molina
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Cleofas Marcial-Medina
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Yanin Chavarri-Guerra
- Department of Hemato-Oncology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Enrique Soto-Pérez-de-Celis
- Department of Geriatrics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Department of Medicine, Division of Medical Oncology, University of Colorado Cancer Center, Denver, CO, United States
| | - Andrea Morales-Alfaro
- Department of Medicine, Division of Medical Oncology, University of Colorado Cancer Center, Denver, CO, United States
| | - Ayerim Esquivel-López
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Fernando Candanedo-González
- Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Armando Gamboa-Domínguez
- Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Rubén Cortes-González
- Surgical Oncology Service, Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alejandro Alfaro-Goldaracena
- Surgical Oncology Service, Department of Surgery, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Sara E Vázquez-Manjarrez
- Department of Radiology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Guido Grajales-Figueroa
- Department of Gastrointestinal Endoscopy, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Beatriz Astudillo-Romero
- Department of Gastrointestinal Endoscopy, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jesús Ruiz-Manriquez
- Department of Gastrointestinal Endoscopy, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - A César Poot-Hernández
- Unidad de Bioinformática y Manejo de Información, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Paula Licona-Limón
- Department of Cellular and Developmental Biology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Molecular Genetics Department, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
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2
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Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y, Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA, Lupien M, Feng FY. Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer. Nat Genet 2024; 56:1689-1700. [PMID: 39020220 PMCID: PMC11319208 DOI: 10.1038/s41588-024-01826-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
The impact of variations in the three-dimensional structure of the genome has been recognized, but solid cancer tissue studies are limited. Here, we performed integrated deep Hi-C sequencing with matched whole-genome sequencing, whole-genome bisulfite sequencing, 5-hydroxymethylcytosine (5hmC) sequencing and RNA sequencing across a cohort of 80 biopsy samples from patients with metastatic castration-resistant prostate cancer. Dramatic differences were present in gene expression, 5-methylcytosine/5hmC methylation and in structural variation versus mutation rate between A and B (open and closed) chromatin compartments. A subset of tumors exhibited depleted regional chromatin contacts at the AR locus, linked to extrachromosomal circular DNA (ecDNA) and worse response to AR signaling inhibitors. We also identified topological subtypes associated with stark differences in methylation structure, gene expression and prognosis. Our data suggested that DNA interactions may predispose to structural variant formation, exemplified by the recurrent TMPRSS2-ERG fusion. This comprehensive integrated sequencing effort represents a unique clinical tumor resource.
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Grants
- P50 CA097186 NCI NIH HHS
- 1DP2CA271832-01, P30 CA014520 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- DP2 CA271832 NCI NIH HHS
- P50 CA186786 NCI NIH HHS
- R01 CA251245, P50 CA097186, P50 CA186786, P50 CA186786-07S1, P30 CA046592, and W81XWH-20-1-0405 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- P30 CA046592 NCI NIH HHS
- R01 CA251245 NCI NIH HHS
- P30 CA014520 NCI NIH HHS
- W81XWH2010799 U.S. Department of Defense (United States Department of Defense)
- W81XWH-21-1-0046 U.S. Department of Defense (United States Department of Defense)
- SU2C-AACR-DT0812 EIF | Stand Up To Cancer (SU2C)
- Prostate Cancer Foundation (PCF)
- UCSF Benioff Initiative for Prostate Cancer Research
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- Canadian Institute of Health Research (CIHR) (FRN-153234 & 168933), the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) (FRN-158225), the Ontario Institute for Cancer Research (OICR) through funding provided by the Government of Ontario (IA 031), and the Princess Margaret Cancer Foundation.
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Affiliation(s)
- Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Madison, WI, USA
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Thaidy Moreno-Rodriguez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Arian Lundberg
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Chu Pan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - James R Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alana S Weinstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa N Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas R Rydzewski
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly Lynch
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshi J Alumkal
- Department of Internal Medicine, Division of Hematology-Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Hansen H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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3
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Lucini F, Petrini C, Salviato E, Pal K, Rosti V, Gorini F, Santarelli P, Quadri R, Lembo G, Graziano G, Di Patrizio Soldateschi E, Tagliaferri I, Pinatel E, Sebestyén E, Rotta L, Gentile F, Vaira V, Lanzuolo C, Ferrari F. Biochemical properties of chromatin domains define genome compartmentalization. Nucleic Acids Res 2024; 52:e54. [PMID: 38808669 PMCID: PMC11229364 DOI: 10.1093/nar/gkae454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/22/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10 000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their compartmentalization in one single experiment.
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Affiliation(s)
- Federica Lucini
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Cristiano Petrini
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Elisa Salviato
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Koustav Pal
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Valentina Rosti
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Francesca Gorini
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Philina Santarelli
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Roberto Quadri
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
| | - Giovanni Lembo
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Giulia Graziano
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Emanuele Di Patrizio Soldateschi
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | | | - Eva Pinatel
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Endre Sebestyén
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Luca Rotta
- IEO, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Francesco Gentile
- Fondazione IRCCS Ca’ Granda-Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Valentina Vaira
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Lanzuolo
- INGM, Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan 20122, Italy
- ITB-CNR, Institute of Biomedical Technologies, National Research Council, Segrate 20054, Italy
| | - Francesco Ferrari
- IFOM-ETS, The AIRC Institute of Molecular Oncology, Milan 20139, Italy
- IGM-CNR, Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Pavia 27100, Italy
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4
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Mulet-Lazaro R, van Herk S, Nuetzel M, Sijs-Szabo A, Díaz N, Kelly K, Erpelinck-Verschueren C, Schwarzfischer-Pfeilschifter L, Stanewsky H, Ackermann U, Glatz D, Raithel J, Fischer A, Pohl S, Rijneveld A, Vaquerizas JM, Thiede C, Plass C, Wouters BJ, Delwel R, Rehli M, Gebhard C. Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia. Nat Commun 2024; 15:5693. [PMID: 38972954 PMCID: PMC11228033 DOI: 10.1038/s41467-024-49811-y] [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: 08/11/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Leukemias with ambiguous lineage comprise several loosely defined entities, often without a clear mechanistic basis. Here, we extensively profile the epigenome and transcriptome of a subgroup of such leukemias with CpG Island Methylator Phenotype. These leukemias exhibit comparable hybrid myeloid/lymphoid epigenetic landscapes, yet heterogeneous genetic alterations, suggesting they are defined by their shared epigenetic profile rather than common genetic lesions. Gene expression enrichment reveals similarity with early T-cell precursor acute lymphoblastic leukemia and a lymphoid progenitor cell of origin. In line with this, integration of differential DNA methylation and gene expression shows widespread silencing of myeloid transcription factors. Moreover, binding sites for hematopoietic transcription factors, including CEBPA, SPI1 and LEF1, are uniquely inaccessible in these leukemias. Hypermethylation also results in loss of CTCF binding, accompanied by changes in chromatin interactions involving key transcription factors. In conclusion, epigenetic dysregulation, and not genetic lesions, explains the mixed phenotype of this group of leukemias with ambiguous lineage. The data collected here constitute a useful and comprehensive epigenomic reference for subsequent studies of acute myeloid leukemias, T-cell acute lymphoblastic leukemias and mixed-phenotype leukemias.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Aniko Sijs-Szabo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Renewable Marine Resources Department, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Katherine Kelly
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Erpelinck-Verschueren
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Raithel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sandra Pohl
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Anita Rijneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital 8 Campus, London, United Kingdom
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bas J Wouters
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
| | - Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
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5
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Murtaza G, Butaney B, Wagner J, Singh R. scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression. Bioinformatics 2024; 40:i490-i500. [PMID: 38940151 PMCID: PMC11256916 DOI: 10.1093/bioinformatics/btae223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
SUMMARY Single-cell Hi-C (scHi-C) protocol helps identify cell-type-specific chromatin interactions and sheds light on cell differentiation and disease progression. Despite providing crucial insights, scHi-C data is often underutilized due to the high cost and the complexity of the experimental protocol. We present a deep learning framework, scGrapHiC, that predicts pseudo-bulk scHi-C contact maps using pseudo-bulk scRNA-seq data. Specifically, scGrapHiC performs graph deconvolution to extract genome-wide single-cell interactions from a bulk Hi-C contact map using scRNA-seq as a guiding signal. Our evaluations show that scGrapHiC, trained on seven cell-type co-assay datasets, outperforms typical sequence encoder approaches. For example, scGrapHiC achieves a substantial improvement of 23.2% in recovering cell-type-specific Topologically Associating Domains over the baselines. It also generalizes to unseen embryo and brain tissue samples. scGrapHiC is a novel method to generate cell-type-specific scHi-C contact maps using widely available genomic signals that enables the study of cell-type-specific chromatin interactions. AVAILABILITY AND IMPLEMENTATION The GitHub link: https://github.com/rsinghlab/scGrapHiC contains the source code of scGrapHiC and associated scripts to preprocess publicly available datasets to produce the results and visualizations we have discuss in this manuscript.
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Affiliation(s)
- Ghulam Murtaza
- Department of Computer Science, Brown University, 115 Waterman Street, Providence, RI, 02912, United States
| | - Byron Butaney
- Department of Computer Science, Brown University, 115 Waterman Street, Providence, RI, 02912, United States
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, United States
| | - Ritambhara Singh
- Department of Computer Science, Brown University, 115 Waterman Street, Providence, RI, 02912, United States
- Center for Computational Molecular Biology, Brown University, 164 Angell Street, Providence, RI, 02912, United States
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6
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Liu R, Xu R, Yan S, Li P, Jia C, Sun H, Sheng K, Wang Y, Zhang Q, Guo J, Xin X, Li X, Guo D. Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells. Front Genet 2024; 15:1377238. [PMID: 38586584 PMCID: PMC10995239 DOI: 10.3389/fgene.2024.1377238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianhao Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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7
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Romero MA, Pyle AD. 'Enhancing' skeletal muscle and stem cells in three-dimensions: genome regulation of skeletal muscle in development and disease. Curr Opin Genet Dev 2023; 83:102133. [PMID: 37951138 PMCID: PMC10872784 DOI: 10.1016/j.gde.2023.102133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/09/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
The noncoding genome imparts important regulatory control over gene expression. In particular, gene enhancers represent a critical layer of control that integrates developmental and differentiation signals outside the cell into transcriptional outputs inside the cell. Recently, there has been an explosion in genomic techniques to probe enhancer control, function, and regulation. How enhancers are regulated and integrate signals in stem cell development and differentiation is largely an open question. In this review, we focus on the role gene enhancers play in muscle stem cell specification, differentiation, and progression. We pay specific attention toward the identification of muscle-specific enhancers, the binding of transcription factors to these enhancers, and how enhancers communicate to their target genes via three-dimensional looping.
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Affiliation(s)
- Matthew A Romero
- Department of Microbiology, Immunology and Molecular Genetics, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
| | - April D Pyle
- Department of Microbiology, Immunology and Molecular Genetics, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA.
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8
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Ing-Simmons E, Machnik N, Vaquerizas JM. Reply to: Revisiting the use of structural similarity index in Hi-C. Nat Genet 2023; 55:2053-2055. [PMID: 38052961 DOI: 10.1038/s41588-023-01595-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/25/2023] [Indexed: 12/07/2023]
Affiliation(s)
- Elizabeth Ing-Simmons
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Nick Machnik
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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9
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Lee H, Blumberg B, Lawrence MS, Shioda T. Revisiting the use of structural similarity index in Hi-C. Nat Genet 2023; 55:2049-2052. [PMID: 38052962 DOI: 10.1038/s41588-023-01594-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/17/2023] [Indexed: 12/07/2023]
Affiliation(s)
- Hanjun Lee
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Pathology, Harvard Medical School, Charlestown, MA, USA.
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Michael S Lawrence
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Harvard Medical School, Charlestown, MA, USA
| | - Toshihiro Shioda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, USA.
- Department of Medicine, Harvard Medical School, Charlestown, MA, USA.
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10
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Dai D, Xie C, Zhou Y, Bo D, Zhang S, Mao S, Liao Y, Cui S, Zhu Z, Wang X, Li F, Peng D, Zheng J, Sun M. Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization. Nat Commun 2023; 14:7156. [PMID: 37935661 PMCID: PMC10630426 DOI: 10.1038/s41467-023-42700-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
The formation and consequences of polyploidization in animals with clonal reproduction remain largely unknown. Clade I root-knot nematodes (RKNs), characterized by parthenogenesis and allopolyploidy, show a widespread geographical distribution and extensive agricultural destruction. Here, we generated 4 unzipped polyploid RKN genomes and identified a putative novel alternative telomeric element. Then we reconstructed 4 chromosome-level assemblies and resolved their genome structures as AAB for triploid and AABB for tetraploid. The phylogeny of subgenomes revealed polyploid RKN origin patterns as hybridization between haploid and unreduced gametes. We also observed extensive chromosomal fusions and homologous gene expression decrease after polyploidization, which might offset the disadvantages of clonal reproduction and increase fitness in polyploid RKNs. Our results reveal a rare pathway of polyploidization in parthenogenic polyploid animals and provide a large number of high-precision genetic resources that could be used for RKN prevention and control.
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Affiliation(s)
- Dadong Dai
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuanshuai Xie
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yayi Zhou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dexin Bo
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shurong Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengqiang Mao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yucheng Liao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Simeng Cui
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhaolu Zhu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueyu Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fanling Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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11
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Ishibashi R. Multidimensional scaling methods can reconstruct genomic DNA loops using Hi-C data properties. PLoS One 2023; 18:e0289651. [PMID: 37590265 PMCID: PMC10434948 DOI: 10.1371/journal.pone.0289651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/23/2023] [Indexed: 08/19/2023] Open
Abstract
This paper proposes multidimensional scaling (MDS) applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Currently, the mechanisms underlying the regulation of gene expression are poorly understood, and where and when DNA loops are formed remains undetermined. Previous studies have focused on reproducing the entire three-dimensional structure of chromatin; however, identifying DNA loops using these data is time-consuming and difficult. MDS is an unsupervised method for reconstructing the original coordinates from a distance matrix. Here, MDS was applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Hi-C data were converted to distances by taking the inverse to reproduce loops via MDS, and the missing values were set to zero. Using the converted data, MDS was applied to the log-transformed genomic coordinate distances and this process successfully reproduced the DNA loops in the given structure. Consequently, the reconstructed DNA loops revealed significantly more DNA-transcription factor interactions involved in DNA loop formation than those obtained from previously applied methods. Furthermore, the reconstructed DNA loops were significantly consistent with chromatin immunoprecipitation followed by sequencing (ChIP-seq) peak positions. In conclusion, the proposed method is an improvement over previous methods for identifying DNA loops.
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Affiliation(s)
- Ryo Ishibashi
- Department of Physics, Chuo University, Tokyo, Japan
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12
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Li H, He X, Kurowski L, Zhang R, Zhao D, Zeng J. Improving comparative analyses of Hi-C data via contrastive self-supervised learning. Brief Bioinform 2023; 24:bbad193. [PMID: 37287135 DOI: 10.1093/bib/bbad193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Hi-C is a widely applied chromosome conformation capture (3C)-based technique, which has produced a large number of genomic contact maps with high sequencing depths for a wide range of cell types, enabling comprehensive analyses of the relationships between biological functionalities (e.g. gene regulation and expression) and the three-dimensional genome structure. Comparative analyses play significant roles in Hi-C data studies, which are designed to make comparisons between Hi-C contact maps, thus evaluating the consistency of replicate Hi-C experiments (i.e. reproducibility measurement) and detecting statistically differential interacting regions with biological significance (i.e. differential chromatin interaction detection). However, due to the complex and hierarchical nature of Hi-C contact maps, it remains challenging to conduct systematic and reliable comparative analyses of Hi-C data. Here, we proposed sslHiC, a contrastive self-supervised representation learning framework, for precisely modeling the multi-level features of chromosome conformation and automatically producing informative feature embeddings for genomic loci and their interactions to facilitate comparative analyses of Hi-C contact maps. Comprehensive computational experiments on both simulated and real datasets demonstrated that our method consistently outperformed the state-of-the-art baseline methods in providing reliable measurements of reproducibility and detecting differential interactions with biological meanings.
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Affiliation(s)
- Han Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Xuan He
- Machine Learning Department, Silexon AI Technology Co., Ltd., 210000 Nanjing, China
| | - Lawrence Kurowski
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Ruotian Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084 Beijing, China
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13
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Stephenson-Gussinye A, Furlan-Magaril M. Chromosome conformation capture technologies as tools to detect structural variations and their repercussion in chromatin 3D configuration. Front Cell Dev Biol 2023; 11:1219968. [PMID: 37457299 PMCID: PMC10346842 DOI: 10.3389/fcell.2023.1219968] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
3D genome organization regulates gene expression in different physiological and pathological contexts. Characterization of chromatin structure at different scales has provided information about how the genome organizes in the nuclear space, from chromosome territories, compartments of euchromatin and heterochromatin, topologically associated domains to punctual chromatin loops between genomic regulatory elements and gene promoters. In recent years, chromosome conformation capture technologies have also been used to characterize structural variations (SVs) de novo in pathological conditions. The study of SVs in cancer, has brought information about transcriptional misregulation that relates directly to the incidence and prognosis of the disease. For example, gene fusions have been discovered arising from chromosomal translocations that upregulate oncogenes expression, and other types of SVs have been described that alter large genomic regions encompassing many genes. However, studying SVs in 2D cannot capture all their regulatory implications in the genome. Recently, several bioinformatic tools have been developed to identify and classify SVs from chromosome conformation capture data and clarify how they impact chromatin structure in 3D, resulting in transcriptional misregulation. Here, we review recent literature concerning bioinformatic tools to characterize SVs from chromosome conformation capture technologies and exemplify their vast potential to rebuild the 3D landscape of genomes in cancer. The study of SVs from the 3D perspective can produce essential information about drivers, molecular targets, and disease evolution.
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14
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Guo Q, Wu S, Geschwind DH. Characterization of Gene Regulatory Elements in Human Fetal Cortical Development: Enhancing Our Understanding of Neurodevelopmental Disorders and Evolution. Dev Neurosci 2023; 46:69-83. [PMID: 37231806 DOI: 10.1159/000530929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
The neocortex is the region that most distinguishes human brain from other mammals and primates [Annu Rev Genet. 2021 Nov;55(1):555-81]. Studying the development of human cortex is important in understanding the evolutionary changes occurring in humans relative to other primates, as well as in elucidating mechanisms underlying neurodevelopmental disorders. Cortical development is a highly regulated process, spatially and temporally coordinated by expression of essential transcriptional factors in response to signaling pathways [Neuron. 2019 Sep;103(6):980-1004]. Enhancers are the most well-understood cis-acting, non-protein-coding regulatory elements that regulate gene expression [Nat Rev Genet. 2014 Apr;15(4):272-86]. Importantly, given the conservation of both DNA sequence and molecular function of the majority of proteins across mammals [Genome Res. 2003 Dec;13(12):2507-18], enhancers [Science. 2015 Mar;347(6226):1155-9], which are far more divergent at the sequence level, likely account for the phenotypes that distinguish the human brain by changing the regulation of gene expression. In this review, we will revisit the conceptual framework of gene regulation during human brain development, as well as the evolution of technologies to study transcriptional regulation, with recent advances in genome biology that open a window allowing us to systematically characterize cis-regulatory elements in developing human brain [Hum Mol Genet. 2022 Oct;31(R1):R84-96]. We provide an update on work to characterize the suite of all enhancers in the developing human brain and the implications for understanding neuropsychiatric disorders. Finally, we discuss emerging therapeutic ideas that utilize our emerging knowledge of enhancer function.
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Affiliation(s)
- Qiuyu Guo
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, USA
- Center for Autism Research and Treatment, Semel Institute, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Sarah Wu
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, USA
| | - Daniel H Geschwind
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, USA
- Center for Autism Research and Treatment, Semel Institute, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Institute of Precision Health, University of California Los Angeles, Los Angeles, California, USA
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15
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Dozmorov MG, Marshall MA, Rashid NS, Grible JM, Valentine A, Olex AL, Murthy K, Chakraborty A, Reyna J, Figueroa DS, Hinojosa-Gonzalez L, Da-Inn Lee E, Baur BA, Roy S, Ay F, Harrell JC. Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Sci Rep 2023; 13:5420. [PMID: 37012431 PMCID: PMC10070455 DOI: 10.1038/s41598-023-32568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. Cancer-associated copy number variants and single nucleotide polymorphisms promote rewiring of chromatin loops, disruption of topologically associating domains (TADs), active/inactive chromatin state switching, leading to oncogene expression and silencing of tumor suppressors. However, little is known about 3D changes during cancer progression to a chemotherapy-resistant state. We integrated chromatin conformation capture (Hi-C), RNA-seq, and whole-genome sequencing obtained from triple-negative breast cancer patient-derived xenograft primary tumors (UCD52) and carboplatin-resistant samples and found increased short-range (< 2 Mb) interactions, chromatin looping, formation of TAD, chromatin state switching into a more active state, and amplification of ATP-binding cassette transporters. Transcriptome changes suggested the role of long-noncoding RNAs in carboplatin resistance. Rewiring of the 3D genome was associated with TP53, TP63, BATF, FOS-JUN family of transcription factors and led to activation of aggressiveness-, metastasis- and other cancer-related pathways. Integrative analysis highlighted increased ribosome biogenesis and oxidative phosphorylation, suggesting the role of mitochondrial energy metabolism. Our results suggest that 3D genome remodeling may be a key mechanism underlying carboplatin resistance.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| | - Maggie A Marshall
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Narmeen S Rashid
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Jacqueline M Grible
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aaron Valentine
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Biochemistry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Kavita Murthy
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Abhijit Chakraborty
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Joaquin Reyna
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Daniela Salgado Figueroa
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Laura Hinojosa-Gonzalez
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Erika Da-Inn Lee
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Brittany A Baur
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Ferhat Ay
- Center for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
- Department of Pediatrics, UC San Diego-School of Medicine, La Jolla, CA, 92093, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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16
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Weigert R, Hetzel S, Bailly N, Haggerty C, Ilik IA, Yung PYK, Navarro C, Bolondi A, Kumar AS, Anania C, Brändl B, Meierhofer D, Lupiáñez DG, Müller FJ, Aktas T, Elsässer SJ, Kretzmer H, Smith ZD, Meissner A. Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nat Cell Biol 2023; 25:579-591. [PMID: 37024684 PMCID: PMC10104784 DOI: 10.1038/s41556-023-01114-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/21/2023] [Indexed: 04/08/2023]
Abstract
DNA and Histone 3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb repressive complexes regulate the unmethylated CpG-rich promoters of developmental genes. In contrast to this general framework, the extra-embryonic lineages display non-canonical, globally intermediate DNA methylation levels, including disruption of local Polycomb domains. Here, to better understand this unusual landscape's molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse trophoblast stem cells. We find that the extra-embryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized molecular appearance, our data point to a highly controlled equilibrium between counteracting repressors within extra-embryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.
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Affiliation(s)
- Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Medical Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Nina Bailly
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Chuck Haggerty
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Ibrahim A Ilik
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Philip Yuk Kwong Yung
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Carmen Navarro
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chiara Anania
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Björn Brändl
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany
| | - David Meierhofer
- Mass Spectrometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Franz-Josef Müller
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany
| | - Tugce Aktas
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA.
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, US.
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17
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Gridina MM, Vesna E, Minzhenkova ME, Shilova NV, Ryzhkova OP, Nazarenko LP, Belyaeva EO, Lebedev IN, Fishman VS. Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries. Vavilovskii Zhurnal Genet Selektsii 2023; 27:83-87. [PMID: 36923477 PMCID: PMC10009481 DOI: 10.18699/vjgb-23-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023] Open
Abstract
The genome-wide variant of the chromatin conformation capture technique (Hi-C) is a powerful tool for revealing patterns of genome spatial organization, as well as for understanding the effects of their disturbance on disease development. In addition, Hi-C can be used to detect chromosomal rearrangements, including balanced translocations and inversions. The use of the Hi-C method for the detection of chromosomal rearrangements is becoming more widespread. Modern high-throughput methods of genome analysis can effectively reveal point mutations and unbalanced chromosomal rearrangements. However, their sensitivity for determining translocations and inversions remains rather low. The storage of whole blood samples can affect the amount and integrity of genomic DNA, and it can distort the results of subsequent analyses if the storage was not under proper conditions. The Hi-C method is extremely demanding on the input material. The necessary condition for successfully applying Hi-C and obtaining high-quality data is the preservation of the spatial chromatin organization within the nucleus. The purpose of this study was to determine the optimal storage conditions of blood samples for subsequent Hi-C analysis. We selected 10 different conditions for blood storage and sample processing. For each condition, we prepared and sequenced Hi-C libraries. The quality of the obtained data was compared. As a result of the work, we formulated the requirements for the storage and processing of samples to obtain high-quality Hi-C data. We have established the minimum volume of blood sufficient for conducting Hi-C analysis. In addition, we have identified the most suitable methods for isolation of peripheral blood mononuclear cells and their long-term storage. The main requirement we have formulated is not to freeze whole blood.
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Affiliation(s)
- M M Gridina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E Vesna
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - N V Shilova
- Research Centre for Medical Genetics, Moscow, Russia
| | - O P Ryzhkova
- Research Centre for Medical Genetics, Moscow, Russia
| | - L P Nazarenko
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E O Belyaeva
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I N Lebedev
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V S Fishman
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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18
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Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JHY, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F. Subtype-specific 3D genome alteration in acute myeloid leukaemia. Nature 2022; 611:387-398. [PMID: 36289338 PMCID: PMC10060167 DOI: 10.1038/s41586-022-05365-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.
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Affiliation(s)
- Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Fan Song
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Bioinformatics and Genomics Graduate Program, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Huijue Lyu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mikoto Kobayashi
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Baozhen Zhang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ziyu Zhao
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bei Jia
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Lena Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Josiah Hiu-Yuen Wong
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yihao Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA
| | - Sinisa Dovat
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Yue Yang
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Tomoko Yamada
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Aaron D Viny
- Division of Hematology/Oncology and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Claxton
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Penn State University, Hershey, PA, USA
| | - Hong Zheng
- Department of Medicine, Division of Hematology and Oncology, Penn State Cancer Institute, Penn State University, Hershey, PA, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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19
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Gridina M, Taskina A, Lagunov T, Nurislamov A, Kulikova T, Krasikova A, Fishman V. Comparison and critical assessment of single-cell Hi-C protocols. Heliyon 2022; 8:e11023. [PMID: 36281413 PMCID: PMC9587272 DOI: 10.1016/j.heliyon.2022.e11023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/13/2022] [Accepted: 10/06/2022] [Indexed: 01/24/2023] Open
Abstract
Advances in single-cell sequencing technologies make it possible to study the genome architecture in single cells. The rapid growth of the field has been fueled by the development of innovative single-cell Hi-C protocols. However, the protocols vary considerably in their efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. Here, we compare the two most commonly used single-cell Hi-C protocols. We use long-read sequencing to analyze molecular products of the Hi-C assay and show that whole-genome amplification step results in increased number of artifacts, larger coverage biases, and increased amount of noise compared to PCR-based amplification. Our comparison provides guidance for researchers studying chromatin architecture in individual cells.
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20
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Rico D, Kent D, Karataraki N, Mikulasova A, Berlinguer-Palmini R, Walker BA, Javierre BM, Russell LJ, Brackley CA. High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation. Genome Res 2022; 32:1355-1366. [PMID: 35863900 PMCID: PMC9341513 DOI: 10.1101/gr.276028.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
Genomic rearrangements are known to result in proto-oncogene deregulation in many cancers, but the link to 3D genome structure remains poorly understood. Here, we used the highly predictive heteromorphic polymer (HiP-HoP) model to predict chromatin conformations at the proto-oncogene CCND1 in healthy and malignant B cells. After confirming that the model gives good predictions of Hi-C data for the nonmalignant human B cell-derived cell line GM12878, we generated predictions for two cancer cell lines, U266 and Z-138. These possess genome rearrangements involving CCND1 and the immunoglobulin heavy locus (IGH), which we mapped using targeted genome sequencing. Our simulations showed that a rearrangement in U266 cells where a single IGH super-enhancer is inserted next to CCND1 leaves the local topologically associated domain (TAD) structure intact. We also observed extensive changes in enhancer-promoter interactions within the TAD, suggesting that it is the downstream chromatin remodeling which gives rise to the oncogene activation, rather than the presence of the inserted super-enhancer DNA sequence per se. Simulations of the IGH-CCND1 reciprocal translocation in Z-138 cells revealed that an oncogenic fusion TAD is created, encompassing CCND1 and the IGH super-enhancers. We predicted how the structure and expression of CCND1 changes in these different cell lines, validating this using qPCR and fluorescence in situ hybridization microscopy. Our work demonstrates the power of polymer simulations to predict differences in chromatin interactions and gene expression for different translocation breakpoints.
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Affiliation(s)
- Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Kent
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nefeli Karataraki
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana 46202, USA
| | - Biola M Javierre
- Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Campus ICO-Germans Trias i Pujol, Ctra de Can Ruti, 08916 Badalona, Barcelona, Spain
| | - Lisa J Russell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Chris A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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21
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Khunsriraksakul C, McGuire D, Sauteraud R, Chen F, Yang L, Wang L, Hughey J, Eckert S, Dylan Weissenkampen J, Shenoy G, Marx O, Carrel L, Jiang B, Liu DJ. Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies. Nat Commun 2022; 13:3258. [PMID: 35672318 PMCID: PMC9171100 DOI: 10.1038/s41467-022-30956-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/25/2022] [Indexed: 02/08/2023] Open
Abstract
Transcriptome-wide association studies (TWAS) are popular approaches to test for association between imputed gene expression levels and traits of interest. Here, we propose an integrative method PUMICE (Prediction Using Models Informed by Chromatin conformations and Epigenomics) to integrate 3D genomic and epigenomic data with expression quantitative trait loci (eQTL) to more accurately predict gene expressions. PUMICE helps define and prioritize regions that harbor cis-regulatory variants, which outperforms competing methods. We further describe an extension to our method PUMICE +, which jointly combines TWAS results from single- and multi-tissue models. Across 79 traits, PUMICE + identifies 22% more independent novel genes and increases median chi-square statistics values at known loci by 35% compared to the second-best method, as well as achieves the narrowest credible interval size. Lastly, we perform computational drug repurposing and confirm that PUMICE + outperforms other TWAS methods.
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Affiliation(s)
- Chachrit Khunsriraksakul
- grid.29857.310000 0001 2097 4281Bioinformatics and Genomics Graduate Program, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Daniel McGuire
- grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Renan Sauteraud
- grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Fang Chen
- grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Lina Yang
- grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Lida Wang
- grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Jordan Hughey
- grid.29857.310000 0001 2097 4281Bioinformatics and Genomics Graduate Program, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Scott Eckert
- grid.29857.310000 0001 2097 4281Bioinformatics and Genomics Graduate Program, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - J. Dylan Weissenkampen
- grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Ganesh Shenoy
- grid.29857.310000 0001 2097 4281Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Olivia Marx
- grid.29857.310000 0001 2097 4281Biomedical Science Program, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Laura Carrel
- grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Bibo Jiang
- grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Dajiang J. Liu
- grid.29857.310000 0001 2097 4281Bioinformatics and Genomics Graduate Program, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
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22
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Zhang Y, Tian GG, Wang X, Hou C, Hu X, Wu J. Retinoic acid induced meiosis initiation in female germline stem cells by remodelling three-dimensional chromatin structure. Cell Prolif 2022; 55:e13242. [PMID: 35633286 PMCID: PMC9251051 DOI: 10.1111/cpr.13242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 12/11/2022] Open
Abstract
Objectives This study aimed to clarify the regulation and mechanism of meiotic initiation in FGSC development. Materials and Methods FGSCs were induced to differentiate into meiosis in differentiation medium. RNA sequencing was performed to analysis the difference of transcription level. High‐through chromosome conformation capture sequencing (Hi‐C) was performed to analysis changes of three‐dimensional chromatin structure. Chromosome conformation capture further confirmed a spatial chromatin loop. ChIP‐qPCR and dual luciferase reporter were used to test the interaction between Stimulated by retinoic acid gene 8 (STRA8) protein and Trip13 promoter. Results Compared with FGSCs, the average diameter of STRA8‐positive germ cells increased from 13 μm to 16.8 μm. Furthermore, there were 4788 differentially expressed genes between the two cell stages; Meiosis and chromatin structure‐associated terms were significantly enriched. Additionally, Hi‐C results showed that FGSCs underwent A/B compartment switching (switch rate was 29.81%), the number of topologically associating domains (TADs) increasing, the average size of TADs decreasing, and chromatin loop changes at genome region of Trip13 from undifferentiated stage to meiosis‐initiation stage. Furthermore, we validated that Trip13 promoter contacted distal enhancer to form spatial chromatin loop and STRA8 could bind Trip13 promoter to promote gene expression. Conclusion FGSCs underwent chromatin structure remodelling from undifferentiated stage to meiosis‐initiation stage, which facilitated STRA8 binding to Trip13 promoter and promoting its expression.
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Affiliation(s)
- Yabin Zhang
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Geng G Tian
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Wang
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China
| | - Changliang Hou
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaopeng Hu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China
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23
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Sati S, Jones P, Kim HS, Zhou LA, Rapp-Reyes E, Leung TH. HiCuT: An efficient and low input method to identify protein-directed chromatin interactions. PLoS Genet 2022; 18:e1010121. [PMID: 35320278 PMCID: PMC8979432 DOI: 10.1371/journal.pgen.1010121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/04/2022] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
3D genome organization regulates gene expression, and disruption of these long-range (>20kB) DNA-protein interactions results in pathogenic phenotypes. Chromosome conformation methods in conjunction with chromatin immunoprecipitation were used to decipher protein-directed chromatin interactions. However, these methods required abundant starting material (>500,000 cells), sizable number of sequencing reads (>100 million reads), and elaborate data processing methods to reduce background noise, which limited their use in primary cells. Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT) is a new transposase-assisted tagmentation method that generates high-resolution protein directed long-range chromatin interactions as efficiently as existing methods, HiChIP and ChIA-PET, despite using 100,000 cells (5-fold less) and 12 million sequencing reads (8-fold fewer). Moreover, HiCuT generates high resolution fragment libraries with low background signal that are easily interpreted with minimal computational processing. We used HiCuT in human primary skin cells to link previously identified single nucleotide polymorphisms (SNPs) in skin disease to candidate genes and to identify functionally relevant transcription factors in an unbiased manner. HiCuT broadens the capacity for genomic profiling in systems previously unmeasurable, including primary cells, human tissue samples, and rare cell populations, and may be a useful tool for all investigators studying human genetics and personalized epigenomics. DNA is precisely packaged and organized within a nucleus to regulate gene expression. Altering this structure results in disease and developmental abnormalities. Current methods to probe 3D genome organization require a minimum of 500,000 cells, 100 million sequencing reads, and elaborate computational genomics skills. This limits general adoption and prevents use in small populations of cells, including primary tissues. We report a new method called Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT). This method couples current 3D genome methods in conjunction with target specific tagmentation, an enzyme-assisted approach to cut and tag DNA. We benchmarked HiCuT against existing methods and found similar efficiency and specificity in assessing target specific 3D genome organization despite reducing assay requirements to 100,000 cells (5-fold less) and 12 million sequencing reads (8-fold fewer). Strikingly, HiCuT data exhibited reduced background noise and required minimal computational processing. Taken together, HiCuT broadens the capacity for 3D genome profiling in cell populations previously unmeasurable, including primary cells and human tissues, reduces sequencing costs, and lowers the need for computational expertise. HiCuT will benefit all investigators studying gene regulation and disease pathophysiology.
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Affiliation(s)
- Satish Sati
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Parker Jones
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hali S. Kim
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Linda A. Zhou
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Emmanuel Rapp-Reyes
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thomas H. Leung
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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24
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Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses. Cell 2022; 185:266-282.e15. [PMID: 35026153 PMCID: PMC8809251 DOI: 10.1016/j.cell.2021.12.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 10/17/2021] [Accepted: 12/10/2021] [Indexed: 01/09/2023]
Abstract
HIV-1-infected cells that persist despite antiretroviral therapy (ART) are frequently considered "transcriptionally silent," but active viral gene expression may occur in some cells, challenging the concept of viral latency. Applying an assay for profiling the transcriptional activity and the chromosomal locations of individual proviruses, we describe a global genomic and epigenetic map of transcriptionally active and silent proviral species and evaluate their longitudinal evolution in persons receiving suppressive ART. Using genome-wide epigenetic reference data, we show that proviral transcriptional activity is associated with activating epigenetic chromatin features in linear proximity of integration sites and in their inter- and intrachromosomal contact regions. Transcriptionally active proviruses were actively selected against during prolonged ART; however, this pattern was violated by large clones of virally infected cells that may outcompete negative selection forces through elevated intrinsic proliferative activity. Our results suggest that transcriptionally active proviruses are dynamically evolving under selection pressure by host factors.
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25
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Hu X, Wang H, Tian GG, Hou C, Xu B, Zhao X, Zhao Y, Fang Q, Li X, He L, Chen X, Li S, Wu J. Offspring production of haploid spermatid-like cells derived from mouse female germline stem cells with chromatin condensation. Cell Biosci 2022; 12:5. [PMID: 34983631 PMCID: PMC8729121 DOI: 10.1186/s13578-021-00697-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/06/2021] [Indexed: 12/04/2022] Open
Abstract
Background During male meiosis, the Y chromosome can form perfect pairing with the X chromosome. However, it is unclear whether mammalian Female germline stem cells (FGSCs) without a Y chromosome can transdifferentiate into functional haploid spermatid-like cells (SLCs). Results We found that spermatogenesis was restarted by transplanting FGSCs into Kitw/wv mutant testes. Complete meiosis and formation of SLCs was induced in vitro by testicular cells of Kitw/wv mutant mice, cytokines and retinoic acid. Healthy offspring were produced by sperm and SLCs derived from the in vivo and in vitro transdifferentiation of FGSCs, respectively. Furthermore, high-throughput chromosome conformation capture sequencing(Hi-C-seq) and “bivalent” (H3K4me3-H3K27me3) micro chromatin immunoprecipitation sequencing (μChIP-seq) experiments showed that stimulated by retinoic acid gene 8 (STRA8)/protamine 1 (PRM1)-positive transdifferentiated germ cells (tGCs) and male germ cells (mGCs) display similar chromatin dynamics and chromatin condensation during in vitro spermatogenesis. Conclusion This study demonstrates that sperm can be produced from FGSCs without a Y chromosome. This suggests a strategy for dairy cattle breeding to produce only female offspring with a high-quality genetic background. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00697-z.
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Affiliation(s)
- Xiaopeng Hu
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Hu Wang
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Geng G Tian
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Changliang Hou
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Bo Xu
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xinyan Zhao
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China
| | - Yongqiang Zhao
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Qian Fang
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xinyue Li
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Lin He
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Xuejin Chen
- Department of Laboratory Animal Science, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Shangang Li
- State Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China. .,Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Ji Wu
- Bio-X Institutes, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China. .,Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China. .,Shanghai Key Laboratory of Reproductive Medicine, Shanghai, 200025, China.
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26
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Jeffery D, Lochhead M, Almouzni G. CENP-A: A Histone H3 Variant with Key Roles in Centromere Architecture in Healthy and Diseased States. Results Probl Cell Differ 2022; 70:221-261. [PMID: 36348109 DOI: 10.1007/978-3-031-06573-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Centromeres are key architectural components of chromosomes. Here, we examine their construction, maintenance, and functionality. Focusing on the mammalian centromere- specific histone H3 variant, CENP-A, we highlight its coevolution with both centromeric DNA and its chaperone, HJURP. We then consider CENP-A de novo deposition and the importance of centromeric DNA recently uncovered with the added value from new ultra-long-read sequencing. We next review how to ensure the maintenance of CENP-A at the centromere throughout the cell cycle. Finally, we discuss the impact of disrupting CENP-A regulation on cancer and cell fate.
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Affiliation(s)
- Daniel Jeffery
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Marina Lochhead
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Geneviève Almouzni
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France.
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27
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Tiscareño-Andrade M, Oktaba K, Vielle-Calzada JP. Isolation of Boechera stricta Developing Embryos for Hi-C. Methods Mol Biol 2022; 2512:249-257. [PMID: 35818009 DOI: 10.1007/978-1-0716-2429-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The possibility of analyzing chromatin topology in developing plant embryos is hampered by inaccessibility of the embryo sac, deeply embedded in the maternal seed tissue, following double fertilization. Here we describe a protocol to isolate, purify, and prepare developing Boechera stricta embryos for chromosome conformation capture-based methods as in situ Hi-C experiments. Early globular embryos can be isolated by air-pressure microaspiration, and subsequently washed to eliminate residual cells from the endosperm and maternal seed coat, allowing for pure sampling of selected stages of embryogenesis. This protocol allows for the possibility of comparing genome topology during plant embryonic differentiation since early until late embryo development stages.
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Affiliation(s)
- Mariana Tiscareño-Andrade
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Katarzyna Oktaba
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Jean-Philippe Vielle-Calzada
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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28
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Maresca M, Liu NQ, de Wit E. Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome. Methods Mol Biol 2022; 2532:311-331. [PMID: 35867256 DOI: 10.1007/978-1-0716-2497-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The organization of the genome inside the nucleus facilitates many nuclear processes. Because the nuclear genome is highly dynamic and often regulated by essential proteins, rapid depletion strategies are necessary to perform loss-of-function analyses. Fortunately, in recent years, various methods have been developed to manipulate the cellular levels of a protein directly and acutely. Here, we describe different methods that have been developed to rapidly deplete proteins from cells, with a focus on auxin inducible degron and dTAG methods, as these are most commonly used in 3D genome organization studies. We outline best practices for designing a knockin strategy, as well as generation and validation of knockin cell lines. Acute depletion strategies have been transformative for the study of the 3D genome and will be important tools for delineating the processes and factors that determine organization of the genome inside the nucleus.
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Affiliation(s)
- Michela Maresca
- Division Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ning Qing Liu
- Division Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elzo de Wit
- Division Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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29
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Abstract
In situ HiC uses the relative frequency of DNA-DNA ligation events to reconstruct the three-dimensional architecture of a genome. As such, restriction enzyme digested ends of genomic DNA within fixed nuclei are tagged with biotinylated dNTPs. DNA-DNA ligation events generated via proximity ligation are then captured, amplified and next generation sequenced to determine their linear genomic position, but also their three-dimensional relationship. Here, we describe these steps in detail.
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Affiliation(s)
- Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
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30
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Hawley JR, Zhou S, Arlidge C, Grillo G, Kron KJ, Hugh-White R, van der Kwast TH, Fraser M, Boutros PC, Bristow RG, Lupien M. Reorganization of the 3D genome pinpoints non-coding drivers of primary prostate tumors. Cancer Res 2021; 81:5833-5848. [PMID: 34642184 DOI: 10.1158/0008-5472.can-21-2056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/13/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Prostate cancer is a heterogeneous disease whose progression is linked to genome instability. However, the impact of this instability on the non-coding genome and its three-dimensional organization to aid progression is unclear. Using primary benign and tumor tissue, we find a high concordance in higher order three-dimensional genome organization. This concordance argues for constraints to the topology of prostate tumor genomes. Nonetheless, we identified changes in focal chromatin interactions, typical of loops bridging non-coding cis-regulatory elements, and showed how structural variants can induce these changes to guide cis-regulatory element hijacking. Such events resulted in opposing differential expression of genes found at antipodes of rearrangements. Collectively, these results argue that changes to focal chromatin interactions, as opposed to higher order genome organization, allow for aberrant gene regulation and are repeatedly mediated by structural variants in primary prostate cancer.
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Affiliation(s)
- James R Hawley
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | - Stanley Zhou
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | | | - Giacomo Grillo
- Medical Biophysics, University of Toronto, Princess Margaret Cancer Center-University Health Network, Ontario Institute for Cancer Research
| | | | | | | | | | | | | | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network
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31
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Luo H, Li X, Tian GG, Li D, Hou C, Ding X, Hou L, Lyu Q, Yang Y, Cooney AJ, Xie W, Xiong J, Wang H, Zhao X, Wu J. Offspring production of ovarian organoids derived from spermatogonial stem cells by defined factors with chromatin reorganization. J Adv Res 2021; 33:81-98. [PMID: 34603780 PMCID: PMC8463929 DOI: 10.1016/j.jare.2021.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/08/2021] [Accepted: 03/13/2021] [Indexed: 11/30/2022] Open
Abstract
Introduction Fate determination of germline stem cells remains poorly understood at the chromatin structure level. Objectives Our research hopes to develop successful offspring production of ovarian organoids derived from spermatogonial stem cells (SSCs) by defined factors. Methods The offspring production from oocytes transdifferentiated from mouse SSCs with tracking of transplanted SSCs in vivo, single cell whole exome sequencing, and in 3D cell culture reconstitution of the process of oogenesis derived from SSCs. The defined factors were screened with ovarian organoids. We uncovered extensive chromatin reorganization during SSC conversion into induced germline stem cells (iGSCs) using high throughput chromosome conformation. Results We demonstrate successful production of offspring from oocytes transdifferentiated from mouse spermatogonial stem cells (SSCs). Furthermore, we demonstrate direct induction of germline stem cells (iGSCs) differentiated into functional oocytes by transduction of H19, Stella, and Zfp57 and inactivation of Plzf in SSCs after screening with ovarian organoids. We uncovered extensive chromatin reorganization during SSC conversion into iGSCs, which was highly similar to female germline stem cells. We observed that although topologically associating domains were stable during SSC conversion, chromatin interactions changed in a striking manner, altering 35% of inactive and active chromosomal compartments throughout the genome. Conclusion We demonstrate successful offspring production of ovarian organoids derived from SSCs by defined factors with chromatin reorganization. These findings have important implications in various areas including mammalian gametogenesis, genetic and epigenetic reprogramming, biotechnology, and medicine.
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Affiliation(s)
- Huacheng Luo
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Xiaoyong Li
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Geng G Tian
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Changliang Hou
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Xinbao Ding
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Lin Hou
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Qifeng Lyu
- Shanghai Ninth People's Hospital Affiliated Shanghai Jiao Tong University Schoolof Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yunze Yang
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Austin J Cooney
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wenhai Xie
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Ji Xiong
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Hu Wang
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China
| | - Xiaodong Zhao
- Shanghai Center for Systems Biomedicine, Shanghai Jiao TongUniversity, Shanghai 200240, China
| | - Ji Wu
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China.,Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China
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32
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Afanasyeva TAV, Corral-Serrano JC, Garanto A, Roepman R, Cheetham ME, Collin RWJ. A look into retinal organoids: methods, analytical techniques, and applications. Cell Mol Life Sci 2021; 78:6505-6532. [PMID: 34420069 PMCID: PMC8558279 DOI: 10.1007/s00018-021-03917-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/14/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022]
Abstract
Inherited retinal diseases (IRDs) cause progressive loss of light-sensitive photoreceptors in the eye and can lead to blindness. Gene-based therapies for IRDs have shown remarkable progress in the past decade, but the vast majority of forms remain untreatable. In the era of personalised medicine, induced pluripotent stem cells (iPSCs) emerge as a valuable system for cell replacement and to model IRD because they retain the specific patient genome and can differentiate into any adult cell type. Three-dimensional (3D) iPSCs-derived retina-like tissue called retinal organoid contains all major retina-specific cell types: amacrine, bipolar, horizontal, retinal ganglion cells, Müller glia, as well as rod and cone photoreceptors. Here, we describe the main applications of retinal organoids and provide a comprehensive overview of the state-of-art analysis methods that apply to this model system. Finally, we will discuss the outlook for improvements that would bring the cellular model a step closer to become an established system in research and treatment development of IRDs.
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Affiliation(s)
- Tess A V Afanasyeva
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | | | - Alejandro Garanto
- Department of Pediatrics, Amalia Children's Hospital and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael E Cheetham
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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33
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Animesh S, Choudhary R, Wong BJH, Koh CTJ, Ng XY, Tay JKX, Chong WQ, Jian H, Chen L, Goh BC, Fullwood MJ. Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach. Front Genet 2021; 12:673530. [PMID: 34539729 PMCID: PMC8446523 DOI: 10.3389/fgene.2021.673530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/31/2021] [Indexed: 11/16/2022] Open
Abstract
Nasopharyngeal cancer (NPC), a cancer derived from epithelial cells in the nasopharynx, is a cancer common in China, Southeast Asia, and Africa. The three-dimensional (3D) genome organization of nasopharyngeal cancer is poorly understood. A major challenge in understanding the 3D genome organization of cancer samples is the lack of a method for the characterization of chromatin interactions in solid cancer needle biopsy samples. Here, we developed Biop-C, a modified in situ Hi-C method using solid cancer needle biopsy samples. We applied Biop-C to characterize three nasopharyngeal cancer solid cancer needle biopsy patient samples. We identified topologically associated domains (TADs), chromatin interaction loops, and frequently interacting regions (FIREs) at key oncogenes in nasopharyngeal cancer from the Biop-C heatmaps. We observed that the genomic features are shared at some important oncogenes, but the patients also display extensive heterogeneity at certain genomic loci. On analyzing the super enhancer landscape in nasopharyngeal cancer cell lines, we found that the super enhancers are associated with FIREs and can be linked to distal genes via chromatin loops in NPC. Taken together, our results demonstrate the utility of our Biop-C method in investigating 3D genome organization in solid cancers.
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Affiliation(s)
- Sambhavi Animesh
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Ruchi Choudhary
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Charlotte Tze Jia Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xin Yi Ng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Joshua Kai Xun Tay
- Department of Otolaryngology - Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Wan-Qin Chong
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Han Jian
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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34
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Zhang C, Xu Z, Yang S, Sun G, Jia L, Zheng Z, Gu Q, Tao W, Cheng T, Li C, Cheng H. tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis. Cell Rep 2021; 32:108206. [PMID: 32997998 DOI: 10.1016/j.celrep.2020.108206] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/08/2020] [Accepted: 09/08/2020] [Indexed: 01/10/2023] Open
Abstract
Spatiotemporal chromatin reorganization during hematopoietic differentiation has not been comprehensively characterized, mainly because of the large numbers of starting cells required for current chromatin conformation capture approaches. Here, we introduce a low-input tagmentation-based Hi-C (tagHi-C) method to capture the chromatin structures of hundreds of cells. Using tagHi-C, we are able to map the spatiotemporal dynamics of chromatin structure in ten primary hematopoietic stem, progenitor, and differentiated cell populations from mouse bone marrow. Our results reveal that changes in compartment dynamics and the Rabl configuration occur during hematopoietic cell differentiation. We identify gene-body-associating domains (GADs) as general structures for highly expressed genes. Moreover, we extend the body of knowledge regarding genes influenced by genome-wide association study (GWAS) loci through spatial chromatin looping. Our study provides the tagHi-C method for studying the three-dimensional (3D) genome of a small number of cells and maps the comprehensive 3D chromatin landscape of bone marrow hematopoietic cells.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China; Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China; PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Peking University, Beijing, China
| | - Zihan Xu
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China
| | - Shangda Yang
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lumeng Jia
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China
| | - Zhaofeng Zheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Quan Gu
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wei Tao
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China.
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China.
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences, Tianjin, China; National Clinical Research Center for Blood Diseases, Tianjin, China; Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China.
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35
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Highsmith M, Cheng J. Four-Dimensional Chromosome Structure Prediction. Int J Mol Sci 2021; 22:ijms22189785. [PMID: 34575948 PMCID: PMC8465368 DOI: 10.3390/ijms22189785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/28/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
Chromatin conformation plays an important role in a variety of genomic processes, including genome replication, gene expression, and gene methylation. Hi-C data is frequently used to analyze structural features of chromatin, such as AB compartments, topologically associated domains, and 3D structural models. Recently, the genomics community has displayed growing interest in chromatin dynamics. Here, we present 4DMax, a novel method, which uses time-series Hi-C data to predict dynamic chromosome conformation. Using both synthetic data and real time-series Hi-C data from processes, such as induced pluripotent stem cell reprogramming and cardiomyocyte differentiation, we construct smooth four-dimensional models of individual chromosomes. These predicted 4D models effectively interpolate chromatin position across time, permitting prediction of unknown Hi-C contact maps at intermittent time points. Furthermore, 4DMax correctly recovers higher order features of chromatin, such as AB compartments and topologically associated domains, even at time points where Hi-C data is not made available to the algorithm. Contact map predictions made using 4DMax outperform naïve numerical interpolation in 87.7% of predictions on the induced pluripotent stem cell dataset. A/B compartment profiles derived from 4DMax interpolation showed higher similarity to ground truth than at least one profile generated from a neighboring time point in 100% of induced pluripotent stem cell experiments. Use of 4DMax may alleviate the cost of expensive Hi-C experiments by interpolating intermediary time points while also providing valuable visualization of dynamic chromatin changes.
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36
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Danieli A, Papantonis A. Spatial genome architecture and the emergence of malignancy. Hum Mol Genet 2021; 29:R197-R204. [PMID: 32619215 DOI: 10.1093/hmg/ddaa128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 01/30/2023] Open
Abstract
Human chromosomes are large spatially and hierarchically structured entities, the integrity of which needs to be preserved throughout the lifespan of the cell and in conjunction with cell cycle progression. Preservation of chromosomal structure is important for proper deployment of cell type-specific gene expression programs. Thus, aberrations in the integrity and structure of chromosomes will predictably lead to disease, including cancer. Here, we provide an updated standpoint with respect to chromatin misfolding and the emergence of various cancer types. We discuss recent studies implicating the disruption of topologically associating domains, switching between active and inactive compartments, rewiring of promoter-enhancer interactions in malignancy as well as the effects of single nucleotide polymorphisms in non-coding regions involved in long-range regulatory interactions. In light of these findings, we argue that chromosome conformation studies may now also be useful for patient diagnosis and drug target discovery.
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Affiliation(s)
- Adi Danieli
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
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37
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van Schoonhoven A, Huylebroeck D, Hendriks RW, Stadhouders R. 3D genome organization during lymphocyte development and activation. Brief Funct Genomics 2021; 19:71-82. [PMID: 31819944 PMCID: PMC7115705 DOI: 10.1093/bfgp/elz030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Chromosomes have a complex three-dimensional (3D) architecture comprising A/B compartments, topologically associating domains and promoter-enhancer interactions. At all these levels, the 3D genome has functional consequences for gene transcription and therefore for cellular identity. The development and activation of lymphocytes involves strict control of gene expression by transcription factors (TFs) operating in a three-dimensionally organized chromatin landscape. As lymphocytes are indispensable for tissue homeostasis and pathogen defense, and aberrant lymphocyte activity is involved in a wide range of human morbidities, acquiring an in-depth understanding of the molecular mechanisms that control lymphocyte identity is highly relevant. Here we review current knowledge of the interplay between 3D genome organization and transcriptional control during B and T lymphocyte development and antigen-dependent activation, placing special emphasis on the role of TFs.
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Affiliation(s)
- Anne van Schoonhoven
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.,Department of Cell Biology,Erasmus MC, Rotterdam, the Netherlands
| | | | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.,Department of Cell Biology,Erasmus MC, Rotterdam, the Netherlands
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38
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Allahyar A, Pieterse M, Swennenhuis J, Los-de Vries GT, Yilmaz M, Leguit R, Meijers RWJ, van der Geize R, Vermaat J, Cleven A, van Wezel T, Diepstra A, van Kempen LC, Hijmering NJ, Stathi P, Sharma M, Melquiond ASJ, de Vree PJP, Verstegen MJAM, Krijger PHL, Hajo K, Simonis M, Rakszewska A, van Min M, de Jong D, Ylstra B, Feitsma H, Splinter E, de Laat W. Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing. Nat Commun 2021; 12:3361. [PMID: 34099699 PMCID: PMC8184748 DOI: 10.1038/s41467-021-23695-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/10/2021] [Indexed: 12/03/2022] Open
Abstract
In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens.
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Affiliation(s)
- Amin Allahyar
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mark Pieterse
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - G Tjitske Los-de Vries
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | - Roos Leguit
- University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands
| | - Ruud W J Meijers
- University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands
| | | | - Joost Vermaat
- Leiden University Medical Centre, Department of Hematology, Leiden, the Netherlands
| | - Arjen Cleven
- Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands
| | - Tom van Wezel
- Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands
| | - Arjan Diepstra
- University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands
| | - Léon C van Kempen
- University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands
| | - Nathalie J Hijmering
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Phylicia Stathi
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Milan Sharma
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Adrien S J Melquiond
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paula J P de Vree
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marjon J A M Verstegen
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | | | - Daphne de Jong
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | | | - Wouter de Laat
- Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
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39
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Wike CL, Guo Y, Tan M, Nakamura R, Shaw DK, Díaz N, Whittaker-Tademy AF, Durand NC, Aiden EL, Vaquerizas JM, Grunwald D, Takeda H, Cairns BR. Chromatin architecture transitions from zebrafish sperm through early embryogenesis. Genome Res 2021; 31:981-994. [PMID: 34006569 PMCID: PMC8168589 DOI: 10.1101/gr.269860.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/07/2021] [Indexed: 11/25/2022]
Abstract
Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish gamete cells to discern whether it either resembles or informs early pre-ZGA zebrafish embryo chromatin architecture. First, we assessed the higher-order architecture through advanced low-cell in situ Hi-C. The structure of zebrafish sperm, packaged by histones, lacks topological associated domains and instead displays “hinge-like” domains of ∼150 kb that repeat every 1–2 Mbs, suggesting a condensed repeating structure resembling mitotic chromosomes. The pre-ZGA embryos lacked chromosomal structure, in contrast to prior work, and only developed structure post-ZGA. During post-ZGA, we find chromatin architecture beginning to form at small contact domains of a median length of ∼90 kb. These small contact domains are established at enhancers, including super-enhancers, and chemical inhibition of Ep300a (p300) and Crebbpa (CBP) activity, lowering histone H3K27ac, but not transcription inhibition, diminishes these contacts. Together, this study reveals hinge-like domains in histone-packaged zebrafish sperm chromatin and determines that the initial formation of high-order chromatin architecture in zebrafish embryos occurs after ZGA primarily at enhancers bearing high H3K27ac.
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Affiliation(s)
- Candice L Wike
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Yixuan Guo
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mengyao Tan
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Dana Klatt Shaw
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Aneasha F Whittaker-Tademy
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - David Grunwald
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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40
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Scourzic L, Salataj E, Apostolou E. Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. Front Immunol 2021; 12:669881. [PMID: 34054841 PMCID: PMC8160312 DOI: 10.3389/fimmu.2021.669881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Proper lymphopoiesis and immune responses depend on the spatiotemporal control of multiple processes, including gene expression, DNA recombination and cell fate decisions. High-order 3D chromatin organization is increasingly appreciated as an important regulator of these processes and dysregulation of genomic architecture has been linked to various immune disorders, including lymphoid malignancies. In this review, we present the general principles of the 3D chromatin topology and its dynamic reorganization during various steps of B and T lymphocyte development and activation. We also discuss functional interconnections between architectural, epigenetic and transcriptional changes and introduce major key players of genomic organization in B/T lymphocytes. Finally, we present how alterations in architectural factors and/or 3D genome organization are linked to dysregulation of the lymphopoietic transcriptional program and ultimately to hematological malignancies.
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Affiliation(s)
| | | | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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41
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Fiorillo L, Musella F, Conte M, Kempfer R, Chiariello AM, Bianco S, Kukalev A, Irastorza-Azcarate I, Esposito A, Abraham A, Prisco A, Pombo A, Nicodemi M. Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin. Nat Methods 2021; 18:482-490. [PMID: 33963348 PMCID: PMC8416658 DOI: 10.1038/s41592-021-01135-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/31/2021] [Indexed: 12/11/2022]
Abstract
Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled, framework against known 3D structures of polymer models of murine and human loci, which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed fluorescence in situ hybridization (FISH) single-molecule conformations. We find that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D structures whereas single-cell data reflect strong variability among single molecules. The minimal number of cells required in replicate experiments to return statistically similar contacts is different across the technologies, being lowest in SPRITE and highest in GAM under the same conditions. Noise-to-signal levels follow an inverse power law with detection efficiency and grow with genomic distance differently among the three methods, being lowest in GAM for genomic separations >1 Mb.
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Affiliation(s)
- Luca Fiorillo
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Francesco Musella
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Rieke Kempfer
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.,Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy.,Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Alexander Kukalev
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Ibai Irastorza-Azcarate
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | | | - Ana Pombo
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.,Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy. .,Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany.
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42
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Gridina M, Mozheiko E, Valeev E, Nazarenko LP, Lopatkina ME, Markova ZG, Yablonskaya MI, Voinova VY, Shilova NV, Lebedev IN, Fishman V. A cookbook for DNase Hi-C. Epigenetics Chromatin 2021; 14:15. [PMID: 33743768 PMCID: PMC7981840 DOI: 10.1186/s13072-021-00389-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 03/08/2021] [Indexed: 12/23/2022] Open
Abstract
Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming. Conclusions We propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00389-5.
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Affiliation(s)
- Maria Gridina
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia
| | - Evgeniy Mozheiko
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia
| | - Emil Valeev
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia.,Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia
| | - Ludmila P Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Kooperativny Str, 5, Tomsk, Russia
| | - Maria E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Kooperativny Str, 5, Tomsk, Russia
| | - Zhanna G Markova
- Research Centre for Medical Genetics, Moskvorechie str., 1, Moscow, Russia
| | - Maria I Yablonskaya
- Clinical Research Institute of Pediatrics Named After Acad. Y.E. Veltischev, Moscow, Russia
| | - Viktoria Yu Voinova
- Clinical Research Institute of Pediatrics Named After Acad. Y.E. Veltischev, Moscow, Russia
| | - Nadezhda V Shilova
- Research Centre for Medical Genetics, Moskvorechie str., 1, Moscow, Russia
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Kooperativny Str, 5, Tomsk, Russia
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia. .,Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia.
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43
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Zheng W, Yang Z, Ge X, Feng Y, Wang Y, Liu C, Luan Y, Cai K, Vakal S, You F, Guo W, Wang W, Feng Z, Li F. Freeze substitution Hi-C, a convenient and cost-effective method for capturing the natural 3D chromatin conformation from frozen samples. J Genet Genomics 2021; 48:237-247. [PMID: 33573880 DOI: 10.1016/j.jgg.2020.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 11/28/2022]
Abstract
Chromatin interactions functionally affect genome architecture and gene regulation, but to date, only fresh samples must be used in High-through chromosome conformation capture (Hi-C) to keep natural chromatin conformation intact. This requirement has impeded the advancement of 3D genome research by limiting sample collection and storage options for researchers and severely limiting the number of samples that can be processed in a short time. Here, we develop a freeze substitution Hi-C (FS-Hi-C) technique that overcomes the need for fresh samples. FS-Hi-C can be used with samples stored in liquid nitrogen (LN2): the water in a vitreous form in the sample cells is replaced with ethanol via automated freeze substitution. After confirming that the FS step preserves the natural chromosome conformation during sample thawing, we tested the performance of FS-Hi-C with Drosophila melanogaster and Gossypium hirsutum. Beyond allowing the use of frozen samples and confirming that FS-Hi-C delivers robust data for generating contact heat maps and delineating A/B compartments and topologically associating domains, we found that FS-Hi-C outperforms the in situ Hi-C in terms of library quality, reproducibility, and valid interactions. Thus, FS-Hi-C will probably extend the application of 3D genome structure analysis to the vast number of experimental contexts in biological and medical research for which Hi-C methods have been unfeasible to date.
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Affiliation(s)
- Wu Zheng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Wenzhou Medical University, Wenzhou 325027, China
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyang Ge
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yijia Feng
- Wenzhou Medical University, Wenzhou 325027, China
| | - Ye Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chengwei Liu
- Wenzhou Medical University, Wenzhou 325027, China
| | - Yanan Luan
- Wenzhou Medical University, Wenzhou 325027, China
| | - Kun Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Serhii Vakal
- Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, Turku 20520, Finland
| | - Feng You
- Wenzhou Medical University, Wenzhou 325027, China
| | - Wei Guo
- Wenzhou Medical University, Wenzhou 325027, China
| | - Wei Wang
- Department of Otorhinolaryngology-Head and Neck Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200000, China
| | - Zhenhua Feng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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44
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van Belzen IAEM, Schönhuth A, Kemmeren P, Hehir-Kwa JY. Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology. NPJ Precis Oncol 2021; 5:15. [PMID: 33654267 PMCID: PMC7925608 DOI: 10.1038/s41698-021-00155-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023] Open
Abstract
Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.
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Affiliation(s)
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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45
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Chen L, Cao W, Aita R, Aldea D, Flores J, Gao N, Bonder EM, Ellison CE, Verzi MP. Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4. Cell Rep 2021; 34:108679. [PMID: 33503426 PMCID: PMC7899294 DOI: 10.1016/j.celrep.2020.108679] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022] Open
Abstract
Cells in renewing tissues exhibit dramatic transcriptional changes as they differentiate. The contribution of chromatin looping to tissue renewal is incompletely understood. Enhancer-promoter interactions could be relatively stable as cells transition from progenitor to differentiated states; alternatively, chromatin looping could be as dynamic as the gene expression from their loci. The intestinal epithelium is the most rapidly renewing mammalian tissue. Proliferative cells in crypts of Lieberkühn sustain a stream of differentiated cells that are continually shed into the lumen. We apply chromosome conformation capture combined with chromatin immunoprecipitation (HiChIP) and sequencing to measure enhancer-promoter interactions in progenitor and differentiated cells of the intestinal epithelium. Despite dynamic gene regulation across the differentiation axis, we find that enhancer-promoter interactions are relatively stable. Functionally, we find HNF4 transcription factors are required for chromatin looping at target genes. Depletion of HNF4 disrupts local chromatin looping, histone modifications, and target gene expression. This study provides insights into transcriptional regulatory mechanisms governing homeostasis in renewing tissues. Chen et al. provide a survey of enhancer-promoter 3D looping in the intestinal epithelium by HiChIP, in vivo. They find that enhancer-promoter interactions are highly dependent upon the key intestinal transcription factor HNF4. Their findings provide insights into transcriptional regulatory mechanisms governing homeostasis in renewing tissues.
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Affiliation(s)
- Lei Chen
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Rohit Aita
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Dennis Aldea
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Christopher E Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA.
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46
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Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat Genet 2021; 53:487-499. [PMID: 33795866 PMCID: PMC8035076 DOI: 10.1038/s41588-021-00799-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/21/2021] [Indexed: 02/01/2023]
Abstract
The relationship between chromatin organization and gene regulation remains unclear. While disruption of chromatin domains and domain boundaries can lead to misexpression of developmental genes, acute depletion of regulators of genome organization has a relatively small effect on gene expression. It is therefore uncertain whether gene expression and chromatin state drive chromatin organization or whether changes in chromatin organization facilitate cell-type-specific activation of gene expression. Here, using the dorsoventral patterning of the Drosophila melanogaster embryo as a model system, we provide evidence for the independence of chromatin organization and dorsoventral gene expression. We define tissue-specific enhancers and link them to expression patterns using single-cell RNA-seq. Surprisingly, despite tissue-specific chromatin states and gene expression, chromatin organization is largely maintained across tissues. Our results indicate that tissue-specific chromatin conformation is not necessary for tissue-specific gene expression but rather acts as a scaffold facilitating gene expression when enhancers become active.
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47
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Kruse K, Hug CB, Vaquerizas JM. FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data. Genome Biol 2020; 21:303. [PMID: 33334380 PMCID: PMC7745377 DOI: 10.1186/s13059-020-02215-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data ( https://github.com/vaquerizaslab/fanc ). Due to its compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.
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Affiliation(s)
- Kai Kruse
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany
| | - Clemens B Hug
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149, Muenster, Germany.
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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48
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Di Stefano M, Paulsen J, Jost D, Marti-Renom MA. 4D nucleome modeling. Curr Opin Genet Dev 2020; 67:25-32. [PMID: 33253996 PMCID: PMC8098745 DOI: 10.1016/j.gde.2020.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/18/2020] [Accepted: 10/24/2020] [Indexed: 02/01/2023]
Abstract
The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in regulating DNA transcription, replication, and damage-repair among other nuclear functions. With this increased awareness, reinforced over the last ten years, many new experimental techniques, mainly based on microscopy and chromosome conformation capture, have been introduced to study the genome in space and time. Owing to the increasing complexity of these cutting-edge techniques, computational approaches have become of paramount importance to interpret, contextualize, and complement such experiments with new insights. Hence, it is becoming crucial for experimental biologists to have a clear understanding of the diverse theoretical modeling approaches available and the biological information each of them can provide.
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Affiliation(s)
- Marco Di Stefano
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
| | - Jonas Paulsen
- EVOGENE, Department of Biosciences, Faculty of Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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49
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Ingram SP, Henthorn NT, Warmenhoven JW, Kirkby NF, Mackay RI, Kirkby KJ, Merchant MJ. Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage. PLoS Comput Biol 2020; 16:e1008476. [PMID: 33326415 PMCID: PMC7773326 DOI: 10.1371/journal.pcbi.1008476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/30/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Developments in the genome organisation field has resulted in the recent methodology to infer spatial conformations of the genome directly from experimentally measured genome contacts (Hi-C data). This provides a detailed description of both intra- and inter-chromosomal arrangements. Chromosomal intermingling is an important driver for radiation-induced DNA mis-repair. Which is a key biological endpoint of relevance to the fields of cancer therapy (radiotherapy), public health (biodosimetry) and space travel. For the first time, we leverage these methods of inferring genome organisation and couple them to nano-dosimetric radiation track structure modelling to predict quantities and distribution of DNA damage within cell-type specific geometries. These nano-dosimetric simulations are highly dependent on geometry and are benefited from the inclusion of experimentally driven chromosome conformations. We show how the changes in Hi-C contract maps impact the inferred geometries resulting in significant differences in chromosomal intermingling. We demonstrate how these differences propagate through to significant changes in the distribution of DNA damage throughout the cell nucleus, suggesting implications for DNA repair fidelity and subsequent cell fate. We suggest that differences in the geometric clustering for the chromosomes between the cell-types are a plausible factor leading to changes in cellular radiosensitivity. Furthermore, we investigate changes in cell shape, such as flattening, and show that this greatly impacts the distribution of DNA damage. This should be considered when comparing in vitro results to in vivo systems. The effect may be especially important when attempting to translate radiosensitivity measurements at the experimental in vitro level to the patient or human level.
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Affiliation(s)
- Samuel P. Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Nicholas T. Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John W. Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Norman F. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Ranald I. Mackay
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Karen J. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Michael J. Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
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50
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Takayama N, Murison A, Takayanagi SI, Arlidge C, Zhou S, Garcia-Prat L, Chan-Seng-Yue M, Zandi S, Gan OI, Boutzen H, Kaufmann KB, Trotman-Grant A, Schoof E, Kron K, Díaz N, Lee JJY, Medina T, De Carvalho DD, Taylor MD, Vaquerizas JM, Xie SZ, Dick JE, Lupien M. The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization. Cell Stem Cell 2020; 28:488-501.e10. [PMID: 33242413 DOI: 10.1016/j.stem.2020.11.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/17/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023]
Abstract
Lifelong blood production requires long-term hematopoietic stem cells (LT-HSCs), marked by stemness states involving quiescence and self-renewal, to transition into activated short-term HSCs (ST-HSCs) with reduced stemness. As few transcriptional changes underlie this transition, we used single-cell and bulk assay for transposase-accessible chromatin sequencing (ATAC-seq) on human HSCs and hematopoietic stem and progenitor cell (HSPC) subsets to uncover chromatin accessibility signatures, one including LT-HSCs (LT/HSPC signature) and another excluding LT-HSCs (activated HSPC [Act/HSPC] signature). These signatures inversely correlated during early hematopoietic commitment and differentiation. The Act/HSPC signature contains CCCTC-binding factor (CTCF) binding sites mediating 351 chromatin interactions engaged in ST-HSCs, but not LT-HSCs, enclosing multiple stemness pathway genes active in LT-HSCs and repressed in ST-HSCs. CTCF silencing derepressed stemness genes, restraining quiescent LT-HSCs from transitioning to activated ST-HSCs. Hence, 3D chromatin interactions centrally mediated by CTCF endow a gatekeeper function that governs the earliest fate transitions HSCs make by coordinating disparate stemness pathways linked to quiescence and self-renewal.
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Affiliation(s)
- Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Cell Therapy Project, R&D Division, Kirin Holdings Company, Limited, Kanagawa 236-0004, Japan
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Sasan Zandi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Héléna Boutzen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Aaron Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Erwin Schoof
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ken Kron
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Tiago Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michael D Taylor
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Munster 48149, Germany
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
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