1
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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [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] [Indexed: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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2
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Conte MI, Fuentes-Trillo A, Domínguez Conde C. Opportunities and tradeoffs in single-cell transcriptomic technologies. Trends Genet 2024; 40:83-93. [PMID: 37953195 DOI: 10.1016/j.tig.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
Recent technological and algorithmic advances enable single-cell transcriptomic analysis with remarkable depth and breadth. Nonetheless, a persistent challenge is the compromise between the ability to profile high numbers of cells and the achievement of full-length transcript coverage. Currently, the field is progressing and developing new and creative solutions that improve cellular throughput, gene detection sensitivity and full-length transcript capture. Furthermore, long-read sequencing approaches for single-cell transcripts are breaking frontiers that have previously blocked full transcriptome characterization. We here present a comprehensive overview of available options for single-cell transcriptome profiling, highlighting the key advantages and disadvantages of each approach.
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Affiliation(s)
- Matilde I Conte
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
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3
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Sun Y, Wiese M, Hmadi R, Karayol R, Seyfferth J, Martinez Greene JA, Erdogdu NU, Deboutte W, Arrigoni L, Holz H, Renschler G, Hirsch N, Foertsch A, Basilicata MF, Stehle T, Shvedunova M, Bella C, Pessoa Rodrigues C, Schwalb B, Cramer P, Manke T, Akhtar A. MSL2 ensures biallelic gene expression in mammals. Nature 2023; 624:173-181. [PMID: 38030723 PMCID: PMC10700137 DOI: 10.1038/s41586-023-06781-3] [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: 05/29/2022] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter-enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.
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Affiliation(s)
- Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Meike Wiese
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Raed Hmadi
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Remzi Karayol
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Juan Alfonso Martinez Greene
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gina Renschler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Naama Hirsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Arion Foertsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Thomas Stehle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Chiara Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bjoern Schwalb
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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4
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Kravitz SN, Ferris E, Love MI, Thomas A, Quinlan AR, Gregg C. Random allelic expression in the adult human body. Cell Rep 2023; 42:111945. [PMID: 36640362 PMCID: PMC10484211 DOI: 10.1016/j.celrep.2022.111945] [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: 04/14/2022] [Revised: 10/17/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Genes are typically assumed to express both parental alleles similarly, yet cell lines show random allelic expression (RAE) for many autosomal genes that could shape genetic effects. Thus, understanding RAE in human tissues could improve our understanding of phenotypic variation. Here, we develop a methodology to perform genome-wide profiling of RAE and biallelic expression in GTEx datasets for 832 people and 54 tissues. We report 2,762 autosomal genes with some RAE properties similar to randomly inactivated X-linked genes. We found that RAE is associated with rapidly evolving regions in the human genome, adaptive signaling processes, and genes linked to age-related diseases such as neurodegeneration and cancer. We define putative mechanistic subtypes of RAE distinguished by gene overlaps on sense and antisense DNA strands, aggregation in clusters near telomeres, and increased regulatory complexity and inputs compared with biallelic genes. We provide foundations to study RAE in human phenotypes, evolution, and disease.
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Affiliation(s)
- Stephanie N Kravitz
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Elliott Ferris
- Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alun Thomas
- Department of Internal Medicine, Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Christopher Gregg
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA.
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5
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Kubasova N, Alves-Pereira CF, Gupta S, Vinogradova S, Gimelbrant A, Barreto VM. In Vivo Clonal Analysis Reveals Random Monoallelic Expression in Lymphocytes That Traces Back to Hematopoietic Stem Cells. Front Cell Dev Biol 2022; 10:827774. [PMID: 36003148 PMCID: PMC9393635 DOI: 10.3389/fcell.2022.827774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Evaluating the epigenetic landscape in the stem cell compartment at the single-cell level is essential to assess the cells’ heterogeneity and predict their fate. Here, using a genome-wide transcriptomics approach in vivo, we evaluated the allelic expression imbalance in the progeny of single hematopoietic cells (HSCs) as a read-out of epigenetic marking. After 4 months of extensive proliferation and differentiation, we found that X-chromosome inactivation (XCI) is tightly maintained in all single-HSC derived hematopoietic cells. In contrast, the vast majority of the autosomal genes did not show clonal patterns of random monoallelic expression (RME). However, a persistent allele-specific autosomal transcription in HSCs and their progeny was found in a rare number of cases, none of which has been previously reported. These data show that: 1) XCI and RME in the autosomal chromosomes are driven by different mechanisms; 2) the previously reported high frequency of genes under RME in clones expanded in vitro (up to 15%) is not found in clones undergoing multiple differentiation steps in vivo; 3) prior to differentiation, HSCs have stable patterns of autosomal RME. We propose that most RME patterns in autosomal chromosomes are erased and established de novo during cell lineage differentiation.
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Affiliation(s)
- Nadiya Kubasova
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- Genetagus, Egas Moniz – Cooperativa de Ensino Superior, CRL, Monte de Caparica, Portugal
| | - Clara F. Alves-Pereira
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Saumya Gupta
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Svetlana Vinogradova
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Alexander Gimelbrant
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
| | - Vasco M. Barreto
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Costa da Caparica, Portugal
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
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6
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Basilicata MF, Keller Valsecchi CI. The good, the bad, and the ugly: Evolutionary and pathological aspects of gene dosage alterations. PLoS Genet 2021; 17:e1009906. [PMID: 34882671 PMCID: PMC8659298 DOI: 10.1371/journal.pgen.1009906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Diploid organisms contain a maternal and a paternal genome complement that is thought to provide robustness and allow developmental progression despite genetic perturbations that occur in heterozygosity. However, changes affecting gene dosage from the chromosome down to the individual gene level possess a significant pathological potential and can lead to developmental disorders (DDs). This indicates that expression from a balanced gene complement is highly relevant for proper cellular and organismal function in eukaryotes. Paradoxically, gene and whole chromosome duplications are a principal driver of evolution, while heteromorphic sex chromosomes (XY and ZW) are naturally occurring aneuploidies important for sex determination. Here, we provide an overview of the biology of gene dosage at the crossroads between evolutionary benefit and pathogenicity during disease. We describe the buffering mechanisms and cellular responses to alterations, which could provide a common ground for the understanding of DDs caused by copy number alterations.
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7
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Sands B, Yun S, Mendenhall AR. Introns control stochastic allele expression bias. Nat Commun 2021; 12:6527. [PMID: 34764277 PMCID: PMC8585970 DOI: 10.1038/s41467-021-26798-4] [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: 11/04/2019] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.
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Affiliation(s)
- Bryan Sands
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Soo Yun
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Alexander R. Mendenhall
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
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8
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Marion-Poll L, Forêt B, Zielinski D, Massip F, Attia M, Carter AC, Syx L, Chang HY, Gendrel AV, Heard E. Locus specific epigenetic modalities of random allelic expression imbalance. Nat Commun 2021; 12:5330. [PMID: 34504093 PMCID: PMC8429725 DOI: 10.1038/s41467-021-25630-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
Most autosomal genes are thought to be expressed from both alleles, with some notable exceptions, including imprinted genes and genes showing random monoallelic expression (RME). The extent and nature of RME has been the subject of debate. Here we investigate the expression of several candidate RME genes in F1 hybrid mouse cells before and after differentiation, to define how they become persistently, monoallelically expressed. Clonal monoallelic expression is not present in embryonic stem cells, but we observe high frequencies of monoallelism in neuronal progenitor cells by assessing expression status in more than 200 clones. We uncover unforeseen modes of allelic expression that appear to be gene-specific and epigenetically regulated. This non-canonical allelic regulation has important implications for development and disease, including autosomal dominant disorders and opens up therapeutic perspectives.
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Affiliation(s)
- Lucile Marion-Poll
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
- Directors' research, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Benjamin Forêt
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Dina Zielinski
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, Paris, France
| | - Florian Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mikael Attia
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Laurène Syx
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, Paris, France
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Anne-Valerie Gendrel
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
| | - Edith Heard
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
- Directors' research, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Collège de France, Paris, France.
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9
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Abstract
Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to cis-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes.
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Affiliation(s)
- Siobhan Cleary
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
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10
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Gregg C. Starvation and Climate Change—How to Constrain Cancer Cell Epigenetic Diversity and Adaptability to Enhance Treatment Efficacy. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.693781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Advanced metastatic cancer is currently not curable and the major barrier to eliminating the disease in patients is the resistance of subpopulations of tumor cells to drug treatments. These resistant subpopulations can arise stochastically among the billions of tumor cells in a patient or emerge over time during therapy due to adaptive mechanisms and the selective pressures of drug therapies. Epigenetic mechanisms play important roles in tumor cell diversity and adaptability, and are regulated by metabolic pathways. Here, I discuss knowledge from ecology, evolution, infectious disease, species extinction, metabolism and epigenetics to synthesize a roadmap to a clinically feasible approach to help homogenize tumor cells and, in combination with drug treatments, drive their extinction. Specifically, cycles of starvation and hyperthermia could help synchronize tumor cells and constrain epigenetic diversity and adaptability by limiting substrates and impairing the activity of chromatin modifying enzymes. Hyperthermia could also help prevent cancer cells from entering dangerous hibernation-like states. I propose steps to a treatment paradigm to help drive cancer extinction that builds on the successes of fasting, hyperthermia and immunotherapy and is achievable in patients. Finally, I highlight the many unknowns, opportunities for discovery and that stochastic gene and allele level epigenetic mechanisms pose a major barrier to cancer extinction that warrants deeper investigation.
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11
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Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HES, Loux SC, Esteller-Vico A, Norris JK, Anand L, Scoggin KE, Rodriguez Lopez CM, Breen J, Bailey E, Daels P, Ball BA. Parental bias in expression and interaction of genes in the equine placenta. Proc Natl Acad Sci U S A 2021; 118:e2006474118. [PMID: 33853939 PMCID: PMC8072238 DOI: 10.1073/pnas.2006474118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a workflow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.
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Affiliation(s)
- Pouya Dini
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Theodore Kalbfleisch
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202
| | - José M Uribe-Salazar
- Department of Biochemistry and Molecular Medicine, Genome Center, Medical Investigation of Neurodevelopmental Disorders Institute, University of California, Davis, CA 95616
| | - Mariano Carossino
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, 35516, Egypt
| | - Shavahn C Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Alejandro Esteller-Vico
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Jamie K Norris
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Ernest Bailey
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Peter Daels
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Barry A Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503;
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12
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Rv P, Sundaresh A, Karunyaa M, Arun A, Gayen S. Autosomal Clonal Monoallelic Expression: Natural or Artifactual? Trends Genet 2020; 37:206-211. [PMID: 33234351 DOI: 10.1016/j.tig.2020.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 01/08/2023]
Abstract
The prevalence of mitotically heritable clonal random monoallelic expression of autosomal genes (aRME) remains controversial. Specifically, presence of clonal aRME is well supported in vitro but remains elusive in vivo. Here, we provide critical insights into this matter and discuss whether prevalent clonal aRME is natural or artifactual.
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Affiliation(s)
- P Rv
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - A Sundaresh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - M Karunyaa
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - A Arun
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - S Gayen
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India.
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13
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Cell Communication-mediated Nonself-Recognition and -Intolerance in Representative Species of the Animal Kingdom. J Mol Evol 2020; 88:482-500. [PMID: 32572694 DOI: 10.1007/s00239-020-09955-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/07/2020] [Indexed: 12/27/2022]
Abstract
Why has histo-incompatibility arisen in evolution and can cause self-intolerance? Compatible/incompatible reactions following natural contacts between genetically-different (allogeneic) colonies of marine organisms have inspired the conception that self-nonself discrimination has developed to reduce invasion threats by migratory foreign germ/somatic stem cells, in extreme cases resulting in conquest of the whole body by a foreign genome. Two prominent model species for allogeneic discrimination are the marine invertebrates Hydractinia (Cnidaria) and Botryllus (Ascidiacea). In Hydractinia, self-nonself recognition is based on polymorphic surface markers encoded by two genes (alr1, alr2), with self recognition enabled by homophilic binding of identical ALR molecules. Variable expression patterns of alr alleles presumably account for the first paradigm of autoaggression in an invertebrate. In Botryllus, self-nonself recognition is controlled by a single polymorphic gene locus (BHF) with hundreds of codominantly expressed alleles. Fusion occurs when both partners share at least one BHF allele while rejection develops when no allele is shared. Molecules involved in allorecognition frequently contain immunoglobulin or Ig-like motifs, case-by-case supplemented by additional molecules enabling homophilic interaction, while the mechanisms applied to destroy allogeneic grafts or neighbors include taxon-specific tools besides common facilities of natural immunity. The review encompasses comparison with allorecognition in mammals based on MHC-polymorphism in transplantation and following feto-maternal cell trafficking.
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14
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Blay N, Casas E, Galván-Femenía I, Graffelman J, de Cid R, Vavouri T. Assessment of kinship detection using RNA-seq data. Nucleic Acids Res 2020; 47:e136. [PMID: 31501877 PMCID: PMC6868348 DOI: 10.1093/nar/gkz776] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 08/23/2019] [Accepted: 08/29/2019] [Indexed: 01/23/2023] Open
Abstract
Analysis of RNA sequencing (RNA-seq) data from related individuals is widely used in clinical and molecular genetics studies. Prediction of kinship from RNA-seq data would be useful for confirming the expected relationships in family based studies and for highlighting samples from related individuals in case-control or population based studies. Currently, reconstruction of pedigrees is largely based on SNPs or microsatellites, obtained from genotyping arrays, whole genome sequencing and whole exome sequencing. Potential problems with using RNA-seq data for kinship detection are the low proportion of the genome that it covers, the highly skewed coverage of exons of different genes depending on expression level and allele-specific expression. In this study we assess the use of RNA-seq data to detect kinship between individuals, through pairwise identity by descent (IBD) estimates. First, we obtained high quality SNPs after successive filters to minimize the effects due to allelic imbalance as well as errors in sequencing, mapping and genotyping. Then, we used these SNPs to calculate pairwise IBD estimates. By analysing both real and simulated RNA-seq data we show that it is possible to identify up to second degree relationships using RNA-seq data of even low to moderate sequencing depth.
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Affiliation(s)
- Natalia Blay
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona 08916, Spain.,Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona 08916, Spain.,Masters Programme in Bioinformatics and Biostatistics, Universitat Oberta de Catalunya (UOC), Barcelona 08035, Spain
| | - Eduard Casas
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona 08916, Spain.,Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona 08916, Spain.,Doctoral Programme in Biomedicine, Universitat de Barcelona, Barcelona 08007, Spain
| | - Iván Galván-Femenía
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona 08916, Spain.,Genomes for Life - GCAT lab Group - Germans Trias i Pujol Research Institute, Can Ruti Campus, Ctra de Can Ruti, Camí de les Escoles s/n, Badalona, Barcelona 08916, Spain
| | - Jan Graffelman
- Department of Statistics and Operations Research Universitat Politècnica de Catalunya, Barcelona 08028, Spain.,Department of Biostatistics, University of Washington, Seattle, WA 98105-946, USA
| | - Rafael de Cid
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona 08916, Spain.,Genomes for Life - GCAT lab Group - Germans Trias i Pujol Research Institute, Can Ruti Campus, Ctra de Can Ruti, Camí de les Escoles s/n, Badalona, Barcelona 08916, Spain
| | - Tanya Vavouri
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona 08916, Spain.,Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona 08916, Spain
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15
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da Silva Francisco Junior R, Dos Santos Ferreira C, Santos E Silva JC, Terra Machado D, Côrtes Martins Y, Ramos V, Simões Carnivali G, Garcia AB, Medina-Acosta E. Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins. Front Genet 2019; 10:1178. [PMID: 31850058 PMCID: PMC6887657 DOI: 10.3389/fgene.2019.01178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/24/2019] [Indexed: 01/19/2023] Open
Abstract
Despite being developed from one zygote, heterokaryotypic monozygotic (MZ) co-twins exhibit discordant karyotypes. Epigenomic studies in biological samples from heterokaryotypic MZ co-twins are of the most significant value for assessing the effects on gene- and allele-specific expression of an extranumerary chromosomal copy or structural chromosomal disparities in otherwise nearly identical germline genetic contributions. Here, we use RNA-Seq data from existing repositories to establish within-pair correlations for the breadth and magnitude of allele-specific expression (ASE) in heterokaryotypic MZ co-twins discordant for trisomy 21 and maternal 21q inheritance, as well as homokaryotypic co-twins. We show that there is a genome-wide disparity at ASE sites between the heterokaryotypic MZ co-twins. Although most of the disparity corresponds to changes in the magnitude of biallelic imbalance, ASE sites switching from either strictly monoallelic to biallelic imbalance or the reverse occur in few genes that are known or predicted to be imprinted, subject to X-chromosome inactivation or A-to-I(G) RNA edited. We also uncovered comparable ASE differences between homokaryotypic MZ twins. The extent of ASE discordance in MZ twins (2.7%) was about 10-fold lower than the expected between pairs of unrelated, non-twin males or females. The results indicate that the observed within-pair dissimilarities in breadth and magnitude of ASE sites in the heterokaryotypic MZ co-twins could not solely be attributable to the aneuploidy and the missing allelic heritability at 21q.
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Affiliation(s)
| | - Cristina Dos Santos Ferreira
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Juan Carlo Santos E Silva
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Yasmmin Côrtes Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Victor Ramos
- Department of Genetics, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo Simões Carnivali
- Department of Computational Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Beatriz Garcia
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
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16
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Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019; 47:2981-2995. [PMID: 30698752 PMCID: PMC6451136 DOI: 10.1093/nar/gkz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function.
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Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Qing Mao
- Complete Genomics, Inc., San Jose, CA 95112, USA
| | - Brock A Peters
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Huebsch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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17
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Kravitz SN, Gregg C. New subtypes of allele-specific epigenetic effects: implications for brain development, function and disease. Curr Opin Neurobiol 2019; 59:69-78. [PMID: 31153086 DOI: 10.1016/j.conb.2019.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/24/2019] [Indexed: 01/15/2023]
Abstract
Typically, it is assumed that the maternal and paternal alleles for most genes are equally expressed. Known exceptions include canonical imprinted genes, random X-chromosome inactivation, olfactory receptors and clustered protocadherins. Here, we highlight recent studies showing that allele-specific expression is frequent in the genome and involves subtypes of epigenetic allelic effects that differ in terms of heritability, clonality and stability over time. Different forms of epigenetic allele regulation could have different roles in brain development, function, and disease. An emerging area involves understanding allelic effects in a cell-type and developmental stage-specific manner and determining how these effects influence the impact of genetic variants and mutations on the brain. A deeper understanding of epigenetics at the allele and cellular level in the brain could help clarify the mechanisms underlying phenotypic variance.
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Affiliation(s)
- Stephanie N Kravitz
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Christopher Gregg
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA.
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18
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van der Veeken J, Zhong Y, Sharma R, Mazutis L, Dao P, Pe'er D, Leslie CS, Rudensky AY. Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells. Immunity 2019; 50:1202-1217.e7. [PMID: 31027997 DOI: 10.1016/j.immuni.2019.03.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/15/2019] [Accepted: 03/27/2019] [Indexed: 12/29/2022]
Abstract
Stable changes in chromatin states and gene expression in cells of the immune system form the basis for memory of infections and other challenges. Here, we used naturally occurring cis-regulatory variation in wild-derived inbred mouse strains to explore the mechanisms underlying long-lasting versus transient gene regulation in CD8 T cells responding to acute viral infection. Stably responsive DNA elements were characterized by dramatic and congruent chromatin remodeling events affecting multiple neighboring sites and required distinct transcription factor (TF) binding motifs for their accessibility. Specifically, we found that cooperative recruitment of T-box and Runx family transcription factors to shared targets mediated stable chromatin remodeling upon T cell activation. Our observations provide insights into the molecular mechanisms driving virus-specific CD8 T cell responses and suggest a general mechanism for the formation of transcriptional and epigenetic memory applicable to other immune and non-immune cells.
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Affiliation(s)
- Joris van der Veeken
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Zhong
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Phuong Dao
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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19
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Reinius B, Sandberg R. Reply to 'High prevalence of clonal monoallelic expression'. Nat Genet 2019; 50:1199-1200. [PMID: 30082784 DOI: 10.1038/s41588-018-0189-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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20
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Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. PLoS Genet 2019; 15:e1007874. [PMID: 30625149 PMCID: PMC6342324 DOI: 10.1371/journal.pgen.1007874] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/22/2019] [Accepted: 12/04/2018] [Indexed: 12/03/2022] Open
Abstract
Extensive cell-to-cell variation exists even among putatively identical cells, and there is great interest in understanding how the properties of transcription relate to this heterogeneity. Differential expression from the two gene copies in diploid cells could potentially contribute, yet our ability to measure from which gene copy individual RNAs originated remains limited, particularly in the context of tissues. Here, we demonstrate quantitative, single molecule allele-specific RNA FISH adapted for use on tissue sections, allowing us to determine the chromosome of origin of individual RNA molecules in formaldehyde-fixed tissues. We used this method to visualize the allele-specific expression of Xist and multiple autosomal genes in mouse kidney. By combining these data with mathematical modeling, we evaluated models for allele-specific heterogeneity, in particular demonstrating that apparent expression from only one of the alleles in single cells can arise as a consequence of low-level mRNA abundance and transcriptional bursting. In mammals, most cells of the body contain two genetic datasets: one from the mother and one from the father, and—in theory—these two sets of information could contribute equally to produce the molecules in a given cell. In practice, however, this is not always the case, which can have dramatic implications for many traits, including visible features (such as fur color) and even disease outcomes. However, it remains difficult to measure the parental origin of individual molecules in a given cell and thus to assess what processes lead to an imbalance of the maternal and paternal contribution. We adapted a microscopy technique—called allele-specific single molecule RNA FISH—that uses a combination of fluorescent tags to specifically label one type of molecule, RNA, depending on its origin, for use in mouse kidney sections. Focusing on RNAs that were previously reported to show imbalance, we performed measurements and combined these with mathematical modeling to quantify imbalance in tissues and explain how these can arise. We found that we could recapitulate the observed imbalances using models that only take into account the random processes that produce RNA, without the need to invoke special regulatory mechanisms to create unequal contributions.
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