1
|
Rojas J, Hose J, Dutcher HA, Place M, Wolters JF, Hittinger CT, Gasch AP. Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model. CELL GENOMICS 2024; 4:100656. [PMID: 39317188 DOI: 10.1016/j.xgen.2024.100656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/10/2024] [Accepted: 08/20/2024] [Indexed: 09/26/2024]
Abstract
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74%-94% of the variance in aneuploid strains' growth rates is explained by the cumulative cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of small nucleolar RNAs (snoRNAs) and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.
Collapse
Affiliation(s)
- Julie Rojas
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John F Wolters
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chris Todd Hittinger
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
2
|
Spealman P, de Santana C, De T, Gresham D. Multilevel gene expression changes in lineages containing adaptive copy number variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.20.563336. [PMID: 37961325 PMCID: PMC10634702 DOI: 10.1101/2023.10.20.563336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Copy-number variants (CNVs) are an important class of recurrent variants that mediate adaptive evolution. While CNVs can increase the relative fitness of the organism, they can also incur a cost. We previously evolved populations of Saccharomyces cerevisiae over hundreds of generations in glutamine-limited (Gln-) chemostats and observed the recurrent evolution of CNVs at the GAP1 locus. To understand the role that expression plays in adaptation, both in relation to the adaptation of the organism to the selective condition, and as a consequence of the CNV, we measured the transcriptome, translatome, and proteome of 4 strains of evolved yeast, each with a unique CNV, and their ancestor in Gln- conditions. We find CNV-amplified genes correlate with higher RNA abundance; however, this effect is reduced at the level of the proteome, consistent with post-transcriptional dosage compensation. By normalizing each level of expression by the abundance of the preceding step we were able to identify widespread divergence in the efficiency of each step in the gene in the efficiency of each step in gene expression. Genes with significantly different translational efficiency were enriched for potential regulatory mechanisms including either upstream open reading frames, RNA binding sites for SSD1, or both. Genes with lower protein expression efficiency were enriched for genes encoding proteins in protein complexes. Taken together, our study reveals widespread changes in gene expression at multiple regulatory levels in lineages containing adaptive CNVs highlighting the diverse ways in which adaptive evolution shapes gene expression.
Collapse
Affiliation(s)
- Pieter Spealman
- Center for Genomics and Systems Biology, Department of Biology, New York University
| | - Carolina de Santana
- Laboratório de Microbiologia Ambiental e Saúde Pública - Universidade Estadual de Feira de Santana (UEFS), Bahia
| | - Titir De
- Center for Genomics and Systems Biology, Department of Biology, New York University
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University
| |
Collapse
|
3
|
Wang S, Leng L, Wang Q, Gu Y, Li J, An Y, Deng Q, Xie P, Cheng C, Chen X, Zhou Q, Lu J, Chen F, Liu L, Yang H, Wang J, Xu X, Hou Y, Gong F, Hu L, Lu G, Shang Z, Lin G. A single-cell transcriptome atlas of human euploid and aneuploid blastocysts. Nat Genet 2024; 56:1468-1481. [PMID: 38839885 DOI: 10.1038/s41588-024-01788-6] [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: 03/24/2023] [Accepted: 05/06/2024] [Indexed: 06/07/2024]
Abstract
Aneuploidy is frequently detected in early human embryos as a major cause of early pregnancy failure. However, how aneuploidy affects cellular function remains elusive. Here, we profiled the transcriptomes of 14,908 single cells from 203 human euploid and aneuploid blastocysts involving autosomal and sex chromosomes. Nearly all of the blastocysts contained four lineages. In aneuploid chromosomes, 19.5% ± 1.2% of the expressed genes showed a dosage effect, and 90 dosage-sensitive domains were identified. Aneuploidy leads to prevalent genome-wide transcriptome alterations. Common effects, including apoptosis, were identified, especially in monosomies, partially explaining the lower cell numbers in autosomal monosomies. We further identified lineage-specific effects causing unstable epiblast development in aneuploidies, which was accompanied by the downregulation of TGF-β and FGF signaling, which resulted in insufficient trophectoderm maturation. Our work provides crucial insights into the molecular basis of human aneuploid blastocysts and may shed light on the cellular interaction during blastocyst development.
Collapse
Affiliation(s)
- Shengpeng Wang
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lizhi Leng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | | | - Yifan Gu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | | | | | - Qiuting Deng
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pingyuan Xie
- Hunan Normal University School of Medicine, Changsha, China
- National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Can Cheng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
| | - Xueqin Chen
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
| | - Qinwei Zhou
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Jia Lu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
| | - Fang Chen
- BGI Research, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, BGI Research, Shenzhen, China
| | - Longqi Liu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huanming Yang
- BGI Research, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jian Wang
- BGI Research, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Xun Xu
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Yong Hou
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fei Gong
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Guangxiu Lu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
- National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Zhouchun Shang
- BGI Research, Shenzhen, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China.
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Changsha, China.
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China.
- National Engineering and Research Center of Human Stem Cell, Changsha, China.
| |
Collapse
|
4
|
Escalante LE, Hose J, Howe H, Paulsen N, Place M, Gasch AP. Premature aging in aneuploid yeast is caused in part by aneuploidy-induced defects in Ribosome Quality Control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.22.600216. [PMID: 38948718 PMCID: PMC11213126 DOI: 10.1101/2024.06.22.600216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Premature aging is a hallmark of Down syndrome, caused by trisomy of human chromosome 21, but the reason is unclear and difficult to study in humans. We used an aneuploid model in wild yeast to show that chromosome amplification disrupts nutrient-induced cell-cycle arrest, quiescence entry, and healthy aging, across genetic backgrounds and amplified chromosomes. We discovered that these defects are due in part to aneuploidy-induced dysfunction in Ribosome Quality Control (RQC). Compared to euploids, aneuploids entering quiescence display aberrant ribosome profiles, accumulate RQC intermediates, and harbor an increased load of protein aggregates. Although they have normal proteasome capacity, aneuploids show signs of ubiquitin dysregulation, which impacts cyclin abundance to disrupt arrest. Remarkably, inducing ribosome stalling in euploids produces similar aberrations, while up-regulating limiting RQC subunits or proteins in ubiquitin metabolism alleviates many of the aneuploid defects. Our results provide implications for other aneuploidy disorders including Down syndrome.
Collapse
Affiliation(s)
- Leah E. Escalante
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Hollis Howe
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Norah Paulsen
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706
| | - Audrey P. Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706
| |
Collapse
|
5
|
Storchová Z. Cells cope with altered chromosome numbers by enhancing protein breakdown. Nature 2024; 630:41-43. [PMID: 38831150 DOI: 10.1038/d41586-024-01360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
|
6
|
Muenzner J, Trébulle P, Agostini F, Zauber H, Messner CB, Steger M, Kilian C, Lau K, Barthel N, Lehmann A, Textoris-Taube K, Caudal E, Egger AS, Amari F, De Chiara M, Demichev V, Gossmann TI, Mülleder M, Liti G, Schacherer J, Selbach M, Berman J, Ralser M. Natural proteome diversity links aneuploidy tolerance to protein turnover. Nature 2024; 630:149-157. [PMID: 38778096 PMCID: PMC11153158 DOI: 10.1038/s41586-024-07442-9] [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: 04/07/2022] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions and allows the generalizability of laboratory findings to be assessed. One notable discovery made in natural isolates of Saccharomyces cerevisiae is that aneuploidy-an imbalance in chromosome copy numbers-is frequent1,2 (around 20%), which seems to contradict the substantial fitness costs and transient nature of aneuploidy when it is engineered in the laboratory3-5. Here we generate a proteomic resource and merge it with genomic1 and transcriptomic6 data for 796 euploid and aneuploid natural isolates. We find that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins-especially subunits of protein complexes-show reduced expression, but the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage compensated, and average protein levels are shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and shows the utility of exploiting the natural diversity of species to attain generalizable molecular insights into complex biological processes.
Collapse
Affiliation(s)
- Julia Muenzner
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Pauline Trébulle
- Molecular Biology of Metabolism Laboratory, Francis Crick Institute, London, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Henrik Zauber
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Christoph B Messner
- Molecular Biology of Metabolism Laboratory, Francis Crick Institute, London, UK
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Martin Steger
- Evotec (München), Martinsried, Germany
- NEOsphere Biotechnologies, Martinsried, Germany
| | - Christiane Kilian
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Kate Lau
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Natalie Barthel
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Andrea Lehmann
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Kathrin Textoris-Taube
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
- Core Facility High-Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Elodie Caudal
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Anna-Sophia Egger
- Molecular Biology of Metabolism Laboratory, Francis Crick Institute, London, UK
| | - Fatma Amari
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
- Core Facility High-Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | | | - Vadim Demichev
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, Francis Crick Institute, London, UK
| | - Toni I Gossmann
- Computational Systems Biology, Faculty of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Michael Mülleder
- Core Facility High-Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | | | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany.
- Molecular Biology of Metabolism Laboratory, Francis Crick Institute, London, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| |
Collapse
|
7
|
Dutcher HA, Hose J, Howe H, Rojas J, Gasch AP. The response to single-gene duplication implicates translation as a key vulnerability in aneuploid yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589582. [PMID: 38659764 PMCID: PMC11042342 DOI: 10.1101/2024.04.15.589582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Aneuploidy produces myriad consequences in health and disease, yet models of the deleterious effects of chromosome amplification are still widely debated. To distinguish the molecular determinants of aneuploidy stress, we measured the effects of duplicating individual genes in cells with varying chromosome duplications, in wild-type cells and cells sensitized to aneuploidy by deletion of RNA-binding protein Ssd1. We identified gene duplications that are nearly neutral in wild-type euploid cells but significantly deleterious in euploids lacking SSD1 or SSD1+ aneuploid cells with different chromosome duplications. Several of the most deleterious genes are linked to translation; in contrast, duplication of other translational regulators, including eI5Fa Hyp2, benefit ssd1Δ aneuploids over controls. Using modeling of aneuploid growth defects, we propose that the deleterious effects of aneuploidy emerge from an interaction between the cumulative burden of many amplified genes on a chromosome and a subset of duplicated genes that become toxic in that context. Our results suggest that the mechanism behind their toxicity is linked to a key vulnerability in translation in aneuploid cells. These findings provide a perspective on the dual impact of individual genes and overall genomic burden, offering new avenues for understanding aneuploidy and its cellular consequences.
Collapse
|
8
|
Boyd SS, Robarts DR, Nguyen K, Villar M, Alghusen I, Kotulkar M, Denson A, Fedosyuk H, Whelan SA, Lee NCY, Hanover J, Dias WB, Tan EP, McGreal SR, Artigues A, Swerdlow RH, Thompson JA, Apte U, Slawson C. Multi-Omics after O-GlcNAc Alteration Identifies Cellular Processes Working Synergistically to Promote Aneuploidy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589379. [PMID: 38659829 PMCID: PMC11042281 DOI: 10.1101/2024.04.16.589379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Pharmacologic or genetic manipulation of O-GlcNAcylation, an intracellular, single sugar post-translational modification, are difficult to interpret due to the pleotropic nature of O-GlcNAc and the vast signaling pathways it regulates. To address this issue, we employed either OGT (O-GlcNAc transferase), OGA (O-GlcNAcase) liver knockouts, or pharmacological inhibition of OGA coupled with multi-Omics analysis and bioinformatics. We identified numerous genes, proteins, phospho-proteins, or metabolites that were either inversely or equivalently changed between conditions. Moreover, we identified pathways in OGT knockout samples associated with increased aneuploidy. To test and validate these pathways, we induced liver growth in OGT knockouts by partial hepatectomy. OGT knockout livers showed a robust aneuploidy phenotype with disruptions in mitosis, nutrient sensing, protein metabolism/amino acid metabolism, stress response, and HIPPO signaling demonstrating how OGT is essential in controlling aneuploidy pathways. Moreover, these data show how a multi-Omics platform can discern how OGT can synergistically fine-tune multiple cellular pathways.
Collapse
|
9
|
Rojas J, Hose J, Auguste Dutcher H, Place M, Wolters JF, Hittinger CT, Gasch AP. Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588778. [PMID: 38645209 PMCID: PMC11030387 DOI: 10.1101/2024.04.09.588778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will only be maintained if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74-94% of the variance in aneuploid strains' growth rates is explained by the additive cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of snoRNAs and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.
Collapse
Affiliation(s)
- Julie Rojas
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John F Wolters
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chris Todd Hittinger
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, 53706, USA
| |
Collapse
|
10
|
Kohanovski I, Pontz M, Vande Zande P, Selmecki A, Dahan O, Pilpel Y, Yona AH, Ram Y. Aneuploidy Can Be an Evolutionary Diversion on the Path to Adaptation. Mol Biol Evol 2024; 41:msae052. [PMID: 38427813 PMCID: PMC10951435 DOI: 10.1093/molbev/msae052] [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: 11/23/2023] [Revised: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024] Open
Abstract
Aneuploidy is common in eukaryotes, often leading to decreased fitness. However, evidence from fungi and human tumur cells suggests that specific aneuploidies can be beneficial under stressful conditions and facilitate adaptation. In a previous evolutionary experiment with yeast, populations evolving under heat stress became aneuploid, only to later revert to euploidy after beneficial mutations accumulated. It was therefore suggested that aneuploidy is a "stepping stone" on the path to adaptation. Here, we test this hypothesis. We use Bayesian inference to fit an evolutionary model with both aneuploidy and mutation to the experimental results. We then predict the genotype frequency dynamics during the experiment, demonstrating that most of the evolved euploid population likely did not descend from aneuploid cells, but rather from the euploid wild-type population. Our model shows how the beneficial mutation supply-the product of population size and beneficial mutation rate-determines the evolutionary dynamics: with low supply, much of the evolved population descends from aneuploid cells; but with high supply, beneficial mutations are generated fast enough to outcompete aneuploidy due to its inherent fitness cost. Our results suggest that despite its potential fitness benefits under stress, aneuploidy can be an evolutionary "diversion" rather than a "stepping stone": it can delay, rather than facilitate, the adaptation of the population, and cells that become aneuploid may leave less descendants compared to cells that remain diploid.
Collapse
Affiliation(s)
- Ilia Kohanovski
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- School of Computer Science, Reichman University, Herzliya, Israel
| | - Martin Pontz
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Pétra Vande Zande
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Avihu H Yona
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
11
|
Joy J, Fusari E, Milán M. Aneuploidy-induced cellular behaviors: Insights from Drosophila. Dev Cell 2024; 59:295-307. [PMID: 38320484 DOI: 10.1016/j.devcel.2023.12.009] [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: 02/02/2023] [Revised: 08/09/2023] [Accepted: 12/15/2023] [Indexed: 02/08/2024]
Abstract
A balanced gene complement is crucial for proper cell function. Aneuploidy, the condition of having an imbalanced chromosome set, alters the stoichiometry of gene copy numbers and protein complexes and has dramatic consequences at the cellular and organismal levels. In humans, aneuploidy is associated with different pathological conditions including cancer, microcephaly, mental retardation, miscarriages, and aging. Over the last century, Drosophila has provided a valuable system for studying the consequences of systemic aneuploidies. More recently, it has contributed to the identification and molecular dissection of aneuploidy-induced cellular behaviors and their impact at the tissue and organismal levels. In this perspective, we review this active field of research, first by comparing knowledge from yeast, mouse, and human cells, then by highlighting the contributions of Drosophila. The aim of these discussions was to further our understanding of the functional interplay between aneuploidy, cell physiology, and tissue homeostasis in human development and disease.
Collapse
Affiliation(s)
- Jery Joy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Elena Fusari
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Marco Milán
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys, 23, 08010 Barcelona, Spain.
| |
Collapse
|
12
|
Yasukawa T, Iwama R, Yamasaki Y, Masuo N, Noda Y. Yeast Rim11 kinase responds to glutathione-induced stress by regulating the transcription of phospholipid biosynthetic genes. Mol Biol Cell 2024; 35:ar8. [PMID: 37938929 PMCID: PMC10881166 DOI: 10.1091/mbc.e23-03-0116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Glutathione (GSH), a tripeptide composed of glycine, cysteine, and glutamic acid, is an abundant thiol found in a wide variety of cells, ranging from bacterial to mammalian cells. Adequate levels of GSH are essential for maintaining iron homeostasis. The ratio of oxidized/reduced GSH is strictly regulated in each organelle to maintain the cellular redox potential. Cellular redox imbalances cause defects in physiological activities, which can lead to various diseases. Although there are many reports regarding the cellular response to GSH depletion, studies on stress response to high levels of GSH are limited. Here, we performed genome-scale screening in the yeast Saccharomyces cerevisiae and identified RIM11, BMH1, and WHI2 as multicopy suppressors of the growth defect caused by GSH stress. The deletion strains of each gene were sensitive to GSH. We found that Rim11, a kinase important in the regulation of meiosis, was activated via autophosphorylation upon GSH stress in a glucose-rich medium. Furthermore, RNA-seq revealed that transcription of phospholipid biosynthetic genes was downregulated under GSH stress, and introduction of multiple copies of RIM11 counteracted this effect. These results demonstrate that S. cerevisiae copes with GSH stress via multiple stress-responsive pathways, including a part of the adaptive pathway to glucose limitation.
Collapse
Affiliation(s)
- Taishi Yasukawa
- Mitsubishi Corporation Life Sciences Limited, Tokyo Takarazuka Building 14F, 1-1-3 Yurakucho, Chiyoda-ku, Tokyo 100-0006, Japan
| | - Ryo Iwama
- Collaborative Research Institute for Innovative Microbiology, Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuriko Yamasaki
- Mitsubishi Corporation Life Sciences Limited, Tokyo Takarazuka Building 14F, 1-1-3 Yurakucho, Chiyoda-ku, Tokyo 100-0006, Japan
| | - Naohisa Masuo
- Mitsubishi Corporation Life Sciences Limited, Tokyo Takarazuka Building 14F, 1-1-3 Yurakucho, Chiyoda-ku, Tokyo 100-0006, Japan
| | - Yoichi Noda
- Collaborative Research Institute for Innovative Microbiology, Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
13
|
Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [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: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
Collapse
Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
14
|
Tobin MP, Pfeifer CR, Zhu PK, Hayes BH, Wang M, Vashisth M, Xia Y, Phan SH, Belt SA, Irianto J, Discher DE. Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters. Mol Biol Cell 2023; 34:br19. [PMID: 37903225 PMCID: PMC10848937 DOI: 10.1091/mbc.e23-06-0207] [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: 06/05/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
Chromosome numbers often change dynamically in tumors and cultured cells, which complicates therapy as well as understanding genotype-mechanotype relationships. Here we use a live-cell "ChReporter" method to identify cells with a single chromosomal loss in efforts to better understand differences in cell shape, motility, and growth. We focus on a standard cancer line and first show clonal populations that retain the ChReporter exhibit large differences in cell and nuclear morphology as well as motility. Phenotype metrics follow simple rules, including migratory persistence scaling with speed, and cytoskeletal differences are evident from drug responses, imaging, and single-cell RNA sequencing. However, mechanotype-genotype relationships between fluorescent ChReporter-positive clones proved complex and motivated comparisons of clones that differ only in loss or retention of a Chromosome-5 ChReporter. When lost, fluorescence-null cells show low expression of Chromosome-5 genes, including a key tumor suppressor APC that regulates microtubules and proliferation. Colonies are compact, nuclei are rounded, and cells proliferate more, with drug results implicating APC, and patient survival data indicating an association in multiple tumor-types. Visual identification of genotype with ChReporters can thus help clarify mechanotype and mechano-evolution.
Collapse
Affiliation(s)
- Michael P. Tobin
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | | | | | - Brandon H. Hayes
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Mai Wang
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Manasvita Vashisth
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Yuntao Xia
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Steven H. Phan
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Susanna A. Belt
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Jerome Irianto
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| | - Dennis E. Discher
- Mol. Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
15
|
Crozier L, Foy R, Adib R, Kar A, Holt JA, Pareri AU, Valverde JM, Rivera R, Weston WA, Wilson R, Regnault C, Whitfield P, Badonyi M, Bennett LG, Vernon EG, Gamble A, Marsh JA, Staples CJ, Saurin AT, Barr AR, Ly T. CDK4/6 inhibitor-mediated cell overgrowth triggers osmotic and replication stress to promote senescence. Mol Cell 2023; 83:4062-4077.e5. [PMID: 37977118 DOI: 10.1016/j.molcel.2023.10.016] [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: 09/12/2022] [Revised: 07/10/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Abnormal increases in cell size are associated with senescence and cell cycle exit. The mechanisms by which overgrowth primes cells to withdraw from the cell cycle remain unknown. We address this question using CDK4/6 inhibitors, which arrest cells in G0/G1 and are licensed to treat advanced HR+/HER2- breast cancer. We demonstrate that CDK4/6-inhibited cells overgrow during G0/G1, causing p38/p53/p21-dependent cell cycle withdrawal. Cell cycle withdrawal is triggered by biphasic p21 induction. The first p21 wave is caused by osmotic stress, leading to p38- and size-dependent accumulation of p21. CDK4/6 inhibitor washout results in some cells entering S-phase. Overgrown cells experience replication stress, resulting in a second p21 wave that promotes cell cycle withdrawal from G2 or the subsequent G1. We propose that the levels of p21 integrate signals from overgrowth-triggered stresses to determine cell fate. This model explains how hypertrophy can drive senescence and why CDK4/6 inhibitors have long-lasting effects in patients.
Collapse
Affiliation(s)
- Lisa Crozier
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Reece Foy
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Rozita Adib
- MRC Laboratory of Medical Sciences, London, UK
| | - Ananya Kar
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK
| | | | - Aanchal U Pareri
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Juan M Valverde
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Rene Rivera
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK
| | | | - Rona Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Clement Regnault
- Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK
| | - Phil Whitfield
- Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK
| | - Mihaly Badonyi
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Laura G Bennett
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Ellen G Vernon
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Amelia Gamble
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Christopher J Staples
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Adrian T Saurin
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK.
| | - Alexis R Barr
- MRC Laboratory of Medical Sciences, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Tony Ly
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK.
| |
Collapse
|
16
|
Shen Y, Gao F, Wang Y, Wang Y, Zheng J, Gong J, Zhang J, Luo Z, Schindler D, Deng Y, Ding W, Lin T, Swidah R, Zhao H, Jiang S, Zeng C, Chen S, Chen T, Wang Y, Luo Y, Mitchell L, Bader JS, Zhang G, Shen X, Wang J, Fu X, Dai J, Boeke JD, Yang H, Xu X, Cai Y. Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. CELL GENOMICS 2023; 3:100364. [PMID: 38020968 PMCID: PMC10667312 DOI: 10.1016/j.xgen.2023.100364] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/03/2023] [Accepted: 07/06/2023] [Indexed: 12/01/2023]
Abstract
Aneuploidy compromises genomic stability, often leading to embryo inviability, and is frequently associated with tumorigenesis and aging. Different aneuploid chromosome stoichiometries lead to distinct transcriptomic and phenotypic changes, making it helpful to study aneuploidy in tightly controlled genetic backgrounds. By deploying the engineered SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) system to the newly synthesized megabase Sc2.0 chromosome VII (synVII), we constructed a synthetic disomic yeast and screened hundreds of SCRaMbLEd derivatives with diverse chromosomal rearrangements. Phenotypic characterization and multi-omics analysis revealed that fitness defects associated with aneuploidy could be restored by (1) removing most of the chromosome content or (2) modifying specific regions in the duplicated chromosome. These findings indicate that both chromosome copy number and specific chromosomal regions contribute to the aneuploidy-related phenotypes, and the synthetic chromosome resource opens new paradigms in studying aneuploidy.
Collapse
Affiliation(s)
- Yue Shen
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Gao
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yun Wang
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Yuerong Wang
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju Zheng
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | | | | | - Zhouqing Luo
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Yang Deng
- BGI Research, Shenzhen 518083, China
| | - Weichao Ding
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Lin
- BGI Research, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Reem Swidah
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Hongcui Zhao
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Shuangying Jiang
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Cheng Zeng
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | | | - Tai Chen
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yong Wang
- BGI Research, Shenzhen 518083, China
| | - Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Leslie Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guojie Zhang
- University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Xia Shen
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Center for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Jian Wang
- BGI Research, Shenzhen 518083, China
| | - Xian Fu
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Junbiao Dai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | | | - Xun Xu
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| |
Collapse
|
17
|
Wang Y, Sun Z, Ping J, Tang J, He B, Chang T, Zhou Q, Yuan S, Tang Z, Li X, Lu Y, He R, He X, Liu Z, Yin L, Wu N. Cell volume controlled by LRRC8A-formed volume-regulated anion channels fine-tunes T cell activation and function. Nat Commun 2023; 14:7075. [PMID: 37925509 PMCID: PMC10625614 DOI: 10.1038/s41467-023-42817-y] [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: 02/15/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Biosynthesis drives the cell volume increase during T cell activation. However, the contribution of cell volume regulation in TCR signaling during T lymphoblast formation and its underlying mechanisms remain unclear. Here we show that cell volume regulation is required for optimal T cell activation. Inhibition of VRACs (volume-regulated anion channels) and deletion of leucine-rich repeat-containing protein 8A (LRRC8A) channel components impair T cell activation and function, particularly under weak TCR stimulation. Additionally, LRRC8A has distinct influences on mRNA transcriptional profiles, indicating the prominent effects of cell volume regulation for T cell functions. Moreover, cell volume regulation via LRRC8A controls T cell-mediated antiviral immunity and shapes the TCR repertoire in the thymus. Mechanistically, LRRC8A governs stringent cell volume increase via regulated volume decrease (RVD) during T cell blast formation to keep the TCR signaling molecules at an adequate density. Together, our results show a further layer of T cell activation regulation that LRRC8A functions as a cell volume controlling "valve" to facilitate T cell activation.
Collapse
Affiliation(s)
- Yuman Wang
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zaiqiao Sun
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jieming Ping
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianlong Tang
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Boxiao He
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Teding Chang
- Department of Traumatic Surgery, Tongji Trauma Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Zhou
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shijie Yuan
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaohui Tang
- Department of Traumatic Surgery, Tongji Trauma Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Li
- Medical Research Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Lu
- Department of Clinical Immunology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ran He
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China.
| | - Ning Wu
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Cell Architecture Research Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- The First Affiliated Hospital of Anhui Medical University, Institute of Clinical Immunology, Anhui Medical University, Hefei, China.
| |
Collapse
|
18
|
Ren K, Feng J, Bi H, Sun Q, Li X, Han D. AFM-Based Poroelastic@Membrane Analysis of Cells and its Opportunities for Translational Medicine. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303610. [PMID: 37403276 DOI: 10.1002/smll.202303610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/09/2023] [Indexed: 07/06/2023]
Abstract
Cell mechanics is an emerging field of research for translational medicine. Here, the cell is modeled as poroelastic cytoplasm wrapped by tensile membrane (poroelastic@membrane model) and is characterized by the atomic force microscopy (AFM). The parameters of cytoskeleton network modulus EC , cytoplasmic apparent viscosity ηC , and cytoplasmic diffusion coefficient DC are used to describe the mechanical behavior of cytoplasm, and membrane tension γ is used to evaluate the cell membrane. Poroelastic@membrane analysis of breast cells and urothelial cells show that non-cancer cells and cancer cells have different distribution regions and distribution trends in the four-dimensional space composed of EC , ηC . From non-cancer to cancer cells, there is often a trend of γ, EC , ηC decreases and DC increases. Patients with urothelial carcinoma at different malignant stages can be distinguished at high sensitivity and specificity by analyzing the urothelial cells from tissue or urine. However, sampling directly from tumor tissues is an invasive method, may lead to undesirable consequences. Thus, AFM-based poroelastic@membrane analysis of urothelial cells from urine may provide a non-invasive and no-bio-label method to detecting urothelial carcinoma.
Collapse
Affiliation(s)
- Keli Ren
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No.11 ZhongGuanCun BeiYiTiao, Haidian, Beijing, 100191, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou Distric, Beijing, 100190, China
| | - Jiantao Feng
- Artemisinin Research Center and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No.16, Nanxiao street, Dongzhimen, Dongcheng, Beijing, 100700, China
| | - Hai Bi
- Department of Urology, Peking University Third Hospital, 49 North Garden Rd., Haidian, Beijing, 100191, China
| | - Quanmei Sun
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No.11 ZhongGuanCun BeiYiTiao, Haidian, Beijing, 100191, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou Distric, Beijing, 100190, China
| | - Xiang Li
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No.11 ZhongGuanCun BeiYiTiao, Haidian, Beijing, 100191, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou Distric, Beijing, 100190, China
| | - Dong Han
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No.11 ZhongGuanCun BeiYiTiao, Haidian, Beijing, 100191, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Rd, Huairou Distric, Beijing, 100190, China
| |
Collapse
|
19
|
Dumeaux V, Massahi S, Bettauer V, Mottola A, Dukovny A, Khurdia SS, Costa ACBP, Omran RP, Simpson S, Xie JL, Whiteway M, Berman J, Hallett MT. Candida albicans exhibits heterogeneous and adaptive cytoprotective responses to antifungal compounds. eLife 2023; 12:e81406. [PMID: 37888959 PMCID: PMC10699808 DOI: 10.7554/elife.81406] [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: 06/25/2022] [Accepted: 10/26/2023] [Indexed: 10/28/2023] Open
Abstract
Candida albicans, an opportunistic human pathogen, poses a significant threat to human health and is associated with significant socio-economic burden. Current antifungal treatments fail, at least in part, because C. albicans can initiate a strong drug tolerance response that allows some cells to grow at drug concentrations above their minimal inhibitory concentration. To better characterize this cytoprotective tolerance program at the molecular single-cell level, we used a nanoliter droplet-based transcriptomics platform to profile thousands of individual fungal cells and establish their subpopulation characteristics in the absence and presence of antifungal drugs. Profiles of untreated cells exhibit heterogeneous expression that correlates with cell cycle stage with distinct metabolic and stress responses. At 2 days post-fluconazole exposure (a time when tolerance is measurable), surviving cells bifurcate into two major subpopulations: one characterized by the upregulation of genes encoding ribosomal proteins, rRNA processing machinery, and mitochondrial cellular respiration capacity, termed the Ribo-dominant (Rd) state; and the other enriched for genes encoding stress responses and related processes, termed the Stress-dominant (Sd) state. This bifurcation persists at 3 and 6 days post-treatment. We provide evidence that the ribosome assembly stress response (RASTR) is activated in these subpopulations and may facilitate cell survival.
Collapse
Affiliation(s)
- Vanessa Dumeaux
- Department of Anatomy and Cell Biology, Western University, London, Canada
| | - Samira Massahi
- Department of Biology, Concordia University, Montreal, Canada
| | - Van Bettauer
- Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada
| | - Austin Mottola
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Anna Dukovny
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, Israel
| | | | | | | | - Shawn Simpson
- Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada
| | - Jinglin Lucy Xie
- Department of Chemical and Systems Biology, Stanford University, Stanford, United States
| | | | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, Israel
| | | |
Collapse
|
20
|
Marques JF, Kops GJPL. Permission to pass: on the role of p53 as a gatekeeper for aneuploidy. Chromosome Res 2023; 31:31. [PMID: 37864038 PMCID: PMC10589155 DOI: 10.1007/s10577-023-09741-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023]
Abstract
Aneuploidy-the karyotype state in which the number of chromosomes deviates from a multiple of the haploid chromosome set-is common in cancer, where it is thought to facilitate tumor initiation and progression. However, it is poorly tolerated in healthy cells: during development and tissue homeostasis, aneuploid cells are efficiently cleared from the population. It is still largely unknown how cancer cells become, and adapt to being, aneuploid. P53, the gatekeeper of the genome, has been proposed to guard against aneuploidy. Aneuploidy in cancer genomes strongly correlates with mutations in TP53, and p53 is thought to prevent the propagation of aneuploid cells. Whether p53 also participates in preventing the mistakes in cell division that lead to aneuploidy is still under debate. In this review, we summarize the current understanding of the role of p53 in protecting cells from aneuploidy, and we explore the consequences of functional p53 loss for the propagation of aneuploidy in cancer.
Collapse
Affiliation(s)
- Joana F Marques
- Royal Netherlands Academy of Arts and Sciences (KNAW), Hubrecht Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
- University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521AL, Utrecht, the Netherlands
| | - Geert J P L Kops
- Royal Netherlands Academy of Arts and Sciences (KNAW), Hubrecht Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands.
- University Medical Center Utrecht, Heidelberglaan 100, 3584CX, Utrecht, the Netherlands.
- Oncode Institute, Jaarbeursplein 6, 3521AL, Utrecht, the Netherlands.
| |
Collapse
|
21
|
McCoy RC, Summers MC, McCollin A, Ottolini CS, Ahuja K, Handyside AH. Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos. Genome Med 2023; 15:77. [PMID: 37779206 PMCID: PMC10544495 DOI: 10.1186/s13073-023-01231-1] [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: 12/14/2022] [Accepted: 09/12/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND The high incidence of aneuploidy in early human development, arising either from errors in meiosis or postzygotic mitosis, is the primary cause of pregnancy loss, miscarriage, and stillbirth following natural conception as well as in vitro fertilization (IVF). Preimplantation genetic testing for aneuploidy (PGT-A) has confirmed the prevalence of meiotic and mitotic aneuploidies among blastocyst-stage IVF embryos that are candidates for transfer. However, only about half of normally fertilized embryos develop to the blastocyst stage in vitro, while the others arrest at cleavage to late morula or early blastocyst stages. METHODS To achieve a more complete view of the impacts of aneuploidy, we applied low-coverage sequencing-based PGT-A to a large series (n = 909) of arrested embryos and trophectoderm biopsies. We then correlated observed aneuploidies with abnormalities of the first two cleavage divisions using time-lapse imaging (n = 843). RESULTS The combined incidence of meiotic and mitotic aneuploidies was strongly associated with blastocyst morphological grading, with the proportion ranging from 20 to 90% for the highest to lowest grades, respectively. In contrast, the incidence of aneuploidy among arrested embryos was exceptionally high (94%), dominated by mitotic aneuploidies affecting multiple chromosomes. In turn, these mitotic aneuploidies were strongly associated with abnormal cleavage divisions, such that 51% of abnormally dividing embryos possessed mitotic aneuploidies compared to only 23% of normally dividing embryos. CONCLUSIONS We conclude that the combination of meiotic and mitotic aneuploidies drives arrest of human embryos in vitro, as development increasingly relies on embryonic gene expression at the blastocyst stage.
Collapse
Affiliation(s)
- Rajiv C McCoy
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21212, USA.
| | - Michael C Summers
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
- Present Address: London Women's Clinic, The Chesterfield, Nuffield Health Clinic, 3 Clifton Hill, Bristol, BS8 1BN, UK
| | - Abeo McCollin
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
| | - Christian S Ottolini
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
- Department of Maternal and Fetal Medicine, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
- Present Address: Juno Genetics Italia, Via Di Quarto Peperino 22, 00188, Rome, Italy
| | - Kamal Ahuja
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
| | - Alan H Handyside
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
| |
Collapse
|
22
|
Johnson BA, Liu AZ, Bi T, Dong Y, Li T, Zhou D, Narkar A, Wu Y, Sun SX, Larman TC, Zhu J, Li R. Differential effects of aneuploidy on growth and differentiation in human intestinal stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559117. [PMID: 37790420 PMCID: PMC10542480 DOI: 10.1101/2023.09.23.559117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Aneuploidy, a near ubiquitous genetic feature of tumors, is a context-dependent driver of cancer evolution; however, the mechanistic basis of this role remains unclear. Here, by inducing heterogeneous aneuploidy in non-transformed human colon organoids (colonoids), we investigate how the effects of aneuploidy on cell growth and differentiation may promote malignant transformation. Single-cell RNA sequencing reveals that the gene expression signature across over 100 unique aneuploid karyotypes is enriched with p53 responsive genes. The primary driver of p53 activation is karyotype complexity. Complex aneuploid cells with multiple unbalanced chromosomes activate p53 and undergo G1 cell-cycle arrest, independent of DNA damage and without evidence of senescence. By contrast, simple aneuploid cells with 1-3 chromosomes gained or lost continue to proliferate, demonstrated by single cell tracking in colonoids. Notably, simple aneuploid cells exhibit impaired differentiation when niche factors are withdrawn. These findings suggest that while complex aneuploid cells are eliminated from the normal epithelium due to p53 activation, simple aneuploid cells can escape this checkpoint and may contribute to niche factor-independent growth of cancer-initiating cells.
Collapse
|
23
|
Vande Zande P, Zhou X, Selmecki A. The Dynamic Fungal Genome: Polyploidy, Aneuploidy and Copy Number Variation in Response to Stress. Annu Rev Microbiol 2023; 77:341-361. [PMID: 37307856 PMCID: PMC10599402 DOI: 10.1146/annurev-micro-041320-112443] [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] [Indexed: 06/14/2023]
Abstract
Fungal species have dynamic genomes and often exhibit genomic plasticity in response to stress. This genome plasticity often comes with phenotypic consequences that affect fitness and resistance to stress. Fungal pathogens exhibit genome plasticity in both clinical and agricultural settings and often during adaptation to antifungal drugs, posing significant challenges to human health. Therefore, it is important to understand the rates, mechanisms, and impact of large genomic changes. This review addresses the prevalence of polyploidy, aneuploidy, and copy number variation across diverse fungal species, with special attention to prominent fungal pathogens and model species. We also explore the relationship between environmental stress and rates of genomic changes and highlight the mechanisms underlying genotypic and phenotypic changes. A comprehensive understanding of these dynamic fungal genomes is needed to identify novel solutions for the increase in antifungal drug resistance.
Collapse
Affiliation(s)
- Pétra Vande Zande
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA;
| |
Collapse
|
24
|
Avecilla G, Spealman P, Matthews J, Caudal E, Schacherer J, Gresham D. Copy number variation alters local and global mutational tolerance. Genome Res 2023; 33:1340-1353. [PMID: 37652668 PMCID: PMC10547251 DOI: 10.1101/gr.277625.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/07/2023] [Indexed: 09/02/2023]
Abstract
Copy number variants (CNVs), duplications and deletions of genomic sequences, contribute to evolutionary adaptation but can also confer deleterious effects and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs of differing sizes and structures. Here, we investigated Saccharomyces cerevisiae (yeast) strains that acquired adaptive CNVs of variable structures and copy numbers following experimental evolution in glutamine-limited chemostats. Although beneficial in the selective environment, CNVs result in decreased fitness compared with the euploid ancestor in rich media. We used transposon mutagenesis to investigate mutational tolerance and genome-wide genetic interactions in CNV strains. We find that CNVs increase mutational target size, confer increased mutational tolerance in amplified essential genes, and result in novel genetic interactions with unlinked genes. We validated a novel genetic interaction between different CNVs and BMH1 that was common to multiple strains. We also analyzed global gene expression and found that transcriptional dosage compensation does not affect most genes amplified by CNVs, although gene-specific transcriptional dosage compensation does occur for ∼12% of amplified genes. Furthermore, we find that CNV strains do not show previously described transcriptional signatures of aneuploidy. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs with implications for genome evolution and CNV-associated diseases, such as cancer.
Collapse
Affiliation(s)
- Grace Avecilla
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Pieter Spealman
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Julia Matthews
- Department of Biology, New York University, New York, New York 10003, USA
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Elodie Caudal
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
- Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France
| | - David Gresham
- Department of Biology, New York University, New York, New York 10003, USA;
- Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| |
Collapse
|
25
|
Pompei S, Cosentino Lagomarsino M. A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains. Proc Natl Acad Sci U S A 2023; 120:e2211687120. [PMID: 37018197 PMCID: PMC10104565 DOI: 10.1073/pnas.2211687120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/19/2023] [Indexed: 04/06/2023] Open
Abstract
The early development of aneuploidy from an accidental chromosome missegregation shows contrasting effects. On the one hand, it is associated with significant cellular stress and decreased fitness. On the other hand, it often carries a beneficial effect and provides a quick (but typically transient) solution to external stress. These apparently controversial trends emerge in several experimental contexts, particularly in the presence of duplicated chromosomes. However, we lack a mathematical evolutionary modeling framework that comprehensively captures these trends from the mutational dynamics and the trade-offs involved in the early stages of aneuploidy. Here, focusing on chromosome gains, we address this point by introducing a fitness model where a fitness cost of chromosome duplications is contrasted by a fitness advantage from the dosage of specific genes. The model successfully captures the experimentally measured probability of emergence of extra chromosomes in a laboratory evolution setup. Additionally, using phenotypic data collected in rich media, we explored the fitness landscape, finding evidence supporting the existence of a per-gene cost of extra chromosomes. Finally, we show that the substitution dynamics of our model, evaluated in the empirical fitness landscape, explains the relative abundance of duplicated chromosomes observed in yeast population genomics data. These findings lay a firm framework for the understanding of the establishment of newly duplicated chromosomes, providing testable quantitative predictions for future observations.
Collapse
Affiliation(s)
- Simone Pompei
- IFOM ETS (Ente del Terzo Settore) - The AIRC (Associazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology, Milano20139, Italy
| | - Marco Cosentino Lagomarsino
- IFOM ETS (Ente del Terzo Settore) - The AIRC (Associazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology, Milano20139, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, Milano20133, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Milano, Milano20133, Italy
| |
Collapse
|
26
|
Kakade P, Sircaik S, Maufrais C, Ene IV, Bennett RJ. Aneuploidy and gene dosage regulate filamentation and host colonization by Candida albicans. Proc Natl Acad Sci U S A 2023; 120:e2218163120. [PMID: 36893271 PMCID: PMC10089209 DOI: 10.1073/pnas.2218163120] [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: 10/24/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023] Open
Abstract
Aneuploidy is a frequent occurrence in fungal species where it can alter gene expression and promote adaptation to a variety of environmental cues. Multiple forms of aneuploidy have been observed in the opportunistic fungal pathogen Candida albicans, which is a common component of the human gut mycobiome but can escape this niche and cause life-threatening systemic disease. Using a barcode sequencing (Bar-seq) approach, we evaluated a set of diploid C. albicans strains and found that a strain carrying a third copy of chromosome (Chr) 7 was associated with increased fitness during both gastrointestinal (GI) colonization and systemic infection. Our analysis revealed that the presence of a Chr 7 trisomy resulted in decreased filamentation, both in vitro and during GI colonization, relative to isogenic euploid controls. A target gene approach demonstrated that NRG1, encoding a negative regulator of filamentation located on Chr 7, contributes to increased fitness of the aneuploid strain due to inhibition of filamentation in a gene dosage-dependent fashion. Together, these experiments establish how aneuploidy enables the reversible adaptation of C. albicans to its host via gene dosage-dependent regulation of morphology.
Collapse
Affiliation(s)
- Pallavi Kakade
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Shabnam Sircaik
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Corinne Maufrais
- Institut Pasteur Bioinformatic Hub, Université Paris Cité, Paris75015, France
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Richard J. Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| |
Collapse
|
27
|
Garner RM, Molines AT, Theriot JA, Chang F. Vast heterogeneity in cytoplasmic diffusion rates revealed by nanorheology and Doppelgänger simulations. Biophys J 2023; 122:767-783. [PMID: 36739478 PMCID: PMC10027447 DOI: 10.1016/j.bpj.2023.01.040] [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: 07/28/2022] [Revised: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The cytoplasm is a complex, crowded, actively driven environment whose biophysical characteristics modulate critical cellular processes such as cytoskeletal dynamics, phase separation, and stem cell fate. Little is known about the variance in these cytoplasmic properties. Here, we employed particle-tracking nanorheology on genetically encoded multimeric 40 nm nanoparticles (GEMs) to measure diffusion within the cytoplasm of individual fission yeast (Schizosaccharomyces pombe) cellscells. We found that the apparent diffusion coefficients of individual GEM particles varied over a 400-fold range, while the differences in average particle diffusivity among individual cells spanned a 10-fold range. To determine the origin of this heterogeneity, we developed a Doppelgänger simulation approach that uses stochastic simulations of GEM diffusion that replicate the experimental statistics on a particle-by-particle basis, such that each experimental track and cell had a one-to-one correspondence with their simulated counterpart. These simulations showed that the large intra- and inter-cellular variations in diffusivity could not be explained by experimental variability but could only be reproduced with stochastic models that assume a wide intra- and inter-cellular variation in cytoplasmic viscosity. The simulation combining intra- and inter-cellular variation in viscosity also predicted weak nonergodicity in GEM diffusion, consistent with the experimental data. To probe the origin of this variation, we found that the variance in GEM diffusivity was largely independent of factors such as temperature, the actin and microtubule cytoskeletons, cell-cyle stage, and spatial locations, but was magnified by hyperosmotic shocks. Taken together, our results provide a striking demonstration that the cytoplasm is not "well-mixed" but represents a highly heterogeneous environment in which subcellular components at the 40 nm size scale experience dramatically different effective viscosities within an individual cell, as well as in different cells in a genetically identical population. These findings carry significant implications for the origins and regulation of biological noise at cellular and subcellular levels.
Collapse
Affiliation(s)
- Rikki M Garner
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Arthur T Molines
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Julie A Theriot
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts
| |
Collapse
|
28
|
Todd RT, Soisangwan N, Peters S, Kemp B, Crooks T, Gerstein A, Selmecki A. Antifungal Drug Concentration Impacts the Spectrum of Adaptive Mutations in Candida albicans. Mol Biol Evol 2023; 40:6989826. [PMID: 36649220 PMCID: PMC9887641 DOI: 10.1093/molbev/msad009] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Invasive fungal infections are a leading global cause of human mortality. Only three major classes of antifungal drugs are widely used, and resistance to all three classes can arise rapidly. The most widely prescribed antifungal drug, fluconazole, disseminates rapidly and reaches a wide range of concentrations throughout the body. The impact of drug concentration on the spectrum and effect of mutations acquired during adaptation is not known for any fungal pathogen, and how the specific level of a given stress influences the distribution of beneficial mutations has been poorly explored in general. We evolved 144 lineages from three genetically distinct clinical isolates of Candida albicans to four concentrations of fluconazole (0, 1, 8, and 64 μg/ml) and performed comprehensive phenotypic and genomic comparisons of ancestral and evolved populations. Adaptation to different fluconazole concentrations resulted in distinct adaptive trajectories. In general, lineages evolved to drug concentrations close to their MIC50 (the level of drug that reduces growth by 50% in the ancestor) tended to rapidly evolve an increased MIC50 and acquired distinct segmental aneuploidies and copy number variations. By contrast, lineages evolved to drug concentrations above their ancestral MIC50 tended to acquire a different suite of mutational changes and increased in drug tolerance (the ability of a subpopulation of cells to grow slowly above their MIC50). This is the first evidence that different concentrations of drug can select for different genotypic and phenotypic outcomes in vitro and may explain observed in vivo drug response variation.
Collapse
Affiliation(s)
- Robert T Todd
- Present address: Department of Biology, Bard College, Annandale-on-Hudson, New York
| | | | - Sam Peters
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Bailey Kemp
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Taylor Crooks
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Aleeza Gerstein
- Department of Microbiology, The University of Manitoba, Winnipeg, Manitoba, Canada,Department of Statistics, The University of Manitoba, Winnipeg, Manitoba, Canada
| | | |
Collapse
|
29
|
Sandlin CW, Gu S, Xu J, Deshpande C, Feldman MD, Good MC. Epithelial cell size dysregulation in human lung adenocarcinoma. PLoS One 2022; 17:e0274091. [PMID: 36201559 PMCID: PMC9536599 DOI: 10.1371/journal.pone.0274091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Human cells tightly control their dimensions, but in some cancers, normal cell size control is lost. In this study we measure cell volumes of epithelial cells from human lung adenocarcinoma progression in situ. By leveraging artificial intelligence (AI), we reconstruct tumor cell shapes in three dimensions (3D) and find airway type 2 cells display up to 10-fold increases in volume. Surprisingly, cell size increase is not caused by altered ploidy, and up to 80% of near-euploid tumor cells show abnormal sizes. Size dysregulation is not explained by cell swelling or senescence because cells maintain cytoplasmic density and proper organelle size scaling, but is correlated with changes in tissue organization and loss of a novel network of processes that appear to connect alveolar type 2 cells. To validate size dysregulation in near-euploid cells, we sorted cells from tumor single-cell suspensions on the basis of size. Our study provides data of unprecedented detail for cell volume dysregulation in a human cancer. Broadly, loss of size control may be a common feature of lung adenocarcinomas in humans and mice that is relevant to disease and identification of these cells provides a useful model for investigating cell size control and consequences of cell size dysregulation.
Collapse
Affiliation(s)
- Clifford W. Sandlin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
| | - Song Gu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Jun Xu
- Nanjing University of Information Science and Technology, Nanjing, China
| | - Charuhas Deshpande
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew C. Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CWS); (MCG)
| |
Collapse
|
30
|
Du M, Zhang S, Liu X, Xu C, Zhang X. Nondiploid cancer cells: Stress, tolerance and therapeutic inspirations. Biochim Biophys Acta Rev Cancer 2022; 1877:188794. [PMID: 36075287 DOI: 10.1016/j.bbcan.2022.188794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 11/19/2022]
Abstract
Aberrant ploidy status is a prominent characteristic in malignant neoplasms. Approximately 90% of solid tumors and 75% of haematopoietic malignancies contain aneuploidy cells, and 30%-60% of tumors undergo whole-genome doubling, indicating that nondiploidy might be a prevalent genomic aberration in cancer. Although the role of aneuploid and polyploid cells in cancer remains to be elucidated, recent studies have suggested that nondiploid cells might be a dangerous minority that severely challenges cancer management. Ploidy shifts cause multiple fitness coasts for cancer cells, mainly including genomic, proteotoxic, metabolic and immune stresses. However, nondiploid comprises a well-adopted subpopulation, with many tolerance mechanisms evident in cells along with ploidy shifts. Aneuploid and polyploid cells elegantly maintain an autonomous balance between the stress and tolerance during adaptive evolution in cancer. Breaking the balance might provide some inspiration for ploidy-selective cancer therapy and alleviation of ploidy-related chemoresistance. To understand of the complex role and therapeutic potential of nondiploid cells better, we reviewed the survival stresses and adaptive tolerances within nondiploid cancer cells and summarized therapeutic ploidy-selective alterations for potential use in developing future cancer therapy.
Collapse
Affiliation(s)
- Ming Du
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
| | - Shuo Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
| | - Xiaoxia Liu
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, People's Republic of China.
| | - Xiaoyan Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200011, People's Republic of China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, People's Republic of China.
| |
Collapse
|
31
|
Bao M, Cornwall-Scoones J, Sanchez-Vasquez E, Cox AL, Chen DY, De Jonghe J, Shadkhoo S, Hollfelder F, Thomson M, Glover DM, Zernicka-Goetz M. Stem cell-derived synthetic embryos self-assemble by exploiting cadherin codes and cortical tension. Nat Cell Biol 2022; 24:1341-1349. [PMID: 36100738 PMCID: PMC9481465 DOI: 10.1038/s41556-022-00984-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/20/2022] [Indexed: 12/21/2022]
Abstract
Mammalian embryos sequentially differentiate into trophectoderm and an inner cell mass, the latter of which differentiates into primitive endoderm and epiblast. Trophoblast stem (TS), extraembryonic endoderm (XEN) and embryonic stem (ES) cells derived from these three lineages can self-assemble into synthetic embryos, but the mechanisms remain unknown. Here, we show that a stem cell-specific cadherin code drives synthetic embryogenesis. The XEN cell cadherin code enables XEN cell sorting into a layer below ES cells, recapitulating the sorting of epiblast and primitive endoderm before implantation. The TS cell cadherin code enables TS cell sorting above ES cells, resembling extraembryonic ectoderm clustering above epiblast following implantation. Whereas differential cadherin expression drives initial cell sorting, cortical tension consolidates tissue organization. By optimizing cadherin code expression in different stem cell lines, we tripled the frequency of correctly formed synthetic embryos. Thus, by exploiting cadherin codes from different stages of development, lineage-specific stem cells bypass the preimplantation structure to directly assemble a postimplantation embryo.
Collapse
Affiliation(s)
- Min Bao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jake Cornwall-Scoones
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- The Francis Crick Institute, London, UK
| | - Estefania Sanchez-Vasquez
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andy L Cox
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dong-Yuan Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Joachim De Jonghe
- The Francis Crick Institute, London, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Shahriar Shadkhoo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David M Glover
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Magdalena Zernicka-Goetz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| |
Collapse
|
32
|
Swamy KBS, Lee HY, Ladra C, Liu CFJ, Chao JC, Chen YY, Leu JY. Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast. Nat Commun 2022; 13:4394. [PMID: 35906261 PMCID: PMC9338014 DOI: 10.1038/s41467-022-32107-4] [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: 11/04/2021] [Accepted: 07/18/2022] [Indexed: 02/08/2023] Open
Abstract
Dobzhansky–Muller incompatibilities represent a major driver of reproductive isolation between species. They are caused when interacting components encoded by alleles from different species cannot function properly when mixed. At incipient stages of speciation, complex incompatibilities involving multiple genetic loci with weak effects are frequently observed, but the underlying mechanisms remain elusive. Here we show perturbed proteostasis leading to compromised mitosis and meiosis in Saccharomyces cerevisiae hybrid lines carrying one or two chromosomes from Saccharomyces bayanus var. uvarum. Levels of proteotoxicity are correlated with the number of protein complexes on replaced chromosomes. Proteomic approaches reveal that multi-protein complexes with subunits encoded by replaced chromosomes tend to be unstable. Furthermore, hybrid defects can be alleviated or aggravated, respectively, by up- or down-regulating the ubiquitin-proteasomal degradation machinery, suggesting that destabilized complex subunits overburden the proteostasis machinery and compromise hybrid fitness. Our findings reveal the general role of impaired protein complex assembly in complex incompatibilities. Hybrid incompatibility can be an important element of reproductive isolation and speciation. Using chromosome replacement lines of yeast, the authors show that perturbed proteostasis caused by destabilized hybrid protein complexes may represent a general mechanism of hybrid incompatibility.
Collapse
Affiliation(s)
- Krishna B S Swamy
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.,Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, 380009, India
| | - Hsin-Yi Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Carmina Ladra
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chien-Fu Jeff Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
33
|
Abstract
Mechanisms of evolution and evolution of antibiotic resistance are both fundamental and world health problems. Stress-induced mutagenesis defines mechanisms of mutagenesis upregulated by stress responses, which drive adaptation when cells are maladapted to their environments—when stressed. Work in mutagenesis induced by antibiotics had produced tantalizing clues but not coherent mechanisms. We review recent advances in antibiotic-induced mutagenesis that integrate how reactive oxygen species (ROS), the SOS and general stress responses, and multichromosome cells orchestrate a stress response-induced switch from high-fidelity to mutagenic repair of DNA breaks. Moreover, while sibling cells stay stable, a mutable “gambler” cell subpopulation is induced by differentially generated ROS, which signal the general stress response. We discuss other evolvable subpopulations and consider diverse evolution-promoting molecules as potential targets for drugs to slow evolution of antibiotic resistance, cross-resistance, and immune evasion. An FDA-approved drug exemplifies “stealth” evolution-slowing drugs that avoid selecting resistance to themselves or antibiotics.
Collapse
|
34
|
Nikitina TV, Lebedev IN. Stem Cell-Based Trophoblast Models to Unravel the Genetic Causes of Human Miscarriages. Cells 2022; 11:1923. [PMID: 35741051 PMCID: PMC9221414 DOI: 10.3390/cells11121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 02/01/2023] Open
Abstract
Miscarriage affects approximately 15% of clinically recognized pregnancies, and 1-3% of couples experience pregnancy loss recurrently. Approximately 50-60% of miscarriages result from chromosomal abnormalities, whereas up to 60% of euploid recurrent abortions harbor variants in candidate genes. The growing number of detected genetic variants requires an investigation into their role in adverse pregnancy outcomes. Since placental defects are the main cause of first-trimester miscarriages, the purpose of this review is to provide a survey of state-of-the-art human in vitro trophoblast models that can be used for the functional assessment of specific abnormalities/variants implicated in pregnancy loss. Since 2018, when primary human trophoblast stem cells were first derived, there has been rapid growth in models of trophoblast lineage. It has been found that a proper balance between self-renewal and differentiation in trophoblast progenitors is crucial for the maintenance of pregnancy. Different responses to aneuploidy have been shown in human embryonic and extra-embryonic lineages. Stem cell-based models provide a powerful tool to explore the effect of a specific aneuploidy/variant on the fetus through placental development, which is important, from a clinical point of view, for deciding on the suitability of embryos for transfer after preimplantation genetic testing for aneuploidy.
Collapse
Affiliation(s)
- Tatiana V. Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, 634050 Tomsk, Russia;
| | | |
Collapse
|
35
|
Wu Y, Pegoraro AF, Weitz DA, Janmey P, Sun SX. The correlation between cell and nucleus size is explained by an eukaryotic cell growth model. PLoS Comput Biol 2022; 18:e1009400. [PMID: 35180215 PMCID: PMC8893647 DOI: 10.1371/journal.pcbi.1009400] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 03/03/2022] [Accepted: 01/12/2022] [Indexed: 12/19/2022] Open
Abstract
In eukaryotes, the cell volume is observed to be strongly correlated with the nuclear volume. The slope of this correlation depends on the cell type, growth condition, and the physical environment of the cell. We develop a computational model of cell growth and proteome increase, incorporating the kinetics of amino acid import, protein/ribosome synthesis and degradation, and active transport of proteins between the cytoplasm and the nucleoplasm. We also include a simple model of ribosome biogenesis and assembly. Results show that the cell volume is tightly correlated with the nuclear volume, and the cytoplasm-nucleoplasm transport rates strongly influence the cell growth rate as well as the cell/nucleus volume ratio (C/N ratio). Ribosome assembly and the ratio of ribosomal proteins to mature ribosomes also influence the cell volume and the cell growth rate. We find that in order to regulate the cell growth rate and the cell/nucleus volume ratio, the cell must optimally control groups of kinetic and transport parameters together, which could explain the quantitative roles of canonical growth pathways. Finally, although not explicitly demonstrated in this work, we point out that it is possible to construct a detailed proteome distribution using our model and RNAseq data, provided that a quantitative cell division mechanism is known.
Collapse
Affiliation(s)
- Yufei Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - David A. Weitz
- Department of Physics, Harvard University, Boston, Massachusetts, United States of America
| | - Paul Janmey
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sean X. Sun
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
36
|
Abstract
Aneuploidy, a genomic alternation characterized by deviations in the copy number of chromosomes, affects organisms from early development through to aging. Although it is a main cause of human pregnancy loss and a hallmark of cancer, how aneuploidy affects cellular function has been elusive. The last two decades have seen rapid advances in the understanding of the causes and consequences of aneuploidy at the molecular and cellular levels. These studies have uncovered effects of aneuploidy that can be beneficial or detrimental to cells and organisms in an environmental context-dependent and karyotype-dependent manner. Aneuploidy also imposes general stress on cells that stems from an imbalanced genome and, consequently, also an imbalanced proteome. These insights provide the fundamental framework for understanding the impact of aneuploidy in genome evolution, human pathogenesis and drug resistance.
Collapse
|
37
|
Xian S, Dosset M, Almanza G, Searles S, Sahani P, Waller TC, Jepsen K, Carter H, Zanetti M. The unfolded protein response links tumor aneuploidy to local immune dysregulation. EMBO Rep 2021; 22:e52509. [PMID: 34698427 PMCID: PMC8647024 DOI: 10.15252/embr.202152509] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 12/19/2022] Open
Abstract
Aneuploidy is a chromosomal abnormality associated with poor prognosis in many cancer types. Here, we tested the hypothesis that the unfolded protein response (UPR) mechanistically links aneuploidy and local immune dysregulation. Using a single somatic copy number alteration (SCNA) score inclusive of whole‐chromosome, chromosome arm, and focal alterations in a pan‐cancer analysis of 9,375 samples in The Cancer Genome Atlas (TCGA) database, we found an inverse correlation with a cytotoxicity (CYT) score across disease stages. Co‐expression patterns of UPR genes changed substantially between SCNAlow and SCNAhigh groups. Pathway activity scores showed increased activity of multiple branches of the UPR in response to aneuploidy. The PERK branch showed the strongest association with a reduced CYT score. The conditioned medium of aneuploid cells transmitted XBP1 splicing and caused IL‐6 and arginase 1 transcription in receiver bone marrow‐derived macrophages and markedly diminished the production of IFN‐γ and granzyme B in activated human T cells. We propose the UPR as a mechanistic link between aneuploidy and immune dysregulation in the tumor microenvironment.
Collapse
Affiliation(s)
- Su Xian
- Division of Medical Genetics Biostatistics, Department of Medicine, Bioinformatics and System Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Magalie Dosset
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Gonzalo Almanza
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Stephen Searles
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Paras Sahani
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - T Cameron Waller
- Division of Medical Genetics Biostatistics, Department of Medicine, Bioinformatics and System Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Division of Medical Genetics Biostatistics, Department of Medicine, Bioinformatics and System Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Maurizio Zanetti
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|
38
|
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.
Collapse
|
39
|
Disruption of Chromatin Dynamics by Hypotonic Stress Suppresses HR and Shifts DSB Processing to Error-Prone SSA. Int J Mol Sci 2021; 22:ijms222010957. [PMID: 34681628 PMCID: PMC8535785 DOI: 10.3390/ijms222010957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022] Open
Abstract
The processing of DNA double-strand breaks (DSBs) depends on the dynamic characteristics of chromatin. To investigate how abrupt changes in chromatin compaction alter these dynamics and affect DSB processing and repair, we exposed irradiated cells to hypotonic stress (HypoS). Densitometric and chromosome-length analyses show that HypoS transiently decompacts chromatin without inducing histone modifications known from regulated local chromatin decondensation, or changes in Micrococcal Nuclease (MNase) sensitivity. HypoS leaves undisturbed initial stages of DNA-damage-response (DDR), such as radiation-induced ATM activation and H2AX-phosphorylation. However, detection of ATM-pS1981, γ-H2AX and 53BP1 foci is reduced in a protein, cell cycle phase and cell line dependent manner; likely secondary to chromatin decompaction that disrupts the focal organization of DDR proteins. While HypoS only exerts small effects on classical nonhomologous end-joining (c-NHEJ) and alternative end-joining (alt-EJ), it markedly suppresses homologous recombination (HR) without affecting DNA end-resection at DSBs, and clearly enhances single-strand annealing (SSA). These shifts in pathway engagement are accompanied by decreases in HR-dependent chromatid-break repair in the G2-phase, and by increases in alt-EJ and SSA-dependent chromosomal translocations. Consequently, HypoS sensitizes cells to ionizing radiation (IR)-induced killing. We conclude that HypoS-induced global chromatin decompaction compromises regulated chromatin dynamics and genomic stability by suppressing DSB-processing by HR, and allowing error-prone processing by alt-EJ and SSA.
Collapse
|
40
|
Narkar A, Johnson BA, Li R. Complex interplay between p53 and chromosome stability. Mol Cell Oncol 2021; 8:1938479. [PMID: 34616871 DOI: 10.1080/23723556.2021.1938479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
TP53-dependent cell cycle arrest has been proposed to limit the proliferation of aneuploid cells. We investigated the cellular response to aneuploidy in cell lines and organoid cultures and found that TP53 (also known as p53) is not activated following aneuploidy induction in organoids. However, we confirmed that p53 is required for high mitotic fidelity. Our findings provide a revised view on how p53 safeguards against aneuploidy.
Collapse
Affiliation(s)
- Akshay Narkar
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Blake A Johnson
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.,Mechanobiology Institute and Department of Biological Science, National University of Singapore, Singapore, Singapore
| |
Collapse
|
41
|
The Interplay Between Neutral and Adaptive Processes Shapes Genetic Variation During Candida Species Evolution. CURRENT CLINICAL MICROBIOLOGY REPORTS 2021. [DOI: 10.1007/s40588-021-00171-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
42
|
Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021; 12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.
Collapse
Affiliation(s)
- Anton Gorkovskiy
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| |
Collapse
|
43
|
Thomson GJ, Kakade P, Hirakawa MP, Ene IV, Bennett RJ. Adaptation to the dietary sugar D-tagatose via genome instability in polyploid Candida albicans cells. G3-GENES GENOMES GENETICS 2021; 11:6219300. [PMID: 33836061 PMCID: PMC8495922 DOI: 10.1093/g3journal/jkab110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
The opportunistic fungal pathogen Candida albicans undergoes an unusual parasexual cycle wherein diploid cells mate to form tetraploid cells that can generate genetically diverse progeny via a non-meiotic program of chromosome loss. The genetic diversity afforded by parasex impacts clinically relevant features including drug resistance and virulence, and yet the factors influencing genome instability in C. albicans are not well defined. To understand how environmental cues impact genome instability, we monitored ploidy change following tetraploid cell growth in a panel of different carbon sources. We found that growth in one carbon source, D-tagatose, led to high levels of genomic instability and chromosome loss in tetraploid cells. This sugar is a stereoisomer of L-sorbose which was previously shown to promote karyotypic changes in C. albicans. However, while expression of the SOU1 gene enabled utilization of L-sorbose, overexpression of this gene did not promote growth in D-tagatose, indicating differences in assimilation of the two sugars. In addition, genome sequencing of multiple progeny recovered from D-tagatose cultures revealed increased relative copy numbers of chromosome 4, suggestive of chromosome-level regulation of D-tagatose metabolism. Together, these studies identify a novel environmental cue that induces genome instability in C. albicans, and further implicate chromosomal changes in supporting metabolic adaptation in this species.
Collapse
Affiliation(s)
- Gregory J Thomson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Pallavi Kakade
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Matthew P Hirakawa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.,Department of Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Iuliana V Ene
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.,Mycology Department, Pasteur Institute, Paris 75015, France
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| |
Collapse
|
44
|
Yang F, Todd RT, Selmecki A, Jiang YY, Cao YB, Berman J. The fitness costs and benefits of trisomy of each Candida albicans chromosome. Genetics 2021; 218:6218773. [PMID: 33837402 DOI: 10.1093/genetics/iyab056] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/01/2021] [Indexed: 01/05/2023] Open
Abstract
Candida albicans is a prevalent human fungal pathogen. Rapid genomic change, due to aneuploidy, is a common mechanism that facilitates survival from multiple types of stresses including the few classes of available antifungal drugs. The stress survival of aneuploids occurs despite the fitness costs attributed to most aneuploids growing under idealized lab conditions. Systematic study of the aneuploid state in C. albicans has been hindered by the lack of a comprehensive collection of aneuploid strains. Here, we describe a collection of diploid C. albicans aneuploid strains, each carrying one extra copy of each chromosome, all from the same genetic background. We tested the fitness of this collection under several physiological conditions including shifts in pH, low glucose, oxidative stress, temperature, high osmolarity, membrane stress, and cell wall stress. We found that most aneuploids, under most conditions, were less fit than their euploid parent, yet there were specific conditions under which specific aneuploid isolates provided a fitness benefit relative to the euploid parent strain. Importantly, this fitness benefit was attributable to the change in the copy number of specific chromosomes. Thus, C. albicans can tolerate aneuploidy of each chromosome and some aneuploids confer improved growth under conditions that the yeast encounters in its host niches.
Collapse
Affiliation(s)
- Feng Yang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200086, China.,Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Yuan-Ying Jiang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yong-Bing Cao
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200086, China
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
45
|
Dick JM. Water as a reactant in the differential expression of proteins in cancer. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021. [DOI: 10.1002/cso2.1007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Jeffrey M. Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education School of Geosciences and Info‐Physics Central South University Changsha China
| |
Collapse
|
46
|
Luo Z, Yu K, Xie S, Monti M, Schindler D, Fang Y, Zhao S, Liang Z, Jiang S, Luan M, Xiao C, Cai Y, Dai J. Compacting a synthetic yeast chromosome arm. Genome Biol 2021; 22:5. [PMID: 33397424 PMCID: PMC7780613 DOI: 10.1186/s13059-020-02232-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel way to understand the core principles of life. The synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) system is a unique feature implanted in the synthetic yeast genome (Sc2.0), which is proposed as an effective tool for genome minimization. As the Sc2.0 project is nearing its completion, we have begun to explore the application of the SCRaMbLE system in genome compaction. RESULTS We develop a method termed SCRaMbLE-based genome compaction (SGC) and demonstrate that a synthetic chromosome arm (synXIIL) can be efficiently reduced. The pre-introduced episomal essential gene array significantly enhances the compacting ability of SGC, not only by enabling the deletion of nonessential genes located in essential gene containing loxPsym units but also by allowing more chromosomal sequences to be removed in a single SGC process. Further compaction is achieved through iterative SGC, revealing that at least 39 out of 65 nonessential genes in synXIIL can be removed collectively without affecting cell viability at 30 °C in rich medium. Approximately 40% of the synthetic sequence, encoding 28 genes, is found to be dispensable for cell growth at 30 °C in rich medium and several genes whose functions are needed under specified conditions are identified. CONCLUSIONS We develop iterative SGC with the aid of eArray as a generic yet effective tool to compact the synthetic yeast genome.
Collapse
Affiliation(s)
- Zhouqing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Kang Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shangqian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, 570228, China
| | - Marco Monti
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Present Address: Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Yuan Fang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shijun Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhenzhen Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Meiwei Luan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University, Haikou, 570228, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yizhi Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| |
Collapse
|
47
|
Wlodarski M, Mancini L, Raciti B, Sclavi B, Lagomarsino MC, Cicuta P. Cytosolic Crowding Drives the Dynamics of Both Genome and Cytosol in Escherichia coli Challenged with Sub-lethal Antibiotic Treatments. iScience 2020; 23:101560. [PMID: 33083729 PMCID: PMC7522891 DOI: 10.1016/j.isci.2020.101560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/22/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022] Open
Abstract
In contrast to their molecular mode of action, the system-level effect of antibiotics on cells is only beginning to be quantified. Molecular crowding is expected to be a relevant global regulator, which we explore here through the dynamic response phenotypes in Escherichia coli, at single-cell resolution, under sub-lethal regimes of different classes of clinically relevant antibiotics, acting at very different levels in the cell. We measure chromosomal mobility through tracking of fast (<15 s timescale) fluctuations of fluorescently tagged chromosomal loci, and we probe the fluidity of the cytoplasm by tracking cytosolic aggregates. Measuring cellular density, we show how the overall levels of macromolecular crowding affect both quantities, regardless of antibiotic-specific effects. The dominant trend is a strong correlation between the effects in different parts of the chromosome and between the chromosome and cytosol, supporting the concept of an overall global role of molecular crowding in cellular physiology.
Collapse
Affiliation(s)
- Michal Wlodarski
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Dipartimento di Fisica and I.N.F.N., Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
| | - Leonardo Mancini
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Bianca Raciti
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Bianca Sclavi
- Laboratory of Biology and Applied Pharmacology (UMR 8113 CNRS), École Normale Supérieure, Paris-Saclay, France
| | | | - Pietro Cicuta
- IFOM Foundation FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| |
Collapse
|
48
|
Moyer AJ, Gardiner K, Reeves RH. All Creatures Great and Small: New Approaches for Understanding Down Syndrome Genetics. Trends Genet 2020; 37:444-459. [PMID: 33097276 DOI: 10.1016/j.tig.2020.09.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/26/2022]
Abstract
Human chromosome 21 (Hsa21) contains more than 500 genes, making trisomy 21 one of the most complex genetic perturbations compatible with life. The ultimate goal of Down syndrome (DS) research is to design therapies that improve quality of life for individuals with DS by understanding which subsets of Hsa21 genes contribute to DS-associated phenotypes throughout the lifetime. However, the complexity of DS pathogenesis has made developing appropriate animal models an ongoing challenge. Here, we examine lessons learned from a variety of model systems, including yeast, nematode, fruit fly, and zebrafish, and discuss emerging methods for creating murine models that better reflect the genetic basis of trisomy 21.
Collapse
Affiliation(s)
- Anna J Moyer
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Katheleen Gardiner
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA (retired)
| | - Roger H Reeves
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
49
|
Larrimore KE, Barattin-Voynova NS, Reid DW, Ng DTW. Aneuploidy-induced proteotoxic stress can be effectively tolerated without dosage compensation, genetic mutations, or stress responses. BMC Biol 2020; 18:117. [PMID: 32900371 PMCID: PMC7487686 DOI: 10.1186/s12915-020-00852-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport, and degradation within a cell. Failure to maintain proteostasis is associated with aging and disease, leading to concerted efforts to study how the network responds to various proteotoxic stresses. This is often accomplished using ectopic overexpression of well-characterized, model misfolded protein substrates. However, how cells tolerate large-scale, diverse burden to the proteostasis network is not understood. Aneuploidy, the state of imbalanced chromosome content, adversely affects the proteostasis network by dysregulating the expression of hundreds of proteins simultaneously. Using aneuploid haploid yeast cells as a model, we address whether cells can tolerate large-scale, diverse challenges to the proteostasis network. RESULTS Here we characterize several aneuploid Saccharomyces cerevisiae strains isolated from a collection of stable, randomly generated yeast aneuploid cells. These strains exhibit robust growth and resistance to multiple drugs which induce various forms of proteotoxic stress. Whole genome re-sequencing of the strains revealed this was not the result of genetic mutations, and transcriptome profiling combined with ribosome footprinting showed that genes are expressed and translated in accordance to chromosome copy number. In some strains, various facets of the proteostasis network are mildly upregulated without chronic activation of environmental stress response or heat shock response pathways. No severe defects were observed in the degradation of misfolded proteins, using model misfolded substrates of endoplasmic reticulum-associated degradation or cytosolic quality control pathways, and protein biosynthesis capacity was not impaired. CONCLUSIONS We show that yeast strains of some karyotypes in the genetic background studied here can tolerate the large aneuploidy-associated burden to the proteostasis machinery without genetic changes, dosage compensation, or activation of canonical stress response pathways. We suggest that proteotoxic stress, while common, is not always an obligate consequence of aneuploidy, but rather certain karyotypes and genetic backgrounds may be able to tolerate the excess protein burden placed on the protein homeostasis machinery. This may help clarify how cancer cells are paradoxically both highly aneuploid and highly proliferative at the same time.
Collapse
Affiliation(s)
- Katherine E Larrimore
- Temasek Life Sciences Laboratory, Singapore, 117604, Singapore.
- Current address: Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.
| | | | - David W Reid
- Duke-NUS Graduate Medical School, Singapore, 169857, Singapore
- Current address: Moderna Inc., Cambridge, MA, 02139, USA
| | - Davis T W Ng
- Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
- Duke-NUS Graduate Medical School, Singapore, 169857, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| |
Collapse
|
50
|
Vydzhak O, Bender K, Klermund J, Busch A, Reimann S, Luke B. Checkpoint adaptation in recombination-deficient cells drives aneuploidy and resistance to genotoxic agents. DNA Repair (Amst) 2020; 95:102939. [PMID: 32777450 DOI: 10.1016/j.dnarep.2020.102939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/19/2022]
Abstract
Human cancers frequently harbour mutations in DNA repair genes, rendering the use of DNA damaging agents as an effective therapeutic intervention. As therapy-resistant cells often arise, it is important to better understand the molecular pathways that drive resistance in order to facilitate the eventual targeting of such processes. We employ recombination-defective diploid yeast as a model to demonstrate that, in response to genotoxic challenges, nearly all cells eventually undergo checkpoint adaptation, resulting in the generation of aneuploid cells with whole chromosome losses that have acquired resistance to the initial genotoxic challenge. We demonstrate that adaptation inhibition, either pharmacologically, or genetically, drastically reduces the occurrence of resistant cells. Additionally, the aneuploid phenotypes of the resistant cells can be specifically targeted to induce cytotoxicity. We provide evidence that TORC1 inhibition with rapamycin, in combination with DNA damaging agents, can prevent both checkpoint adaptation and the continued growth of aneuploid resistant cells.
Collapse
Affiliation(s)
- Olga Vydzhak
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany; Johannes Gutenberg University Mainz, Faculty of Biology, Institute of Developmental Biology and Neurobiology, Mainz, 55128, Germany
| | - Katharina Bender
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany; Johannes Gutenberg University Mainz, Faculty of Biology, Institute of Developmental Biology and Neurobiology, Mainz, 55128, Germany
| | - Julia Klermund
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Stefanie Reimann
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany; Johannes Gutenberg University Mainz, Faculty of Biology, Institute of Developmental Biology and Neurobiology, Mainz, 55128, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany; Johannes Gutenberg University Mainz, Faculty of Biology, Institute of Developmental Biology and Neurobiology, Mainz, 55128, Germany.
| |
Collapse
|