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Wallace AD, Blue NR, Morgan T, Workalemahu T, Silver RM, Quinlan AR. Placental somatic mutation in human stillbirth and live birth: A pilot case-control study of paired placental, fetal, and maternal whole genomes. Placenta 2024; 154:137-144. [PMID: 38972082 PMCID: PMC11368634 DOI: 10.1016/j.placenta.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION A high frequency of single nucleotide somatic mutations in the placenta has been recently described, but its relationship to placental dysfunction is unknown. METHODS We performed a pilot case-control study using paired fetal, maternal, and placental samples collected from healthy live birth controls (n = 10), live births with fetal growth restriction (FGR) due to placental insufficiency (n = 7), and stillbirths with FGR and placental insufficiency (n = 11). We quantified single nucleotide and structural somatic variants using bulk whole genome sequencing (30-60X coverage) in four biopsies from each placenta. We also assessed their association with clinical and histological evidence of placental dysfunction. RESULTS Seventeen pregnancies had sufficiently high-quality placental, fetal, and maternal DNA for analysis. Each placenta had a median of 473 variants (range 111-870), with 95 % arising in just one biopsy within each placenta. In controls, live births with FGR, and stillbirths, the median variant counts per placenta were 514 (IQR 381-779), 582 (450-735), and 338 (245-441), respectively. After adjusting for depth of sequencing coverage and gestational age at birth, the somatic mutation burden was similar between groups (FGR live births vs. controls, adjusted diff. 59, 95 % CI -218 to +336; stillbirths vs controls, adjusted diff. -34, -351 to +419), and with no association with placental dysfunction (p = 0.7). DISCUSSION We confirmed the high prevalence of somatic mutation in the human placenta and conclude that the placenta is highly clonal. We were not able to identify any relationship between somatic mutation burden and clinical or histologic placental insufficiency.
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Affiliation(s)
- Amelia D Wallace
- University of Utah Health, Department of Human Genetics, 15 N 2030 E, Eccles Institute of Human Genetics Rm 7160B, Salt Lake City, UT, 84112, USA; Utah Center for Genetic Discovery, 15 N 2030 E, #2100, Salt Lake City, UT, 4112, USA
| | - Nathan R Blue
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA
| | - Terry Morgan
- Oregon Health & Science University, Departments of Pathology and Obstetrics and Gynecology, 3181 SW Sam Jackson Park Rd, L-113, Portland, OR, 97239, USA
| | - Tsegaselassie Workalemahu
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA
| | - Robert M Silver
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA.
| | - Aaron R Quinlan
- University of Utah Health, Department of Human Genetics, 15 N 2030 E, Eccles Institute of Human Genetics Rm 7160B, Salt Lake City, UT, 84112, USA; Utah Center for Genetic Discovery, 15 N 2030 E, #2100, Salt Lake City, UT, 4112, USA.
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2
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Herriage HC, Huang YT, Calvi BR. The antagonistic relationship between apoptosis and polyploidy in development and cancer. Semin Cell Dev Biol 2024; 156:35-43. [PMID: 37331841 PMCID: PMC10724375 DOI: 10.1016/j.semcdb.2023.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023]
Abstract
One of the important functions of regulated cell death is to prevent cells from inappropriately acquiring extra copies of their genome, a state known as polyploidy. Apoptosis is the primary cell death mechanism that prevents polyploidy, and defects in this apoptotic response can result in polyploid cells whose subsequent error-prone chromosome segregation are a major contributor to genome instability and cancer progression. Conversely, some cells actively repress apoptosis to become polyploid as part of normal development or regeneration. Thus, although apoptosis prevents polyploidy, the polyploid state can actively repress apoptosis. In this review, we discuss progress in understanding the antagonistic relationship between apoptosis and polyploidy in development and cancer. Despite recent advances, a key conclusion is that much remains unknown about the mechanisms that link apoptosis to polyploid cell cycles. We suggest that drawing parallels between the regulation of apoptosis in development and cancer could help to fill this knowledge gap and lead to more effective therapies.
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Affiliation(s)
- Hunter C Herriage
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Yi-Ting Huang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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3
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Wang Y, Tamori Y. Polyploid Cancer Cell Models in Drosophila. Genes (Basel) 2024; 15:96. [PMID: 38254985 PMCID: PMC10815460 DOI: 10.3390/genes15010096] [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: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Cells with an abnormal number of chromosomes have been found in more than 90% of solid tumors, and among these, polyploidy accounts for about 40%. Polyploidized cells most often have duplicate centrosomes as well as genomes, and thus their mitosis tends to promote merotelic spindle attachments and chromosomal instability, which produces a variety of aneuploid daughter cells. Polyploid cells have been found highly resistant to various stress and anticancer therapies, such as radiation and mitogenic inhibitors. In other words, common cancer therapies kill proliferative diploid cells, which make up the majority of cancer tissues, while polyploid cells, which lurk in smaller numbers, may survive. The surviving polyploid cells, prompted by acute environmental changes, begin to mitose with chromosomal instability, leading to an explosion of genetic heterogeneity and a concomitant cell competition and adaptive evolution. The result is a recurrence of the cancer during which the tenacious cells that survived treatment express malignant traits. Although the presence of polyploid cells in cancer tissues has been observed for more than 150 years, the function and exact role of these cells in cancer progression has remained elusive. For this reason, there is currently no effective therapeutic treatment directed against polyploid cells. This is due in part to the lack of suitable experimental models, but recently several models have become available to study polyploid cells in vivo. We propose that the experimental models in Drosophila, for which genetic techniques are highly developed, could be very useful in deciphering mechanisms of polyploidy and its role in cancer progression.
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Affiliation(s)
| | - Yoichiro Tamori
- Department of Molecular Oncology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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4
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Andrawus M, Sharvit L, Touitou N, Lerrer B, Cohen HY, Atzmon G. Copy number variation as a tool for implementing pregnancy as an aging model. Aging (Albany NY) 2023; 15:7922-7932. [PMID: 37639552 PMCID: PMC10496986 DOI: 10.18632/aging.204936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/10/2023] [Indexed: 08/31/2023]
Abstract
Copy number variations (CNV) are a major contributor to genome variability and have been linked to aging and other degradable phenotypes such as pregnancy physiology. To demonstrate how pregnancy can be used as a model of aging, we used CNVs from pregnant mice. Candidate CNVs were selected by applying case-control analysis in human centenarians compared with control groups. These CNVs were aligned with the mouse genome and their copy variation was assessed using qRT-PCR in liver and blood tissue samples from pregnant mice throughout pregnancy (baseline; first, second, and third trimester; post-partum). Eight of the ten selected CNVs demonstrated a significant decline/increase trend throughout the pregnancy followed by opposite direction soon after delivery in the liver and blood of the mouse tissues. Furthermore, significant differential expression was detected among the candidate CNVs' close vicinity genes (APA2A, LSS, RBDHF1, PLAAT1, and SCL17A2), but not in the WSCD2 gene. Establishing a genetic link between longevity and pregnancy is a significant step toward implementing the pregnancy process as a model for aging. These results in pregnant mice highlight the mechanism and similarities between pregnancy and aging. Investigating the mechanisms that cause such rejuvenation after labor could change our aging treatment paradigm.
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Affiliation(s)
- Mariana Andrawus
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
| | - Lital Sharvit
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
| | - Noga Touitou
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Batia Lerrer
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Haim Y. Cohen
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Gil Atzmon
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
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5
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Weier JF, Ferlatte C, Baumgartner A, Nguyen HN, Weier BA, Weier HUG. Analysis of human invasive cytotrophoblasts demonstrates mosaic aneuploidy. PLoS One 2023; 18:e0284317. [PMID: 37478076 PMCID: PMC10361533 DOI: 10.1371/journal.pone.0284317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/28/2023] [Indexed: 07/23/2023] Open
Abstract
A total of 24 chromosome-specific fluorescence in situ hybridization probes for interphase nucleus analysis were developed to determine the chromosomal content of individual human invasive cytotrophoblasts derived from in vitro cultured assays. At least 75% of invasive cytotrophoblasts were hyperdiploid and the total number of chromosomes ranged from 47 to 61. The results also demonstrated that these hyperdiploid invasive cytotrophoblasts showed significant heterogeneity. The most copy number gains were observed for chromosomes 13, 14, 15, 19, 21, and 22 with average copy number greater than 2.3. A parallel study using primary invasive cytotrophoblasts also showed a similar trend of copy number changes. Conclusively, 24-chromosome analysis of human non-proliferating cytotrophoblasts (interphase nuclei) was achieved. Hyperdiploidy and chromosomal heterogeneity without endoduplication in invasive cytotrophoblasts may suggest a selective advantage for invasion and short lifespan during normal placental development.
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Affiliation(s)
- Jingly F Weier
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California (U.C.), San Francisco, California, United States of America
- Life Sciences Division, U.C. E.O. Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Christy Ferlatte
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California (U.C.), San Francisco, California, United States of America
| | - Adolf Baumgartner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California (U.C.), San Francisco, California, United States of America
- Life Sciences Division, U.C. E.O. Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Ha Nam Nguyen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California (U.C.), San Francisco, California, United States of America
| | - Beatrice A Weier
- Golden State Dermatology, Walnut Creek, California, United States of America
| | - Heinz-Ulrich G Weier
- Life Sciences Division, U.C. E.O. Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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6
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Edwards MM, Zuccaro MV, Sagi I, Ding Q, Vershkov D, Benvenisty N, Egli D, Koren A. Delayed DNA replication in haploid human embryonic stem cells. Genome Res 2021; 31:2155-2169. [PMID: 34810218 PMCID: PMC8647822 DOI: 10.1101/gr.275953.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Ido Sagi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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7
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Morey R, Farah O, Kallol S, Requena DF, Meads M, Moretto-Zita M, Soncin F, Laurent LC, Parast MM. Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast. Front Cell Dev Biol 2021; 9:702046. [PMID: 34540826 PMCID: PMC8446284 DOI: 10.3389/fcell.2021.702046] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022] Open
Abstract
During pregnancy, conceptus-derived extravillous trophoblast (EVT) invades the endomyometrium, anchors the placenta to the maternal uterus, and remodels the spiral arteries in order to establish maternal blood supply to the fetoplacental unit. Recent reports have described early gestation EVT as polyploid and senescent. Here, we extend these reports by performing comprehensive profiling of both the genomic organization and transcriptome of first trimester and term EVT. We define pathways and gene regulatory networks involved in both initial differentiation and maturation of this important trophoblast lineage at the maternal-fetal interface. Our results suggest that like first trimester EVT, term EVT undergoes senescence and endoreduplication, is primarily tetraploid, and lacks high rates of copy number variations. Additionally, we have highlighted senescence and polyploidy-related genes, pathways, networks, and transcription factors that appeared to be important in normal EVT differentiation and maturation and validated a key role for the unfolded protein response in this context.
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Affiliation(s)
- Robert Morey
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Omar Farah
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Sampada Kallol
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Daniela F Requena
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Matteo Moretto-Zita
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Francesca Soncin
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal-Fetal Medicine, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Mana M Parast
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States.,Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, United States
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8
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Kimmel GJ, Dane M, Heiser LM, Altrock PM, Andor N. Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments. Cancer Res 2020; 80:5109-5120. [PMID: 32938640 DOI: 10.1158/0008-5472.can-20-1231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/30/2020] [Accepted: 09/11/2020] [Indexed: 12/22/2022]
Abstract
Breast cancer progresses in a multistep process from primary tumor growth and stroma invasion to metastasis. Nutrient-limiting environments promote chemotaxis with aggressive morphologies characteristic of invasion. It is unknown how coexisting cells differ in their response to nutrient limitations and how this impacts invasion of the metapopulation as a whole. In this study, we integrate mathematical modeling with microenvironmental perturbation data to investigate invasion in nutrient-limiting environments inhabited by one or two cancer cell subpopulations. Subpopulations were defined by their energy efficiency and chemotactic ability. Invasion distance traveled by a homogeneous population was estimated. For heterogeneous populations, results suggest that an imbalance between nutrient efficacy and chemotactic superiority accelerates invasion. Such imbalance will spatially segregate the two populations and only one type will dominate at the invasion front. Only if these two phenotypes are balanced, the two subpopulations compete for the same space, which decelerates invasion. We investigate ploidy as a candidate biomarker of this phenotypic heterogeneity and discuss its potential to inform the dose of mTOR inhibitors (mTOR-I) that can inhibit chemotaxis just enough to facilitate such competition. SIGNIFICANCE: This study identifies the double-edged sword of high ploidy as a prerequisite to personalize combination therapies with cytotoxic drugs and inhibitors of signal transduction pathways such as mTOR-Is. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/22/5109/F1.large.jpg.
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Affiliation(s)
- Gregory J Kimmel
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Mark Dane
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Laura M Heiser
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida.,Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Philipp M Altrock
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Noemi Andor
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida.
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Kolesnikova TD, Kolodyazhnaya AV, Pokholkova GV, Schubert V, Dovgan VV, Romanenko SA, Prokopov DY, Zhimulev IF. Effects of Mutations in the Drosophila melanogaster Rif1 Gene on the Replication and Underreplication of Pericentromeric Heterochromatin in Salivary Gland Polytene Chromosomes. Cells 2020; 9:cells9061501. [PMID: 32575592 PMCID: PMC7349278 DOI: 10.3390/cells9061501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023] Open
Abstract
In Drosophila salivary gland polytene chromosomes, a substantial portion of heterochromatin is underreplicated. The combination of mutations SuURES and Su(var)3-906 results in the polytenization of a substantial fraction of unique and moderately repeated sequences but has almost no effect on satellite DNA replication. The Rap1 interacting factor 1 (Rif) protein is a conserved regulator of replication timing, and in Drosophila, it affects underreplication in polytene chromosomes. We compared the morphology of pericentromeric regions and labeling patterns of in situ hybridization of heterochromatin-specific DNA probes between wild-type salivary gland polytene chromosomes and the chromosomes of Rif1 mutants and SuUR Su(var)3-906 double mutants. We show that, despite general similarities, heterochromatin zones exist that are polytenized only in the Rif1 mutants, and that there are zones that are under specific control of Su(var)3-9. In the Rif1 mutants, we found additional polytenization of the largest blocks of satellite DNA (in particular, satellite 1.688 of chromosome X and simple satellites in chromosomes X and 4) as well as partial polytenization of chromosome Y. Data on pulsed incorporation of 5-ethynyl-2′-deoxyuridine (EdU) into polytene chromosomes indicated that in the Rif1 mutants, just as in the wild type, most of the heterochromatin becomes replicated during the late S phase. Nevertheless, a significantly increased number of heterochromatin replicons was noted. These results suggest that Rif1 regulates the activation probability of heterochromatic origins in the satellite DNA region.
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Affiliation(s)
- Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
| | - Alexandra V. Kolodyazhnaya
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Galina V. Pokholkova
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Seeland, Germany;
| | - Viktoria V. Dovgan
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
| | - Dmitry Yu. Prokopov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.V.K.); (G.V.P.); (V.V.D.); (S.A.R.); (D.Y.P.); (I.F.Z.)
- Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
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Singh VP, McKinney S, Gerton JL. Persistent DNA Damage and Senescence in the Placenta Impacts Developmental Outcomes of Embryos. Dev Cell 2020; 54:333-347.e7. [PMID: 32800293 DOI: 10.1016/j.devcel.2020.05.025] [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: 12/30/2019] [Revised: 04/17/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cohesin is an evolutionarily conserved chromosome-associated protein complex essential for chromosome segregation, gene expression, and repair of DNA damage. Mutations that affect this complex cause the human developmental disorder Cornelia de Lange syndrome (CdLS), thought to arise from defective embryonic transcription. We establish a significant role for placental defects in the development of CdLS mouse embryos (Nipbl and Hdac8). Placenta is a naturally senescent tissue; we demonstrate that persistent DNA damage potentiates senescence and activates cytokine signaling. Mutant embryo developmental outcomes are significantly improved in the context of a wild-type placenta or by genetically restricting cytokine signaling. Our study highlights that cohesin is required for maintaining ploidy and the repair of spontaneous DNA damage in placental cells, suggesting that genotoxic stress and ensuing placental senescence and cytokine production could represent a broad theme in embryo health and viability.
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Affiliation(s)
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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11
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Eaton M, Davies AH, Devine J, Zhao X, Simmons DG, Maríusdóttir E, Natale DRC, Matyas JR, Bering EA, Workentine ML, Hallgrimsson B, Cross JC. Complex patterns of cell growth in the placenta in normal pregnancy and as adaptations to maternal diet restriction. PLoS One 2020; 15:e0226735. [PMID: 31917811 PMCID: PMC6952106 DOI: 10.1371/journal.pone.0226735] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023] Open
Abstract
The major milestones in mouse placental development are well described, but our understanding is limited to how the placenta can adapt to damage or changes in the environment. By using stereology and expression of cell cycle markers, we found that the placenta grows under normal conditions not just by hyperplasia of trophoblast cells but also through extensive polyploidy and cell hypertrophy. In response to feeding a low protein diet to mothers prior to and during pregnancy, to mimic chronic malnutrition, we found that this normal program was altered and that it was influenced by the sex of the conceptus. Male fetuses showed intrauterine growth restriction (IUGR) by embryonic day (E) 18.5, just before term, whereas female fetuses showed IUGR as early as E16.5. This difference was correlated with differences in the size of the labyrinth layer of the placenta, the site of nutrient and gas exchange. Functional changes were implied based on up-regulation of nutrient transporter genes. The junctional zone was also affected, with a reduction in both glycogen trophoblast and spongiotrophoblast cells. These changes were associated with increased expression of Phlda2 and reduced expression of Egfr. Polyploidy, which results from endoreduplication, is a normal feature of trophoblast giant cells (TGC) but also spongiotrophoblast cells. Ploidy was increased in sinusoidal-TGCs and spongiotrophoblast cells, but not parietal-TGCs, in low protein placentas. These results indicate that the placenta undergoes a range of changes in development and function in response to poor maternal diet, many of which we interpret are aimed at mitigating the impacts on fetal and maternal health.
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Affiliation(s)
- Malcolm Eaton
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary Alberta
| | - Alastair H. Davies
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary Alberta
| | - Jay Devine
- Department of Anatomy and Cell Biology, Cumming School of Medicine, University of Calgary, Calgary Alberta
| | - Xiang Zhao
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary Alberta
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary Alberta
| | - David G. Simmons
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary Alberta
| | - Elín Maríusdóttir
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary Alberta
| | - David R. C. Natale
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary Alberta
| | - John R. Matyas
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary Alberta
| | - Elizabeth A. Bering
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary Alberta
| | | | - Benedikt Hallgrimsson
- Department of Anatomy and Cell Biology, Cumming School of Medicine, University of Calgary, Calgary Alberta
| | - James C. Cross
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary Alberta
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary Alberta
- * E-mail:
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12
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Fischer U, Backes C, Fehlmann T, Galata V, Keller A, Meese E. Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing. J Mol Med (Berl) 2019; 97:1099-1111. [PMID: 31134286 PMCID: PMC6647207 DOI: 10.1007/s00109-019-01792-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 12/03/2022]
Abstract
Abstract Gene amplification is an evolutionarily well-conserved and highly efficient mechanism to increase the amount of specific proteins. In humans, gene amplification is a hallmark of cancer and has recently been found during stem cell differentiation. Amplifications in stem cells are restricted to specific tissue areas and time windows, rendering their detection difficult. Here, we report on the performance of deep WGS sequencing (average 82-fold depth of coverage) on the BGISEQ with nanoball technology to detect amplifications in human mesenchymal and neural stem cells. As reference technology, we applied array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), and qPCR. Using different in silico strategies for amplification detection, we analyzed the potential of WGS for amplification detection. Our results provide evidence that WGS accurately identifies changes of the copy number profiles in human stem cell differentiation. However, the identified changes are not in all cases consistent between WGS and aCGH. The results between WGS and the validation by qPCR were concordant in 83.3% of all tested 36 cases. In sum, both genome-wide techniques, aCGH and WGS, have unique advantages and specific challenges, calling for locus-specific confirmation by the low-throughput approaches qPCR or FISH. Key messages WGS allows for the identification of dynamic copy number changes in human stem cells. Less stringent threshold setting is crucial for detection of copy number increase. Broad knowledge of dynamic copy number is pivotal to estimate stem cell capabilities.
Electronic supplementary material The online version of this article (10.1007/s00109-019-01792-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ulrike Fischer
- Department of Human Genetics, Saarland University, Building 60, 66421, Homburg/Saar, Germany.
| | - Christina Backes
- Clinical Bioinformatics, Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Valentina Galata
- Clinical Bioinformatics, Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Building 60, 66421, Homburg/Saar, Germany
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13
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H3K9 Promotes Under-Replication of Pericentromeric Heterochromatin in Drosophila Salivary Gland Polytene Chromosomes. Genes (Basel) 2019; 10:genes10020093. [PMID: 30700014 PMCID: PMC6409945 DOI: 10.3390/genes10020093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/11/2022] Open
Abstract
Chromatin structure and its organization contributes to the proper regulation and timing of DNA replication. Yet, the precise mechanism by which chromatin contributes to DNA replication remains incompletely understood. This is particularly true for cell types that rely on polyploidization as a developmental strategy for growth and high biosynthetic capacity. During Drosophila larval development, cells of the salivary gland undergo endoreplication, repetitive rounds of DNA synthesis without intervening cell division, resulting in ploidy values of ~1350C. S phase of these endocycles displays a reproducible pattern of early and late replicating regions of the genome resulting from the activity of the same replication initiation factors that are used in diploid cells. However, unlike diploid cells, the latest replicating regions of polyploid salivary gland genomes, composed primarily of pericentric heterochromatic enriched in H3K9 methylation, are not replicated each endocycle, resulting in under-replicated domains with reduced ploidy. Here, we employ a histone gene replacement strategy in Drosophila to demonstrate that mutation of a histone residue important for heterochromatin organization and function (H3K9) but not mutation of a histone residue important for euchromatin function (H4K16), disrupts proper endoreplication in Drosophila salivary gland polyploid genomes thereby leading to DNA copy gain in pericentric heterochromatin. These findings reveal that H3K9 is necessary for normal levels of under-replication of pericentric heterochromatin and suggest that under-replication at pericentric heterochromatin is mediated through H3K9 methylation.
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14
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Gjelsvik KJ, Besen-McNally R, Losick VP. Solving the Polyploid Mystery in Health and Disease. Trends Genet 2019; 35:6-14. [PMID: 30470486 PMCID: PMC6457904 DOI: 10.1016/j.tig.2018.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/12/2018] [Accepted: 10/22/2018] [Indexed: 01/12/2023]
Abstract
Polyploidy (the more than doubling of a cell's genome) frequently arises during organogenesis, tissue repair, and age-associated diseases. Despite its prevalence, major gaps exist in how polyploid cells emerge and affect tissue function. Studies have begun to elucidate the signals required for polyploid cell growth as well as the advantages and disadvantages of polyploidy in health and disease. This review highlights the recent advances on the role and regulation of polyploidy in Drosophila and vertebrate models. The newly discovered versatility of polyploid cells has the potential to provide alternative strategies to promote tissue growth and repair, while limiting disease and dysfunction.
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Affiliation(s)
- K J Gjelsvik
- MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA
| | - R Besen-McNally
- MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA
| | - V P Losick
- MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA.
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15
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Munden A, Rong Z, Sun A, Gangula R, Mallal S, Nordman JT. Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila. eLife 2018; 7:e39140. [PMID: 30277458 PMCID: PMC6185109 DOI: 10.7554/elife.39140] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022] Open
Abstract
Control of DNA copy number is essential to maintain genome stability and ensure proper cell and tissue function. In Drosophila polyploid cells, the SNF2-domain-containing SUUR protein inhibits replication fork progression within specific regions of the genome to promote DNA underreplication. While dissecting the function of SUUR's SNF2 domain, we identified an interaction between SUUR and Rif1. Rif1 has many roles in DNA metabolism and regulates the replication timing program. We demonstrate that repression of DNA replication is dependent on Rif1. Rif1 localizes to active replication forks in a partially SUUR-dependent manner and directly regulates replication fork progression. Importantly, SUUR associates with replication forks in the absence of Rif1, indicating that Rif1 acts downstream of SUUR to inhibit fork progression. Our findings uncover an unrecognized function of the Rif1 protein as a regulator of replication fork progression.
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Affiliation(s)
- Alexander Munden
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Zhan Rong
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Amanda Sun
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
| | - Rama Gangula
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
| | - Simon Mallal
- Department of MedicineVanderbilt University School of MedicineNashvilleUnited States
- Department of Pathology, Microbiology and ImmunologyVanderbilt University School of MedicineNashvilleUnited States
| | - Jared T Nordman
- Department of Biological SciencesVanderbilt UniversityNashvilleUnited States
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16
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Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. Genome amplification and cellular senescence are hallmarks of human placenta development. PLoS Genet 2018; 14:e1007698. [PMID: 30312291 PMCID: PMC6200260 DOI: 10.1371/journal.pgen.1007698] [Citation(s) in RCA: 60] [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: 04/10/2018] [Revised: 10/24/2018] [Accepted: 09/17/2018] [Indexed: 12/16/2022] Open
Abstract
Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM.
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Affiliation(s)
- Philipp Velicky
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Gudrun Meinhardt
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Kerstin Plessl
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Sigrid Vondra
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Tamara Weiss
- Children's Cancer Research Institute, St. Anna Children´s Hospital, Vienna, Austria
| | - Peter Haslinger
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Thomas Lendl
- Biooptics Facility of Institute of Molecular Pathology, Institute of Molecular Biotechnology and Gregor Mendel Institute, Vienna, Austria
| | - Karin Aumayr
- Biooptics Facility of Institute of Molecular Pathology, Institute of Molecular Biotechnology and Gregor Mendel Institute, Vienna, Austria
| | - Mario Mairhofer
- Department of Gynecological Endocrinology and Reproductive Medicine, Medical University of Vienna, Vienna, Austria
| | - Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America
| | - Birgit Schütz
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Roberta L. Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert Lindau
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Beatrix Weil
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jürgen Neesen
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Mario Mikula
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Clemens Röhrl
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Tasha and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford, California, United States of America
| | - Julie Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Martin Knöfler
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Jürgen Pollheimer
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
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17
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Dynamic changes in ORC localization and replication fork progression during tissue differentiation. BMC Genomics 2018; 19:623. [PMID: 30134926 PMCID: PMC6103881 DOI: 10.1186/s12864-018-4992-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/02/2018] [Indexed: 12/23/2022] Open
Abstract
Background Genomic regions repressed for DNA replication, resulting in either delayed replication in S phase or underreplication in polyploid cells, are thought to be controlled by inhibition of replication origin activation. Studies in Drosophila polytene cells, however, raised the possibility that impeding replication fork progression also plays a major role. Results We exploited genomic regions underreplicated (URs) with tissue specificity in Drosophila polytene cells to analyze mechanisms of replication repression. By localizing the Origin Recognition Complex (ORC) in the genome of the larval fat body and comparing this to ORC binding in the salivary gland, we found that sites of ORC binding show extensive tissue specificity. In contrast, there are common domains nearly devoid of ORC in the salivary gland and fat body that also have reduced density of ORC binding sites in diploid cells. Strikingly, domains lacking ORC can still be replicated in some polytene tissues, showing absence of ORC and origins is insufficient to repress replication. Analysis of the width and location of the URs with respect to ORC position indicates that whether or not a genomic region lacking ORC is replicated is controlled by whether replication forks formed outside the region are inhibited. Conclusions These studies demonstrate that inhibition of replication fork progression can block replication across genomic regions that constitutively lack ORC. Replication fork progression can be inhibited in both tissue-specific and genome region-specific ways. Consequently, when evaluating sources of genome instability it is important to consider altered control of replication forks in response to differentiation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4992-3) contains supplementary material, which is available to authorized users.
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18
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Okano-Uchida T, Kent LN, Ouseph MM, McCarty B, Frank JJ, Kladney R, Cuitino MC, Thompson JC, Coppola V, Asano M, Leone G. Endoreduplication of the mouse genome in the absence of ORC1. Genes Dev 2018; 32:978-990. [PMID: 29967292 PMCID: PMC6075035 DOI: 10.1101/gad.311910.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/09/2018] [Indexed: 01/24/2023]
Abstract
In this study, Okano-Uchida et al. describe the physiological role of ORC1 in mice by generating knock-in mice with LoxP sites flanking exons encoding the critical ATPase domain of ORC1. They show that ORC1 ablation in extraembryonic trophoblasts and hepatocytes failed to impede genome endoreduplication and organ development and function and conclude that ORC1 in mice is essential for mitotic cell divisions but dispensable for endoreduplication. The largest subunit of the origin recognition complex (ORC1) is essential for assembly of the prereplicative complex, firing of DNA replication origins, and faithful duplication of the genome. Here, we generated knock-in mice with LoxP sites flanking exons encoding the critical ATPase domain of ORC1. Global or tissue-specific ablation of ORC1 function in mouse embryo fibroblasts and fetal and adult diploid tissues blocked DNA replication, cell lineage expansion, and organ development. Remarkably, ORC1 ablation in extraembryonic trophoblasts and hepatocytes, two polyploid cell types in mice, failed to impede genome endoreduplication and organ development and function. Thus, ORC1 in mice is essential for mitotic cell divisions but dispensable for endoreduplication. We propose that DNA replication of mammalian polyploid genomes uses a distinct ORC1-independent mechanism.
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Affiliation(s)
- Takayuki Okano-Uchida
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Lindsey N Kent
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Madhu M Ouseph
- Solid Tumor Biology Program, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Britney McCarty
- Solid Tumor Biology Program, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Jeffrey J Frank
- Solid Tumor Biology Program, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Raleigh Kladney
- Solid Tumor Biology Program, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Maria C Cuitino
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - John C Thompson
- Solid Tumor Biology Program, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Vincenzo Coppola
- Solid Tumor Biology Program, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA.,Department of Cancer Biology and Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Maki Asano
- Solid Tumor Biology Program, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA.,Department of Molecular Cellular and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
| | - Gustavo Leone
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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19
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Moreno-Marín N, Merino JM, Alvarez-Barrientos A, Patel DP, Takahashi S, González-Sancho JM, Gandolfo P, Rios RM, Muñoz A, Gonzalez FJ, Fernández-Salguero PM. Aryl Hydrocarbon Receptor Promotes Liver Polyploidization and Inhibits PI3K, ERK, and Wnt/β-Catenin Signaling. iScience 2018; 4:44-63. [PMID: 30240752 PMCID: PMC6147018 DOI: 10.1016/j.isci.2018.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/25/2018] [Accepted: 05/09/2018] [Indexed: 01/02/2023] Open
Abstract
Aryl hydrocarbon receptor (AhR) deficiency alters tissue homeostasis. However, how AhR regulates organ maturation and differentiation remains mostly unknown. Liver differentiation entails a polyploidization process fundamental for cell growth, metabolism, and stress responses. Here, we report that AhR regulates polyploidization during the preweaning-to-adult mouse liver maturation. Preweaning AhR-null (AhR−/−) livers had smaller hepatocytes, hypercellularity, altered cell cycle regulation, and enhanced proliferation. Those phenotypes persisted in adult AhR−/− mice and correlated with compromised polyploidy, predominance of diploid hepatocytes, and enlarged centrosomes. Phosphatidylinositol-3-phosphate kinase (PI3K), extracellular signal-regulated kinase (ERK), and Wnt/β-catenin signaling remained upregulated from preweaning to adult AhR-null liver, likely increasing mammalian target of rapamycin (mTOR) activation. Metabolomics revealed the deregulation of mitochondrial oxidative phosphorylation intermediates succinate and fumarate in AhR−/− liver. Consistently, PI3K, ERK, and Wnt/β-catenin inhibition partially rescued polyploidy in AhR−/− mice. Thus, AhR may integrate survival, proliferation, and metabolism for liver polyploidization. Since tumor cells tend to be polyploid, AhR modulation could have therapeutic value in the liver. AhR is required for liver polyploidization during preweaning-to-adult transition INS-R/PI3K/AKT, ERK, Wnt/β-Cat and mTOR are downregulated during liver polyploidization Reduced polyploidy relates with enhanced mitochondrial metabolism in AhR-null liver Understanding how AhR modulates polyploidy may provide strategies against cancer
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Affiliation(s)
- Nuria Moreno-Marín
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Badajoz 06071, Spain
| | - Jaime M Merino
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Badajoz 06071, Spain
| | - Alberto Alvarez-Barrientos
- Servicio de Técnicas Aplicadas a las Biociencias (STAB), Universidad de Extremadura, Badajoz, Badajoz 06071, Spain
| | - Daxeshkumar P Patel
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shogo Takahashi
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - José M González-Sancho
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, and CIBER de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Pablo Gandolfo
- Cell Signaling Department, CABIMER-CSIC, Sevilla 41092, Spain
| | - Rosa M Rios
- Cell Signaling Department, CABIMER-CSIC, Sevilla 41092, Spain
| | - Alberto Muñoz
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, and CIBER de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Frank J Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro M Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Badajoz, Badajoz 06071, Spain.
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20
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Nucleosomes of polyploid trophoblast giant cells mostly consist of histone variants and form a loose chromatin structure. Sci Rep 2018; 8:5811. [PMID: 29643413 PMCID: PMC5895725 DOI: 10.1038/s41598-018-23832-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/20/2018] [Indexed: 12/31/2022] Open
Abstract
Trophoblast giant cells (TGCs) are one of the cell types that form the placenta and play multiple essential roles in maintaining pregnancy in rodents. TGCs have large, polyploid nuclei resulting from endoreduplication. While previous studies have shown distinct gene expression profiles of TGCs, their chromatin structure remains largely unknown. An appropriate combination of canonical and non-canonical histones, also known as histone variants, allows each cell to exert its cell type-specific functions. Here, we aimed to reveal the dynamics of histone usage and chromatin structure during the differentiation of trophoblast stem cells (TSCs) into TGCs. Although the expression of most genes encoding canonical histones was downregulated, the expression of a few genes encoding histone variants such as H2AX, H2AZ, and H3.3 was maintained at a relatively high level in TGCs. Both the micrococcal nuclease digestion assay and nucleosome stability assay using a microfluidic device indicated that chromatin became increasingly loose as TSCs differentiated. Combinatorial experiments involving H3.3-knockdown and -overexpression demonstrated that variant H3.3 resulted in the formation of loose nucleosomes in TGCs. In conclusion, our study revealed that TGCs possessed loose nucleosomes owing to alterations in their histone composition during differentiation.
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21
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Shu Z, Row S, Deng WM. Endoreplication: The Good, the Bad, and the Ugly. Trends Cell Biol 2018; 28:465-474. [PMID: 29567370 DOI: 10.1016/j.tcb.2018.02.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 01/08/2023]
Abstract
To battle adverse internal and external conditions and maintain homeostasis, diploid organisms employ various cellular processes, such as proliferation and apoptosis. In some tissues, an alternative mechanism, endoreplication, is employed toward similar goals. Endoreplication is an evolutionarily conserved cell cycle program during which cells replicate their genomes without division, resulting in polyploid cells. Importantly, endoreplication is reported to be indispensable for normal development and organ formation across various organisms, from fungi to humans. In recent years, more attention has been drawn to delineating its connections to wound healing and tumorigenesis. In this Review, we discuss mechanisms of endoreplication and polyploidization, their essential and positive roles in normal development and tissue homeostasis, and the relationship between polyploidy and cancer.
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Affiliation(s)
- Zhiqiang Shu
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Sarayu Row
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
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22
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DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression. Genetics 2017; 207:29-47. [PMID: 28874453 PMCID: PMC5586379 DOI: 10.1534/genetics.115.186627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 05/19/2017] [Indexed: 12/11/2022] Open
Abstract
Proper control of DNA replication is critical to ensure genomic integrity during cell proliferation. In addition, differential regulation of the DNA replication program during development can change gene copy number to influence cell size and gene expression. Drosophila melanogaster serves as a powerful organism to study the developmental control of DNA replication in various cell cycle contexts in a variety of differentiated cell and tissue types. Additionally, Drosophila has provided several developmentally regulated replication models to dissect the molecular mechanisms that underlie replication-based copy number changes in the genome, which include differential underreplication and gene amplification. Here, we review key findings and our current understanding of the developmental control of DNA replication in the contexts of the archetypal replication program as well as of underreplication and differential gene amplification. We focus on the use of these latter two replication systems to delineate many of the molecular mechanisms that underlie the developmental control of replication initiation and fork elongation.
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23
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Spradling AC. Polytene Chromosome Structure and Somatic Genome Instability. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:293-304. [PMID: 29167281 DOI: 10.1101/sqb.2017.82.033670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Polytene chromosomes have for 80 years provided the highest resolution view of interphase genome structure in an animal cell nucleus. These chromosomes represent the normal genomic state of nearly all Drosophila larval and many adult cells, and a better understanding of their striking banded structure has been sought for decades. A more recently appreciated characteristic of Drosophila polytene cells is somatic genome instability caused by unfinished replication (UR). Repair of stalled forks generates enough deletions in polytene salivary gland cells to alter 10%-90% of the DNA strands within more than 100 UR regions comprising 20% of the euchromatic genome. We accurately map UR regions and show that most approximate large polytene bands, indicating that replication forks frequently stall near band boundaries in late S phase. Chromosome conformation capture has recently identified dense topologically associated domains (TADs) in many genomes and most UR bands are similar or slightly smaller than a cognate Drosophila TAD. We argue that bands serve the evolutionarily ancient function of coordinating genome replication with local gene activity. We also discuss the relatively recent evolution of polyteny and somatic instability in Diptera and propose that these processes helped propel the amazing success of two-winged flies in becoming the most ecologically diverse insect group, with 200 times the number of species as mammals.
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Affiliation(s)
- Allan C Spradling
- Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, Maryland 21218
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24
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Stormo BM, Fox DT. Polyteny: still a giant player in chromosome research. Chromosome Res 2017; 25:201-214. [PMID: 28779272 PMCID: PMC5768140 DOI: 10.1007/s10577-017-9562-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/17/2022]
Abstract
In this era of high-resolution mapping of chromosome territories, topological interactions, and chromatin states, it is increasingly appreciated that the positioning of chromosomes and their interactions within the nucleus is critical for cellular function. Due to their large size and distinctive structure, polytene chromosomes have contributed a wealth of knowledge regarding chromosome regulation. In this review, we discuss the diversity of polytene chromosomes in nature and in disease, examine the recurring structural features of polytene chromosomes in terms of what they reveal about chromosome biology, and discuss recent advances regarding how polytene chromosomes are assembled and disassembled. After over 130 years of study, these giant chromosomes are still powerful tools to understand chromosome biology.
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Affiliation(s)
- Benjamin M Stormo
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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25
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Guernsey MW, Chuong EB, Cornelis G, Renfree MB, Baker JC. Molecular conservation of marsupial and eutherian placentation and lactation. eLife 2017; 6. [PMID: 28895534 PMCID: PMC5595433 DOI: 10.7554/elife.27450] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/24/2017] [Indexed: 12/18/2022] Open
Abstract
Eutherians are often mistakenly termed 'placental mammals', but marsupials also have a placenta to mediate early embryonic development. Lactation is necessary for both infant and fetal development in eutherians and marsupials, although marsupials have a far more complex milk repertoire that facilitates morphogenesis of developmentally immature young. In this study, we demonstrate that the anatomically simple tammar placenta expresses a dynamic molecular program that is reminiscent of eutherian placentation, including both fetal and maternal signals. Further, we provide evidence that genes facilitating fetal development and nutrient transport display convergent co-option by placental and mammary gland cell types to optimize offspring success.
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Affiliation(s)
- Michael W Guernsey
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Edward B Chuong
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Guillaume Cornelis
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Marilyn B Renfree
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
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26
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Deficient Vitamin E Uptake During Development Impairs Neural Tube Closure in Mice Lacking Lipoprotein Receptor SR-BI. Sci Rep 2017; 7:5182. [PMID: 28701710 PMCID: PMC5507922 DOI: 10.1038/s41598-017-05422-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/30/2017] [Indexed: 12/31/2022] Open
Abstract
SR-BI is the main receptor for high density lipoproteins (HDL) and mediates the bidirectional transport of lipids, such as cholesterol and vitamin E, between these particles and cells. During early development, SR-BI is expressed in extraembryonic tissue, specifically in trophoblast giant cells in the parietal yolk sac. We previously showed that approximately 50% of SR-BI-/- embryos fail to close the anterior neural tube and develop exencephaly, a perinatal lethal condition. Here, we evaluated the role of SR-BI in embryonic vitamin E uptake during murine neural tube closure. Our results showed that SR-BI-/- embryos had a very low vitamin E content in comparison to SR-BI+/+ embryos. Whereas SR-BI-/- embryos with closed neural tubes (nSR-BI-/-) had high levels of reactive oxygen species (ROS), intermediate ROS levels between SR-BI+/+ and nSR-BI-/- embryos were detected in SR-BI-/- with NTD (NTD SR-BI-/-). Reduced expression of Pax3, Alx1 and Alx3 genes was found in NTD SR-BI-/- embryos. Maternal α-tocopherol dietary supplementation prevented NTD almost completely (from 54% to 2%, p < 0.001) in SR-BI-/- embryos and normalized ROS and gene expression levels. In sum, our results suggest the involvement of SR-BI in the maternal provision of embryonic vitamin E to the mouse embryo during neural tube closure.
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27
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Brown SC, Bourge M, Maunoury N, Wong M, Wolfe Bianchi M, Lepers-Andrzejewski S, Besse P, Siljak-Yakovlev S, Dron M, Satiat-Jeunemaître B. DNA Remodeling by Strict Partial Endoreplication in Orchids, an Original Process in the Plant Kingdom. Genome Biol Evol 2017; 9:1051-1071. [PMID: 28419219 PMCID: PMC5546068 DOI: 10.1093/gbe/evx063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA remodeling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analyzed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodeling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome 2C, plus 2-32 additional copies of a complementary part of the genome. The fixed proportion ranged from 89% of the genome in Vanilla mexicana down to 19% in V. pompona, the lowest value for all 148 orchids reported. Insterspecific hybridization did not suppress this phenomenon. Interestingly, this process was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of endocopies present, coherent with high transcription activity in endoreplicated nuclei. Our analyses suggest species-specific chromatin rearrangement. Towards understanding endoreplication, V. planifolia constitutes a tractable system for isolating the genomic sequences that confer an advantage via endoreplication from those that apparently suffice at diploid level.
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Affiliation(s)
- Spencer C. Brown
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nicolas Maunoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Maurice Wong
- Service du Développement Rural, Papeete Tahiti, French Polynesia,
France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | | | - Pascale Besse
- UMR 53, PVBMT Université de la Réunion – Cirad, Pôle de Protection des
Plantes, St Pierre, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech,
Université Paris-Saclay, Orsay Cedex, France
| | - Michel Dron
- Institute of Plant Sciences Paris Saclay IPS2, Université Paris-Sud, CNRS,
INRA, Université Evry, Université Paris Diderot, Sorbonne Paris-Cité, Université
Paris-Saclay, Orsay, France
| | - Béatrice Satiat-Jeunemaître
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
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28
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Abstract
As the ratio of the copy number of the most replicated to the unreplicated regions in the same chromosome, the definition of chromosomal replication complexity (CRC) appears to leave little room for variation, being either two during S-phase or one otherwise. However, bacteria dividing faster than they replicate their chromosome spike CRC to four and even eight. A recent experimental inquiry about the limits of CRC in Escherichia coli revealed two major reasons to avoid elevating it further: (i) increased chromosomal fragmentation and (ii) complications with subsequent double-strand break repair. Remarkably, examples of stable elevated CRC in eukaryotic chromosomes are well known under various terms like "differential replication," "underreplication," "DNA puffs," "onion-skin replication," or "re-replication" and highlight the phenomenon of static replication fork (sRF). To accurately describe the resulting "amplification by overinitiation," I propose a new term: "replification" (subchromosomal overreplication). In both prokaryotes and eukaryotes, replification, via sRF processing, causes double-strand DNA breaks and, with their repair elevating chromosomal rearrangements, represents a novel genome instability factor. I suggest how static replication bubbles could be stabilized and speculate that some tandem duplications represent such persistent static bubbles. Moreover, I propose how static replication bubbles could be transformed into tandem duplications, double minutes, or inverted triplications. Possible experimental tests of these models are discussed.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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29
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Abstract
Evolutionary gene duplication, developmental endoreduplication and selective gene amplification are alternative strategies for increasing gene copy number. When these processes occur together, things get really interesting, and new work shows that is the lifestyle of cells in the placenta.
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Affiliation(s)
- James C Cross
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, T1S 1A2 Canada.
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30
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Bretscher HS, Fox DT. Proliferation of Double-Strand Break-Resistant Polyploid Cells Requires Drosophila FANCD2. Dev Cell 2016; 37:444-57. [PMID: 27270041 PMCID: PMC4901310 DOI: 10.1016/j.devcel.2016.05.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 02/22/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022]
Abstract
Conserved DNA-damage responses (DDRs) sense genome damage and prevent mitosis of broken chromosomes. How cells lacking DDRs cope with broken chromosomes during mitosis is poorly understood. DDRs are frequently inactivated in cells with extra genomes (polyploidy), suggesting that study of polyploidy can reveal how cells with impaired DDRs/genome damage continue dividing. Here, we show that continued division and normal organ development occurs in polyploid, DDR-impaired Drosophila papillar cells. As papillar cells become polyploid, they naturally accumulate broken acentric chromosomes but do not apoptose/arrest the cell cycle. To survive mitosis with acentric chromosomes, papillar cells require Fanconi anemia proteins FANCD2 and FANCI, as well as Blm helicase, but not canonical DDR signaling. FANCD2 acts independently of previous S phases to promote alignment and segregation of acentric DNA produced by double-strand breaks, thus avoiding micronuclei and organ malformation. Because polyploidy and impaired DDRs can promote cancer, our findings provide insight into disease-relevant DNA-damage tolerance mechanisms.
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Affiliation(s)
- Heidi S Bretscher
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, DUMC Box 3813, Durham, NC 27710, USA
| | - Donald T Fox
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, DUMC Box 3813, Durham, NC 27710, USA.
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31
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Stormo BM, Fox DT. Distinct responses to reduplicated chromosomes require distinct Mad2 responses. eLife 2016; 5. [PMID: 27159240 PMCID: PMC4898934 DOI: 10.7554/elife.15204] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/08/2016] [Indexed: 01/17/2023] Open
Abstract
Duplicating chromosomes once each cell cycle produces sister chromatid pairs, which separate accurately at anaphase. In contrast, reduplicating chromosomes without separation frequently produces polytene chromosomes, a barrier to accurate mitosis. Chromosome reduplication occurs in many contexts, including: polytene tissue development, polytene tumors, and following treatment with mitosis-blocking chemotherapeutics. However, mechanisms responding to or resolving polyteny during mitosis are poorly understood. Here, using Drosophila, we uncover two distinct reduplicated chromosome responses. First, when reduplicated polytene chromosomes persist into metaphase, an anaphase delay prevents tissue malformation and apoptosis. Second, reduplicated polytene chromosomes can also separate prior to metaphase through a spindle-independent mechanism termed Separation-Into-Recent-Sisters (SIRS). Both reduplication responses require the spindle assembly checkpoint protein Mad2. While Mad2 delays anaphase separation of metaphase polytene chromosomes, Mad2’s control of overall mitotic timing ensures efficient SIRS. Our results pinpoint mechanisms enabling continued proliferation after genome reduplication, a finding with implications for cancer progression and prevention. DOI:http://dx.doi.org/10.7554/eLife.15204.001 Before a cell divides, it duplicates all its genetic information, which is stored on chromosomes. Then, each chromosome evenly divides into two new cells so that each cell ends up with identical copies of the genetic information. Because the cellular machinery that evenly divides chromosomes is built to recognize chromosomes that were duplicated exactly once, it is important to maintain this pattern of alternating one round of duplication with one round of division. Cells that instead duplicate their chromosomes more than once can make mistakes during division that are associated with diseases such as cancer. Chromosomes with extra duplications are present in normal tissues such as the placenta of mammals. They can also occur in human diseases and may even result from chemotherapy treatment. However, we know almost nothing about how cells respond to these problematic chromosomes when dividing. By studying cells from the Drosophila melanogaster species of fruit fly, Stormo and Fox discovered two distinct ways in which cells respond to extra chromosome duplications. One response occurs in cells that were experimentally engineered to undergo an extra chromosome duplication. These cells delay division so that the chromosome separation machinery can somehow adapt to the challenge of separating more than two chromosome copies at once. The second response occurs in cells that naturally undergo extra chromosome duplications before division. In these cells, Stormo and Fox discovered a new type of chromosome separation, whereby the extra chromosome copies move apart from each other before cell division. In doing so the chromosomes can better interact with the chromosome separation machinery during division. Stormo and Fox also found that a protein named Mad2 is important in both responses, and gives the cell enough time to respond to extra chromosome copies. Without Mad2, the separation of chromosomes with extra duplications is too hasty, and can lead to severe cell division errors and cause organs to form incorrectly. Having uncovered two new responses that cells use to adapt to extra chromosomes, it will now be important to find other proteins like Mad2 that are important in these events. Understanding these processes and the proteins involved in more detail could help to prevent diseases that are associated with extra chromosomes. DOI:http://dx.doi.org/10.7554/eLife.15204.002
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Affiliation(s)
- Benjamin M Stormo
- Department of Cell Biology, Duke University Medical Center, Durham, United States
| | - Donald T Fox
- Department of Cell Biology, Duke University Medical Center, Durham, United States.,Department of Pharamacology and Cancer biology, Duke University Medical Center, Durham, United States
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32
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Affiliation(s)
- Thomas W Glover
- Departments of Human Genetics and Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Departments of Human Genetics and Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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33
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Biron-Shental T, Sharony R, Shtorch-Asor A, Keiser M, Sadeh-Mestechkin D, Laish I, Amiel A. Genomic Alterations Are Enhanced in Placentas from Pregnancies with Fetal Growth Restriction and Preeclampsia: Preliminary Results. Mol Syndromol 2016; 6:276-80. [PMID: 27022328 DOI: 10.1159/000444064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2015] [Indexed: 11/19/2022] Open
Abstract
Fetal growth restriction (FGR) secondary to placental insufficiency and preeclampsia (PE) are associated with substantially increased childhood and adult morbidity and mortality. The long-term outcomes are related to placental aberrations and intrauterine programming. Advances in microarray technology allow high-resolution, genome-wide evaluation for DNA copy number variations - deletions and duplications. The aim of our study was to demonstrate the usefulness of microarray testing in FGR placentas. Using Affymetrix GeneChip for chromosomal microarray (CMA), we analyzed 10 placentas from pregnancies with FGR attributed to placental insufficiency; 5 with FGR below the 5th percentile and 5 from the 5th to <10th percentiles. All fetuses had normal anomaly scans and karyotypes. We also analyzed 5 third-trimester placentas from pregnancies complicated by PE with severe features and 5 from PE without severe features, all with appropriately grown fetuses. The results were compared to 10 placentas from uncomplicated pregnancies with healthy neonates. CMA analysis identified more genomic alterations in FGR (p < 0.05) and in PE (p < 0.05) placentas than in healthy controls. There was a correlation to the severity of FGR and PE. The genomic alterations were below the resolution of normal karyotyping. The altered genes are related to adult human height, stress reactions and to cellular migration, differentiation and adhesion. Though very preliminary, our data support evaluating FGR and PE placentas using CMA. Larger data sets are needed for further evaluation of the findings and their clinical implications.
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Affiliation(s)
- Tal Biron-Shental
- Department of Obstetrics and Gynecology, Meir Medical Center, Kfar Saba, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Reuven Sharony
- Department of Obstetrics and Gynecology, Meir Medical Center, Kfar Saba, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Meirav Keiser
- Genetics Institute, Meir Medical Center, Kfar Saba, Israel
| | - Dana Sadeh-Mestechkin
- Department of Obstetrics and Gynecology, Meir Medical Center, Kfar Saba, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Laish
- Genetics Institute, Meir Medical Center, Kfar Saba, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aliza Amiel
- Genetics Institute, Meir Medical Center, Kfar Saba, Israel; Faculty of Life Science, Bar Ilan University, Ramat Gan, Israel
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34
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Selective Amplification of the Genome Surrounding Key Placental Genes in Trophoblast Giant Cells. Curr Biol 2016; 26:230-236. [PMID: 26774788 DOI: 10.1016/j.cub.2015.11.060] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/10/2015] [Accepted: 11/16/2015] [Indexed: 12/23/2022]
Abstract
While most cells maintain a diploid state, polyploid cells exist in many organisms and are particularly prevalent within the mammalian placenta [1], where they can generate more than 900 copies of the genome [2]. Polyploidy is thought to be an efficient method of increasing the content of the genome by avoiding the costly and slow process of cytokinesis [1, 3, 4]. Polyploidy can also affect gene regulation by amplifying a subset of genomic regions required for specific cellular function [1, 3, 4]. This mechanism is found in the fruit fly Drosophila melanogaster, where polyploid ovarian follicle cells amplify genomic regions containing chorion genes, which facilitate secretion of eggshell proteins [5]. Here, we report that genomic amplification also occurs in mammals at selective regions of the genome in parietal trophoblast giant cells (p-TGCs) of the mouse placenta. Using whole-genome sequencing (WGS) and digital droplet PCR (ddPCR) of mouse p-TGCs, we identified five amplified regions, each containing a gene family known to be involved in mammalian placentation: the prolactins (two clusters), serpins, cathepsins, and the natural killer (NK)/C-type lectin (CLEC) complex [6-12]. We report here the first description of amplification at selective genomic regions in mammals and present evidence that this is an important mode of genome regulation in placental TGCs.
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35
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Kim M, Cooper BA, Venkat R, Phillips JB, Eidem HR, Hirbo J, Nutakki S, Williams SM, Muglia LJ, Capra JA, Petren K, Abbot P, Rokas A, McGary KL. GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. Nucleic Acids Res 2016; 44:D908-16. [PMID: 26567549 PMCID: PMC4702823 DOI: 10.1093/nar/gkv1137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/30/2015] [Accepted: 10/16/2015] [Indexed: 01/24/2023] Open
Abstract
Mammalian gestation and pregnancy are fast evolving processes that involve the interaction of the fetal, maternal and paternal genomes. Version 1.0 of the GEneSTATION database (http://genestation.org) integrates diverse types of omics data across mammals to advance understanding of the genetic basis of gestation and pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans. GEneSTATION is built using tools from the Generic Model Organism Database project, including the biology-aware database CHADO, new tools for rapid data integration, and algorithms that streamline synthesis and user access. GEneSTATION contains curated life history information on pregnancy and reproduction from 23 high-quality mammalian genomes. For every human gene, GEneSTATION contains diverse evolutionary (e.g. gene age, population genetic and molecular evolutionary statistics), organismal (e.g. tissue-specific gene and protein expression, differential gene expression, disease phenotype), and molecular data types (e.g. Gene Ontology Annotation, protein interactions), as well as links to many general (e.g. Entrez, PubMed) and pregnancy disease-specific (e.g. PTBgene, dbPTB) databases. By facilitating the synthesis of diverse functional and evolutionary data in pregnancy-associated tissues and phenotypes and enabling their quick, intuitive, accurate and customized meta-analysis, GEneSTATION provides a novel platform for comprehensive investigation of the function and evolution of mammalian pregnancy.
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Affiliation(s)
- Mara Kim
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Brian A Cooper
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Rohit Venkat
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Julie B Phillips
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Haley R Eidem
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Jibril Hirbo
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Sashank Nutakki
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Scott M Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Louis J Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - J Anthony Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Kenneth Petren
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Kriston L McGary
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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36
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Tuteja G, Chung T, Bejerano G. Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network. Placenta 2015; 37:45-55. [PMID: 26604129 DOI: 10.1016/j.placenta.2015.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Trophoblast invasion establishes adequate blood flow between mother and fetus in early placental development. However, little is known about the cis-regulatory mechanisms underlying this important process. We aimed to identify enhancer elements that are active during trophoblast invasion, and build a trophoblast invasion gene-enhancer network. METHODS We carried out ChIP-Seq for an enhancer-associated mark (H3k27Ac) at two time points during early placental development in mouse. One time point when invasion is at its peak (e7.5) and another time point shortly afterwards (e9.5). We use computational analysis to identify putative enhancers, as well as the transcription factor binding sites within them, that are specific to the time point of trophoblast invasion. RESULTS We compared read profiles at e7.5 and e9.5 to identify 1,977 e7.5-specific enhancers. Within a subset of e7.5-specific enhancers, we discovered a cell migration associated regulatory code, consisting of three transcription factor motifs: AP1, Ets, and Tcfap2. To validate differential expression of the transcription factors that bind these motifs, we performed RNA-Seq in the same context. Finally, we integrated these data with publicly available protein-protein interaction data and constructed a trophoblast invasion gene-enhancer network. DISCUSSION The data we generated and analysis we carried out improves our understanding of the regulatory mechanisms of trophoblast invasion, by suggesting a transcriptional code exists in the enhancers of cell migration genes. Furthermore, the network we constructed highlights novel candidate genes that may be critical for trophoblast invasion.
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Affiliation(s)
- Geetu Tuteja
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Tisha Chung
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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Abstract
The placenta sits at the interface between the maternal and fetal vascular beds where it mediates nutrient and waste exchange to enable in utero existence. Placental cells (trophoblasts) accomplish this via invading and remodeling the uterine vasculature. Amazingly, despite being of fetal origin, trophoblasts do not trigger a significant maternal immune response. Additionally, they maintain a highly reliable hemostasis in this extremely vascular interface. Decades of research into how the placenta differentiates itself from embryonic tissues to accomplish these and other feats have revealed a previously unappreciated level of complexity with respect to the placenta's cellular composition. Additionally, novel insights with respect to roles played by the placenta in guiding fetal development and metabolism have sparked a renewed interest in understanding the interrelationship between fetal and placental well-being. Here, we present an overview of emerging research in placental biology that highlights these themes and the importance of the placenta to fetal and adult health.
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Abstract
Polyploid cells, which contain more than two genome copies, occur throughout nature. Beyond well-established roles in increasing cell size/metabolic output, polyploidy can also promote nonuniform genome, transcriptome, and metabolome alterations. Polyploidy also frequently confers resistance to environmental stresses not tolerated by diploid cells. Recent progress has begun to unravel how this fascinating phenomenon contributes to normal physiology and disease.
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Affiliation(s)
- Kevin P Schoenfelder
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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Abstract
Polyploidy is defined as an increase in genome DNA content. Throughout the plant and animal kingdoms specific cell types become polyploid as part of their differentiation programs. When this occurs in subsets of tissues within an organism it is termed somatic polyploidy, because it is distinct from the increase in ploidy that is inherited through the germline and present in every cell type of the organism. Germline polyploidy is common in plants and occurs in some animals, such as amphibians, but will not be discussed further here. Somatic polyploid cells can be mononucleate or multinucleate, and the replicated sister chromatids can remain attached and aligned, producing polytene chromosomes, or they can be dispersed (Figure 1). In this Primer, we focus on why somatic polyploidy occurs and how cells become polyploid — the first of these issues being more speculative, given the status of the field.
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Nordman JT, Orr-Weaver TL. Understanding replication fork progression, stability, and chromosome fragility by exploiting the Suppressor of Underreplication protein. Bioessays 2015; 37:856-61. [PMID: 26059810 DOI: 10.1002/bies.201500021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
There are many layers of regulation governing DNA replication to ensure that genetic information is accurately transmitted from mother cell to daughter cell. While much of the control occurs at the level of origin selection and firing, less is known about how replication fork progression is controlled throughout the genome. In Drosophila polytene cells, specific regions of the genome become repressed for DNA replication, resulting in underreplication and decreased copy number. Importantly, underreplicated domains share properties with common fragile sites. The Suppressor of Underreplication protein SUUR is essential for this repression. Recent work established that SUUR functions by directly inhibiting replication fork progression, raising several interesting questions as to how replication fork progression and stability can be modulated within targeted regions of the genome. Here we discuss potential mechanisms by which replication fork inhibition can be achieved and the consequences this has on genome stability and copy number control.
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Affiliation(s)
- Jared T Nordman
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Terry L Orr-Weaver
- Department of Biology, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
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Meinhardt G, Kaltenberger S, Fiala C, Knöfler M, Pollheimer J. ERBB2 gene amplification increases during the transition of proximal EGFR(+) to distal HLA-G(+) first trimester cell column trophoblasts. Placenta 2015; 36:803-8. [PMID: 26071215 DOI: 10.1016/j.placenta.2015.05.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2015] [Accepted: 05/27/2015] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Although, DNA copy-number alterations (CNAs) have been well documented in a number of adverse phenotypic conditions, accumulating data suggest that CNAs also occur during physiological processes. Interestingly, extravillous trophoblasts induce the expression of the transforming, proto-oncogene ERBB2, which is frequently amplified in human cancer. However, no data are available to address whether trophoblast-related ERBB2 expression might also be linked to genomic amplification. METHODS Dual color silver as well as fluorescence in situ hybridization analyses were carried out to evaluate frequency and degree of ERBB2 gene and chromosome 17 copy numbers in first trimester placental cell columns and isolated trophoblasts. Proliferative EGFR(+) and differentiated HLA-G(+) trophoblasts were identified or separated by means of in situ immunofluorescence co-stainings and magnetic beads cell isolation, respectively. RESULTS ERBB2 gene amplification is detected in approximately 40% of isolated HLA-G(+) trophoblasts. Although already detectable in EGFR(+) cells, the percentage and extent of ERBB2 amplification was markedly increased in HLA-G(+) trophoblasts in situ and after isolation. Accordingly, HLA-G(+) trophoblasts highly express ERBB2 on protein level. Finally, ERBB2 copy number variations occur independently of aneuploidy as the majority of ERBB2 amplifying cells were cytogenetically diploid for chromosome 17. DISCUSSION ERBB2 gene amplification is a frequent event during EVT differentiation. This finding challenges the long standing paradigm, which associates gene amplification with pathological conditions and further supports recent evidences suggesting that CNAs are a normal feature of developmental processes.
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Affiliation(s)
- G Meinhardt
- Department of Obstetrics and Fetal-Maternal Medicine, Reproductive Biology Unit, Medical University of Vienna, Austria
| | - S Kaltenberger
- Clinical Institute of Pathology, Medical University of Vienna, Austria
| | - C Fiala
- Gynmed Clinic, Vienna, Austria
| | - M Knöfler
- Department of Obstetrics and Fetal-Maternal Medicine, Reproductive Biology Unit, Medical University of Vienna, Austria
| | - J Pollheimer
- Department of Obstetrics and Fetal-Maternal Medicine, Reproductive Biology Unit, Medical University of Vienna, Austria.
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Haplotype phasing and inheritance of copy number variants in nuclear families. PLoS One 2015; 10:e0122713. [PMID: 25853576 PMCID: PMC4390228 DOI: 10.1371/journal.pone.0122713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.
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Kasak L, Rull K, Vaas P, Teesalu P, Laan M. Extensive load of somatic CNVs in the human placenta. Sci Rep 2015; 5:8342. [PMID: 25666259 PMCID: PMC4914949 DOI: 10.1038/srep08342] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/15/2015] [Indexed: 11/09/2022] Open
Abstract
Placenta is a temporary, but indispensable organ in mammalian pregnancy. From its basic nature, it exhibits highly invasive tumour-like properties facilitating effective implantation through trophoblast cell proliferation and migration, and a critical role in pregnancy success. We hypothesized that similarly to cancer, somatic genomic rearrangements are promoted in the support of placental function. Here we present the first profiling of copy number variations (CNVs) in human placental genomes, showing an extensive load of somatic CNVs, especially duplications and suggesting that this phenomenon may be critical for normal gestation. Placental somatic CNVs were significantly enriched in genes involved in cell adhesion, immunity, embryonic development and cell cycle. Overrepresentation of imprinted genes in somatic duplications suggests that amplified gene copies may represent an alternative mechanism to support parent-of-origin specific gene expression. Placentas from pregnancy complications exhibited significantly altered CNV profile compared to normal gestations, indicative to the clinical implications of the study.
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Affiliation(s)
- Laura Kasak
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
| | - Kristiina Rull
- 1] Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia [2] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [3] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Vaas
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Teesalu
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
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Yarosh W, Spradling AC. Incomplete replication generates somatic DNA alterations within Drosophila polytene salivary gland cells. Genes Dev 2014; 28:1840-55. [PMID: 25128500 PMCID: PMC4197960 DOI: 10.1101/gad.245811.114] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA replication remains unfinished in many Drosophila polyploid cells, which harbor disproportionately fewer copies of late-replicating chromosomal regions. Using NextGen sequencing of DNA from giant polytene cells of the larval salivary gland, Yarosh and Spradling show that sporadic, incomplete replication during the endocycle S phase alters the Drosophila genome at thousands of sites that differ in every cell; similar events occur in the ovary. The authors propose that the extensive somatic DNA instability described here underlies position effect variegation and molds the structure of polytene chromosomes. DNA replication remains unfinished in many Drosophila polyploid cells, which harbor disproportionately fewer copies of late-replicating chromosomal regions. By analyzing paired-end high-throughput sequence data from polytene larval salivary gland cells, we define 112 underreplicated (UR) euchromatic regions 60–480 kb in size. To determine the effects of underreplication on genome integrity, we analyzed anomalous read pairs and breakpoint reads throughout the euchromatic genome. Each UR euchromatic region contains many different deletions 10–500 kb in size, while very few deletions are present in fully replicated chromosome regions or UR zones from embryo DNA. Thus, during endocycles, stalled forks within UR regions break and undergo local repair instead of remaining stable and generating nested forks. As a result, each salivary gland cell contains hundreds of unique deletions that account for their copy number reductions. Similar UR regions and deletions were observed in ovarian DNA, suggesting that incomplete replication, fork breakage, and repair occur widely in polytene cells. UR regions are enriched in genes encoding immunoglobulin superfamily proteins and contain many neurally expressed and homeotic genes. We suggest that the extensive somatic DNA instability described here underlies position effect variegation, molds the structure of polytene chromosomes, and should be investigated for possible functions.
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Affiliation(s)
- Will Yarosh
- Howard Hughes Medical Institute, Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Allan C Spradling
- Howard Hughes Medical Institute, Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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Cross JC. More of a good thing or less of a bad thing: gene copy number variation in polyploid cells of the placenta. PLoS Genet 2014; 10:e1004330. [PMID: 24784435 PMCID: PMC4006710 DOI: 10.1371/journal.pgen.1004330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- James C. Cross
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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