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Flowers AE, Gonzalez TL, Wang Y, Santiskulvong C, Clark EL, Novoa A, Jefferies CA, Lawrenson K, Chan JL, Joshi NV, Zhu Y, Tseng HR, Wang ET, Ishimori M, Karumanchi SA, Williams J, Pisarska MD. High-throughput mRNA sequencing of human placenta shows sex differences across gestation. Placenta 2024; 150:8-21. [PMID: 38537412 DOI: 10.1016/j.placenta.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 05/04/2024]
Abstract
INTRODUCTION Fetal sex affects fetal and maternal health outcomes in pregnancy, but this connection remains poorly understood. As the placenta is the route of fetomaternal communication and derives from the fetal genome, placental gene expression sex differences may explain these outcomes. OBJECTIVES We utilized next generation sequencing to study the normal human placenta in both sexes in first and third trimester to generate a normative transcriptome based on sex and gestation. STUDY DESIGN We analyzed 124 first trimester (T1, 59 female and 65 male) and 43 third trimester (T3, 18 female and 25 male) samples for sex differences within each trimester and sex-specific gestational differences. RESULTS Placenta shows more significant sexual dimorphism in T1, with 94 T1 and 26 T3 differentially expressed genes (DEGs). The sex chromosomes contributed 60.6% of DEGs in T1 and 80.8% of DEGs in T3, excluding X/Y pseudoautosomal regions. There were 6 DEGs from the pseudoautosomal regions, only significant in T1 and all upregulated in males. The distribution of DEGs on the X chromosome suggests genes on Xp (the short arm) may be particularly important in placental sex differences. Dosage compensation analysis of X/Y homolog genes shows expression is primarily contributed by the X chromosome. In sex-specific analyses of first versus third trimester, there were 2815 DEGs common to both sexes upregulated in T1, and 3263 common DEGs upregulated in T3. There were 7 female-exclusive DEGs upregulated in T1, 15 female-exclusive DEGs upregulated in T3, 10 male-exclusive DEGs upregulated in T1, and 20 male-exclusive DEGs upregulated in T3. DISCUSSION This is the largest cohort of placentas across gestation from healthy pregnancies defining the normative sex dimorphic gene expression and sex common, sex specific and sex exclusive gene expression across gestation. The first trimester has the most sexually dimorphic transcripts, and the majority were upregulated in females compared to males in both trimesters. The short arm of the X chromosome and the pseudoautosomal region is particularly critical in defining sex differences in the first trimester placenta. As pregnancy is a dynamic state, sex specific DEGs across gestation may contribute to sex dimorphic changes in overall outcomes.
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Affiliation(s)
- Amy E Flowers
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Tania L Gonzalez
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Yizhou Wang
- Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Chintda Santiskulvong
- CS Cancer Applied Genomics Shared Resource, CS Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Ekaterina L Clark
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Allynson Novoa
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Caroline A Jefferies
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Kate Lawrenson
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica L Chan
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Nikhil V Joshi
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Yazhen Zhu
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA; California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Erica T Wang
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mariko Ishimori
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - S Ananth Karumanchi
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - John Williams
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Margareta D Pisarska
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.
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Affiliation(s)
| | - Brandon D. Pickett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Monika Cechova
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Karol Pal
- Penn State University, University Park, PA, USA
| | - Sergey Nurk
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - DongAhn Yoo
- University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Johns Hopkins University, Baltimore, MD, USA
| | - Prajna Hebbar
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | | | | | - Erich Bomberg
- University of Münster, Münster, Germany
- MPI for Developmental Biology, Tübingen, Germany
| | - Gerard G. Bouffard
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelise Y. Brooks
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Carbone
- Oregon Health & Science University, Portland, OR, USA
- Oregon National Primate Research Center, Hillsboro, OR, USA
| | - Laura Carrel
- Penn State University School of Medicine, Hershey, PA, USA
| | | | | | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | | | | | | | - Mark Diekhans
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Amalia Dutra
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gage H. Garcia
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Glenn Hickey
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - David A. Hillis
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Hyeonsoo Jeong
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benedict Paten
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Arang Rhie
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | | | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | - Steven J. Solar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sweetalana
- Penn State University, University Park, PA, USA
| | - Alex Sweeten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Alice C. Young
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xinru Zhang
- Penn State University, University Park, PA, USA
| | | | | | | | - Soojin V. Yi
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Evan Eichler
- University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Kim H, Choo H, Cha J, Jang M, Son J, Jeong T, Choi BH, Lim Y, Chai HH, Lee J, Lim D, Shin D, Park W, Park JE. Blood transcriptome comparison between sexes and their function in 4-week Rhode Island red chickens. Anim Cells Syst (Seoul) 2022; 26:358-368. [PMID: 36605592 PMCID: PMC9809412 DOI: 10.1080/19768354.2022.2146187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sex is a major biological factor in the development and physiology of a sexual reproductive organism, and its role in the growing process is needed to be investigated in various species. We compare blood transcriptome between 5 males and 5 females in 4-week-old Rhode Island Red chickens and perform functional annotation of differentially expressed genes (DEGs). The results are as follows. 141 and 109 DEGs were located in autosomes and sex chromosomes, respectively. The gene ontology (GO) terms are significantly (p < 0.05) enriched, which were limb development, inner ear development, positive regulation of dendrite development, the KEGG pathway the TGF-beta signaling pathway, and melanogenesis (p < 0.05). These pathways are related to morphological maintenance and growth of the tissues. In addition, the SMAD2W and the BMP5 were involved in the TGF-beta signaling pathway, and both play an important role in maintaining tissue development. The major DEGs related to the development of neurons and synapses include the up-regulated NRN1, GDF10, SLC1A1, BMP5, NBEA, and NRXN1. Also, 7 DEGs were validated using RT-qPCR with high correlation (r 2 = 0.74). In conclusion, the differential expression of blood tissue in the early growing chicken was enriched in TGF-beta signaling and related to the development of neurons and synapses including SMAD2W and BMP5. These results suggest that blood in the early growing stage is differentially affected in tissue development, nervous system, and pigmentation by sex. For future research, experimental characterization of DEGs and a holistic investigation of various tissues and growth stages will be required.
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Affiliation(s)
- Hana Kim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Hyojun Choo
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang, Korea
| | - Jihye Cha
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Myoungjin Jang
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Juhwan Son
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Taejoon Jeong
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Bong-Hwan Choi
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Youngjo Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Han-Ha Chai
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, Korea
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Korea
| | - Woncheoul Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
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