1
|
Galy B, Conrad M, Muckenthaler M. Mechanisms controlling cellular and systemic iron homeostasis. Nat Rev Mol Cell Biol 2024; 25:133-155. [PMID: 37783783 DOI: 10.1038/s41580-023-00648-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2023] [Indexed: 10/04/2023]
Abstract
In mammals, hundreds of proteins use iron in a multitude of cellular functions, including vital processes such as mitochondrial respiration, gene regulation and DNA synthesis or repair. Highly orchestrated regulatory systems control cellular and systemic iron fluxes ensuring sufficient iron delivery to target proteins is maintained, while limiting its potentially deleterious effects in iron-mediated oxidative cell damage and ferroptosis. In this Review, we discuss how cells acquire, traffick and export iron and how stored iron is mobilized for iron-sulfur cluster and haem biogenesis. Furthermore, we describe how these cellular processes are fine-tuned by the combination of various sensory and regulatory systems, such as the iron-regulatory protein (IRP)-iron-responsive element (IRE) network, the nuclear receptor co-activator 4 (NCOA4)-mediated ferritinophagy pathway, the prolyl hydroxylase domain (PHD)-hypoxia-inducible factor (HIF) axis or the nuclear factor erythroid 2-related factor 2 (NRF2) regulatory hub. We further describe how these pathways interact with systemic iron homeostasis control through the hepcidin-ferroportin axis to ensure appropriate iron fluxes. This knowledge is key for the identification of novel therapeutic opportunities to prevent diseases of cellular and/or systemic iron mismanagement.
Collapse
Affiliation(s)
- Bruno Galy
- German Cancer Research Center (DKFZ), Division of Virus-associated Carcinogenesis (F170), Heidelberg, Germany
| | - Marcus Conrad
- Helmholtz Zentrum München, Institute of Metabolism and Cell Death, Neuherberg, Germany
| | - Martina Muckenthaler
- Department of Paediatric Hematology, Oncology and Immunology, University of Heidelberg, Heidelberg, Germany.
- Molecular Medicine Partnership Unit, University of Heidelberg, Heidelberg, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany.
| |
Collapse
|
2
|
Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet 2024; 56:258-272. [PMID: 38200130 PMCID: PMC11005318 DOI: 10.1038/s41588-023-01626-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.
Collapse
Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Xie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Human Phenome Institute, School of Life Science, Fudan University, Shanghai, China
| | - Joshua Saskin
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Chao Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN); Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Elena Oancea
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
3
|
Holst JD, Murphy LG, Gorman MJ, Ragan EJ. Comparison of insect and human cytochrome b561 proteins: Insights into candidate ferric reductases in insects. PLoS One 2023; 18:e0291564. [PMID: 38039324 PMCID: PMC10691727 DOI: 10.1371/journal.pone.0291564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/19/2023] [Indexed: 12/03/2023] Open
Abstract
Cytochrome b561 (cytb561) proteins comprise a family of transmembrane oxidoreductases that transfer single electrons across a membrane. Most eukaryotic species, including insects, possess multiple cytb561 homologs. To learn more about this protein family in insects, we carried out a bioinformatics-based investigation of cytb561 family members from nine species representing eight insect orders. We performed a phylogenetic analysis to classify insect cytb561 ortholog groups. We then conducted sequence analyses and analyzed protein models to predict structural elements that may impact the biological functions and localization of these proteins, with a focus on possible ferric reductase activity. Our study revealed three ortholog groups, designated CG1275, Nemy, and CG8399, and a fourth group of less-conserved genes. We found that CG1275 and Nemy proteins are similar to a human ferric reductase, duodenal cytochrome b561 (Dcytb), and have many conserved amino acid residues that function in substrate binding in Dcytb. Notably, CG1275 and Nemy proteins contain a conserved histidine and other residues that play a role in ferric ion reduction by Dcytb. Nemy proteins were distinguished by a novel cysteine-rich cytoplasmic loop sequence. CG8399 orthologs are similar to a putative ferric reductase in humans, stromal cell-derived receptor 2. Like other members of the CYBDOM class of cytb561 proteins, these proteins contain reeler, DOMON, and cytb561 domains. Drosophila melanogaster CG8399 is the only insect cytb561 with known ferric reductase activity. Our investigation of the DOMON domain in CG8399 proteins revealed a probable heme-binding site and a possible site for ferric reduction. The fourth group includes a subgroup of proteins with a conserved "KXXXXKXH" non-cytoplasmic loop motif that may be a substrate binding site and is present in a potential ferric reductase, human tumor suppressor cytochrome b561. This study provides a foundation for future investigations of the biological functions of cytb561 genes in insects.
Collapse
Affiliation(s)
- Jessica D. Holst
- Department of Chemistry and Biochemistry, Metropolitan State University of Denver, Denver, Colorado, United States of America
| | - Laura G. Murphy
- Department of Chemistry and Biochemistry, Metropolitan State University of Denver, Denver, Colorado, United States of America
| | - Maureen J. Gorman
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
| | - Emily J. Ragan
- Department of Chemistry and Biochemistry, Metropolitan State University of Denver, Denver, Colorado, United States of America
| |
Collapse
|
4
|
Shi Y, Guo Y, Zhou J, Cui G, Cheng J, Wu Y, Zhao Y, Fang L, Han X, Yang Y, Sun Y. A spatiotemporal gene expression and cell atlases of the developing rat ovary. Cell Prolif 2023; 56:e13516. [PMID: 37309718 PMCID: PMC10693188 DOI: 10.1111/cpr.13516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023] Open
Abstract
Normal ovarian development is necessary for the production of healthy oocytes. However, the characteristics of oocytes development at different stages and the regulatory relationship between oocytes and somatic cells remain to be fully explained. Here, we combined scRNA-seq and spatial transcriptomic sequencing to profile the transcriptomic atlas of developing ovarian of the rat. We identified four components from developing granulosa cells including cumulus, primitive, mural, and luteal cells, and constructed their differential transcriptional regulatory networks. Several novel growth signals from oocytes to cumulus cells were identified, such as JAG1-NOTCH2 and FGF9-FGFR2. Moreover, we observed three cumulus sequential phases during follicle development determined by the key transcriptional factors in each cumulus phase (Bckaf1, Gata6, Cebpb, etc.), as well as the potential pinpointed roles of macrophages in luteal regression. Altogether, the single-cell spatial transcriptomic profile of the ovary provides not only a new research dimension for temporal and spatial analysis of ovary development, but also valuable data resources and a research basis for in-depth excavation of the mechanisms of mammalian ovary development.
Collapse
Affiliation(s)
- Yong Shi
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- Academy of medical sciencesZhengzhou UniversityZhengzhouChina
| | - Yanjie Guo
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jiayi Zhou
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guanshen Cui
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
| | - Jung‐Chien Cheng
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Ying Wu
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yong‐Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lanlan Fang
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xiao Han
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
| | - Yun‐Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
- China National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Institute of Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
| | - Yingpu Sun
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive MedicineThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| |
Collapse
|
5
|
Yu T, Xu-Monette ZY, Yu L, Li Y, Young KH. Mechanisms of ferroptosis and targeted therapeutic approaches in lymphoma. Cell Death Dis 2023; 14:771. [PMID: 38007476 PMCID: PMC10676406 DOI: 10.1038/s41419-023-06295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Lymphoma is the sixth most common type of cancer worldwide. Under the current treatment standards, patients with lymphoma often fail to respond to treatment or relapse early and require further therapy. Hence, novel therapeutic strategies need to be explored and our understanding of the molecular underpinnings of lymphomas should be expanded. Ferroptosis, a non-apoptotic regulated cell death, is characterized by increased reactive oxygen species and lipid peroxidation due to metabolic dysfunction. Excessive or lack of ferroptosis has been implicated in tumor development. Current preclinical evidences suggest that ferroptosis participates in tumorigenesis, progression, and drug resistance of lymphoma, identifying a potential biomarker and an attractive molecular target. Our review summarizes the core mechanisms and regulatory networks of ferroptosis and discusses existing evidences of ferroptosis induction for the treatment of lymphoma, with intent to provide a framework for understanding the role of ferroptosis in lymphomagenesis and a new perspective of lymphoma treatment.
Collapse
Affiliation(s)
- Tiantian Yu
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, USA
- Department of Hematology and Oncology, The Second Affiliated Hospital of NanChang University, Nanchang, China
| | - Zijun Y Xu-Monette
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Li Yu
- Department of Hematology and Oncology, The Second Affiliated Hospital of NanChang University, Nanchang, China
| | - Yong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Ken H Young
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, USA.
- Duke Cancer Institute, Durham, NC, USA.
| |
Collapse
|
6
|
Zhou X, Guo X, Han J, Wang M, Liu Z, Ren D, Zhao J, Li Z. Cytochrome b561 regulates iron metabolism by activating the Akt/mTOR pathway to promote Breast Cancer Cells proliferation. Exp Cell Res 2023; 431:113760. [PMID: 37634562 DOI: 10.1016/j.yexcr.2023.113760] [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: 06/25/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Breast cancer (BC) is the leading cause of cancer-related mortality in women, necessitating the development of novel therapeutic targets. While cytochrome b561 (CYB561) expression is associated with poor prognosis in BC, the precise role of CYB561 in BC and its potential mechanisms remain unclear. In the present study, we found that CYB561 plays an essential role in BC growth. CYB561 expression was up-regulated in surgically resected cancerous tissues and in six BC cell lines. Lentivirus-mediated CYB561 knockdown in BC cells significantly reduced their proliferation, migration, and invasiveness. CYB561 participates in the regulation of iron metabolism in BC. CYB561 knockdown reduced total iron content, increased ferrous iron content, and down-regulated the expression of proteins associated with iron metabolism (transferrin receptor 1, divalent metal transporter 1, and ferritin heavy chain 1). Conversely, up-regulation of CYB561 through co-incubation with exogenous iron (ferric ammonium citrate) produced contrary outcomes. Additionally, CYB561 activated the protein kinase B/mammalian target of rapamycin (Akt/mTOR) signaling pathway in BC cells. Down-regulation of CYB561 expression inhibited the Akt/mTOR signaling pathway activity. The application of an mTOR agonist (MHY1485) rescued this negative effect, as well as the inhibitory effect of CYB561 knockdown on cell proliferation. Importantly, the dual mTOR inhibitor MLN0128 (50 nM, 48 h) down-regulated CYB561 expression and the iron metabolism-related proteins transferrin receptor, divalent metal transporter 1, and ferritin heavy chain 1, whereas the mTOR agonist MHY1485 rescued the down-regulation of CYB561 knockdown on iron metabolism-related proteins. We conclude that CYB561 promotes the proliferation of BC cells by regulating iron metabolism through the activation of the Akt/mTOR signaling pathway.
Collapse
Affiliation(s)
- Xiaofeng Zhou
- Research Center for High Altitude Medicine, Qinghai University, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Xining, 810001, China; Pathology Department, Affiliated Hospital of Qinghai University, Xining, 810001, China
| | - Xinjian Guo
- Pathology Department, Affiliated Hospital of Qinghai University, Xining, 810001, China
| | - Jingqi Han
- Pathology Department, Affiliated Hospital of Qinghai University, Xining, 810001, China
| | - Miaozhou Wang
- Research Center for High Altitude Medicine, Qinghai University, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Xining, 810001, China; Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Xining, 810001, China
| | - Zhen Liu
- Research Center for High Altitude Medicine, Qinghai University, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Xining, 810001, China; Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Xining, 810001, China
| | - Dengfeng Ren
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Xining, 810001, China
| | - Jiuda Zhao
- Research Center for High Altitude Medicine, Qinghai University, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Xining, 810001, China; Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Xining, 810001, China.
| | - Zhanquan Li
- Research Center for High Altitude Medicine, Qinghai University, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Xining, 810001, China; Department of Hematopathology, Affiliated Hospital of Qinghai University, Xining, 810001, China.
| |
Collapse
|
7
|
Zhou C, Huang H, Wang Y, Sendinc E, Shi Y. Selective regulation of tuft cell-like small cell lung cancer by novel transcriptional co-activators C11orf53 and COLCA2. Cell Discov 2022; 8:112. [PMID: 36253350 PMCID: PMC9576728 DOI: 10.1038/s41421-022-00470-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/13/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Chen Zhou
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.,Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Hui Huang
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Yunyi Wang
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Erdem Sendinc
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Shi
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK. .,Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
8
|
Guan D, Halstead MM, Islas-Trejo AD, Goszczynski DE, Cheng HH, Ross PJ, Zhou H. Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing. Front Genet 2022; 13:997460. [PMID: 36246588 PMCID: PMC9561881 DOI: 10.3389/fgene.2022.997460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 11/22/2022] Open
Abstract
To identify and annotate transcript isoforms in the chicken genome, we generated Nanopore long-read sequencing data from 68 samples that encompassed 19 diverse tissues collected from experimental adult male and female White Leghorn chickens. More than 23.8 million reads with mean read length of 790 bases and average quality of 18.2 were generated. The annotation and subsequent filtering resulted in the identification of 55,382 transcripts at 40,547 loci with mean length of 1,700 bases. We predicted 30,967 coding transcripts at 19,461 loci, and 16,495 lncRNA transcripts at 15,512 loci. Compared to existing reference annotations, we found ∼52% of annotated transcripts could be partially or fully matched while ∼47% were novel. Seventy percent of novel transcripts were potentially transcribed from lncRNA loci. Based on our annotation, we quantified transcript expression across tissues and found two brain tissues (i.e., cerebellum and cortex) expressed the highest number of transcripts and loci. Furthermore, ∼22% of the transcripts displayed tissue specificity with the reproductive tissues (i.e., testis and ovary) exhibiting the most tissue-specific transcripts. Despite our wide sampling, ∼20% of Ensembl reference loci were not detected. This suggests that deeper sequencing and additional samples that include different breeds, cell types, developmental stages, and physiological conditions, are needed to fully annotate the chicken genome. The application of Nanopore sequencing in this study demonstrates the usefulness of long-read data in discovering additional novel loci (e.g., lncRNA loci) and resolving complex transcripts (e.g., the longest transcript for the TTN locus).
Collapse
Affiliation(s)
- Dailu Guan
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Michelle M. Halstead
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Alma D. Islas-Trejo
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Daniel E. Goszczynski
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Hans H. Cheng
- USDA, ARS, USNPRC, Avian Disease and Oncology Laboratory, East Lansing, MI, United States
| | - Pablo J. Ross
- Department of Animal Science, University of California Davis, Davis, CA, United States
- *Correspondence: Pablo J. Ross, ; Huaijun Zhou,
| | - Huaijun Zhou
- Department of Animal Science, University of California Davis, Davis, CA, United States
- *Correspondence: Pablo J. Ross, ; Huaijun Zhou,
| |
Collapse
|
9
|
Ni S, Yuan Y, Song S, Li X. A double-edged sword with a therapeutic target: iron and ferroptosis in immune regulation. Nutr Rev 2022; 81:587-596. [PMID: 36130411 DOI: 10.1093/nutrit/nuac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cellular activities such as DNA synthesis, adenosine triphosphate production, and mitochondrial respiration are affected by iron metabolism. Disturbance of iron homeostasis usually leads to damage in cells and organs in the context of iron overload or deficiency. Thus, iron, a key regulator in nutritional immunity, was shown to be critical in innate and adaptive immunity. Unlike apoptosis, ferroptosis, a feature of iron-dependent lipid peroxidation, is thought to be associated with immune regulation because of its immunogenic nature. In this review, we summarize the role of iron and ferroptosis in immune regulation and discuss their therapeutic potential in the treatment of arthropathies like osteoarthritis and rheumatoid arthritis.
Collapse
Affiliation(s)
- Shuo Ni
- Department of Orthopedic Surgery and Shanghai Institute of Microsurgery on Extremities, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yin Yuan
- the State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shangdao Song
- the Department of Rehabilitation Medicine, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaolin Li
- the Department of Orthopedic Surgery and Shanghai Institute of Microsurgery on Extremities, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| |
Collapse
|
10
|
Unlu G, Prizer B, Erdal R, Yeh HW, Bayraktar EC, Birsoy K. Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability. Mol Cell 2022; 82:2832-2843.e7. [PMID: 35714613 PMCID: PMC9356996 DOI: 10.1016/j.molcel.2022.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/14/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
Abstract
Iron is the most abundant transition metal essential for numerous cellular processes. Although most mammalian cells acquire iron through transferrin receptors, molecular players of iron utilization under iron restriction are incompletely understood. To address this, we performed metabolism-focused CRISPRa gain-of-function screens, which revealed metabolic limitations under stress conditions. Iron restriction screens identified not only expected members of iron utilization pathways but also SLCO2B1, a poorly characterized membrane carrier. SLCO2B1 expression is sufficient to increase intracellular iron, bypass the essentiality of the transferrin receptor, and enable proliferation under iron restriction. Mechanistically, SLCO2B1 mediates heme analog import in cellular assays. Heme uptake by SLCO2B1 provides sufficient iron for proliferation through heme oxygenases. Notably, SLCO2B1 is predominantly expressed in microglia in the brain, and primary Slco2b1-/- mouse microglia exhibit strong defects in heme analog import. Altogether, our work identifies SLCO2B1 as a microglia-enriched plasma membrane heme importer and provides a genetic platform to identify metabolic limitations under stress conditions.
Collapse
Affiliation(s)
- Gokhan Unlu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Benjamin Prizer
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Ranya Erdal
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY 10065, USA; Medical Scientist Training Program, Hacettepe University Faculty of Medicine, Ankara 06230, Turkey
| | - Hsi-Wen Yeh
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Erol C Bayraktar
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
11
|
Lysosomal iron recycling in mouse macrophages is dependent upon both LcytB and Steap3 reductases. Blood Adv 2022; 6:1692-1707. [PMID: 34982827 PMCID: PMC8941456 DOI: 10.1182/bloodadvances.2021005609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023] Open
Abstract
Iron that is stored in macrophages as ferritin can be made bioavailable by degrading ferritin in the lysosome and releasing iron back into the cytosol. Iron stored in ferritin is found as Fe3+ and must be reduced to Fe2+ before it can be exported from the lysosome. Here we report that the lysosomal reductase Cyb561a3 (LcytB) and the endosomal reductase six-transmembrane epithelial antigen of prostate 3 (Steap3) act as lysosomal ferrireductases in the mouse macrophage cell line RAW264.7 converting Fe3+ to Fe2+ for iron recycling. We determined that when lysosomes were loaded with horse cationic ferritin, reductions or loss of LcytB or Steap3 using CRISPR/Cas9-mediated knockout technology resulted in decreased lysosomal iron export. Loss of both reductases was additive in decreasing lysosomal iron export. Decreased reductase activity resulted in increased transcripts for iron acquisition proteins DMT1 and transferrin receptor 1 (Tfrc1) suggesting that cells were iron limited. We show that transcript expression of LcytB and Steap3 is decreased in macrophages exposed to Escherichia coli pathogen UTI89, which supports a role for these reductases in regulating iron availability for pathogens. We further show that loss of LcytB and Steap3 in macrophages infected with UTI89 led to increased proliferation of intracellular UTI89 suggesting that the endolysosomal system is retaining Fe3+ that can be used for proliferation of intravesicular pathogens. Together, our findings reveal an important role for both LcytB and Steap3 in macrophage iron recycling and suggest that limiting iron recycling by decreasing expression of endolysosomal reductases is an innate immune response to protect against pathogen proliferation and sepsis.
Collapse
|
12
|
Guo Q, Li L, Hou S, Yuan Z, Li C, Zhang W, Zheng L, Li X. The Role of Iron in Cancer Progression. Front Oncol 2021; 11:778492. [PMID: 34858857 PMCID: PMC8631356 DOI: 10.3389/fonc.2021.778492] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/15/2021] [Indexed: 01/19/2023] Open
Abstract
Iron is an essential trace element for the human body, and its deficiency or excess can induce a variety of biological processes. Plenty of evidences have shown that iron metabolism is closely related to the occurrence and development of tumors. In addition, iron plays an important role in cell death, which is very important for the development of potential strategies for tumor treatment. Here, we reviewed the latest research about iron metabolism disorders in various types of tumors, the functions and properties of iron in ferroptosis and ferritinophagy, and new opportunities for iron-based on treatment methods for tumors, providing more information regarding the prevention and treatment of tumors.
Collapse
Affiliation(s)
- Qianqian Guo
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Liwen Li
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Shanshan Hou
- Department of Pharmacy, Zhejiang Pharmaceutical College, Ningbo, China
| | - Ziqiao Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chenhui Li
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wenzhou Zhang
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| |
Collapse
|
13
|
Iron metabolism as a novel therapeutic target. Blood 2021; 138:2155-2156. [PMID: 34854879 DOI: 10.1182/blood.2021013086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/20/2022] Open
|