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Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2024:10.1038/s41587-024-02224-0. [PMID: 38760567 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
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Affiliation(s)
- C C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - C M Wilson
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
| | | | - R Dai
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Q Chen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - N Teyssier
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - S Misiukiewicz
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - A Arab
- Arc Institute, Palo Alto, CA, USA
| | - T O'Loughlin
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - J C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - L A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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2
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Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558350. [PMID: 37781594 PMCID: PMC10541102 DOI: 10.1101/2023.09.18.558350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
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3
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Pance A, Ng BL, Mwikali K, Koutsourakis M, Agu C, Rouhani FJ, Montandon R, Law F, Ponstingl H, Rayner JC. Novel stem cell technologies are powerful tools to understand the impact of human factors on Plasmodium falciparum malaria. Front Cell Infect Microbiol 2023; 13:1287355. [PMID: 38173794 PMCID: PMC10762799 DOI: 10.3389/fcimb.2023.1287355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Plasmodium falciparum parasites have a complex life cycle, but the most clinically relevant stage of the disease is the invasion of erythrocytes and the proliferation of the parasite in the blood. The influence of human genetic traits on malaria has been known for a long time, however understanding the role of the proteins involved is hampered by the anuclear nature of erythrocytes that makes them inaccessible to genetic tools. Here we overcome this limitation using stem cells to generate erythroid cells with an in-vitro differentiation protocol and assess parasite invasion with an adaptation of flow cytometry to detect parasite hemozoin. We combine this strategy with reprogramming of patient cells to Induced Pluripotent Stem Cells and genome editing to understand the role of key genes and human traits in malaria infection. We show that deletion of basigin ablates invasion while deletion of ATP2B4 has a minor effect and that erythroid cells from reprogrammed patient-derived HbBart α-thalassemia samples poorly support infection. The possibility to obtain patient-secific and genetically modifed erythoid cells offers an unparalleled opportunity to study the role of human genes and polymorphisms in malaria allowing preservation of the genomic background to demonstrate their function and understand their mechanisms.
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Affiliation(s)
- Alena Pance
- Wellcome Sanger Institute, Cambridge, United Kingdom
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Bee L. Ng
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Kioko Mwikali
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Chukwuma Agu
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Ruddy Montandon
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Frances Law
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Julian C. Rayner
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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4
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Baro B, Kim CY, Lin C, Kongsomboonvech AK, Tetard M, Peterson NA, Salinas ND, Tolia NH, Egan ES. Plasmodium falciparum exploits CD44 as a coreceptor for erythrocyte invasion. Blood 2023; 142:2016-2028. [PMID: 37832027 PMCID: PMC10783654 DOI: 10.1182/blood.2023020831] [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: 04/13/2023] [Revised: 09/08/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
The malaria parasite Plasmodium falciparum invades and replicates asexually within human erythrocytes. CD44 expressed on erythrocytes was previously identified as an important host factor for P falciparum infection through a forward genetic screen, but little is known about its regulation or function in these cells, nor how it may be used by the parasite. We found that CD44 can be efficiently deleted from primary human hematopoietic stem cells using CRISPR/Cas9 genome editing, and that the efficiency of ex vivo erythropoiesis to enucleated cultured red blood cells (cRBCs) is not affected by lack of CD44. However, the rate of P falciparum invasion was reduced in CD44-null cRBCs relative to isogenic wild-type control cells, validating CD44 as an important host factor for this parasite. We identified 2 P falciparum invasion ligands as binding partners for CD44, erythrocyte binding antigen 175 (EBA-175) and EBA-140 and demonstrated that their ability to bind to human erythrocytes relies primarily on their canonical receptors, glycophorin A and glycophorin C, respectively. We further show that EBA-175 induces phosphorylation of erythrocyte cytoskeletal proteins in a CD44-dependent manner. Our findings support a model in which P falciparum exploits CD44 as a coreceptor during invasion of human erythrocytes, stimulating CD44-dependent phosphorylation of host cytoskeletal proteins that alter host cell deformability and facilitate parasite entry.
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Affiliation(s)
- Barbara Baro
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Chi Yong Kim
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Carrie Lin
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | | | - Marilou Tetard
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | | | - Nichole D. Salinas
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Niraj H. Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Elizabeth S. Egan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
- Chan Zuckerberg Biohub–San Francisco, San Francisco, CA
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5
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Feldman TP, Ryan Y, Egan ES. Plasmodium falciparum infection of human erythroblasts induces transcriptional changes associated with dyserythropoiesis. Blood Adv 2023; 7:5496-5509. [PMID: 37493969 PMCID: PMC10515311 DOI: 10.1182/bloodadvances.2023010844] [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: 05/30/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
During development down the erythroid lineage, hematopoietic stem cells undergo dramatic changes to cellular morphology and function in response to a complex and tightly regulated program of gene expression. In malaria infection, Plasmodium spp parasites accumulate in the bone marrow parenchyma, and emerging evidence suggests erythroblastic islands are a protective site for parasite development into gametocytes. Although it has been observed that Plasmodium falciparum infection in late-stage erythroblasts can delay terminal erythroid differentiation and enucleation, the mechanism(s) underlying this phenomenon are unknown. Here, we apply RNA sequencing after fluorescence-activated cell sorting of infected erythroblasts to identify transcriptional responses to direct and indirect interaction with P falciparum. Four developmental stages of erythroid cells were analyzed: proerythroblast, basophilic erythroblast, polychromatic erythroblast, and orthochromatic erythroblast. We found extensive transcriptional changes in infected erythroblasts compared with that in uninfected cells in the same culture, including dysregulation of genes involved in erythroid proliferation and developmental processes. Although some indicators of cellular oxidative and proteotoxic stress were common across all stages of erythropoiesis, many responses were specific to cellular processes associated with developmental stage. Together, our results evidence multiple possible avenues by which parasite infection can induce dyserythropoiesis at specific points along the erythroid continuum, advancing our understanding of the molecular determinants of malaria anemia.
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Affiliation(s)
- Tamar P. Feldman
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
| | - Yana Ryan
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA
| | - Elizabeth S. Egan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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6
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Feldman TP, Ryan Y, Egan ES. Plasmodium falciparum infection of human erythroblasts induces transcriptional changes associated with dyserythropoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.23.538003. [PMID: 37398027 PMCID: PMC10312461 DOI: 10.1101/2023.04.23.538003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
During development down the erythroid lineage, hematopoietic stem cells undergo dramatic changes to cellular morphology and function in response to a complex and tightly regulated program of gene expression. In malaria infection, Plasmodium spp . parasites accumulate in the bone marrow parenchyma, and emerging evidence suggests erythroblastic islands are a protective site for parasite development into gametocytes. While it has been observed that Plasmodium falciparum infection of late-stage erythroblasts can delay terminal erythroid differentiation and enucleation, the mechanism(s) underlying this phenomenon are unknown. Here, we apply RNA-seq after fluorescence-activated cell sorting (FACS) of infected erythroblasts to identify transcriptional responses to direct and indirect interaction with Plasmodium falciparum . Four developmental stages of erythroid cells were analyzed: proerythroblast, basophilic erythroblast, polychromatic erythroblast, and orthochromatic erythroblast. We found extensive transcriptional changes in infected erythroblasts compared to uninfected cells in the same culture, including dysregulation of genes involved in erythroid proliferation and developmental processes. Whereas some indicators of cellular oxidative and proteotoxic stress were common across all stages of erythropoiesis, many responses were specific to cellular processes associated with developmental stage. Together, our results evidence multiple possible avenues by which parasite infection can induce dyserythropoiesis at specific points along the erythroid continuum, advancing our understanding of the molecular determinants of malaria anemia. Key Points Erythroblasts at different stages of differentiation have distinct responses to infection by Plasmodium falciparum . P. falciparum infection of erythroblasts alters expression of genes related to oxidative and proteotoxic stress and erythroid development.
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Ren Y, Yan C, Yang H. Erythrocytes: Member of the Immune System that Should Not Be Ignored. Crit Rev Oncol Hematol 2023; 187:104039. [PMID: 37236411 DOI: 10.1016/j.critrevonc.2023.104039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/27/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023] Open
Abstract
Erythrocytes are the most abundant type of cells in the blood and have a relatively simple structure when mature; they have a long life-span in the circulatory system. The primary function of erythrocytes is as oxygen carriers; however, they also play an important role in the immune system. Erythrocytes recognize and adhere to antigens and promote phagocytosis. The abnormal morphology and function of erythrocytes are also involved in the pathological processes of some diseases. Owing to the large number and immune properties of erythrocytes, their immune functions should not be ignored. Currently, research on immunity is focused on immune cells other than erythrocytes. However, research on the immune function of erythrocytes and the development of erythrocyte-mediated applications is of great significance. Therefore, we aimed to review the relevant literature and summarize the immune functions of erythrocytes.
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Affiliation(s)
- Yijun Ren
- Department of Neurology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, China, 410000.
| | - Chengkai Yan
- Department of Neurology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, China, 410000.
| | - Huan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, China, 410000.
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8
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Baro-Sastre B, Kim CY, Lin C, Kongsomboonvech AK, Tetard M, Salinas ND, Tolia NH, Egan ES. Plasmodium falciparum exploits CD44 as a co-receptor for erythrocyte invasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536503. [PMID: 37090581 PMCID: PMC10120705 DOI: 10.1101/2023.04.12.536503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The malaria parasite Plasmodium falciparum invades and replicates asexually within human erythrocytes. CD44 expressed on erythrocytes was previously identified as an important host factor for P. falciparum infection through a forward genetic screen, but little is known about its regulation or function in these cells, nor how it may be utilized by the parasite. We found that CD44 can be efficiently deleted from primary human hematopoietic stem cells using CRISPR/Cas9 genome editing, and that the efficiency of ex-vivo erythropoiesis to enucleated cultured red blood cells (cRBCs) is not impacted by lack of CD44. However, the rate of P. falciparum invasion was substantially reduced in CD44-null cRBCs relative to isogenic wild-type (WT) control cells, validating CD44 as an important host factor for this parasite. We identified two P. falciparum invasion ligands as binding partners for CD44, Erythrocyte Binding Antigen-175 (EBA-175) and EBA-140, and demonstrated that their ability to bind to human erythrocytes relies primarily on their canonical receptors-glycophorin A and glycophorin C, respectively. We further show that EBA-175 induces phosphorylation of erythrocyte cytoskeletal proteins in a CD44-dependent manner. Our findings support a model where P. falciparum exploits CD44 as a co-receptor during invasion of human erythrocytes, stimulating CD44-dependent phosphorylation of host cytoskeletal proteins that alter host cell deformability and facilitate parasite entry.
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Wang Z, Wang J, Lan T, Zhang L, Yan Z, Zhang N, Xu Y, Tao Q. Role and mechanism of fibroblast-activated protein-α expression on the surface of fibroblast-like synoviocytes in rheumatoid arthritis. Front Immunol 2023; 14:1135384. [PMID: 37006278 PMCID: PMC10064071 DOI: 10.3389/fimmu.2023.1135384] [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: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Fibroblast-activated protein-α (FAP) is a type II integrated serine protease expressed by activated fibroblasts during fibrosis or inflammation. Fibroblast-like synoviocytes (FLSs) in rheumatoid arthritis (RA) synovial sites abundantly and stably overexpress FAP and play important roles in regulating the cellular immune, inflammatory, invasion, migration, proliferation, and angiogenesis responses in the synovial region. Overexpression of FAP is regulated by the initial inflammatory microenvironment of the disease and epigenetic signaling, which promotes RA development by regulating FLSs or affecting the signaling cross-linking FLSs with other cells at the local synovium and inflammatory stimulation. At present, several treatment options targeting FAP are in the process of development. This review discusses the basic features of FAP expressed on the surface of FLSs and its role in RA pathophysiology and advances in targeted therapies.
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Affiliation(s)
- Zihan Wang
- Traditional Chinese Medicine Department of Rheumatism, China-Japan Friendship Hospital, Beijing, China
- Graduate school, Beijing University of Chinese Medicine, Beijing, China
| | - Jinping Wang
- Traditional Chinese Medicine Department of Rheumatism, China-Japan Friendship Hospital, Beijing, China
| | - Tianyi Lan
- Graduate school, Beijing University of Chinese Medicine, Beijing, China
| | - Liubo Zhang
- Graduate school, Beijing University of Chinese Medicine, Beijing, China
| | - Zeran Yan
- Traditional Chinese Medicine Department of Rheumatism, China-Japan Friendship Hospital, Beijing, China
| | - Nan Zhang
- Traditional Chinese Medicine Department of Rheumatism, China-Japan Friendship Hospital, Beijing, China
| | - Yuan Xu
- Traditional Chinese Medicine Department of Rheumatism, China-Japan Friendship Hospital, Beijing, China
- *Correspondence: Yuan Xu, ; Qingwen Tao,
| | - Qingwen Tao
- Traditional Chinese Medicine Department of Rheumatism, China-Japan Friendship Hospital, Beijing, China
- *Correspondence: Yuan Xu, ; Qingwen Tao,
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Erythrocyte-Plasmodium interactions: genetic manipulation of the erythroid lineage. Curr Opin Microbiol 2022; 70:102221. [PMID: 36242898 DOI: 10.1016/j.mib.2022.102221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 09/12/2022] [Indexed: 01/25/2023]
Abstract
Targeting critical host factors is an emerging concept in the treatment of infectious diseases. As obligate pathogens of erythrocytes, the Plasmodium spp. parasites that cause malaria must exploit erythroid host factors for their survival. However, our understanding of this important aspect of the malaria lifecycle is limited, in part because erythrocytes are enucleated cells that lack a nucleus and DNA, rendering them genetically intractable. Recent advances in genetic analysis of the erythroid lineage using small-hairpin RNAs and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) in red-blood cells derived from stem cells have generated new insights into the functions of several candidate host factors for Plasmodium parasites. Along with efforts in other hematopoietic cells, these advances have also laid a strong foundation for genetic screens to identify novel erythrocyte host factors for malaria.
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Kumari G, Rex DAB, Goswami S, Mukherjee S, Biswas S, Maurya P, Jain R, Garg S, Prasad TSK, Pati S, Ramalingam S, Mohandas N, Singh S. Dynamic Palmitoylation of Red Cell Membrane Proteins Governs Susceptibility to Invasion by the Malaria Parasite, Plasmodium falciparum. ACS Infect Dis 2022; 8:2106-2118. [PMID: 36044540 DOI: 10.1021/acsinfecdis.2c00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Phosphorylation and other post-translational modifications of red blood cell (RBC) proteins govern membrane function and have a role in the invasion of RBCs by the malaria parasite, Plasmodium falciparum. Furthermore, a percentage of RBC proteins are palmitoylated, although the functional consequences are unknown. We establish dynamic palmitoylation of 118 RBC membrane proteins using click chemistry and acyl biotin exchange (ABE)-coupled LC-MS/MS and characterize their involvement in controlling membrane organization and parasite invasion. RBCs were treated with a generic palmitoylation inhibitor, 2-bromopalmitate (2-BMP), and then analyzed using ABE-coupled LC-MS/MS. Only 42 of the 118 palmitoylated proteins detected were palmitoylated in the 2-BMP-treated sample, indicating that palmitoylation is dynamically regulated. Interestingly, membrane receptors such as semaphorin 7A, CR1, and ABCB6, which are known to be involved in merozoite interaction with RBCs and parasite invasion, were found to be dynamically palmitoylated, including the blood group antigen, Kell, whose antigenic abundance was significantly reduced following 2-BMP treatment. To investigate the involvement of Kell in merozoite invasion of RBCs, a specific antibody to its extracellular domain was used. The antibody targeting Kell inhibited merozoite invasion of RBCs by 50%, implying a role of Kell, a dynamically palmitoylated potent host-derived receptor, in parasite invasion. Furthermore, a significant reduction in merozoite contact with the RBC membrane and a consequent decrease in parasite invasion following 2-BMP treatment demonstrated that palmitoylation does indeed regulate RBC susceptibility to parasite invasion. Taken together, our findings revealed the dynamic palmitoylome of RBC membrane proteins and its role in P. falciparum invasion.
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Affiliation(s)
- Geeta Kumari
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore 575018, India.,Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore 575018, India
| | - Sangam Goswami
- CSIR─Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi 110025, India
| | - Soumyadeep Mukherjee
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida 201314, Uttar Pradesh, India
| | - Shreeja Biswas
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Preeti Maurya
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ravi Jain
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Swati Garg
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Soumya Pati
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida 201314, Uttar Pradesh, India
| | - Sivaprakash Ramalingam
- CSIR─Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi 110025, India
| | - Narla Mohandas
- Laboratory of Red Cell Physiology, New York Blood Center, 310 E 67th Street, New York, New York 10065, United States
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
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12
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The impact of human complement on the clinical outcome of malaria infection. Mol Immunol 2022; 151:19-28. [PMID: 36063583 DOI: 10.1016/j.molimm.2022.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022]
Abstract
The tropical disease malaria remains a major cause of global morbidity. Once transmitted to the human by a blood-feeding mosquito, the unicellular malaria parasite comes into contact with the complement system and continues to interact with human complement during its intraerythrocytic replication cycles. In the course of infection, both the classical and the alternative pathway of complement are activated, leading to parasite opsonization and lysis as well as the induction of complement-binding antibodies. While complement activity can be linked to the severity of malaria, it remains to date unclear, whether human complement is beneficial for protective immunity or if extensive complement reactions may rather enhance pathogenesis. In addition, the parasite has evolved molecular strategies to circumvent attack by human complement and has even developed means to utilize complement factors as mediators of host cell infection. In this review, we highlight current knowledge on the role of human complement for the progression of malaria infection. We discuss the various types of interactions between malaria parasites and complement factors with regard to immunity and infection outcome and set a special emphasis on the dual role of complement in the context of parasite fitness.
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Feldman TP, Egan ES. Uncovering a Cryptic Site of Malaria Pathogenesis: Models to Study Interactions Between Plasmodium and the Bone Marrow. Front Cell Infect Microbiol 2022; 12:917267. [PMID: 35719356 PMCID: PMC9201243 DOI: 10.3389/fcimb.2022.917267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
The bone marrow is a critical site of host-pathogen interactions in malaria infection. The discovery of Plasmodium asexual and transmission stages in the bone marrow has renewed interest in the tissue as a niche for cellular development of both host and parasite. Despite its importance, bone marrow in malaria infection remains largely unexplored due to the challenge of modeling the complex hematopoietic environment in vitro. Advancements in modeling human erythropoiesis ex-vivo from primary human hematopoietic stem and progenitor cells provide a foothold to study the host-parasite interactions occurring in this understudied site of malaria pathogenesis. This review focuses on current in vitro methods to recapitulate and assess bone marrow erythropoiesis and their potential applications in the malaria field. We summarize recent studies that leveraged ex-vivo erythropoiesis to shed light on gametocyte development in nucleated erythroid stem cells and begin to characterize host cell responses to Plasmodium infection in the hematopoietic niche. Such models hold potential to elucidate mechanisms of disordered erythropoiesis, an underlying contributor to malaria anemia, as well as understand the biological determinants of parasite sexual conversion. This review compares the advantages and limitations of the ex-vivo erythropoiesis approach with those of in vivo human and animal studies of the hematopoietic niche in malaria infection. We highlight the need for studies that apply single cell analyses to this complex system and incorporate physical and cellular components of the bone marrow that may influence erythropoiesis and parasite development.
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Affiliation(s)
- Tamar P. Feldman
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Elizabeth S. Egan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Elizabeth S. Egan,
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Matteucci KC, Correa AAS, Costa DL. Recent Advances in Host-Directed Therapies for Tuberculosis and Malaria. Front Cell Infect Microbiol 2022; 12:905278. [PMID: 35669122 PMCID: PMC9163498 DOI: 10.3389/fcimb.2022.905278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 04/21/2022] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis, and malaria, caused by parasites from the Plasmodium genus, are two of the major causes of death due to infectious diseases in the world. Both diseases are treatable with drugs that have microbicidal properties against each of the etiologic agents. However, problems related to treatment compliance by patients and emergence of drug resistant microorganisms have been a major problem for combating TB and malaria. This factor is further complicated by the absence of highly effective vaccines that can prevent the infection with either M. tuberculosis or Plasmodium. However, certain host biological processes have been found to play a role in the promotion of infection or in the pathogenesis of each disease. These processes can be targeted by host-directed therapies (HDTs), which can be administered in conjunction with the standard drug treatments for each pathogen, aiming to accelerate their elimination or to minimize detrimental side effects resulting from exacerbated inflammation. In this review we discuss potential new targets for the development of HDTs revealed by recent advances in the knowledge of host-pathogen interaction biology, and present an overview of strategies that have been tested in vivo, either in experimental models or in patients.
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Affiliation(s)
- Kely C. Matteucci
- Plataforma de Medicina Translacional Fundação Oswaldo Cruz/Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - André A. S. Correa
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Diego L. Costa
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- *Correspondence: Diego L. Costa,
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Sánchez-Arcila JC, Jensen KDC. Forward Genetics in Apicomplexa Biology: The Host Side of the Story. Front Cell Infect Microbiol 2022; 12:878475. [PMID: 35646724 PMCID: PMC9133346 DOI: 10.3389/fcimb.2022.878475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Forward genetic approaches have been widely used in parasitology and have proven their power to reveal the complexities of host-parasite interactions in an unbiased fashion. Many aspects of the parasite's biology, including the identification of virulence factors, replication determinants, antibiotic resistance genes, and other factors required for parasitic life, have been discovered using such strategies. Forward genetic approaches have also been employed to understand host resistance mechanisms to parasitic infection. Here, we will introduce and review all forward genetic approaches that have been used to identify host factors involved with Apicomplexa infections, which include classical genetic screens and QTL mapping, GWAS, ENU mutagenesis, overexpression, RNAi and CRISPR-Cas9 library screens. Collectively, these screens have improved our understanding of host resistance mechanisms, immune regulation, vaccine and drug designs for Apicomplexa parasites. We will also discuss how recent advances in molecular genetics give present opportunities to further explore host-parasite relationships.
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Affiliation(s)
- Juan C. Sánchez-Arcila
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA, United States
| | - Kirk D. C. Jensen
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA, United States
- Health Science Research Institute, University of California, Merced, Merced, CA, United States
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