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Exploring transcriptomic landscapes in red cell populations, in their extracellular vesicles and on single cell level

ABSTRACT: Circulating human red blood cells (RBCs) consist of mature erythrocytes, and immature reticulocytes. As being anucleated cells, RBCs lack typical, abundant transcriptomes but are known to contain low amounts of diverse long transcripts and microRNAs. The exact role and importance of these RNAs is, however, lacking. To study this further, we have explored the RNA content of RBCs as well as extracellular vesicles of RBCs using next generation sequencing (NGS). Furthermore, to understand the dynamics of the RBC transcriptome we performed single cell RNA sequencing on RBCs both from fresh blood and blood unit. Analysis of the single cell transcriptomes revealed that while the majority of the cells don’t have detectable RNA the remaining, approximately 10% of the cells fall into three sub-populations based on their RNA content. Overall decrease in the RNA quantity over the populations is observed. Qualitative changes include the differences in the hemoglobin (Hb) content of the cells, and the changes in the expression of ribosomal and mitochondrial genes. A previously unknown transcript of a long non-coding RNA, MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) is the most enriched marker gene for one subpopulation of RBCs suggesting a role for MALAT1 in reticulocyte maturation. Enriched pathways in RBC transcriptome, such as autophagy, reflect the processes required for reticulocyte maturation to erythrocytes. RBC transcriptome is transferred to extracellular vesicles (EVs) suggesting the vesiculation as the mechanism to remove the cellular contents at the final stages of erythrocyte maturation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE108241 | GEO | 2023/04/01

REPOSITORIES: GEO

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Exploring transcriptomic landscapes in red cell populations, in their extracellular vesicles and on single cell level

Project description:Circulating human red blood cells (RBCs) consist of mature erythrocytes, and immature reticulocytes. As being anucleated cells, RBCs lack typical, abundant transcriptomes but are known to contain low amounts of diverse long transcripts and microRNAs. The exact role and importance of these RNAs is, however, lacking. To study this further, we have explored the RNA content of RBCs as well as extracellular vesicles of RBCs using next-generation sequencing (NGS). Furthermore, to understand the dynamics of the RBC transcriptome, we performed single cell RNA sequencing on RBCs both from fresh blood and blood unit. Analysis of the single cell transcriptomes revealed that while the majority of the cells don’t have detectable RNA, the remaining, approximately 10% of the cells fall into three sub-populations based on their RNA content. Overall decrease in the RNA quantity over the populations is observed. Qualitative changes include the differences in the hemoglobin (Hb) content of the cells, and the changes in the expression of ribosomal and mitochondrial genes. A previously unknown transcript of a long non-coding RNA, MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) is the most enriched marker gene for one subpopulation of RBCs, suggesting a role for MALAT1 in reticulocyte maturation. Enriched pathways in RBC transcriptome, such as autophagy, reflect the processes required for reticulocyte maturation to erythrocytes. RBC transcriptome is transferred to extracellular vesicles (EVs), suggesting the vesiculation as the mechanism to remove the cellular contents at the final stages of erythrocyte maturation.

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Comparison of the proteome of human adult and cord erythroid cells and changes in the proteome following reticulocyte maturation.

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microRNA profiling of RBC transcriptome during ex vivo storage

Project description:Mature human red blood cells (RBCs) are terminally differentiated anuclear cells. While initially thought to lack any nucleic acids, human RBCs are found to contain abundant and diverse species of RNA transcripts with functional relevance. Given the absence of novel transcription, RBCs may provide an interesting cellular context to study RNA metabolism over time. One clinically relevant context is the ex vivo storage of RBCs in blood banks for use in blood transfusion. Some studies have indicated that the transfusion of “old” or aged stored RBCs may be associated with adverse outcomes due to various storage changes termed “storage lesions”. However, other studies do not support these effects, and much remains unknown about the relevant changes associated with RBC storage. Here, we employed the NanoString nCounter assay for global miRNA profiling to comprehensively define the miRNA turnover during ex vivo RBC storage. This profiling demonstrates that the abundance of most RBC miRNAs did not change significantly during the 42 days of refrigerated storage, indicating extremely long decay half-lives. Unexpectedly, miR-720, a cleavage product of tRNAThr, increased dramatically in the first two weeks and persisted during storage. Furthermore, we present evidence for a role of angiogenin in tRNA cleavage to generate miR-720 during RBC storage. The dramatic increase in miR-720 may serve as a new characteristic for storage lesion and may be used to monitor transfused RBCs in clinical patients and athletes performing blood doping.

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2024-01-26 | PXD039914 | Pride

The genomic analysis of erythrocyte microRNA expression in sickle cell diseases

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20S proteasomes exported by malaria parasite promote its growth

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