Analysis of transcribed sequences from young and mature zebrafish thrombocytes

Piggyback knockdown screening of unique genes of zebrafish young thrombocytes identifies eight novel genes in thrombopoiesis

Platelet production, or thrombopoiesis, is a critical process involving the differentiation of hematopoietic stem cells into megakaryocytes, which release platelets into circulation. This study employed a comprehensive screening approach through a piggyback knockdown strategy targeting 394 protein-encoding genes expressed explicitly in young thrombocytes. This approach led us to identify eight candidate genes associated with thrombopoiesis, including spi1b, a transcription factor that potentially regulates thrombocyte development. The sequencing of spi1b mutant progeny harboring a termination codon after Arg254 within the conserved ETS transcription factor domain confirmed the lethality of homozygous mutations, highlighting the essential role of Spi1b in embryonic development. Comparative analysis revealed homology between zebrafish Spi1b and human SPI1, suggesting evolutionary conservation of thrombopoiesis regulatory mechanisms. Additionally, analysis of spi1b knockdown zebrafish and the mutant demonstrated increased bleeding, further emphasizing the importance of spi1b in maintaining hemostasis. Our study provides novel insights into the regulatory networks governing thrombopoiesis and identifies Spi1b as a critical regulator of young thrombocyte development in zebrafish. Further investigations into the functional roles of identified genes in thrombocyte biology may elucidate mechanisms underlying thrombopoiesis and inform therapeutic strategies for bleeding disorders.

Knockdown of zebrafish tmem242 enhances the production of ROS that signals to increase f9a expression resulting in DIC-like condition

Transmembrane proteins (TMEMs) are embedded in cell membranes and often have poorly understood functions. Our RNAseq analysis identified 89 tmem genes in zebrafish thrombocytes, leading to further investigation through knockdown experiments and gill bleeding assays. Knockdown of tmem242 significantly increased bleeding, indicating a role in hemostasis. While thrombocyte production and aggregation were unaffected, coagulation was impaired, with delayed fibrin and thrombus formation. Notably, mRNA levels of several clotting factor genes, including coagulation factor 5 (f5), coagulation factor 7 (f7), and coagulation factor 9a (f9a), were elevated, except for coagulation factor 8 (f8). Microthrombi were also observed in larvae after tmem242 knockdown. In parallel studies, impaired ATP synthase assembly in human cells lacking TMEM242 prompted us to hypothesize that reduced ATP synthase could elevate reactive oxygen species (ROS) levels, influencing clotting factor expression. Indeed, tmem242 knockdown increased ROS levels. Inhibition of ATP synthase with oligomycin elevated ROS and f9a transcripts, while ROS inhibition reduced f9a expression, suggesting ROS-mediated regulation. Further analysis revealed increased sirt6 and nrf2 transcripts after tmem242 knockdown, with their knockdown reducing f9a levels. These findings suggest that tmem242 depletion may impair ATP synthase, elevate ROS, upregulate sirt6 and nrf2, and increase f9a transcripts, potentially leading to bleeding tendencies similar to disseminated intravascular coagulation (DIC).

Zebrafish Thrombocyte Transcriptome Analysis and Functional Genomics

Our laboratory is interested in investigating the maturation process of zebrafish thrombocytes, which are functional equivalents to human platelets. We have adopted the zebrafish model to gain insights into mammalian platelet production, or thrombopoiesis. Notably, zebrafish exhibit two distinct populations of thrombocytes in their circulating blood: young and mature thrombocytes. This observation is intriguing because maturation appears to occur in circulation, yet the precise mechanisms governing this maturation remain elusive. Our goal is to understand the mechanisms underlying thrombocyte maturation by conducting single-cell RNA sequencing (scRNA-Seq) on young and mature thrombocytes, analyzing these transcriptomes to identify genes specific to each thrombocyte population, and elucidating the role of these genes in the maturation process, by quantifying thrombocyte numbers after the piggyback knockdown of each of these genes. In this chapter, we present a comprehensive, step-by-step protocol detailing the multifaceted methodology involved in understanding thrombocyte maturation, which encompasses the collection of zebrafish blood, the separation of young and mature thrombocytes using flow cytometry, scRNA-Seq analysis of these distinct thrombocyte populations, identification of genes specific to young and mature thrombocytes, and subsequent validation through gene knockdown techniques.

Discovery of seven hox genes in zebrafish thrombopoiesis

Thrombopoiesis is the production of platelets from megakaryocytes in the bone marrow of mammals. In fish, thrombopoiesis involves the formation of thrombocytes without megakaryocyte-like precursors but derived from erythrocyte thrombocyte bi-functional precursor cells. One unique feature of thrombocyte differentiation involves the maturation of young thrombocytes in circulation. In this study, we investigated the role of hox genes in zebrafish thrombopoiesis to model platelet production. We selected hoxa10b, hoxb2a, hoxc5a, hoxd3a, and hoxc11b from thrombocyte RNA expression data, and checked whether they are expressed in young or mature thrombocytes. We found hoxa10b, hoxb2a, hoxc5a, and hoxd3a were expressed in both young and mature thrombocytes and hoxc11b was expressed in only young thrombocytes. We then performed knockdowns of these 5 hox genes and found hoxc11b knockdown resulted in thrombocytosis and the rest showed thrombocytopenia. To identify hox genes that could have been missed by the above datasets, we performed knockdowns 47 hox genes in the zebrafish genome and found hoxa9a, and hoxb1a knockdowns resulted in thrombocytopenia and they were expressed in both young and mature thrombocytes. In conclusion, our comprehensive knockdown study identified Hoxa10b, Hoxb2a, Hoxc5a, Hoxd3a, Hoxa9a, and Hoxb1a, as positive regulators and Hoxc11b, as a negative regulator for thrombocyte development.

Role of microRNAs and their downstream target transcription factors in zebrafish thrombopoiesis

Previous studies have shown that human platelets and megakaryocytes carry microRNAs suggesting their role in platelet function and megakaryocyte development, respectively. However, a comprehensive study on the microRNAs and their targets has not been undertaken. Zebrafish thrombocytes could be used as a model to study their role in megakaryocyte maturation and platelet function because thrombocytes have both megakaryocyte features and platelet properties. In our laboratory, we identified 15 microRNAs in thrombocytes using single-cell RNA sequencing. We knocked down each of these 15 microRNAs by the piggyback method and found knockdown of three microRNAs, mir-7148, let-7b, and mir-223 in adult zebrafish led to an increase in the percentage of thrombocytes. Functional thrombocyte analysis using plate tilt assay showed no modulatory effect of the three microRNAs on thrombocyte aggregation/agglutination. We also found enhanced thrombosis using arterial laser thrombosis assay in a group of zebrafish larvae after mir-7148, let-7b, and mir-223 knockdowns. These results suggested mir-7148, let-7b, and mir-223 are repressors for thrombocyte production. We then explored miRWalk database for let-7b downstream targets and then selected those that are expressed in thrombocytes, and from this list based on their role in differentiation selected 14 genes, rorca, tgif1, rfx1a, deaf1, zbtb18, mafba, cebpa, spi1a, spi1b, fhl3b, ikzf1, irf5, irf8, and lbx1b that encode transcriptional regulators. The qRT-PCR analysis of expression levels of the above genes following let-7b knockdown showed changes in the expression of 13 targets. We then studied the effect of the 13 targets on thrombocyte production and identified 5 genes, irf5, tgif1, irf8, cebpa, and rorca that showed thrombocytosis and one gene, ikzf1 that showed thrombocytopenia. Furthermore, we tested whether mir-223 regulates any of the above 13 transcription factors after mir-223 knockdown using qRT-PCR. Six of the 13 genes showed similar gene expression as observed with let-7b knockdown and 7 genes showed opposing results. Thus, our results suggested a possible regulatory network in common with both let-7b and mir-223. We also identified that tgif1, cebpa, ikzf1, irf5, irf8, and ikzf1 play a role in thrombopoiesis. Since the ikzf1 gene showed a differential expression profile in let-7b and mir-223 knockdowns but resulted in thrombocytopenia in ikzf1 knockdown in both adults and larvae we also studied an ikzf1 mutant and showed the mutant had thrombocytopenia. Taken together, these studies showed that thrombopoiesis is controlled by a network of transcription regulators that are regulated by multiple microRNAs in both positive and negative manner resulting in overall inhibition of thrombopoiesis.

Role of MicroRNAs and their Downstream Target Transcription Factors in Zebrafish Thrombopoiesis

Previous studies have shown that human platelets and megakaryocytes carry microRNAs suggesting their role in platelet function and megakaryocyte development, respectively. However, a comprehensive study on the microRNAs and their targets has not been undertaken. Zebrafish thrombocytes could be used as a model to study their role in megakaryocyte maturation and platelet function because thrombocytes have both megakaryocyte features and platelet properties. In our laboratory, we identified 15 microRNAs in thrombocytes using single-cell RNA sequencing. We knocked down each of these 15 microRNAs by the piggyback method and found knockdown of three microRNAs, mir-7148, let-7b , and mir-223 in adult zebrafish led to an increase in the percentage of thrombocytes. Functional thrombocyte analysis using plate tilt assay showed no modulatory effect of the three microRNAs on thrombocyte aggregation/agglutination. We also found enhanced thrombosis using arterial laser thrombosis assay in a group of zebrafish larvae after mir-7148, let-7b , and mir-223 knockdowns. These results suggested mir-7148, let-7b , and mir-223 are repressors for thrombocyte production. We then explored miRWalk database for let-7b downstream targets and then selected those that are expressed in thrombocytes, and from this list based on their role in differentiation selected 14 genes, rorca, tgif1, rfx1a, deaf1, zbtb18, mafba, cebpa, spi1a, spi1b, fhl3b, ikzf1, irf5, irf8 , and lbx1b that encode transcriptional regulators. The qRT-PCR analysis of expression levels of the above genes following let-7b knockdown showed changes in the expression of 13 targets. We then studied the effect of the 13 targets on thrombocyte production and identified 5 genes, irf5, tgif1, irf8, cebpa , and rorca that showed thrombocytosis and one gene, ikzf1 that showed thrombocytopenia. Furthermore, we tested whether mir-223 regulates any of the above 13 transcription factors after mir-223 knockdown using qRT-PCR. Six of the 13 genes showed similar gene expression as observed with let-7b knockdown and 7 genes showed opposing results. Thus, our results suggested a possible regulatory network in common with both let-7b and mir-223 . We also identified that tgif1, cebpa, ikzf1, irf5 , irf8 , and ikzf1 play a role in thrombopoiesis. Since the ikzf1 gene showed a differential expression profile in let-7b and mir-223 knockdowns but resulted in thrombocytopenia in ikzf1 knockdown in both adults and larvae we also studied an ikzf1 mutant and showed the mutant had thrombocytopenia. Taken together, these studies showed that thrombopoiesis is controlled by a network of transcription regulators that are regulated by multiple microRNAs in both positive and negative manner resulting in overall inhibition of thrombopoiesis.

Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish

The zebrafish has proven to be a valuable model organism for studying hematopoiesis, but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single-cell RNA sequencing on ∼70,000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus, elucidated B- and T-cell developmental trajectories, and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic-like cell populations and provided evidence in support of the existence of a pre-B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies.