scholarly journals Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage

2021 ◽  
Vol 11 ◽  
Author(s):  
Kathrin Witmer ◽  
Farah Aida Dahalan ◽  
Tom Metcalf ◽  
Arthur M. Talman ◽  
Virginia M. Howick ◽  
...  
Keyword(s):  
Single Cell ◽  
Malaria Parasite ◽  
Clonal Variation ◽  
Environmental Cues ◽  
Anopheles Coluzzii ◽  
Parasite Life Cycle ◽  
Low Input ◽  
Transcriptional Variation ◽  
Transcriptional Changes ◽  
Parasite Populations

The crossing of the mosquito midgut epithelium by the malaria parasite motile ookinete form represents the most extreme population bottleneck in the parasite life cycle and is a prime target for transmission blocking strategies. However, we have little understanding of the clonal variation that exists in a population of ookinetes in the vector, partially because the parasites are difficult to access and are found in low numbers. Within a vector, variation may result as a response to specific environmental cues or may exist independent of those cues as a potential bet-hedging strategy. Here we use single-cell RNA-seq to profile transcriptional variation in Plasmodium berghei ookinetes across different vector species, and between and within individual midguts. We then compare our results to low-input transcriptomes from individual Anopheles coluzzii midguts infected with the human malaria parasite Plasmodium falciparum. Although the vast majority of transcriptional changes in ookinetes are driven by development, we have identified candidate genes that may be responding to environmental cues or are clonally variant within a population. Our results illustrate the value of single-cell and low-input technologies in understanding clonal variation of parasite populations.

scholarly journals Transcriptional variation in malaria parasites: why and how

2019 ◽  
Vol 18 (5) ◽  
pp. 329-341 ◽  
Author(s):  
Oriol Llorà-Batlle ◽  
Elisabet Tintó-Font ◽  
Alfred Cortés
Keyword(s):  
Molecular Mechanisms ◽  
Transcriptional Responses ◽  
Malaria Parasites ◽  
Genetic Changes ◽  
Alternative Phenotypes ◽  
Transcriptional Variation ◽  
Parasite Survival ◽  
Transcriptional Changes ◽  
Stochastic Events ◽  
Parasite Populations

Abstract Transcriptional differences enable the generation of alternative phenotypes from the same genome. In malaria parasites, transcriptional plasticity plays a major role in the process of adaptation to fluctuations in the environment. Multiple studies with culture-adapted parasites and field isolates are starting to unravel the different transcriptional alternatives available to Plasmodium falciparum and the underlying molecular mechanisms. Here we discuss how epigenetic variation, directed transcriptional responses and also genetic changes that affect transcript levels can all contribute to transcriptional variation and, ultimately, parasite survival. Some transcriptional changes are driven by stochastic events. These changes can occur spontaneously, resulting in heterogeneity within parasite populations that provides the grounds for adaptation by dynamic natural selection. However, transcriptional changes can also occur in response to external cues. A better understanding of the mechanisms that the parasite has evolved to alter its transcriptome may ultimately contribute to the design of strategies to combat malaria to which the parasite cannot adapt.

scholarly journals Single-Cell Transcriptional Heterogeneity of Lymphatic Endothelial Cells in Normal and Inflamed Murine Lymph Nodes

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1371
Author(s):  
Eliane Sibler ◽  
Yuliang He ◽  
Luca Ducoli ◽  
Nadja Keller ◽  
Noriki Fujimoto ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Lymph Nodes ◽  
Single Cell ◽  
In Silico Analysis ◽  
Skin Inflammation ◽  
Lymphatic Endothelial Cells ◽  
Depth Analysis ◽  
Subcapsular Sinus ◽  
Transcriptional Changes ◽  
Sinus Floor

The lymphatic system plays a crucial role in immunity and lymph nodes (LNs) undergo drastic remodeling during inflammation. Here, we used single-cell RNA sequencing to investigate transcriptional changes in lymphatic endothelial cells (LECs) in LNs draining naïve and inflamed skin. We found that subsets of LECs lining the different LN sinuses responded individually to skin inflammation, suggesting that they exert distinct functions under pathological conditions. Among the genes dysregulated during inflammation, we confirmed an up-regulation of CD200 in the LECs lining the subcapsular sinus floor with a possible function in immune regulation. Furthermore, by in silico analysis, we predicted numerous possible interactions of LECs with diverse immune cells in the LNs and found similarities in the transcriptional changes of LN LECs in different skin inflammation settings. In summary, we provide an in-depth analysis of the transcriptional landscape of LN LECs in the naïve state and in skin inflammation.

New insights on the genetic diversity of the honeybee parasiteNosema ceranaebased onmultilocussequence analysis

Parasitology ◽  
2013 ◽  
Vol 140 (11) ◽  
pp. 1346-1356 ◽  
Author(s):  
MATHIEU ROUDEL ◽  
JULIE AUFAUVRE ◽  
BRUNO CORBARA ◽  
FREDERIC DELBAC ◽  
NICOLAS BLOT
Keyword(s):  
Ribosomal Rna ◽  
Evolutionary History ◽  
Nucleotide Diversity ◽  
Selective Pressure ◽  
Population Divergence ◽  
Environmental Cues ◽  
Microsporidian Parasite ◽  
High Nucleotide Diversity ◽  
Single Host ◽  
Parasite Populations

SUMMARYThe microsporidian parasiteNosema ceranaeis a common pathogen of the Western honeybee (Apis mellifera) whose variable virulence could be related to its genetic polymorphism and/or its polyphenism responding to environmental cues. Since the genotyping ofN. ceranaebased on unique marker sequences had been unsuccessful, we tested whether amultilocusapproach, assessing the diversity of ten genetic markers – encoding nine proteins and the small ribosomal RNA subunit – allowed the discrimination betweenN. ceranaevariants isolated from singleA. melliferaindividuals in four distant locations. High nucleotide diversity and allele content were observed for all genes. Most importantly, the diversity was mainly present within parasite populations isolated from single honeybee individuals. In contrast the absence of isolate differentiation precluded anytaxadiscrimination, even through amultilocusapproach, but suggested that similar populations of parasites seem to infect honeybees in distant locations. As statistical evolutionary analyses showed that the allele frequency is under selective pressure, we discuss the origin and consequences ofN. ceranaeheterozygosity in a single host and lack of population divergence in the context of the parasite natural and evolutionary history.

scholarly journals Single-Cell Transcriptomics Reveals the Expression of Aging- and Senescence-Associated Genes in Distinct Cancer Cell Populations

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3126
Author(s):  
Dominik Saul ◽  
Robyn Laura Kosinsky
Keyword(s):  
Single Cell ◽  
Myelogenous Leukemia ◽  
Ductal Adenocarcinoma ◽  
Cell Populations ◽  
Rna Seq ◽  
Healthy Control ◽  
Transcriptional Changes ◽  
The Relationship ◽  
Senescence Associated Genes

The human aging process is associated with molecular changes and cellular degeneration, resulting in a significant increase in cancer incidence with age. Despite their potential correlation, the relationship between cancer- and ageing-related transcriptional changes is largely unknown. In this study, we aimed to analyze aging-associated transcriptional patterns in publicly available bulk mRNA-seq and single-cell RNA-seq (scRNA-seq) datasets for chronic myelogenous leukemia (CML), colorectal cancer (CRC), hepatocellular carcinoma (HCC), lung cancer (LC), and pancreatic ductal adenocarcinoma (PDAC). Indeed, we detected that various aging/senescence-induced genes (ASIGs) were upregulated in malignant diseases compared to healthy control samples. To elucidate the importance of ASIGs during cell development, pseudotime analyses were performed, which revealed a late enrichment of distinct cancer-specific ASIG signatures. Notably, we were able to demonstrate that all cancer entities analyzed in this study comprised cell populations expressing ASIGs. While only minor correlations were detected between ASIGs and transcriptome-wide changes in PDAC, a high proportion of ASIGs was induced in CML, CRC, HCC, and LC samples. These unique cellular subpopulations could serve as a basis for future studies on the role of aging and senescence in human malignancies.

scholarly journals Probing Plasmodium falciparum sexual commitment at the single-cell level

2018 ◽  
Vol 3 ◽  
pp. 70 ◽  
Author(s):  
Nicolas M.B. Brancucci ◽  
Mariana De Niz ◽  
Timothy J. Straub ◽  
Deepali Ravel ◽  
Lauriane Sollelis ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Life Cycle ◽  
Single Cell ◽  
Transcriptional Profiling ◽  
Quantitative Imaging ◽  
Complex Life Cycle ◽  
Major Transitions ◽  
Transcriptional Signature ◽  
Life Cycle Stages ◽  
Parasite Populations

Background: Malaria parasites go through major transitions during their complex life cycle, yet the underlying differentiation pathways remain obscure. Here we apply single cell transcriptomics to unravel the program inducing sexual differentiation in Plasmodium falciparum. Parasites have to make this essential life-cycle decision in preparation for human-to-mosquito transmission. Methods: By combining transcriptional profiling with quantitative imaging and genetics, we defined a transcriptional signature in sexually committed cells. Results: We found this transcriptional signature to be distinct from general changes in parasite metabolism that can be observed in response to commitment-inducing conditions. Conclusions: This proof-of-concept study provides a template to capture transcriptional diversity in parasite populations containing complex mixtures of different life-cycle stages and developmental programs, with important implications for our understanding of parasite biology and the ongoing malaria elimination campaign.

scholarly journals Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

2019 ◽  
Author(s):  
Teresa G Krieger ◽  
Stephan M Tirier ◽  
Jeongbin Park ◽  
Tanja Eisemann ◽  
Heike Peterziel ◽  
...  
Keyword(s):  
Single Cell ◽  
Specific Treatment ◽  
Cellular Heterogeneity ◽  
Patient Specific ◽  
Before And After ◽  
Invasive Capacity ◽  
Transcriptional Changes ◽  
Potential Interactions

AbstractGlioblastoma multiforme (GBM) are devastating neoplasms with high invasive capacity. GBM has been difficult to study in vitro. Therapeutic progress is also limited by cellular heterogeneity within and between tumors. To address these challenges, we present an experimental model using human cerebral organoids as a scaffold for patient-derived glioblastoma cell invasion. By tissue clearing and confocal microscopy, we show that tumor cells within organoids extend a network of long microtubes, recapitulating the in vivo behavior of GBM. Single-cell RNA-seq of GBM cells before and after co-culture with organoid cells reveals transcriptional changes implicated in the invasion process that are coherent across patient samples, indicating that GBM cells reactively upregulate genes required for their dispersion. Functional therapeutic targets are identified by an in silico receptor-ligand pairing screen detecting potential interactions between GBM and organoid cells. Taken together, our model has proven useful for studying GBM invasion and transcriptional heterogeneity in vitro, with applications for both pharmacological screens and patient-specific treatment selection at a time scale amenable to clinical practice.

scholarly journals Regulatory Hotspots in the Malaria Parasite Genome Dictate Transcriptional Variation

PLoS Biology ◽  
2008 ◽  
Vol 6 (9) ◽  
pp. e238 ◽  
Author(s):  
Joseph M Gonzales ◽  
Jigar J Patel ◽  
Napawan Ponmee ◽  
Lei Jiang ◽  
Asako Tan ◽  
...  
Keyword(s):  
Malaria Parasite ◽  
Parasite Genome ◽  
Transcriptional Variation

scholarly journals The Malaria Parasite Cyclic GMP-Dependent Protein Kinase Plays a Central Role in Blood-Stage Schizogony

2009 ◽  
Vol 9 (1) ◽  
pp. 37-45 ◽  
Author(s):  
Helen M. Taylor ◽  
Louisa McRobert ◽  
Munira Grainger ◽  
Audrey Sicard ◽  
Anton R. Dluzewski ◽  
...  
Keyword(s):  
Life Cycle ◽  
Protein Kinase ◽  
Cyclic Gmp ◽  
Malaria Parasite ◽  
Kinase Inhibitor ◽  
Blood Stage ◽  
Parasite Life Cycle ◽  
Dependent Protein Kinase ◽  
Asexual Blood Stage ◽  
Dependent Protein

ABSTRACT A role for the Plasmodium falciparum cyclic GMP (cGMP)-dependent protein kinase (PfPKG) in gametogenesis in the malaria parasite was elucidated previously. In the present study we examined the role of PfPKG in the asexual blood-stage of the parasite life cycle, the stage that causes malaria pathology. A specific PKG inhibitor (compound 1, a trisubstituted pyrrole) prevented the progression of P. falciparum schizonts through to ring stages in erythrocyte invasion assays. Addition of compound 1 to ring-stage parasites allowed normal development up to 30 h postinvasion, and segmented schizonts were able to form. However, synchronized schizonts treated with compound 1 for ≥6 h became large and dysmorphic and were unable to rupture or liberate merozoites. To conclusively demonstrate that the effect of compound 1 on schizogony was due to its selective action on PfPKG, we utilized genetically manipulated P. falciparum parasites expressing a compound 1-insensitive PfPKG. The mutant parasites were able to complete schizogony in the presence of compound 1 but not in the presence of the broad-spectrum protein kinase inhibitor staurosporine. This shows that PfPKG is the primary target of compound 1 during schizogony and provides direct evidence of a role for PfPKG in this process. Discovery of essential roles for the P. falciparum PKG in both asexual and sexual development demonstrates that cGMP signaling is a key regulator of both of these crucial life cycle phases and defines this molecule as an exciting potential drug target for both therapeutic and transmission blocking action against malaria.

scholarly journals Dual Plasmepsin-Targeting Antimalarial Agents Disrupt Multiple Stages of the Malaria Parasite Life Cycle

2020 ◽  
Vol 27 (4) ◽  
pp. 642-658.e12 ◽  
Author(s):  
Paola Favuzza ◽  
Manuel de Lera Ruiz ◽  
Jennifer K. Thompson ◽  
Tony Triglia ◽  
Anna Ngo ◽  
...  
Keyword(s):  
Life Cycle ◽  
Malaria Parasite ◽  
Parasite Life Cycle ◽  
Antimalarial Agents ◽  
Multiple Stages

scholarly journals Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

2020 ◽  
Vol 22 (8) ◽  
pp. 1138-1149 ◽  
Author(s):  
Teresa G Krieger ◽  
Stephan M Tirier ◽  
Jeongbin Park ◽  
Katharina Jechow ◽  
Tanja Eisemann ◽  
...  
Keyword(s):  
Single Cell ◽  
Specific Treatment ◽  
Therapy Resistance ◽  
Cellular Heterogeneity ◽  
Patient Specific ◽  
Before And After ◽  
Invasive Capacity ◽  
Transcriptional Changes

Abstract Background Glioblastoma (GBM) consists of devastating neoplasms with high invasive capacity, which have been difficult to study in vitro in a human-derived model system. Therapeutic progress is also limited by cellular heterogeneity within and between tumors, among other factors such as therapy resistance. To address these challenges, we present an experimental model using human cerebral organoids as a scaffold for patient-derived GBM cell invasion. Methods This study combined tissue clearing and confocal microscopy with single-cell RNA sequencing of GBM cells before and after co-culture with organoid cells. Results We show that tumor cells within organoids extend a network of long microtubes, recapitulating the in vivo behavior of GBM. Transcriptional changes implicated in the invasion process are coherent across patient samples, indicating that GBM cells reactively upregulate genes required for their dispersion. Potential interactions between GBM and organoid cells identified by an in silico receptor–ligand pairing screen suggest functional therapeutic targets. Conclusions Taken together, our model has proven useful for studying GBM invasion and transcriptional heterogeneity in vitro, with applications for both pharmacological screens and patient-specific treatment selection on a time scale amenable to clinical practice.

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