Biology subjects

Bozdech, Z.

Publications and source records attributed to Bozdech, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-omic profiling of Plasmodium knowlesi blood stages identifies host adaptation barriers

The zoonotic parasite Plasmodium knowlesi has emerged as a widespread cause of human malaria in Southeast Asia. We assembled a high-resolution transcriptome of zoonotic P. knowlesi across its intraerythrocytic developmental cycle and combined transcriptomics, quantitative proteomics and thermal stability measurements to compare parasites cultured in macaque and human red blood cells. We found that P. knowlesi accelerates through the ring stage to settle at the same developmental pace as P. falciparum during the trophozoite and schizont stages. Subsequent multi-omic analysis revealed broad transcriptional and proteomic adaptations of P. knowlesi to the human host cell environment. Parasites cultured in human cells expressed glutathione synthetase earlier and displayed changes in upstream processes that include NADPH production by the pentose phosphate pathway and glutamine synthesis. These changes were accompanied by further differences in the expression of ribosomal subunits and mitochondrial respiratory complexes. Together, our findings offer a systems-level view of non-genetic adaptations of P. knowlesi to the human red blood cell environment.

microbiology↗

bioRxiv2026

A chromosome-scale Plasmodium cynomolgi Berok genome reveals a distinct subtelomeric architecture and a highly diverged primate malaria lineage

Plasmodium cynomolgi is the closest relative of P. vivax and the primary experimental model for relapsing malaria, hypnozoite biology, and blood-stage drug susceptibility. Yet existing reference genomes remain fragmented, leaving structurally complex, AT-rich regions largely unresolved. We generated a chromosome-scale genome assembly for the K4-A7 cloned line of P. cynomolgi Berok by combining Hi-C chromosome conformation capture, Oxford Nanopore long reads, PacBio, and Illumina sequencing. The assembly spans 14 chromosomes plus mitochondrial and apicoplast genomes, with only seven unplaced minor contigs, the fewest for any non-P. falciparum Plasmodium genome, and an N50 of 3.06 Mb. Critically, this hybrid strategy resolved approximately 8 Mb of extremely AT-rich (~20% GC) sequence onto chromosomes 4, 8, and 13, anchoring what were previously unplaced or absent contigs into a continuous chromosomal framework. These subtelomere-like expansions (SLEs) constitute ~26.5% of the chromosomal genome and are enriched for PIR/VIR, STP1, variable surface antigen, and methyltransferase pseudogene families. Despite low gene density, SLE-encoded genes are transcriptionally active and show stage-specific expression across the erythrocytic cycle. Integrated lifecycle transcriptomics across 7,006 genes revealed a ~54-hour erythrocytic cycle with a "just-in-time" transcriptional cascade closely resembling that of P. vivax. Phylogenomic analyses and pairwise amino acid comparisons across more than 2,600 single-copy orthologs show that Berok forms a deeply diverged P. cynomolgi lineage, suggesting a distinct subspecies. This assembly establishes a high-resolution genomic foundation for comparative malaria biology, drug discovery, and the study of subtelomeric architecture, host adaptation, and lineage boundaries in primate Plasmodium.

microbiology↗

bioRxiv2026

Dihydroartemisinin induces a two-step transcriptional response and stage-specific developmental shifts in malaria parasites, Plasmodium falciparum

The parasite Plasmodium falciparum causes malaria, the deadliest human parasitic disease, which remains fatal when not promptly treated. Evolving parasite resistance to frontline artemisinin-based therapies threatens vulnerable populations and decades of progress toward malaria elimination. Yet the mode of action of dihydroartemisinin (DHA), the active metabolite of these treatments, remains incompletely understood. Here we applied dose-response transcriptomics across the three intraerythrocytic stages - rings, trophozoites, and schizonts, revealing a two-tier transcriptional response to DHA, with low- and high-dose programs consistent with specific drug action and cytotoxic damage. The trophozoite stage mounts the strongest and most coordinated response, including a striking reversal of the developmental cascade in which protein synthesis machinery is broadly downregulated and a ring-like transcriptional profile is reactivated - reminiscent of drug-induced quiescence. Coordinated regulation of multiple protein complexes, most notably Kelch13 and its interacting partners (KIC), points to organized transcriptional control of the parasites drug response. This work provides a stage- and dose-resolved view of DHA action in P. falciparum and a template for future antimalarial mechanism-of-action studies.

Systems Biology↗

bioRxiv2026

Integrative genomics of Plasmodium knowlesi reveals parasite-intrinsic regulators of severe human malaria

To dissect parasite determinants of clinical disease severity in Plasmodium knowlesi, we performed the first integrative genome-wide association (GWAS), transcriptomic, and expression quantitative trait locus (eQTL) analysis from clinical malaria isolates. We identify distinct parasite programs associated with WHO-defined severe disease, characterized by transcriptional activation of stress-response and host-interaction pathways. In contrast, invasion-linked programs were more strongly associated with parasite burden, while immune-evasion pathways showed overlapping but distinct associations with both burden and severity. GWAS and eQTL analyses revealed genetic regulation of transcriptional states, including immune-evasion variant antigen families (SICAvar and kir) and chromatin-associated regulators. Mature gametocyte transcripts were detectable across infections, including those with low parasitaemia, indicating that transmission-stage expression occurs independently of both clinical severity and parasite density. Together, these findings show that severe P. knowlesi malaria is associated with genetically regulated parasite transcriptional programs that are not fully explained by parasite burden.

genomics↗

bioRxiv2026

Thermal proteome profiling identifies new drug targets in Plasmodium falciparum parasites

Spreading resistance to clinically used antimalarial drugs increases the need for identification of new drug targets. Here, we screened 25 antimalarials with known and unknown mode of action to validate old and find new drug targets in P. falciparum. Combining experimental approach by proteome-wide cellular thermal shift assay and computational filtering by molecular docking, we found the drugs to bind to previously known drug targets, validated ACS10 as the target of MMV665915 and discovered new drug targets. Furthermore, we updated the experimental and analytical MS-CETSA pipeline with the inclusion of membrane solubilization step, validated the targets of atovaquone and cipargamin on cell lysates and in intact cells and mapped the parasite response to these antimalarials, identifying monocarboxylate transporter MCP2 as atovaquone transporter.

microbiology↗

bioRxiv2025

Inhibition of PfCLK3 a master regulator of malaria parasite RNA-splicing provides the basis for a radical cure for malaria

Emerging resistance to front-line anti-malarials means there is a race to discover new drugs with novel mechanisms of action that remain effective across multiple stages of the parasite life cycle. Previously we reported the malaria protein kinase, PfCLK3, as a target offering a cure, prophylaxis and transmission blocking. The homology between PfCLK3 and human kinases suggested that the mechanism of parasiticidal activity of PfCLK3 inhibitors is disruption of RNA processing. Here, we use whole genome RNA-sequencing to reveal that selective PfCLK3 inhibition extensively affects RNA-splicing with 2039 splice-junctions across 1125 genes mis-spliced in treated wild type parasites compared to controls. The function of mis-spliced transcripts showed that the affected genes were involved in numerous essential parasite processes associated with multiple life cycle stages and revealed transcripts and introns particularly susceptible to inhibition. Our study supports the role of PfCLK3 as an important regulator of spliceosome activity and establishes the distinct mechanism of parasiticidal activity of PfCLK3 inhibitors from current front-line treatments.

molecular biology↗

bioRxiv2024

Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia.

Sabah, Malaysia, has amongst the highest burden of human Plasmodium knowlesi infection in the country, associated with increasing encroachment on the parasites macaque host habitat. However, the genomic make-up of P. knowlesi in Sabah was previously poorly understood. To inform on local patterns of transmission and putative adaptive drivers, we conduct population-level genetic analyses of P. knowlesi human infections using 52 new whole genomes from Sabah, Malaysia, in combination with publicly available data. We identify the emergence of distinct geographical subpopulations within the macaque-associated clusters using IBD-based connectivity analysis. Secondly, we report on introgression events between the clusters, which may be linked to differentiation of the subpopulations, and that overlap genes critical for survival in human and mosquito hosts. Using village-level locations from P. knowlesi infections, we also identify associations between several introgressed regions and both intact forest perimeter-area ratio and mosquito vector habitat suitability. Our findings provide further evidence of the complex role of changing ecosystems and sympatric macaque hosts in Malaysia driving distinct genetic changes seen in P. knowlesi populations. Future expanded analyses of evolving P. knowlesi genetics and environmental drivers of transmission will be important to guide public health surveillance and control strategies. Author SummaryThe zoonotic P. knowlesi parasite is an emerging, yet understudied, cause of malaria in Southeast Asia. Sabah, Malaysia, has amongst the highest burden of human P. knowlesi infection in the country, however, the region is currently understudied. Thus, we produced a collection of high-quality P. knowlesi genomes from Sabah, and in combination with publicly available data, performed an extensive population genetics analysis. Our work contributes novel insights for Plasmodium knowlesi population genetics and genetic epidemiology.

genomics↗

bioRxiv2024

A complex Plasmodium falciparum cryptotype circulating at low frequency across the African continent

The population structure of the malaria parasite Plasmodium falciparum can reveal underlying demographic and adaptive evolutionary processes. Here, we analyse population structure in 4,376 P. falciparum genomes from 21 countries across Africa. We identified a strongly differentiated cluster of parasites, comprising [~]1.2% of samples analysed, geographically distributed over 13 countries across the continent. Members of this cluster, named AF1, carry a genetic background consisting of a large number of highly differentiated variants, rarely observed outside this cluster, at a multitude of genomic loci distributed across most chromosomes. At these loci, the AF1 haplotypes appear to have common ancestry, irrespective of the sampling location; outside the shared loci, however, AF1 members are genetically similar to their sympatric parasites. AF1 parasites sharing up to 23 genomic co-inherited regions were found in all major regions of Africa, at locations over 7,000 km apart. We coined the term cryptotype to describe a complex common background which is geographically widespread, but concealed by genomic regions of local origin. Most AF1 differentiated variants are functionally related, comprising structural variations and single nucleotide polymorphisms in components of the MSP1 complex and several other genes involved in interactions with red blood cells, including invasion and erythrocyte antigen export. We propose that AF1 parasites have adapted to some as yet unidentified evolutionary niche, by acquiring a complex compendium of interacting variants that rarely circulate separately in Africa. As the cryptotype spread across the continent, it appears to have been maintained mostly intact in spite of recombination events, suggesting a selective advantage. It is possible that other cryptotypes circulate in Africa, and new analysis methods may be needed to identify them.

genomics↗

bioRxiv2023

Repeated Plasmodium vivax blood stage infection provides sterile protection against homologous challenge in non-human primates

The malaria parasite Plasmodium vivax remains a major global public health challenge, causing major morbidity across tropical and subtropical regions. Several candidate vaccines are in preclinical and clinical trials, however no vaccine against P. vivax malaria is approved for use in humans. Here we assessed whether P. vivax strain-transcendent immunity can be achieved by repeated infection in Aotus monkeys. For this purpose, we repeatedly infected six animals with blood stages of the P. vivax Salvador 1 (SAL-1) strain until sterile immune, and then challenged with the AMRU-1 strain. Sterile immunity was achieved in 4/4 Aotus monkeys after two homologous infections with the SAL-1 strain, while partial protection against a heterologous AMRU-1 challenge (i.e., delay to infection and reduction in peak parasitemia compared to control) was achieved in 3/3 monkeys. IgG levels based on P. vivax lysate ELISA and protein microarray increased with repeated infections and correlated with the level of homologous protection. Analysis of parasite transcriptional profiles across inoculation levels provided no evidence of major antigenic switching upon homologous or heterologous challenge. In contrast, we observed significant transcriptional differences in the P. vivax core gene repertoire between SAL-1 and AMRU-1. Together with the strain-specific genetic diversity between SAL-1 and AMRU-1 these data suggest that the partial protection upon heterologous challenge is due to molecular differences between strains (at genome and transcriptome level) rather than immune evasion by antigenic switching. Our study demonstrates that sterile immunity against P. vivax can be achieved by repeated homologous blood stage infection in Aotus monkeys, thus providing a benchmark to test the efficacy of candidate blood stage P. vivax malaria vaccines. Author summaryPlasmodium vivax is the most widespread human malaria parasite. Elimination efforts are complicated due to the peculiar biology of P. vivax including dormant liver forms, cryptic reservoirs in bone marrow and spleen and a large asymptomatic infectious reservoir in affected populations. Currently there is no vaccine against malaria caused by P. vivax. Here we induce sterile immunity by repeated P. vivax infection with the SAL-1 strain in non-human primates. In contrast, heterologous challenge with the AMRU-1 strain only provided partial protection. Antibody levels against a crude antigen and a protein microarray correlated with the level of homologous protection. Parasite transcriptional profiles across inoculation levels failed to show major antigenic switching across SAL-1 infections or upon heterologous challenge, instead suggesting other mechanisms of immune evasion. Our study demonstrates that sterile immunity against P. vivax can be achieved by repeated blood stage infection in Aotus monkeys, thus providing a benchmark to test the efficacy of candidate blood stage P. vivax malaria vaccines.

microbiology↗

bioRxiv2023

The artemisinin-induced dormant stages of Plasmodium falciparum exhibit hallmarks of cellular senescence and drug resilience.

Recrudescent infections with human malaria parasite, Plasmodium falciparum, presented traditionally the major setback of artemisinin-based monotherapies. Although introduction of artemisinin combination therapies (ACT) largely solved the problem, the ability of artemisinin to induce dormant parasites still poses major obstacle for current as well as future malaria chemotherapeutics. Here, we developed a robust laboratory model for induction of dormant P. falciparum parasites and characterized their transcriptome, drug sensitivity profile and cellular ultrastructure. We show that P. falciparum dormancy requires a ~5-days maturation process during which the genome-wide gene expression pattern gradually transitions from the ring-like state to a highly unique form. The transcriptome of the mature dormant stage carries hallmarks of cellular senescence with downregulation of most cellular functions associated with growth and development, but upregulation of selected metabolic functions and DNA repair. Moreover, the P. falciparum dormant stage is considerably more resistant to essentially all antimalaria drugs compared to the fast-growing asexual stages. Finally, the unique cellular ultrastructure further suggests unique properties of this new developmental stage of the P. falciparum life cycle that should be taken into consideration by new malaria control strategies.

microbiology↗

bioRxiv2022

Quinazoline-quinoline bisubstrate inhibitors target eukaryotic translation initiation factor 3 in Plasmodium falciparum

Malaria drug resistance is hampering the fight against the deadliest parasitic disease affecting over 200 million people worldwide. We recently developed quinoline-quinazoline-based inhibitors (as compound 70) as promising new antimalarials. Here we aimed to investigate their mechanism of action by using Thermal Proteome Profiling (TPP). The eukaryotic translation initiation factor 3 (EIF3i) subunit I was identified as the main target of the inhibitor in P. falciparum. This protein is not a known drug target in malaria parasites. P. falciparum parasite lines were generated expressing either a HA tag or an inducible knockdown of the PfEIF3i gene to further characterize the target protein. PfEIF3i was stabilized in presence of the compound 70 in a cellular thermal shift-western blot assay, confirming that PfEIF3i is a target of quinoline-quinazoline-based inhibitors. In addition, PfEIF3i-inducible knock-down blocks intra-erythrocytic development in the trophozoite stage indicating that it has a vital function. We show that PfEIF3i is mostly expressed in late intraerythrocytic stages and localizes in the cytoplasm. Previous mass spectrometry reports show that EIF3i is expressed in all parasite life cycle stages. Hence, quinoline-quinazoline-based inhibitors allowed to identify PfEIF3i as a valuable target for the design of new antimalarial drugs active all along the life cycle of the parasite.

pharmacology and toxicology↗

bioRxiv2022

FKBP35 secures ribosome homeostasis in Plasmodium falciparum

Plasmodium falciparum accounts for the majority of over 600000 malaria-associated deaths annually. Parasites resistant to nearly all antimalarials have emerged and the need for drugs with alternative modes of action is thus undoubted. The FK506-binding protein PfFKBP35 has gained attention as a promising drug target due to its high affinity to the macrolide compound FK506 (tacrolimus). Whilst there is considerable interest in targeting PfFKBP35 with small molecules, a genetic validation of this factor as a drug target is missing and its function in parasite biology remains elusive. Here, we show that limiting PfFKBP35 levels are lethal to P. falciparum and result in a delayed death-like phenotype that is characterized by defective ribosome homeostasis and stalled protein synthesis. Our data furthermore suggest that FK506, unlike the action of this drug in model organisms, exerts its anti-proliferative activity in a PfFKBP35-independent manner and, using cellular thermal shift assays, we identify putative FK506-targets beyond PfFKBP35. In addition to revealing first insights into the function of PfFKBP35, our results show that FKBP-binding drugs can adopt non-canonical modes of action - with major implications for the development of FK506-derived molecules active against Plasmodium parasites and other eukaryotic pathogens.

molecular biology↗

bioRxiv2022

Genomic, transcriptomic, and metabolomic analysis of Traditional Chinese Medicine plant Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites

Natural products from traditional medicinal plants are valuable candidates for clinical cancer therapy. Plants from the Oldenlandia-Hedyotis complex are popular ingredients of Traditional Chinese Medicine (TCM), however a major hurdle in the plant bioprospecting process of TCM plants is that the active metabolites, their biosynthetic pathways, and mode of action are often unknown. We show that Oldenlandia corymbosa extracts are active against breast cancer cell lines. To study the genes involved in the biosynthesis of active compounds in this medicinal plant, we assembled a high-quality genome. We show that the main active compound is ursolic acid and that abiotic stresses cause changes in anti-cancer activity, metabolite composition, and gene expression of plants. To reveal the mode of action of ursolic acid, we show that cancer cells undergo mitotic catastrophe, and we identify three high-confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking.

plant biology↗

bioRxiv2022

Human peroxiredoxin 6 is essential for malaria parasites and provides a host-based drug target

The uptake and digestion of host hemoglobin by malaria parasites during blood stage growth leads to significant oxidative damage of membrane lipids. Repair of lipid peroxidation damage is crucial for parasite survival. Here, we demonstrate that Plasmodium falciparum imports a host antioxidant enzyme, peroxiredoxin 6 (PRDX6), during hemoglobin uptake from the red blood cell cytosol. PRDX6 is a lipid peroxidation repair enzyme with phospholipase A2 (PLA2) activity. Inhibition of PRDX6 with a PLA2 inhibitor, Darapladib, increases lipid peroxidation damage in the parasite and disrupts transport of hemoglobin-containing vesicles to the food vacuole, causing parasite death. Furthermore, inhibition of PRDX6 synergistically reduces the survival of artemisinin-resistant parasites following co-treatment of parasite cultures with artemisinin and Darapladib. Thus, PRDX6 is a unique host-derived drug target for development of antimalarial drugs that could help overcome artemisinin resistance. GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cell biology↗

bioRxiv2021

The mechanism of artemisinin resistance of Plasmodium falciparum malaria parasites originates in their initial transcriptional response.

The emergence and spread of artemisinin resistant Plasmodium falciparum, first in the Greater Mekong Subregion (GMS), and now in East Africa, is a major threat to global malaria eliminations ambitions. To investigate the artemisinin resistance mechanism, transcriptome analysis was conducted of 577 P. falciparum isolates collected in the GMS between 2016-2018. A specific artemisinin resistance-associated transcriptional profile was identified that involves a broad but discrete set of biological functions related to proteotoxic stress, host cytoplasm remodeling and REDOX metabolism. The artemisinin resistance-associated transcriptional profile evolved from initial transcriptional responses of susceptible parasites to artemisinin. The genetic basis for this adapted response is likely to be complex. One sentence summaryThe transcriptional profile that characterize artemisinin resistant infections with malaria parasites Plasmodium falciparum originates in the initial transcriptional response to the drug.

systems biology↗

bioRxiv2021

Identification of an inhibitory pocket in falcilysin bound by chloroquine provides a new avenue for malaria drug development

Despite their widespread use, our understanding of how many antiparasitic drugs work remains limited. We used mass-spectrometry based cellular thermal shift assay (MS-CETSA) to identify possible protein targets of several malaria drugs and drug candidates. We found that falcilysin (FLN) is a common target for several quinoline drugs including chloroquine and mefloquine, as well as drug candidates MK-4815, MMV000848 and MMV665806. At pH 7.5, these compounds all inhibit FLN proteolytic activity with IC50 values ranging from 1.6 to 67.9 {micro}M. Their interaction with FLN was systematically probed by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with depleted FLN expression demonstrated statistically significant increases in susceptibility towards chloroquine, mefloquine, MK-4815 and MMV000848. Taken together, our findings point to a multimodal mechanism of action for several commonly used anti-malaria drugs. Importantly, a common allosteric pocket of FLN appears amenable to inhibition, providing a structural basis to guide the development of novel drugs against malaria.

microbiology↗

bioRxiv2021

The PfAP2-HS transcription factor protects malaria parasites from febrile temperatures

Periodic fever is the most characteristic clinical feature of human malaria1-3, but how parasites survive febrile episodes is not known. While Plasmodium spp. genomes encode a full complement of chaperones4, they lack an ortholog of the conserved transcription factor HSF1, which in most eukaryotes activates the expression of key chaperones upon heat shock (HS)5-8. Here we identified PfAP2-HS, a transcription factor of the ApiAP2 family9-11, as the key regulator of the P. falciparum protective HS response. The PfAP2-HS-dependent HS response is largely restricted to rapid activation of hsp70-1, the predominant direct target of PfAP2-HS, and hsp90. Deletion of PfAP2-HS dramatically reduced HS survival and also resulted in severe growth defects at 37{degrees}C, but not at 35{degrees}C, and increased sensitivity to imbalances in protein homeostasis (proteostasis) produced by artemisinin, the current frontline antimalarial drug12,13. These results demonstrate that PfAP2-HS contributes to general maintenance of proteostasis and drives a rapid chaperone-based protective response against febrile temperatures. While several ApiAP2 transcription factors regulate life cycle transitions in malaria parasites11,14,15, PfAP2-HS is the first identified Plasmodium transcription factor that controls a protective response to a within-host environmental challenge.

microbiology↗

bioRxiv2020

Reverse transcription quantitative PCR to detect low density malaria infections

Targeted malaria elimination strategies require highly sensitive tests to detect low density malaria infections (LDMI). Commonly used methods for malaria diagnosis such as light microscopy and antigen-based rapid diagnostic tests (RDTs) are not sensitive enough for reliable identification of infections with parasitaemia below 200 parasites per milliliter of blood. While targeted malaria elimination efforts on the Thailand-Myanmar border have successfully used high sample volume ultrasensitive quantitative PCR (uPCR) to determine malaria prevalence, the necessity for venous collection and processing of large quantities of patient blood limits the widespread tractability of this method. Here we evaluated a real-time quantitative reverse transcription PCR (qRT-PCR) method that significantly reduces the required sample volume compared to uPCR. To do this, 304 samples collected from an active case detection program in Kayin state, Myanmar were compared using uPCR and qRT-PCR. Plasmodium spp. qRT-PCR confirmed 18 of 21 uPCR Plasmodium falciparum positives, while P. falciparum specific qRT-PCR confirmed 17 of the 21 uPCR P. falciparum positives. Combining both qRT-PCR results increased the sensitivity to 100% and specificity was 95.1%. These results show that malaria detection in areas of low transmission and LDMI, can benefit from the increased sensitivity of qRT-PCR especially where sample volume is limited.

microbiology↗