Single-cell evaluation of red blood cell bio-mechanical and nano-structural alterations upon chemically induced oxidative stress

Erythroid cells, specifically red blood cells (RBCs), are constantly exposed to highly reactive radicals during cellular gaseous exchange. Such exposure often exceeds the cells' innate anti-oxidant defense systems, leading to progressive damage and eventual senescence. One of the contributing factors to this process are alterations to hemoglobin conformation and globin binding to red cell cytoskeleton. However, in addition to the aforementioned changes, it is possible that oxidative damage induces critical changes to the erythrocyte cytoskeleton and corresponding bio-mechanical and nano-structural properties of the red cell membrane. To quantitatively characterize how oxidative damage accounts for such changes, we employed single-cell manipulation techniques such as micropipette aspiration and atomic force microscopy (AFM) on RBCs. These investigations demonstrated visible morphological changes upon chemically induced oxidative damage (using hydrogen peroxide, diamide, primaquine bisphosphate and cumene hydroperoxide). Our results provide previously unavailable observations on remarkable changes in red cell cytoskeletal architecture and membrane stiffness due to oxidative damage. Furthermore, we also demonstrate that a pathogen that infects human blood cells, Plasmodium falciparum was unable to penetrate through the oxidant-exposed RBCs that have damaged cytoskeleton and stiffer membranes. This indicates the importance of bio-physical factors pertinent to aged RBCs and it's relevance to malaria infectivity.Singapore-MIT Alliance for Research and Technology (Singapore. National Research Foundation

Wu's Method can Boost Symbolic AI to Rival Silver Medalists and AlphaGeometry to Outperform Gold Medalists at IMO Geometry

Proving geometric theorems constitutes a hallmark of visual reasoning combining both intuitive and logical skills. Therefore, automated theorem proving of Olympiad-level geometry problems is considered a notable milestone in human-level automated reasoning. The introduction of AlphaGeometry, a neuro-symbolic model trained with 100 million synthetic samples, marked a major breakthrough. It solved 25 of 30 International Mathematical Olympiad (IMO) problems whereas the reported baseline based on Wu's method solved only ten. In this note, we revisit the IMO-AG-30 Challenge introduced with AlphaGeometry, and find that Wu's method is surprisingly strong. Wu's method alone can solve 15 problems, and some of them are not solved by any of the other methods. This leads to two key findings: (i) Combining Wu's method with the classic synthetic methods of deductive databases and angle, ratio, and distance chasing solves 21 out of 30 methods by just using a CPU-only laptop with a time limit of 5 minutes per problem. Essentially, this classic method solves just 4 problems less than AlphaGeometry and establishes the first fully symbolic baseline strong enough to rival the performance of an IMO silver medalist. (ii) Wu's method even solves 2 of the 5 problems that AlphaGeometry failed to solve. Thus, by combining AlphaGeometry with Wu's method we set a new state-of-the-art for automated theorem proving on IMO-AG-30, solving 27 out of 30 problems, the first AI method which outperforms an IMO gold medalist.Comment: Work in Progress. Released for wider feedbac

Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites

International audienceDNA cytosine modifications are key epigenetic regulators of cellular processes in mammalian cells, with their misregulation leading to varied disease states. In the human malaria parasite Plasmodium falciparum, a unicellular eukaryotic pathogen, little is known about the predominant cytosine modifications, cytosine methylation (5mC) and hydroxymethylation (5hmC). Here, we report the first identification of a hydroxymethylcytosine-like (5hmC-like) modification in P. falciparum asexual blood stages using a suite of biochemical methods. In contrast to mammalian cells, we report 5hmC-like levels in the P. falciparum genome of 0.2–0.4%, which are significantly higher than the methylated cytosine (mC) levels of 0.01–0.05%. Immunoprecipitation of hydroxymethylated DNA followed by next generation sequencing (hmeDIP-seq) revealed that 5hmC-like modifications are enriched in gene bodies with minimal dynamic changes during asexual development. Moreover, levels of the 5hmC-like base in gene bodies positively correlated to transcript levels, with more than 2000 genes stably marked with this modification throughout asexual development. Our work highlights the existence of a new predominant cytosine DNA modification pathway in P. falciparum and opens up exciting avenues for gene regulation research and the development of antimalarial

tRNA epitranscriptomics and biased codon are linked to proteome expression in

Among components of the translational machinery, ribonucleoside modifications on tRNAs are emerging as critical regulators of cell physiology and stress response. Here, we demonstrate highly coordinated behavior of the repertoire of tRNA modifications of Plasmodium falciparum throughout the intra-erythrocytic developmental cycle (IDC). We observed both a synchronized increase in 22 of 28 modifications from ring to trophozoite stage, consistent with tRNA maturation during translational up-regulation, and asynchronous changes in six modifications. Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. We thus propose a model in which tRNA modifications modulate the abundance of stage-specific proteins by enhancing translation efficiency of codon-biased transcripts for critical genes. These findings reveal novel epitranscriptomic and translational control mechanisms in the development and pathogenesis of Plasmodium parasites.Singapore. National Research FoundationSingapore-MIT Alliance (Graduate Fellowship

Deciphering the Plasmodium epitranscriptome as a mechanism of translational control

Modifications to nucleosides present in ribonucleic acid (RNA) species have been shown to influence gene expression. Using a LC-MS/MS-based platform, we have characterized the full spectrum of modified ribonucleosides on the transfer RNA (tRNA) and messenger RNA (mRNA) in P. falciparum. We demonstrate that modifications on the wobble position of certain tRNA isoacceptors are associated with efficient translation of corresponding codon biased genes. Of the mRNA modifications, we quantified N6-methyladenosine (m6A) across the intra- erythrocytic lifecycle and characterized the putative “writer” enzyme complex that catalyses this modification. Upon carrying out m6A-sequencing, we find that m6A-associated transcripts have shorter half-lives and lower translation efficiency. Additionally, we quantified tRNA modification levels in the parasites that were exposed to oxidative stressors like hydrogen peroxide, sodium hypochlorite and anti-malarials like artemisinin and chloroquine. The work presented here holds potential for several avenues of new discovery. For one, unique patterns of tRNA modification reprograming can distinguish mechanistically distinct damaging agents which supports the idea the tRNA modification patterns can be used as biomarkers of exposure. Besides these stress-specific patterns of tRNA modification changes are linked to selective translation of codon-biased mRNAs for stress response proteins in other organisms. In order to address this hypothesis in Plasmodium we have carried out a proteomics experiment to determine if the parasite proteins that are upregulated show a marked codon bias which can be tied up with the tRNA modification data. All of these findings together provide new insights into the role of translational control mechanisms involving RNA modifications in the development and pathogenesis of malaria parasites.Doctor of Philosoph

Tissue-guided LASSO for prediction of clinical drug response using preclinical samples

Prediction of clinical drug response (CDR) of cancer patients, based on their clinical and molecular profiles obtained prior to administration of the drug, can play a significant role in individualized medicine. Machine learning models have the potential to address this issue but training them requires data from a large number of patients treated with each drug, limiting their feasibility. While large databases of drug response and molecular profiles of preclinical in-vitro cancer cell lines (CCLs) exist for many drugs, it is unclear whether preclinical samples can be used to predict CDR of real patients. We designed a systematic approach to evaluate how well different algorithms, trained on gene expression and drug response of CCLs, can predict CDR of patients. Using data from two large databases, we evaluated various linear and non-linear algorithms, some of which utilized information on gene interactions. Then, we developed a new algorithm called TG-LASSO that explicitly integrates information on samples’ tissue of origin with gene expression profiles to improve prediction performance. Our results showed that regularized regression methods provide better prediction performance. However, including the network information or common methods of including information on the tissue of origin did not improve the results. On the other hand, TG-LASSO improved the predictions and distinguished resistant and sensitive patients for 7 out of 13 drugs. Additionally, TG-LASSO identified genes associated with the drug response, including known targets and pathways involved in the drugs’ mechanism of action. Moreover, genes identified by TG-LASSO for multiple drugs in a tissue were associated with patient survival. In summary, our analysis suggests that preclinical samples can be used to predict CDR of patients and identify biomarkers of drug sensitivity and survival.Ope

Cohesin contributes to transcriptional repression of stage‐specific genes in the human malaria parasite

The authors would like to acknowledge the use of the Biomics and Flow Cytometry platforms at the Institut Pasteur, as well as the mass spectrometer facilities at A*STAR Institute of Molecular and Cell Biology in the laboratory of Dr. Radoslaw Sabota with the aid of Dr. Wint Wint Phoo.International audienceThe complex life cycle of the human malaria parasite, Plasmodium falciparum , is driven by specific transcriptional programs, but it is unclear how most genes are activated or silenced at specific times. There is an association between transcription and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks key genome‐organizing proteins found in metazoans, it has all core components of the cohesin complex. To investigate the role of cohesin in P. falciparum , we functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown during early stages of the intraerythrocytic developmental cycle (IDC) upregulates a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP‐seq analyses reveal that during the IDC, SMC3 enrichment at the promoter regions of these genes inversely correlates with gene expression and chromatin accessibility. These data suggest that SMC3 binding contributes to the repression of specific genes until their appropriate time of expression, revealing a new mode of stage‐specific gene repression in P. falciparum

Modulation of the Vault Protein-Protein Interaction for Tuning of Molecular Release.

Vaults are naturally occurring ovoid nanoparticles constructed from a protein shell that is composed of multiple copies of major vault protein (MVP). The vault-interacting domain of vault poly(ADP-ribose)-polymerase (INT) has been used as a shuttle to pack biomolecular cargo in the vault lumen. However, the interaction between INT and MVP is poorly understood. It is hypothesized that the release rate of biomolecular cargo from the vault lumen is related to the interaction between MVP and INT. To tune the release of molecular cargos from the vault nanoparticles, we determined the interactions between the isolated INT-interacting MVP domains (iMVP) and wild-type INT and compared them to two structurally modified INT: 15-amino acid deletion at the C terminus (INTΔC15) and histidine substituted at the interaction surface (INT/DSA/3 H) to impart a pH-sensitive response. The apparent affinity constants determined using surface plasmon resonance (SPR) biosensor technology are 262 ± 4 nM for iMVP/INT, 1800 ± 160 nM for iMVP/INTΔC15 at pH 7.4. The INT/DSA/3 H exhibits stronger affinity to iMVP (K Dapp  = 24 nM) and dissociates at a slower rate than wild-type INT at pH 6.0

Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite

International audienceMutually exclusive expression of the var multigene family is key to immune evasion and pathogenesis in Plasmodium falciparum, but few factors have been shown to play a direct role. We adapted a CRISPR-based proteomics approach to identify novel factors associated with var genes in their natural chromatin context. Catalytically inactive Cas9 ("dCas9") was targeted to var gene regulatory elements, immunoprecipitated, and analyzed with mass spectrometry. Known and novel factors were enriched including structural proteins, DNA helicases, and chromatin remodelers. Functional characterization of PfISWI, an evolutionarily divergent putative chromatin remodeler enriched at the var gene promoter, revealed a role in transcriptional activation. Proteomics of PfISWI identified several proteins enriched at the var gene promoter such as acetyl-CoA synthetase, a putative MORC protein, and an ApiAP2 transcription factor. These findings validate the CRISPR/dCas9 proteomics method and define a new var gene-associated chromatin complex. This study establishes a tool for targeted chromatin purification of unaltered genomic loci and identifies novel chromatin-associated factors potentially involved in transcriptional control and/or chromatin organization of virulence genes in the human malaria parasite