Biology subjects

Landry, J. J. M.

Publications and source records attributed to Landry, J. J. M..

6 recordsLinked to original sources

bioRxiv2023

A signalling rheostat controls chromosome segregation fidelity during early lineage specification and neurogenesis by modulating DNA replication stress

The development and homeostasis of organisms rely on the correct replication, maintenance and segregation of their genetic blueprints. How these intracellular processes are monitored across generations of different human cellular lineages, and why the spatio-temporal distribution of mosaicism varies during development remain unknown. Here, we identify several lineage specification signals that regulate chromosome segregation fidelity in both human and mouse pluripotent stem cells. Through epistatic analyses, we find that that WNT, BMP and FGF form a signalling "rheostat" upstream of ATM that monitors replication fork velocity, origin firing and DNA damage during S-phase in pluripotency, which in turn controls spindle polymerisation dynamics and faithful chromosome segregation in the following mitosis. Cell signalling control of chromosome segregation fidelity declines together with ATM activity after pluripotency exit and specification into the three human germ layers, or further differentiation into meso- and endoderm lineages, but re-emerges during neuronal lineage specification. In particular, we reveal that a tug-of-war between FGF and WNT signalling in neural progenitor cells results in DNA damage and chromosome missegregation during cortical neurogenesis, which could provide a rationale for the high levels of mosaicism in the human brain. Our results highlight a moonlighting role of morphogens, patterning signals and growth factors in genome maintenance during pluripotency and lineage specification, which could have important implications for our understanding on how mutations and aneuploidy arise during human development and disease. One sentence summaryDevelopmental signals link genome maintenance to cell fate

cell biology↗

bioRxiv2022

Co-translational binding of importins to nascent proteins

Various cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent misfolding of nascent chains during translation, importins were shown to prevent the aggregation of specific cargoes in a post-translational mechanism prior the import into the nucleoplasm. Here, we hypothesized that importins may already bind ribosome-associated cargo in a co-translational manner. We systematically measured the nascent chain association of all importins in Saccharomyces cerevisiae by selective ribosome profiling. We identified a subset of importins that bind to a wide range of nascent, often uncharacterized cargoes. This included ribosomal proteins, chromatin remodelers and RNA binding proteins that are aggregation prone in the cytosol. We show that importins act consecutively with other ribosome-associated chaperones. Thus, the nuclear import system is directly intertwined with nascent chain folding and chaperoning. One-Sentence SummaryWe describe an unanticipated connection between co-translational protein chaperoning and the nuclear import system.

molecular biology↗

bioRxiv2022

Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia

Inter-patient variability and the similarity of healthy and leukemic stem cells have impeded the characterization of leukemic stem cells (LSCs) in acute myeloid leukemia (AML), and their differentiation landscape. Here, we introduce CloneTracer, a novel method that adds clonal resolution to single-cell RNA-seq datasets. Applied to samples from 19 AML patients, CloneTracer revealed routes of leukemic differentiation. While residual healthy cells dominated the dormant stem cell compartment, active leukemic stem cells resembled their healthy counterpart and retained erythroid capacity. By contrast, downstream myeloid progenitors were highly aberrant and constituted the disease-defining compartment: Their gene expression and differentiation state determined both chemotherapy response and the leukemias ability to differentiate to transcriptomically normal monocytes. Finally, we demonstrated the potential of CloneTracer to identify surface markers mis-regulated specifically in leukemic cells by intra-patient comparisons. Taken together, CloneTracer revealed a differentiation landscape that mimics its healthy counterpart and determines biology and therapy response in AML.

cancer biology↗

bioRxiv2021

Co-translational assembly counteracts promiscuous interactions

During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examined structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally tested candidate structural motifs and identified several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assembled co-translationally in only one but not all of the relevant assembly pathways. Our results highlight the regulatory complexity of assembly pathways.

molecular biology↗

bioRxiv2021

Extensive OMICS resource for Sf21 and Tni cell lines

Insect-derived cell lines, from Spodoptera frugiperda (Sf21) and from Trichoplusia ni (Tni), are the two most widely used cell lines for recombinant protein expression in combination with the Baculoviral Expression Vector System (BEVS). Genomic sequences and annotations are still incomplete for Sf21 and absent for Tni. In this study, we present an approach using different sequencing data types, including short-read sequencing, long synthetic and Oxford Nanopore reads, to build genomes. The Sf21 and Tni assemblies contain 4,020 scaffolds of 463 Mb in size with N50 of 364 Kb and 2,954 scaffolds of 332 Mb in size with N50 of 326 Kb, respectively. Furthermore, we built a new gene prediction workflow, which integrates transcriptome and proteome information using pre-existing tools. Using this approach, we predicted 21,506 Sf21 and 14,159 Tni genes, generated and integrated proteomic datasets to validate predicted genes and could identify 5577 and 4919 proteins in the Sf21 and Tni cell lines respectively. This integrative approach could be theoretically applied to any uncharacterized genome and result in valuable new resources. With this information available, Sf21 and Tni cells will become even better tools for protein expression and could be used in a wider range of applications, from promoter identification to genome engineering and editing.

genomics↗

bioRxiv2017

Single-cell RNA-sequencing redefines blood cell type classification in mosquitoes

Mosquito blood cells are ancestral immune cells that help control infection by vector-borne pathogens. Despite their importance, little is known about mosquito blood cell biology beyond the ambiguous morphological and functional criteria used for their classification. Here we combined the power of single-cell RNA-sequencing, imaging flow cytometry and single-molecule RNA hybridization to analyze blood cells of the malaria mosquito Anopheles gambiae. By demonstrating that blood cells express nearly half of the mosquito transcriptome, our dataset represents an unprecedented view into their transcriptional machinery. Analyses of differentially expressed genes identified transcriptional signatures of two distinct cell types that challenge the current morphology-based classification of these cells. We further demonstrated an active transfer of a cellular marker between blood cells that confounds their identity. We propose that cell-to-cell exchange is broadly relevant for cell type classification and may account for the remarkable cellular diversity observed in nature.

immunology↗