Biology subjects

La, K.

Publications and source records attributed to La, K..

6 recordsLinked to original sources

bioRxiv2024

Glycosaminoglycan-mediated lipoprotein uptake protects cancer cells from ferroptosis

Lipids are essential for tumours because of their structural, energetic, and signaling roles. While many cancer cells upregulate lipid synthesis, growing evidence suggests that tumours simultaneously intensify the uptake of circulating lipids carried by lipoproteins. Which mechanisms promote the uptake of extracellular lipids, and how this pool of lipids contributes to cancer progression, are poorly understood. Here, using functional genetic screens, we find that lipoprotein uptake confers resistance to lipid peroxidation and ferroptotic cell death. Lipoprotein supplementation robustly inhibits ferroptosis across numerous cancer types. Mechanistically, cancer cells take up lipoproteins through a pathway dependent on sulfated glycosaminoglycans (GAGs) linked to cell-surface proteoglycans. Tumour GAGs are a major determinant of the uptake of both low and high density lipoproteins. Impairment of glycosaminoglycan synthesis or acute degradation of surface GAGs decreases the uptake of lipoproteins, sensitizes cells to ferroptosis and reduces tumour growth in mice. We also find that human clear cell renal cell carcinomas, a distinctively lipid-rich tumour type, display elevated levels of lipoprotein-derived antioxidants and the GAG chondroitin sulfate than non-malignant human kidney. Altogether, our work identifies lipoprotein uptake as an essential anti-ferroptotic mechanism for cancer cells to overcome lipid oxidative stress in vivo, and reveals GAG biosynthesis as an unexpected mediator of this process.

cancer biology↗

bioRxiv2022

An updated evolutionary history and taxonomy of Mycobacterium tuberculosis lineage 5, also called M. africanum

Contrarily to other lineages such as L2 and L4, there are still scarce whole-genome-sequence data on L5-L6 MTBC clinical isolates in public genomes repositories. Recent results suggest a high complexity of L5 history in Africa. It is of importance for an adequate assessment of TB infection in Africa, that is still related to the presence of L5-L6 MTBC strains. This study reports a significant improvement of our knowledge of L5 diversity, phylogeographical history, and global population structure of Mycobacterium africanum L5. To achieve this aim, we sequenced new clinical isolates from Northern Nigeria and from proprietary collections, and used a new powerful bioinformatical pipeline, TB-Annotator that explores not only the shared SNPs but also shared missing genes, identical IS6110 insertion sites and shared regions of deletion. This study using both newly sequenced genomes and available public genomes allows to describe new L5 sublineages. We report that the MTBC L5 tree is made-up of at least 12 sublineages from which 6 are new descriptions. We confront our new classification to the most recent published one and suggest new naming for the discovered sublineages. Finally, we discuss the phylogeographical specificity of sublineages 5.1 and sublineage 5.2 and suggest a new hypothesis of L5-L6 emergence in Africa. Impact statementRecent studies on Mycobacterium africanum (L5-L6-L9 of MTBC) genomic diversity and its evolution in Africa discovered three new lineages of the Mycobacterium tuberculosis complex (MTBC) in the last ten years (L7, L8, L9). These discoveries are symptomatic of the delay in characterizing the diversity of the MTBC on the African continent. Another understudied part of MTBC diversity is the intra-lineage diversity of L5 and L6. This study unravels an hidden diversity of L5 in Africa and provides a more exhaustive description of specific genetic features of each sublineage by using a proprietary "TB-Annotator" pipeline. Furthermore, we identify different phylogeographical localization trends between L5.1 and L5.2, suggesting different histories. Our results suggest that a better understanding of the spatiotemporal dynamics of MTBC in Africa absolutely requires a large sampling effort and powerful tools to dig into the retrieved diversity. Data summary[A section describing all supporting external data, software or code, including the DOI(s) and/or accession numbers(s), and the associated URL. If no data was generated or reused in the research, please state this.] The search was done in the TB-Annotator 15901 genomes version which is available at: http://(to be added). The new sequenced genomes are available via NCBI Bioproject accession number: (to be added). The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

genomics↗

bioRxiv2021

Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis

Multiplexed mRNA profiling in the spatial context provides important new information enabling basic research and clinical applications. Unfortunately, most existing spatial transcriptomics methods are limited due to either low multiplexing or assay complexity. Here, we introduce a new spatialomics technology, termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA), that integrates in situ labeling of mRNA and protein markers in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, spectral and time-resolved fluorescence imaging, and machine learning-based target decoding. This technology is the first application combining the biophotonic techniques, Spectral and Fluorescence Lifetime Imaging and Microscopy (FLIM), to the field of spatial transcriptomics. By integrating the time dimension with conventional spectrum-based measurements, MOSAICA enables direct and highly-multiplexed in situ spatial biomarker profiling in a single round of staining and imaging while providing error correction removal of background autofluorescence. We demonstrate mRNA encoding using combinatorial spectral and lifetime labeling and target decoding and quantification using a phasor-based image segmentation and machine learning clustering technique. We then showcase MOSAICAs multiplexing scalability in detecting 10-plex targets in fixed colorectal cancer cells using combinatorial labeling of only five fluorophores with facile error-correction and removal of autofluorescent moieties. MOSAICAs analysis is strongly correlated with sequencing data (Pearsons r = 0.9) and was further benchmarked using RNAscopeand LGC Stellaris. We further apply MOSAICA for multiplexed analysis of clinical melanoma Formalin-Fixed Paraffin-Embedded (FFPE) tissues that have a high degree of tissue scattering and intrinsic autofluorescence, demonstrating the robustness of the approach. We then demonstrate simultaneous co-detection of protein and mRNA in colorectal cancer cells. MOSAICA represents a simple, versatile, and scalable tool for targeted spatial transcriptomics analysis that can find broad utility in constructing human cell atlases, elucidating biological and disease processes in the spatial context, and serving as companion diagnostics for stratified patient care.

bioengineering↗

bioRxiv2021

Enduring motor memory of walking on a split-belt treadmill in young children and adults

Adults and children modify how they move to accommodate persistent changes in their surroundings, called motor adaptation. Walking-related motor adaption can be seen when one walks on a treadmill with two belts running at different speeds, a split-belt treadmill, where a new walking pattern is slowly adopted with practice. This has been suggested as a way to improve left-right symmetry in walking after a stroke. Central to using split-belt walking for rehabilitation is whether the adapted motor pattern is retained over days and weeks, and whether this motor memory is a function of the persons age. When first exposed to split-belt walking, the walking is asymmetric (initial error), resembling a limp. With subsequent exposure, the error is smaller than the initial error, indicating the adaptation was remembered. Here, we explored the persistence of this memory over 24 hours, one week, and two weeks, in young children (3-6 yr old), younger adults (20-30 yr old) and older adults (50-70 yr old). We found that the motor memory declines with the interval duration, but was still evident up to 2 weeks after initial exposure. Retention of the motor memory in children and younger adults was better than older adults. Further, forgetting between trials was seen on the first day of split-belt walking especially in children and older adults, but this forgetting diminished with repeated trials. The results indicate that long-term memory of motor adaptation on the split-belt treadmill is affected by age, but it may be possible to enhance the memory by more frequent and repeated exposure. This suggests that when using split-belt adaptation in rehabilitation, the sessions should ideally be less than one week apart.

neuroscience↗

bioRxiv2021

Adaptive stimulation of macropinocytosis overcomes aspartate limitation in cancer cells under hypoxia

Stress-adaptive mechanisms enable tumor cells to overcome metabolic constraints in nutrient and oxygen poor tumors. Aspartate is an endogenous metabolic limitation under hypoxic conditions, but the nature of the adaptive mechanisms that contribute to aspartate availability and hypoxic tumor growth are poorly understood. Here, using a combination of metabolomics and CRISPR-based genetic screens, we identify GOT2-catalyzed mitochondrial aspartate synthesis as an essential metabolic dependency for the proliferation of pancreatic tumor cells under hypoxic culture conditions. In contrast, GOT2-catalyzed aspartate synthesis is dispensable for pancreatic tumor formation in vivo. The dependence of pancreatic tumor cells on aspartate synthesis is bypassed in part by a hypoxia-induced potentiation of extracellular protein scavenging via macropinocytosis. This effect is mutant KRas-dependent, and is mediated by hypoxia inducible factor 1 (HIF1A) and its canonical target carbonic anhydrase-9 (CA9) through the cooption of the bicarbonate-macropinocytosis signaling axis. Our findings reveal high plasticity of aspartate metabolism and define an adaptive regulatory role for macropinocytosis by which mutant KRas tumors can overcome nutrient deprivation under hypoxic conditions.

cancer biology↗

bioRxiv2020

Respiratory complex and tissue lineage drive mutational patterns in the tumor mitochondrial genome

Mitochondrial DNA (mtDNA) encodes essential protein subunits and translational machinery for four distinct complexes of oxidative phosphorylation (OXPHOS). Using repurposed whole-exome sequencing data, we demonstrate that pathogenic mtDNA mutations arise in tumors at a rate comparable to the most common cancer driver genes. We identify OXPHOS complexes as critical determinants shaping somatic mtDNA mutation patterns across tumor lineages. Loss-of-function mutations accumulate at an elevated rate specifically in Complex I, and often arise at specific homopolymeric hotspots. In contrast, Complex V is depleted of all non-synonymous mutations, suggesting that mutations directly impacting ATP synthesis are under negative selection. Both common truncating mutations and rarer missense alleles are associated with a pan-lineage transcriptional program, even in cancer types where mtDNA mutations are comparatively rare. Pathogenic mutations of mtDNA are associated with substantial increases in overall survival of colorectal adenocarcinoma patients, demonstrating a clear functional relationship between genotype and phenotype. The mitochondrial genome is therefore frequently and functionally disrupted across many cancers, with significant implications for patient stratification, prognosis and therapeutic development.

genomics↗