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Biology subjects

Lewis, C.

Publications and source records attributed to Lewis, C..

At least 19 recordsLinked to original sources

Genome-wide CRISPRi mapping of mycobacteriophage interaction determinants in Mycobacterium smegmatis mc2155

Bacteriophages are highly specific predators of bacterial hosts, but the molecular mechanisms governing their entry across the structurally complex mycobacterial cell envelope remain poorly defined. Utilizing a genome-wide CRISPR interference library in the model organism Mycobacterium smegmatis against a phylogenetically representative collection of 70 mycobacteriophages, we mapped the functional architecture of host susceptibility determinants. This parallelized genetic screen revealed a spatial continuum of infection requirements spanning from outer leaflet surface structures down to deep cytoplasmic machinery. The four major outer membrane Mycobacterium smegmatis porins (Msp) emerged as the dominant candidate receptor family for 46 diverse phages, representing the first protein receptors identified within this group. Interrogating the asymmetric outer bilayer also implicated cell envelope glycolipids as candidate receptors for 14 phages, resolving into glycopeptidolipid sub-lineages. Beneath the mycomembrane, arabinogalactan functions as a candidate secondary receptor for 5 phages, while the inner membrane lipid transporter MmpL11 and the global nucleoid-associated protein Lsr2 represent determinant factors for 14 and 31 phages respectively. While physical deletions of major porins trigger spontaneous regulatory pathways that upregulate silent backup paralogues, acute transcriptional knockdowns circumvent suppressor accumulation, revealing unmasked single-gene dependencies. Structural analysis demonstrated that host determinant usage decouples entirely from whole-genome viral phylogeny, indicating that standard phylogenetic groupings fail to predict surface recognition profiles. Ultimately, mapping this host interactome reveals an evolutionary strategy where phages target highly redundant or abundant host machinery to exploit fixed physiological liabilities, presenting a robust molecular blueprint for the rational engineering of escape-resistant therapeutic phage cocktails.

microbiology↗

Sediment depth-dependent trait expression controls species contributions to nutrient cycling

Global biodiversity loss is restructuring ecological communities and compromising ecosystem functioning. Yet, we still lack an empirical understanding of how specific trait combinations regulate ecosystem processes or how their functional expression is organised within the immediate environment. Here, we investigated trait-expression across 17 functionally contrasting sediment-dwelling marine invertebrate species. We show that while sediment reworking and burrow ventilation are depth dependent, their influence on nutrient concentrations are highly nutrient-specific. Our analyses reveal that nutrient concentrations are better explained by continuous, spatially explicit trait combinations than by categorical bioturbation modes. Surface modification was associated with higher ammonium concentrations, moderated by ventilation, while deeper sediment reworking and biomass were associated with higher nitrite concentrations. Phosphate relationships were weak, and nitrate was not explained by the measured traits. These results establish a mechanistic baseline for species-specific trait-nutrient relationships under controlled conditions. This shift from categorical trait assignments to a spatially explicit, empirically resolved trait-interaction framework provides a mechanistic foundation for predicting how changes in species composition may alter benthic nutrient cycling.

ecology↗

High nitrogen deposition is associated with phosphorus-efficient ectomycorrhizas in Europe's Scots pine forests

Atmospheric inorganic nitrogen (N) deposition has been linked to increased tree phosphorus (P) deficiency and shifts in ectomycorrhizal (ECM) fungal community composition across Europe, but the underlying mechanisms remain poorly understood due to the scarcity of species-level studies of fungal physiology at large spatial scales. Here, we characterized ECM communities in nine Scots pine (Pinus sylvestris L.) stands across Europes largest N deposition gradient to gain mechanistic insight into N-driven ECM community shifts, by assessing morpho-physiological traits (i.e. soil exploration types and ECM root-tip level exoenzyme activities involved in organic N and P acquisition) on individual ectomycorrhizas. Our data revealed high functional variation in foraging strategies across species and sites, including within dominant ECM genera (Cortinarius, Elaphomyces, Lactarius, Piloderma, Russula). Shifts in community-level exoenzyme activities along the N deposition gradient were consistent with increasing P limitation, with a buffering effect of phosphomonoesterase activity on host nutritional status (i.e. reduced foliar N:P). These trends were mainly driven by interspecific differences in enzymatic profiles and species turnover along the gradient, rather than intraspecific variation within widespread species. Dominant low-biomass species in high N sites (e.g. E. citrinopapillatus, L. subdulcis, R. ochroleuca) were efficient P-foragers, with some displaying high oxidative activity, potentially hampering soil carbon storage under elevated N loads. These findings highlight the role of ECM species-specific traits in mediating ecosystem processes and can help understand the future of pine forests under chronic N pollution, with potential implications for applied forestry.

ecology↗

Novel clonal lineages of wheat stem rust in the Southern Cone of South America

Puccinia graminis f. sp. tritici (Pgt) causes wheat stem rust, a devastating disease of cereals. Recent approaches to examine populations at a genomic level have provided valuable information on the genotypic diversity of Pgt populations in Africa, Europe and North America and evolutionary mechanisms underlying the emergence of new races. However, an in-depth characterisation of Pgt populations in South America has been lacking. To bridge this knowledge gap, 91 Pgt isolates were collected from Argentina and Uruguay in 2020 and 2021 and used to generate transcriptome and whole genome sequence data and pathotype information. Phylogenetic analyses revealed that this South American Pgt population includes three clonal lineages, two of which have not been detected elsewhere. The third lineage is globally dispersed, including isolates from Africa and the Middle East. The predominant lineage, unique to South America, encompassed 90% of the samples and showed related pathotypes differing by virulence on single resistance genes consistent with evolution by stepwise mutation within the clonal lineage. There was no evidence of sexual recombination giving rise to new genetic diversity in this population. These observations urge to routinely incorporate and compare genotypic data from South American Pgt isolates to surveillance data from other geographic regions.

evolutionary biology↗

Loss of heterozygosity exposes germline mutations in complex I and drives Warburg metabolism in oncocytic carcinoma of the thyroid

Oncocytic (Hurthle cell) carcinoma of the thyroid (OCT) is characterized by widespread loss of heterozygosity (LOH), mitochondrial accumulation and recurrent mitochondrial DNA mutations leading to impairment of complex I. Here, we establish and characterize a novel OCT cell line, UT946, which displays severe mitochondrial electron transport chain dysfunction and a Warburg metabolic phenotype. Using a series of cytoplasmic hybrids, we establish that the complex I defect in UT946 stems from a nuclear-encoded loss of function mutation in the complex I subunit NDUFS1. To our surprise, the mutation in NDUFS1 was inherited as a recessive germline allele that underwent LOH in the tumor to expose functional loss of complex I. A re-analysis of 91 OCT tumor genomes revealed that LOH-driven exposure of recessive germline mutations in complex I subunits was a recurrent mechanism underlying complex I inactivation in OCT. These findings unveil a new germline-driven mechanism of complex I loss and metabolic reprogramming in cancer, and provide further evidence of the strong selective pressure for complex I impairment in OCT. TeaserGermline mutations in complex I induce aerobic glycolysis in oncocytic carcinoma of the thyroid through somatic loss of heterozygosity.

cancer biology↗

The non-kinase function of CDK6 is a key driver of acquired resistance to CDK4/6 inhibitors in Estrogen Receptor-positive breast cancer

The therapeutic efficacy of CDK4/6 inhibitors in ER+ breast cancer (BC) patients is presumed to arise from inhibition of the kinase function of CDK4 and 6 proteins. Despite their initial efficacy, development of acquired resistance to CDK4/6 inhibitors in metastatic ER+ BC patients is nearly universal, commonly through compensatory overexpression of CDK6. Here, we show that primary ER+ tumors show high CDK4 but very low to undetectable expression of CDK6, which suggests that the therapeutic efficacy of CDK4/6 inhibitors in ER+ BC patients is largely driven by inhibition of CDK4, rather than CDK6. Furthermore, we show that overexpression of CDK6 confers acquired resistance to CDK4/6 inhibitors, largely, through a kinase-independent function. Our findings challenge the dogma that CDK4/6-mediated phosphorylation of retinoblastoma protein (pRB) is necessary to ER+ BC cells to progress from G1 to S phase of cell cycle. Consequently, by taking advantage of the non-kinase function of CDK6, ER+ BC cells acquire independence from the kinase function of CDK4 and 6 for cell cycle progression. These findings highlight the limitations of the current standard-of-care treatments, which focus on merely inhibiting the kinase function of CDK4 and 6, and uncover the non-kinase function of CDK6 as a new targetable vulnerability to overcome acquired resistance to CDK4/6 inhibitors in ER+ BC.

cancer biology↗

Evolutionarily conserved transcriptional regulators control monoaminergic neuron development

To what extent conserved developmental programs specify homologous cell types is a central question in biology. Here, we address this by focusing on reconstructing monoaminergic neuron development in Drosophila melanogaster embryo using time- resolved single-cell genomics, spatial transcript mapping with hybridisation chain reaction, and targeted metabolomics. We uncover a regulatory landscape in which specific transcription factors are activated before biosynthetic enzymes, establishing a prospective temporal architecture for monoaminergic fate specification. Comparative analyses of developmental single-cell atlases from zebrafish and sea urchin indicate that components of this machinery are conserved across [~]550 million years of bilaterian evolution with orthologous transcription factors showing similar temporal dynamics. Together, these findings point to a putatively conserved regulatory core that interfaces with other context-dependent transcription factors; this interplay accommodates monoaminergic multifunction and subtype diversity across distinct neuroanatomies.

evolutionary biology↗

Monoaminergic neurons share transcriptional identity across Bilaterian animals

The evolutionary conservation of cell types over deep time has long been theorised but remains difficult to demonstrate. Monoaminergic neurons, which produce molecules such as serotonin and dopamine, are central to animal behaviour and cognition, yet their evolutionary origins remain unresolved. Here, we analysed single-cell transcriptomes from 16 metazoan species spanning eight phyla. Using a novel integration method, Orthogroup Recoding, together with experimental validation, we show that monoaminergic neurons form consistent transcriptional clusters across Bilateria. These clusters share a regulatory signature involving conserved transcription factors, including homologues of Fev, Lmx1b, Fer2, Insm, and Isl, suggesting a common regulatory program. This signature extends beyond the brain including other monoaminergic cells, such as the gut enterochromaffin cells and larval sensory neurons. By contrast, non-bilaterian lineages lack the coordinated expression of the transcription factors and the biosynthetic machinery that regulate monoamine production. Our observations support the existence of a shared set of TFs that define monoaminergic identity across in bilaterians.

bioinformatics↗

Form Follows Function: A New Paradigm of Pancreatic Cancer Progression

Pancreatic ductal adenocarcinoma (PDAC) exhibits a distinctive propensity to invade nearby organs and infiltrate large blood vessels, even in the absence of distant metastasis. While the genetic and transcriptomic drivers of PDAC progression have been well studied, the mechanisms by which these molecular changes translate into functional, invasive behavior remain largely unknown. Here, we uncover a striking level of tissue organization, characterized by previously unrecognized spatial and geometric properties within and among tumor structures. Leveraging the first large-scale, AI-assisted, human-curated PDAC atlas from hematoxylin and eosin (H&E) images, we annotated, classified, and characterized 144,474 malignant and normal structures from treatment-naive (n=118) and neoadjuvant-treated PDAC patients (n=50). Additionally, we developed a new computational tool, SHAPE, to investigate PDAC aggressiveness through a comprehensive "geometrization" of cancer progression. Using traditional H&E-stained slides and three-dimensional (3D) tissue reconstruction experiments, we observed that invading tumor structures display an eccentric morphology with pronounced local angular coherence. These geometric and spatial properties revealed coherent architectural patterns, with invasive structures closely tracking vessels and nerves as they infiltrate surrounding tissue. Mechanistically, integration of morphological features from 39,045 annotated tumor structures with whole-genome and RNA sequencing data revealed that PDACs with numerous eccentric structures exhibit increased copy number alterations (CNAs), loss of heterozygosity (LoH) on the p-arm of chromosome 17, and a quasi-mesenchymal/basal-like molecular subtype. Spatial transcriptomic analysis of 1,650 tumor structures from six additional PDAC patients further confirmed upregulation of invasive cellular programs within highly eccentric structures, such as epithelial-to-mesenchymal transition (EMT), angiogenesis, coagulation, and complement pathways, underscoring their infiltrative nature. Finally, cross-validation of our AI-based method enabled a fully automated, highly interpretable computational approach to assist pathologists and clinicians in evaluating neoadjuvant chemotherapy response, predicting patient survival, and guiding chemotherapy in adjuvant settings. Collectively, these findings deepen our understanding of PDAC progression, identify a new hallmark of tumor architecture, and pave the way for full integration of AI-driven morphology-based approaches into clinical workflows to improve the management of PDAC patients.

cancer biology↗

ZNF865 (BLST) Regulates Human Cell Senescence and DNA Damage

Senescence has been shown to contribute to the progression of aging related diseases including degenerative disc disease (DDD). However, the mechanisms regulating senescence in the intervertebral disc (IVD) and other tissues/diseases remain poorly understood. Recently, ZNF865 (BLST) was identified as a previously uncharacterized zinc finger protein, that regulates a wide array of genes related to protein processing, cell senescence and DNA damage repair. Here, we show that ZNF865 expression decreases with age and pathology in human and mouse IVD samples. Utilizing CRISPR-guided gene modulation, we show that ZNF865 is necessary for healthy cell function and is a critical protein in regulating senescence and DNA damage in IVD cells, with implications for a wide range of tissues and organs. We also demonstrate that downregulation of ZNF865 induces senescence in asymptomatic human nucleus pulposus (NP) cells. Conversely, restoration in degenerative NP cells mitigates senescence, SASP expression and DNA damage, enhances ECM anabolism, and restores chromatin accessibility and gene expression to a healthy state. In vivo, CRISPRi of ZNF865 induces disc degeneration and painful behaviors. Collectively, our findings establish ZNF865 as a novel regulator of genome stability and a potential therapeutic target for mediating senescence/DNA damage in aging related diseases.

bioengineering↗

HIV-1 accessory protein Vpr possesses a cryptic p300-dependent transcription-promoting activity that is blocked by histone deacetylases in CD4+ T cells.

Antiretroviral therapy (ART) has dramatically improved the clinical prognosis for people with HIV and prevents HIV transmission. However, ART does not cure HIV infection because of a persistent, latent reservoir in long-lived cells such as central memory CD4+ T (TCM) cells. Eliminating or preventing reservoir formation will require a better understanding of HIV-1 latency establishment. We and others have recently shown that host cell factors such as histone deacetylases (HDACs) are critical cellular factors that allow HIV-1 entry into latency. Whether HDACs interact with specific viral factors to regulate latency establishment, however, is unknown. To examine the role of individual HIV-1 accessory proteins, we constructed a panel of HIV-1 reporter strains, each expressing a single HIV-1 accessory protein, and examined them in a primary CD4+ T-cell latency model. Interestingly, we found that the HDAC inhibitor (HDACi) vorinostat potently enhances the effect of the HIV-1 protein Vpr in promoting HIV expression in infected cells, suggesting that Vpr possesses a cryptic transcription-promoting activity that is restricted by HDACs. This activity was dependent on a p300-binding domain of Vpr and inhibited by a selective p300 histone acetyltransferase inhibitor. Interestingly, Vpr expression also resulted in a significant increase in the proportion of infected cells with a central memory (TCM) phenotype. Furthermore, we observed that TCM cells were more resistant to Vpr-induced apoptosis/cell death than other CD4+ T-cell subtypes, indicating that Vpr expression during reservoir formation selects for latent proviruses in TCM cells. Overall, these findings suggest that Vpr plays an important role in shaping the latent reservoir and that HIV-1 latency results, in part, from an HDAC-mediated restriction on Vprs transcription-promoting activity. Understanding how viral factors shape the latent reservoir and how host and viral factors interact during HIV-1 latency establishment in CD4+ T cells will aid in the development of new latency-targeting therapies. Author SummaryAlthough antiretroviral therapy is effective at treating HIV, a cure remains elusive. The primary obstacle to HIV cure is the presence of a long-lived reservoir of latently infected cells in which the virus persists despite therapy. Recent work has shown that a sizable fraction of this latent reservoir forms near the time that therapy is initiated, suggesting it may be possible to prevent some of the reservoir from forming. However, latency prevention will require a better understanding of how HIV enters latency, including how viral gene expression is silenced. We therefore sought to examine the role of the interaction between viral proteins and host factors in turning off viral gene expression and found that, whereas the HIV protein Vpr turns on viral gene expression, host histone deacetylases block this activity. Second, we observed that Vpr expression in infected cells leads to an increase in the relative proportion of central memory CD4+ T cells, a cell type that harbors latent virus. Our findings on the role of the viral protein Vpr in the silencing of viral gene expression and the persistence of certain memory cell types during infection will be important for developing new approaches to targeting latently infected cells.

microbiology↗

Functional Specialization of S-Adenosylmethionine Synthases Links Phosphatidylcholine to Mitochondrial Function and Stress Survival

S-adenosylmethionine (SAM), produced by SAM synthases, is critical for various cellular regulatory pathways and the synthesis of diverse metabolites. Studies have often equated the effects of knocking down one synthase with broader SAM-dependent outcomes such as histone methylation or phosphatidylcholine (PC) production. Humans and many other organisms express multiple SAM synthases. Evidence in Caenorhabditis elegans, which possesses four SAM synthase genes, suggest that the enzymatic source of SAM impacts its function. For instance, loss of sams-1 leads to enhanced heat shock survival and increased lifespan, whereas reducing sams-4 adversely affects heat stress survival. Here, we show that SAMS-1 contributes to a variety of intermediary metabolic pathways, whereas SAMS-4 is more important to generate SAM for methylation reactions. We demonstrate that loss of sams-1 exerts age-dependent effects on nuclear-encoded mitochondrial gene expression, mitochondrial metabolites, and may induce mitophagy. We propose a mechanistic model where reduced SAM from SAMS-1 acts through PC to impact mitochondria, thereby enhancing survival during heat stress.

cell biology↗

Engaging cancer patients on their attitudes towards microbiome engineering technologies

Microbiome engineering aims to develop engineered live biotherapeutic products to diagnose and treat human disease. One of the most active areas is in the engineering of modified bacteria that act as cancer therapeutics, with many products currently in clinical trials. With the emergence of any novel technologies, it is important to consult the public and end users throughout their development to address any concerns that may arise from their use. This is particularly true for therapeutics, for which it is vital that both clinicians and patients have confidence in the treatments that are available to them. Here, we surveyed a cohort of cancer patients and their relatives to gauge their knowledge of modern microbiome engineering techniques. We focus predominately on the use of bacterial eLBPs to treat cancer. Overall, most participants indicated that they would be comfortable taking cancer treatment options based on microbiome engineering technologies.

scientific communication and education↗

Coordinated translational control of multiple immune checkpoints by the integrated stress response pathway in lung cancer

The integrated stress response (ISR) is an adaptive pathway hijacked by cancer cells to survive cellular stresses in the tumor microenvironment. ISR activation potently induces Programmed Death Ligand 1 (PD-L1), leading to suppression of anti-tumor immunity. Here we sought to uncover additional immune checkpoint proteins regulated by the ISR to elucidate mechanisms of tumor immune escape. We show that CD155 and PD-L1 are coordinately induced by the ISR, enhancing translation of both immune checkpoint proteins through bypass of inhibitory upstream open reading frames (uORFs) in their 5' UTRs. Analysis of primary human lung tumors identifies a significant correlation between PD-L1 and CD155 expression. ISR activation accelerates tumorigenesis and inhibits T cell function, effects that can be overcome by combining PD-1 blockade with the ISR inhibitor ISRIB. These studies uncover a novel mechanism by which two immune checkpoint proteins are coordinately regulated and suggest a new therapeutic strategy for lung cancer patients. Statement of SignificanceThis study uncovers a novel mechanism for the coordinated translational regulation of the PD- L1/PD1 and CD155/TIGIT immune checkpoint pathways and highlights the ISR as a therapeutic vulnerability for lung cancer. Inhibition of the ISR pathway bolsters PD-1 blockade, potentially unveiling a new therapeutic strategy for lung cancer patients.

cancer biology↗

Integrated single cell functional-proteomic profiling of human skeletal muscle reveals a shift in cellular specificity in nemaline myopathy

Skeletal muscle is a complex syncytial arrangement of an array of cell types and, in the case of muscle specific cells (myofibers), sub-types. There exists extensive heterogeneity in skeletal muscle functional behaviour and molecular landscape, at the cell composition, myofiber sub-type and intra-myofiber sub-type level. This heterogeneity highlights limitations in currently applied methodological approaches, which has stagnated our understanding of fundamental skeletal muscle biology in both healthy and myopathic contexts. Here, we developed a novel approach that combines a fluorescence based assay for the biophysical examination of the sarcomeric protein, myosin, coupled with same-myofiber high sensitivity proteome profiling, termed Single Myofiber Protein Function-Omics (SMPFO). Successfully applying this approach to healthy human skeletal muscle tissue, we identify the integrate relationship between myofiber functionality and the underlying proteomic landscape that guides divergent, but physiologically important, behaviour in myofiber sub-types. By applying SMPFO to two forms of human nemaline myopathy (ACTA1 and TNNT1 mutations), we reveal significant reduction in the divergence of myofiber sub-types, across both biophysical and proteomic behaviour. Collectively, we develop SMPFO as a novel approach to study skeletal muscle with greater specificity, accuracy and resolution then currently applied methods, facilitating that advancement in understanding of SkM tissue in both healthy and diseased states.

physiology↗

ZNF865 Regulates Senescence and Cell Cycle for Applications to Cell Engineering and Gene Therapy

Zinc finger (ZNF) proteins represent the largest group of regulatory proteins within eukaryotic genomes. However, despite their broad regulatory function, the majority of ZNF protein function remains unknown. Recently, we discovered ZNF865, which has no in-depth publications and has not been functionally characterized. Utilizing CRISPR-guided gene modulation, we show that ZNF865 regulates key cellular and molecular processes associated with healthy cell function by primarily regulating cellular senescence, cell cycle progression, and protein processing. As a result, regulating this gene acts as a primary titratable regulator of cell activity, and we demonstrate the potential of targeted ZNF865 regulation as a tool to control senescence and protein production in multiple clinically relevant cell types for cell engineering/tissue engineering/gene therapy applications. We demonstrate its ability to rescue human senescent cell populations, boost T-cell activity, and dramatically deposit more cartilaginous tissue in a whole organ tissue-engineered intervertebral disc. Overall, we present novel biology and regulatory mechanisms of senescence and cell cycle that were previously unknown and display the power of CRISPR-cell engineering to enhance cell engineering strategies treating disease.

bioengineering↗

Exploring archaeogenetic studies of dental calculus to shed light on past human migrations in Oceania

The Pacific islands have experienced multiple waves of human migrations, providing a case study for exploring the potential of using the microbiome to study human migration. We performed a metagenomic study of archaeological dental calculus from 103 ancient individuals, originating from 12 Pacific islands and spanning a time range of [~]3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone from the Pacific, and comparable to that seen in calculus from temperate regions. Variation in the microbial community composition was minimally driven by time period and geography within the Pacific, while comparison with samples from Europe, Africa, and Asia reveal the microbial communities of Pacific calculus samples to be distinctive. Phylogenies of individual bacterial species in Pacific calculus reflect geography. Archaeological dental calculus shows potential to yield information about past human migrations, complementing studies of the human genome.

microbiology↗

Therapeutic TNF-alpha Delivery After CRISPR Receptor Modulation in the Intervertebral Disc

Low back pain (LBP) ranks among the leading causes of disability worldwide and generates a tremendous socioeconomic cost. Disc degeneration, a leading contributor to LBP, can be characterized by the breakdown of the extracellular matrix of the intervertebral disc (IVD), disc height loss, and inflammation. The inflammatory cytokine TNF- has multiple pathways and has been implicated as a primary mediator of disc degeneration. We tested our ability to regulate the multiple TNF- inflammatory signaling pathways in vivo utilizing CRISPR receptor modulation to slow the progression of disc degeneration in rats. Sprague-Dawley rats were treated with CRISPRi-based epigenome-editing therapeutics targeting TNFR1 and showed a decrease in behavioral pain in a disc degeneration model. Surprisingly, while treatment with the vectors alone was therapeutic, TNF- injection itself became therapeutic after TNFR1 modulation. These results suggest direct inflammatory receptor modulation, to harness beneficial inflammatory signaling pathways, as a potent strategy for treating disc degeneration.

bioengineering↗