Biology subjects

Anderson, K. E.

Publications and source records attributed to Anderson, K. E..

13 recordsLinked to original sources

bioRxiv2026

CASM regulates p62/KEAP1/NRF2 antioxidant responses to lysosome damage

Effective lysosome function is essential for health, and declines with ageing and disease. Upon lysosome damage, cells mount a complex stress response to restore homeostasis. Membrane ATG8ylation plays a central role, orchestrating lysosome repair, replacement and removal, either directly at the damaged membrane, via CASM (conjugation of ATG8s to single membranes), or at nascent autophagosomes, during lysophagy. Here, we identify a novel role for CASM in driving an antioxidant response to lysosome stress. Following damage, CASM regulates both lysosome ubiquitination and p62 recruitment. Membrane-associated p62 undergoes S349-phosphorylation, which permits KEAP1 sequestration, thereby releasing master transcription factor, NRF2. Liberated NRF2 translocates to the nucleus and promotes transcription of antioxidant and detoxifying genes, co-ordinating a cytoprotective response, in a CASM-dependent manner. These findings position CASM as a major upstream response to lysosome stress and uncover the p62/KEAP1/NRF2 axis as a novel effector pathway, termed SOLAR (SQSTM1/p62 Oligomer-mediated lysosome antioxidant response). HighlightsO_LICASM recruits p62/SQSTM1 as an effector protein during lysosome damage C_LIO_LICASM acts upstream to enhance ubiquitination of damaged lysosomes C_LIO_LICASM-recruited p62 engages KEAP1/NRF2 to drive antioxidant gene transcription (SOLAR) C_LI

cell biology↗

bioRxiv2026

Evidence that the protein phosphatase activity of PTEN contributes to embryonic development and tumour suppression in mice

PTEN (phosphatase and tensin homologue deleted on chromosome ten) is a tumour suppressor, the function of which is impaired in many diverse cancers. It has phosphoinositide lipid phosphatase activity by which it suppresses activation of the oncogenic PI3K signalling network but in vitro also displays activity against protein substrates and is able to auto-dephosphorylate its Thr366 residue. Here we generate germline knock-in mice expressing PTEN-Y138L, a mutant enzyme which selectively lacks protein phosphatase activity and retains lipid phosphatase activity. Homozygous PtenY138L/Y138L mice die in utero before E10.5. Primary MEFs and thymocytes with only a single PtenY138L allele display normal low levels of AKT phosphorylation indicating effective regulation of PI3K signalling by endogenous PTEN-Y138L in vivo. Heterozygous Pten+/Y138L mice have reduced overall survival compared to wild type littermates and develop tumours in multiple organs. Our data imply that in addition to its lipid phosphatase activity, the protein phosphatase activity of PTEN is also required for normal embryonic development and tumour suppression.

cancer biology↗

bioRxiv2026

Applying PCR cycle autonormalization to improve PacBio full-length 16S rRNA sequencing

The bacterial 16S rRNA gene is widely used to characterize host-associated and environmental microbiomes, most commonly through sequencing short hypervariable regions. Recent improvements in PacBio sequencing chemistry and concatenation approaches can now enable high-throughput, full-length 16S rRNA gene sequencing with high accuracy and depth. However, PCR-induced errors remain a major limitation, particularly for full-length amplicons where error accumulation may be elevated due to a five-fold increase in sequence lengths. These challenges are exacerbated when samples vary widely in microbial biomass, making it difficult to select a single optimal number of PCR cycles. Here, we evaluated the effects of PCR cycle autonormalization on PacBio Kinnex full-length 16S rRNA gene sequencing across seven agriculturally relevant specimen types. We compared conventional PCR protocols (20, 24, and 30 cycles) with an autonormalization approach in which individual reactions were terminated during exponential amplification based on real-time fluorescence thresholds. Autonormalized reactions consistently retained a higher proportion of sequences following denoising and chimera removal, exhibited fewer substitution-based errors, and produced more even read distributions across samples. Meanwhile, overamplified reactions (30 cycles) showed elevated error rates and higher sequence removal, particularly in samples with greatest microbial biodiversity. Importantly, PCR protocol had minimal effects on overall community composition relative to specimen types. These results demonstrate that PCR cycle autonormalization improves data yield for full-length 16S rRNA sequencing while maintaining robust inferences, while facilitating streamlined workflows for heterogeneous samples. ImportanceAmplicon-based sequencing of the 16S rRNA gene is foundational tool in microbiome research, yet PCR amplification remains a major source of technical error. This challenge is magnified for full-length 16S rRNA sequencing and for workflows that process specimen types with widely varying microbial biomass. Selecting a single PCR cycle number can result in under-amplification of samples with low 16S rRNA copies or over-amplification and error accumulation in high-titer samples. Here, we show that PCR cycle autonormalization, implemented using iconPCR, substantially improves PacBio full-length 16S rRNA sequencing by reducing PCR-induced substitution errors and chimeras while maintaining consistent biological inference. Autonormalization also enables blind pooling of amplicons without post-PCR quantification or equimolar normalization, reducing hands-on time and sample loss. These benefits make cycle autonormalization particularly valuable for high-throughput and production-scale sequencing applications handling diverse specimen types.

microbiology↗

bioRxiv2025

Archetype analysis of lung adenocarcinoma premalignancy links heterogeneity in premalignant lesions to diverging features of invasive disease

ABSTRACTLung adenocarcinoma (LUAD), the most common form of lung cancer, is a heterogeneous disease with highly variable histopathologic features and clinical outcomes. LUAD premalignant lesions (PMLs) are localized proliferative lesions of atypical pneumocytes that proliferate along the alveolar walls. In this study, we characterized the molecular heterogeneity across PMLs, regardless of histologic designation, and identified four unique groups or "archetypes" of PMLs using bulk RNA and exome sequencing data from laser captured microdissected PMLs, normal, and tumor tissue from LUAD resection cases. The archetypes were defined based on expression of recurrent gene co-expression modules discovered using the LUAD PMLs we profiled and three publicly available datasets. One PML archetype, termed "proliferation", was associated with increased expression of genes involved in cell proliferation, a pro-tumor immune environment, and enrichment for EGFR driver mutations. Another archetype, termed "normal-like", was associated with similar features to normal tissue, an anti-tumor immune response, and lacked enrichment for driver mutations compared to other archetypes. We projected the PML archetypes into independent gene expression datasets profiling LUAD and found that tumors closest to the proliferation archetype were enriched for multiple features of aggressive LUAD, including high tumor grade and lymph node invasion, and had significantly lower disease-free survival. Proliferation archetype PMLs may represent a subset of lesions with more aggressive features that could improve patient stratification and suggest novel targets for lung cancer interception.

cancer biology↗

bioRxiv2024

Phospholipase Cgamma regulates lacrimal gland branching by competing with PI3K in phosphoinositide metabolism

Although the regulation of branching morphogenesis by spatially distributed cues is well established, the role of intracellular signaling in determining the branching pattern remains poorly understood. In this study, we investigated the regulation and function of phospholipase C gamma (PLC{gamma}) in Fibroblast Growth Factor (FGF) signaling in lacrimal gland development. We showed that deletion of PLC{gamma}1 in the lacrimal gland epithelium leads to ectopic branching and acinar hyperplasia, which was phenocopied by either mutating the PLC{gamma}1 binding site on Fgfr2 or disabling any of its SH2 domains. PLC{gamma}1 inactivation did not change the level of Fgfr2 or affect MAPK signaling, but instead led to sustained AKT phosphorylation due to increased PIP3 production. Consistent with this, PLC{gamma}1 mutant phenotype can be reproduced by elevation of PI3K signaling in Pten knockout and attenuated by blocking AKT signaling. This study demonstrated that PLC{gamma} modulates PI3K signaling by shifting phosphoinositide metabolism, revealing an important role of signaling dynamics in conjunction with spatial cues in shaping branching morphogenesis.

developmental biology↗

bioRxiv2023

Evaluating the ileal and cecal microbiota composition of a 1940 heritage genetic line and a 2016 commercial line of white leghorns fed representative diets from 1940 and 2016

This study was conducted to identify and evaluate the differences between the microbiome composition of the ileum and ceca of 1940 and 2016 genetic strains of white leghorns fed representative contemporary diets from those times. Ileal and cecal samples were aseptically collected from both genetic lines at 69 weeks of age. The genomic DNA of the ileal and cecal contents were extracted and the V4 region of the 16S rDNA was sequenced on an Illumina Miseq. Microbiota data were filtered and aligned using the QIIME2 2020.2 pipeline. Alpha and beta diversity metrics were generated and the Analysis of Composition of Microbiomes (ANCOM) was utilized to determine significantly different taxa. Data were considered significant at P [≤] 0.05 for main effects and Q [≤] 0.05 for pairwise differences. Alpha diversity of the ileum and ceca were significantly different (P = 0.001; Q = 0.001; however, no differences between genetic lineage were observed (P > 0.05; Q > 0.05). The beta diversity between the ileum and ceca, as well as between the genetic lines (1940 vs. 2016) were significantly different from one another (P = 0.001; Q = 0.001). Using ANCOM, Proteobacteria and Actinobacteriota were significantly different than other phyla (P 0.05) with a higher relative abundance of Proteobacteria being observed among treatment groups 2 and 3, while Actinobacteriota had higher relative abundance in treatment groups 1 and 4. Among the significantly different genera in the ileum, Pseudomonas, Rhizobiaceae, Leuconostoc, and Aeriscardovia were different (P 0.05) with treatment groups 1 and 4 having a higher relative abundance of Aeriscardovia, while treatment groups 2 and 3 had higher relative abundance in both Pseudomonas and Leuconostoc. In the ceca, Proteobacteria, Firmicutes, Actinobacteriota, and Euryarchaeota were significantly different phyla (P 0.05) with Firmicutes having the highest relative abundance across all treatment groups. Among the significantly different genera (Pseudomonas, Leuconostoc, Alloprevotella, and Aeriscardovia), Alloprevotella had the highest relative abundance across all treatment groups 1 and 2, while Leuconostoc and Pseudomonas had the highest relative abundance in treatment group 4. Results from this study suggest that genetic makeup in conjunction with the nutritional composition of laying hens influences the cecal and ileal microbiota of corresponding hens.

microbiology↗

bioRxiv2023

PLEKHS1 drives PI3Ks and remodels pathway homeostasis in PTEN-null prostate

The PIP3/PI3K network is a central regulator of metabolism and is frequently activated in cancer, commonly by loss of the PIP3/PI(3,4)P2-phosphatase, PTEN. Despite huge investment, the drivers of the PI3K network in normal tissues and how they adapt to overactivation are unclear. We find that in healthy mouse prostate PI3K activity is driven by RTK/IRS signalling and constrained by pathway-feedback. In the absence of PTEN, the network is dramatically remodelled. A poorly understood, YXXM and PIP3/PI(3,4)P2-binding PH domain-containing, adaptor, PLEKHS1, became the dominant activator and was required to sustain PIP3, AKT-phosphorylation and growth in PTEN-null prostate. This was because PLEKHS1 evaded pathway-feedback and experienced enhanced PI3K and SRC-family kinase-dependent phosphorylation of Y258XXM, eliciting PI3K activation. hPLEKHS1-mRNA and activating-Y419-phosphorylation of hSRC correlated with PI3K-pathway activity in human prostate cancers. We propose that in PTEN-null cells, receptor-independent, SRC-dependent tyrosine-phosphorylation of PLEKHS1 creates positive-feedback that escapes homeostasis, drives PIP3- signalling and supports tumour progression.

cell biology↗

bioRxiv2023

The LCLAT1/LYCAT acyltransferase supports EGF-mediated phosphatidylinositol-3,4,5-trisphosphate and Akt signalling

Receptor tyrosine kinases such as epidermal growth factor receptor (EGFR) stimulate phosphoinositide 3-kinases (PI3Ks) to convert phosphatidylinositol-4,5-bisphosophate [PtdIns(4,5)P2] into phosphatidylinositol-3,4,5-trisphosphate [PtdIns(3,4,5)P3]. PtdIns(3,4,5)P3 then remodels actin and gene expression, and boosts cell survival and proliferation. PtdIns(3,4,5)P3 partly achieves these functions by triggering activation of the kinase Akt, which phosphorylates targets like Tsc2 and GSK3{beta}. Consequently, unchecked upregulation of PtdIns(3,4,5)P3-Akt signalling promotes tumour progression. Interestingly, 50-70% of PtdIns and PtdInsPs have stearate and arachidonate at sn-1 and sn-2 positions of glycerol, respectively, forming a species known as 38:4-PtdIns/PtdInsPs. LCLAT1 and MBOAT7 acyltransferases partly enrich PtdIns in this acyl format. We previously showed that disruption of LCLAT1 lowered PtdIns(4,5)P2 levels and perturbed endocytosis and endocytic trafficking. However, the role of LCLAT1 in receptor tyrosine kinase and PtdIns(3,4,5)P3 signaling was not explored. Here, we show that LCLAT1 silencing in MDA-MB-231 and ARPE-19 cells abated the levels of PtdIns(3,4,5)P3 in response to EGF signalling. Importantly, LCLAT1-silenced cells were also impaired for EGF-driven and insulin-driven Akt activation and downstream signalling. Thus, our work provides first evidence that the LCLAT1 acyltransferase is required for receptor tyrosine kinase signalling.

cell biology↗

bioRxiv2022

Aspects of flow variability and spatial context predict temporal beta diversity in river metacommunities

O_LIRiver catchments are dynamic networks that contain multiple levels of spatial and temporal complexity. Benthic macroinvertebrates are key indicator taxa throughout catchments and beta diversity has been used as a metric to explore determinants of community composition at the catchment scale. Commonly explored drivers of beta diversity include environmental and spatial variables such as flow, temperature, and spatial distance. While factors influencing spatial beta diversity have been explored, factors explaining temporal beta diversity have been understudied. Temporal beta diversity is predicted to also be important since community assembly mechanisms are not stable over time, and more studies are needed to determine which factors most strongly determine temporal beta diversity patterns. C_LIO_LIWe investigated the effects of local environmental variables, flow variability, and spatial context on temporal beta-diversity using a large, publicly available biomonitoring dataset from river networks in California. Data included benthic macroinvertebrate community composition and environmental data from multiple locations and years, allowing us to explore temporal changes in these communities as a function of site-specific environmental and spatial factors. Associated gage data were used to calculate hydrograph metrics and contextualize the flow regime at each location over long timescales. We then used beta regression to model the relationship between benthic macroinvertebrate temporal beta-diversity, environmental variables, flow regimes, and spatial network context. C_LIO_LIFlow and spatial catchment-related predictors were the strongest predictors of temporal beta diversity, while changes in environmental variables were much weaker. Channel slope, drainage density, and upstream catchment area were the most significant spatial factors. Channel slope showed a negative relationship with temporal beta diversity, while drainage density and upstream catchment area showed positive ones. Temporal beta diversity was also higher when the rate and magnitude of rises and falls in flow was higher in the hydrograph as well as when the number of zero-flow days and the duration of flow rises and falls was higher. C_LIO_LIOverall, our results indicate that temporal beta diversity of freshwater benthic macroinvertebrates is shaped by both long-term hydrological context and spatial context, and that these factors may serve as better predictors of long term community variability than variability in point estimates of environmental measurements. Flow regimes and spatial metrics may provide more environmental context than point-estimate environmental measurements, as the latter may not accurately capture the dynamic conditions that drive variability in metacommunity responses. C_LIO_LIOur study supports the need for biomonitoring efforts at long spatial and temporal timescales, and highlights the need to consider metacommunity change in the management of freshwater systems. C_LI

ecology↗

bioRxiv2021

Body size dependent dispersal influences stability in heterogeneous metacommunities

Body size affects key biological processes across the tree of life, with particular importance for food web dynamics and stability. Traits influencing movement capabilities depend strongly on body size, yet the effects of allometrically-structured dispersal on food web stability are less well understood than other demographic processes. Here we study the stability properties of spatially-arranged model food webs in which larger bodied species occupy higher trophic positions, while species body sizes also determine the rates at which they traverse spatial networks of heterogeneous habitat patches. Our analysis shows an apparent stabilizing effect of positive dispersal rate scaling with body size compared to negative scaling relationships or uniform dispersal. However, as the global coupling strength among patches increases, the benefits of positive body size-dispersal scaling disappear. A permutational analysis shows that breaking allometric dispersal hierarchies while preserving dispersal rate distributions rarely alters qualitative aspects of metacommunity stability. Taken together, these results suggest that the oft-predicted stabilizing effects of large mobile predators may, for some dimensions of ecological stability, be attributed to increased patch coupling per se, and not necessarily coupling by top trophic levels in particular.

ecology↗

bioRxiv2020

Reclassification of seven honey bee symbiont strains as Bombella apis

Honey bees are important pollinators of many major crops and add billions of dollars annually to the US economy through their services. Recent declines in the health of the honey bee have startled researchers and lay people alike as honey bees are agricultures most important pollinator. One factor that may influence colony health is the microbial community. Although honey bee worker guts have a characteristic community of bee-specific microbes, the honey bee queen digestive tracts are colonized predominantly by a single acetic acid bacterium tentatively named "Parasaccharibacter apium". This bacterium is related to flower-associated microbes such as Saccharibacter floricola, and initial phylogenetic analyses placed it as sister to these environmental bacteria. We used a combination of phylogenetic and sequence identity methods to better resolve evolutionary relationships among "P. apium", strains in the genus Saccharibacter, and strains in the closely related genus Bombella. Interestingly, measures of genome-wide average nucleotide identity and aligned fraction, coupled with phylogenetic placement, indicate that many strains labeled as "P. apium" and Saccharibacter sp. are all the same species as Bombella apis. We propose reclassifying these strains as Bombella apis and outline the data supporting that classification below.

microbiology↗

bioRxiv2018

Omnivory does not preclude strong trophic cascades

Omnivory has been cited as an explanation for why trophic cascades are weak in many ecosystems, but empirical support for this prediction is equivocal. Compared to predators that feed only on herbivores, top omnivores -- species that feed on both herbivores and primary producers -- have been observed generating cascades ranging from strong, to moderate, null, and negative. To gain intuition about the sensitivity of cascades to omnivory, we analyzed models describing systems with top omnivores that display either fixed or flexible diets, two foraging strategies that are supported by empirical observations. We identified regions of parameter space wherein omnivores following a fixed foraging strategy, with herbivores and producers comprising a constant proportion of the diet, non-intuitively generate stronger cascades than predators that are otherwise demographically identical: (i) high productivity relative to herbivore mortality, and (ii) small discrepancies in producer versus herbivore reward create conditions in which cascades are stronger with moderate omnivory. In contrast, flexible omnivores that attempt to optimize per capita growth rates during search never induce cascades that are stronger than the case of predators. Although we focus on simple models, the consistency of these general patterns together with prior empirical evidence suggests that omnivores should not be uniformly ruled out as agents of strong trophic cascades.

ecology↗

bioRxiv2018

The Queen Gut Refines with Age: Longevity Phenotypes in a Social Insect Model

BackgroundIn social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short and long-lived host phenotypes are polarized by a suite of age-associated factors including hormones, nutrition, immune senescence and oxidative stress. Similar to other model organisms, the aging gut microbiota of short-lived (worker) honey bees accrue Proteobacteria and are depleted of Lactobacillus and Bifidobacterium, consistent with a suite of host senescence markers. In contrast, long-lived (queen) honey bees maintain youthful cellular function without expressing oxidative stress genes, suggesting a very different host environment for age-associated microbial succession.\n\nResultsWe sequenced the microbiota of 63 honey bee queens exploring two chronological ages and four alimentary tract niches. To control for individual variation we quantified carbonyl accumulation in queen fat body tissue as a proxy for biological aging. We compared our results to the age-specific microbial succession of worker guts. Accounting for queen source variation, two or more bacterial species per niche differed significantly by queen age. Biological aging in queens was correlated with microbiota composition highlighting the relationship of microbiota with oxidative stress. Queens and workers shared many major gut bacterial species, but differ markedly in community structure and age succession. In stark contrast to aging workers, carbonyl accumulation in queens was significantly associated with increased Lactobacillus and Bifidobacterium and depletion of various Proteobacteria.\n\nConclusionsWe present a model system linking changes in gut microbiota to diet and longevity, two of the most confounding variables in human microbiota research. As described for other model systems, metabolic changes associated with diet and host longevity correspond to the changing microbiota. The pattern of age-associated succession in the queen microbiota is largely the reverse of that demonstrated for workers. The guts of short-lived worker phenotypes are progressively dominated by three major Proteobacteria, but these same species were sparse or significantly depleted in long-lived queen phenotypes. More broadly, our results suggest that lifespan evolution formed the context for host-microbial interactions and age-related succession of honey bee microbiota.

microbiology↗