Biology subjects

Basu, A.

Publications and source records attributed to Basu, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Dose- and outcome-dependent effects of bacterial infection on female fecundity in Drosophila melanogaster

The virulence of a pathogenic infection challenge can manifest in the form of increased host mortality rates and/or reduced host fecundity. Reduced fecundity in infected hosts can result from resource-allocation trade-offs: increased investment in immune defences depletes the common pool of resources, which are also required for reproduction. Alternatively, reduced fecundity may result from damage to host organs, especially reproductive organs, caused by the infection. We infected Drosophila melanogaster females with the bacterial pathogen Enterococcus faecalis at different infection doses and found that increasing the infection dose led to greater suppression of fecundity, without a corresponding increase in mortality rates. We further found that the reduction in host fecundity is contingent on the infection outcome (whether the host lives or dies after being infected), particularly in flies infected with a high dose of bacteria. Interestingly, survivors of the infection challenge had exhibited comparable fecundity irrespective of the dose used to infect them, whereas amongst females that died after infection, a higher infection dose led to a lower fecundity. We therefore propose that our results indicate that fecundity suppression in E. faecalis-infected females is likely caused by host organ damage rather than by diversion of limited resources towards immune function.

evolutionary biology↗

bioRxiv2025

Socio-sexual environment influences fecundity, but not response to bacterial infection, in Drosophila melanogaster females

It is common for a host exposed to a pathogenic infection challenge to exhibit suppression of fecundity. This suppression can be driven by either a resource allocation-based trade-off between fecundity and immune function, or by infection-induced damage to host soma (particularly the reproductive organs). Alternatively, hosts can increase their fecundity to compensate for the curtailed lifespan resulting from lethal infection. Various factors, both extrinsic and intrinsic to the host, determine the actual effect of any infection challenge on host fecundity. While the hosts physiological and abiotic environmental factors have been thoroughly explored in this context, the role of the hosts biotic environment - especially its social and sexual environment - is rarely addressed. We investigated whether the socio-sexual environment (SSE) of D. melanogaster females influenced the effect of bacterial infection on their fecundity. We altered the socio-sexual environment of the females by housing them with different numbers of same-sex and opposite-sex companions. Our results indicate that while such alterations of the SSE changed the baseline reproductive effort of the females, they had no role in determining female susceptibility to infections or how infection affected female fecundity.

evolutionary biology↗

bioRxiv2025

Axon Regeneration and Functional Recovery after Spinal Cord Injury is Enhanced by Allele-Specific ApoE Neuronal Action through LRP8

Adult CNS trauma frequently causes neuronal disconnection and persistent deficits due to failed axon regeneration. While model system screening has identified multiple candidate neural repair pathways, ApoE-LRP8 signaling is unique in being implicated clinically. Here, we show that cortical axon regeneration requires LRP8 and is modified by APOE variants. ApoE2-expressing mice show reparative corticospinal and raphespinal axon growth with greater motor function than controls after spinal cord injury. Distinct from ApoE in other settings, there is no change in inflammation or scarring. After axotomy, ApoE exerts allele-specific effects on LRP8 localization and signaling in cortical neurons. APOE alleles regulate synaptic organization gene expression by cortical neurons after injury, with little effect on glial gene expression. AAV-mediated overexpression of ApoE2 in mice after spinal trauma increases locomotor recovery and reparative axon growth. Thus, ApoE-LRP8 signaling for axon regrowth following CNS trauma provides a potential therapeutic intervention site.

neuroscience↗

bioRxiv2025

Sulfatase modifying factors control the timing of zebrafish gastrulation morphogenesis

To shape the emerging body plan, morphogenetic cell movements must be coordinated not only in space, but also in time. Convergence and Extension (C&E) movements that elongate the anteroposterior axis initiate with precise timing during vertebrate gastrulation, but the mechanisms controlling their onset remain unknown. We examined this question using zebrafish embryonic explants that faithfully recapitulate C&E cell movements and their precise timing in culture, in isolation from other gastrulation movements. We determined that new transcription is required at gastrulation onset for C&E in explants and identified sulfatase modifying factor 2 (sumf2) as a candidate trigger gene expressed at this time. sumf2 and its paralog sumf1 encode negative and positive regulators, respectively, of all sulfatase enzymes, which remove sulfate groups from their substrates, altering their biological activity. In zebrafish embryos and explants, sumf1 and sumf2 expression levels invert at gastrulation onset, predicting a reduction in sulfatase activity and consequent increase of substrate sulfation. We found that overexpressing sumf1 and sumf2 causes delayed or precocious C&E onset, respectively, whereas loss of sumf1 and sumf2 function shifts C&E timing in the opposite direction. We further identified Sulf1, an extracellular sulfatase that modifies heparan sulfate proteoglycans (HSPGs), as the key effector by which sumf1 and sumf2 control C&E timing. Accordingly, reduced or increased levels of sulfated heparan sulfate similarly shift C&E onset and suppress sumf1 and sumf2 mutant phenotypes. Together, our work supports a model in which sumf2 expression at zebrafish gastrulation onset reduces sulfatase activity, rewriting HSPG sulfation patterns to promote and/or permit C&E morphogenesis.

developmental biology↗

bioRxiv2025

Glycan Profiling Identifies Chondroitin-4-sulfate as a Biomarker for Platinum Response and Therapeutic Target in Ovarian Cancer

For women with advanced ovarian cancer (OC), remission is typically achieved through surgery and combination chemotherapy, with duration largely dependent on tumor sensitivity to platinum-based drugs. Here, we show that tumor-associated glycosaminoglycans (GAGs) influence platinum drug efficacy in preclinical models of ovarian cancer. Due to the complexity of GAG biosynthesis and the involvement of multiple enzymes, traditional transcriptomic and proteomic approaches cannot accurately estimate their levels or correlation with patient response and survival. To address this, we quantitatively analyzed the full compositional profile of GAGs in OC patient-derived xenograft (PDX) models with known carboplatin sensitivity. Our results revealed a significant correlation between carboplatin resistance and high levels of the predominant GAG sequence, chondroitin-4-sulfate (C4S). Further investigation in cellular models demonstrated that high GAG expression reduces carboplatin uptake, DNA adduct formation, and tumor accumulation, whereas the opposite effect was observed for Triplatin, a GAG-targeting platinum agent. These trends were further validated in vivo, where treatment of OC PDX models with varying C4S levels confirmed that carboplatin efficacy decreases while Triplatin activity increases in tumors with high C4S expression. Based on these findings, we established a C4S cut-off score to predict tumor sensitivity, identifying a threshold above which tumors are likely to be carboplatin-resistant but Triplatin-sensitive. Analysis of patient tissue microarrays estimated that 40-83% of OC tumors, depending on subtype, exhibit high C4S expression. Collectively, these findings highlight the predictive power of C4S as a biomarker for platinum response and support the clinical evaluation of Triplatin as a targeted treatment for patients with carboplatin-resistant tumors expressing high levels of C4S. One Sentence SummaryElevated chondroitin-4-sulfate in ovarian cancer results in resistance to carboplatin and sensitivity to Triplatin.

pharmacology and toxicology↗

bioRxiv2025

Capture, Confine, Characterize: High-Throughput Dielectrophoresis-Based Single-Cell Microfluidics Platform to Analyze Mammalian and Yeast Cells Using Raman Spectroscopy

Single-cell analysis technologies are pivotal in unraveling complex biological mechanisms, yet existing platforms are often limited to sequencing-based end-point measurements, which fail to capture live cell dynamics. Here, we present a microfluidic- microelectronic device, the Microfluidic dielectrophoretic Arresting System (MiDAS) that employs dielectrophoresis (DEP) for high-throughput single-cell and droplet trapping in a compact array. We tested multiple trap geometries, including a 20 m-diameter DEP trap for polymer microbeads, fungal and mammalian cells, and a 40 m-diameter trap for water-in-oil droplets. The platform demonstrates broad sample compatibility, reliably immobilizing cells and beads of varying sizes. By integrating optical imaging and Raman spectroscopy, we enable rapid, non-destructive interrogation of individual cells with temporal resolution. We describe different modes of MiDAS operation to trap and manipulate single-cells or reverse emulsion droplets on demand, with applications in droplet microfluidics. Our MiDAS platforms simple fabrication, robust performance, and broad compatibility with diverse sample types position it as a versatile tool with transformative potential for single-cell analysis, offering researchers an innovative approach to interrogate cellular dynamics with unprecedented precision and throughput.

bioengineering↗

bioRxiv2025

Characterization of intermolecular base pairing using AMT crosslinking in mammalian cells during oxidative stress

Cellular stress induces global translational repression, leading to exposure of RNA sequences that could engage in intermolecular base pairing. However, characterization of these interactions in stressed cells remains limited. Here, we coupled RNA crosslinking with biotin pulldown to probe intermolecular base pairing in mammalian cells during oxidative stress. We found that oxidative stress downregulates intermolecular base pairing of a reporter mRNA engineered to enhance detection of such interactions. Consistently, crosslinking-dependent intermolecular base pairing was not readily detected among candidate mRNAs that accumulate in stress granules - RNA-rich condensates that form during stress. Furthermore, chemical probing of base accessibility revealed that while RNA regions within these transcripts remain structured during stress, they increase in structural diversity in a manner dependent on oxidative stress and the stress granule nucleating proteins G3BP1 and G3BP2. This enhanced structural heterogeneity may help reduce a sustained exposure of interaction-prone RNA sequences during stress such as those prone to crosslinking. We propose that the combined downregulation of intermolecular base pairing and increased RNA structural diversity provides a mechanism to preserve normal function of RNAs during stress, while simultaneously enabling the reversible assembly of stress granules.

molecular biology↗

bioRxiv2025

Epithelia mediate inflammation with myeloid cells in Crohn's disease patients under treatment

Many Crohn's disease patients fail to respond to biologic therapies targeting canonical immune pathways, and the mechanisms underlying treatment non-response remain poorly understood. Integrating single-cell and spatial transcriptomics, we generated a comprehensive mucosal atlas of 380,000 cells spanning the terminal ileum and ascending colon of healthy donors and Crohn's disease patients receiving biologics. We revealed site-specific programs centered on TNF-expressing macrophages embedded within epithelial-stromal networks: follicle-associated enterocytes dictated immune activation in the ileum, while FAP-expressing stromal cells served this role in the colon. Co-expression network analysis further identified lineage-specific programs associating non-response, including a novel epithelial marker BPIFB1 independent of known genetic risk loci. Co-expression marker Z-scores significantly differed between responders and non-responders in published datasets. Together, these findings define a non-responder-specific epithelial-stromal-immune ecosystem that sustains chronic inflammation, providing a framework for stratifying treatment resistance and informing therapeutic strategies in Crohn's disease and other barrier organ disorders.

immunology↗

bioRxiv2025

Heterobifunctional proteomimetic polymers for targeted protein degradation

The burgeoning field of targeted protein degradation (TPD) has opened new avenues for modulating the activity of previously undruggable proteins of interest. To date, TPD has been dominated by small molecules containing separate linked domains for protein engagement and recruitment of cellular degradation machinery. The process of identifying active compounds has required tedious optimization and has been successful largely against a limited set of targets with well-defined, suitable docking pockets. Here we present a polymer chemistry approach termed the HYbrid DegRAding Copolymer (HYDRAC) to overcome standing challenges associated with the development of TPD. These copolymers densely display either peptide-based or small molecule-derived degradation inducers and target-binding peptide sequences for the selective degradation of disease-associated proteins. HYDRACs are synthesized in a facile manner, are modular in design, and are highly selective. Using the intrinsically disordered transcription factor MYC as an initial proof-of-concept, difficult to drug protein target, HYDRACs containing a MYC-inhibitory peptide copolymerized with a validated degron, showed robust and selective degradation of the target protein. Treatment of tumor-bearing mice with MYC-targeted HYDRACs showed decreased cell proliferation and increased tumor apoptosis, leading to significantly suppressed tumor growth in vivo. The versatility of the platform was demonstrated by substituting the degron for recruiters of three different E3 ligases (VHL, KEAP1, and CRBN), which all maintained MYC degradation. To demonstrate generalizability, HYDRACs were further designed against a second elusive target of clinical interest, KRAS, by employing a consensus RAS binding motif. RAS-targeted HYDRACs showed degradation in two cell lines harboring separate KRAS alleles, suggesting potential pan-KRAS activity. We envision the HYDRAC platform as a generalizable approach to developing degraders of proteins of interest, greatly expanding the therapeutic armamentarium for TPD.

bioengineering↗

bioRxiv2025

Searching for Sequence Features that Control DNA Cyclizability

The mechanical properties of DNA molecules are crucial in many biological processes, from DNA packaging to transcription regulation. While the mechanics of long DNA typically follow the worm-like chain polymer model, multiple studies have shown that the mechanics of short DNA - at the length scale of DNA-protein interactions - depend strongly on its sequence content. Motivated by recent high-throughput measurements of sequence-dependent DNA cyclizability - the DNAs tendency to mechanically bend and form a loop, we developed a statistical mechanics approach to systematically explore how cyclizability depends on interactions between individual nucleotides in the sequence. By applying this method to datasets of randomly generated and biologically derived sequences, we identified characteristic sequence features that control DNA cyclizability and extracted the most and least cyclizable sequences, the behavior of which we validated through all-atom molecular dynamics simulations. We found that while highly cyclizable sequences share the same periodic features across datasets, distinct sequence patterns can result in low cyclizability. This work contributes to our understanding of the sequence dependence of DNA mechanics and its role in various biological processes, and has implications for the growing field of DNA nanofabrication.

biophysics↗

bioRxiv2024

Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics

Connections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally, in silico evolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA of Namystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.

biophysics↗

bioRxiv2024

Timing of starvation determines its effects on susceptibility to infection in Drosophila melanogaster females independent of host evolutionary history

An organisms susceptibility to pathogens is contingent on various environmental factors, including the availability of nutrition. Starvation can alter host susceptibility to infections, either directly via depletion of resources essential for proper functioning of the immune system, or indirectly via the various physiological changes it induces within the host body. We tested if the susceptibility of Drosophila melanogaster populations to Enterococcus faecalis infection is affected by (a) whether the hosts are starved before or after the infection, and (b) the evolutionary history of the host. Hosts from laboratory fly populations that have been experimentally evolved to be more resistant to E. faecalis, and their corresponding control populations, were subjected to infection with or without being starved prior to and after being infected. We found that the effect of starvation on susceptibility to E. faecalis changed with the timing of starvation: starvation after infection improved survival of infected hosts, irrespective of how they were treated before infection, while starving only prior to infection (and not after) compromised post-infection survival. The changes in infection susceptibility were uniform in both the evolved and the control populations, suggesting that the effects of starvation are not dependent on pre-existing resistance to the infecting pathogen.

evolutionary biology↗

bioRxiv2024

Phase separated liquid vimentin droplets stabilize actin fibers through wetting

The cytoskeleton is composed of F-actin, microtubules, and intermediate filaments (IFs). Vimentin is the most ubiquitous IF. It is involved in wound healing, tissue fibrosis and cancer metastasis, all of which require rapid vimentin filaments assembly. In this paper, we report that un-polymerized vimentin forms liquid condensates that appear to enable rapid filament growth. Given the transient nature of these droplets, we focus on properties of vimentin-Y117L, a mutant which does not form filaments, enabling us to study these droplets in detail. They dissolve under 1,6-Hexanediol treatment and under decreasing concentration, confirming that they are liquid, and phase separated. These condensates extensively wet actin fibers, rendering them resistant to actin-depolymerizing drugs. We show similar behavior occurs in wild type vimentin during its assembly into filaments.

biophysics↗

bioRxiv2024

Determinants of raffinose family oligosaccharide use in Bacteroides species

Bacteroides species are successful colonizers of the human gut and can utilize a wide variety of complex polysaccharides and oligosaccharides that are indigestible by the host. To do this, they use enzymes encoded in Polysaccharide Utilization Loci (PULs). While recent work has uncovered the PULs required for use of some polysaccharides, how Bacteroides utilize smaller oligosaccharides is less well studied. Raffinose family oligosaccharides (RFOs) are abundant in plants, especially legumes, and consist of variable units of galactose linked by -1,6 bonds to a sucrose (glucose -1-{beta}-2 fructose) moiety. Previous work showed that an -galactosidase, BT1871, is required for RFO utilization in Bacteroides thetaiotaomicron. Here, we identify two different types of mutations that increase BT1871 mRNA levels and improve B. thetaiotaomicron growth on RFOs. First, a novel spontaneous duplication of BT1872 and BT1871 places these genes under control of a ribosomal promoter, driving high BT1871 transcription. Second, nonsense mutations in a gene encoding the PUL24 anti-sigma factor likewise increase BT1871 transcription. We then show that hydrolases from PUL22 work together with BT1871 to break down the sucrose moiety of RFOs and determine that the master regulator of carbohydrate utilization (BT4338) plays a role in RFO utilization in B. thetaiotaomicron. Examining the genomes of other Bacteroides species, we found homologs of BT1871 in subset and show that representative strains of species containing a BT1871 homolog grew better on melibiose than species that lack a BT1871 homolog. Altogether, our findings shed light on how an important gut commensal utilizes an abundant dietary oligosaccharide. ImportanceThe gut microbiome is important in health and disease. The diverse and densely populated environment of the gut makes competition for resources fierce. Hence, it is important to study the strategies employed by microbes for resource usage. Raffinose family oligosaccharides are abundant in plants and are a major source of nutrition for the gut microbiota since they remain undigested by the host. Here, we study how the model gut commensal, Bacteroides thetaiotaomicron utilizes raffinose family oligosaccharides. This work highlights how an important member of the microbiota uses an abundant dietary resource.

microbiology↗

bioRxiv2024

ERK5 Signaling is Required for Type III IFN-mediated Mucosal Antiviral Responses

Type III interferons (IFN{lambda}) are innate immune cytokines that limit viral replication and coordinate tissue repair through the induction of interferon stimulated genes (ISGs). This response must be tightly regulated to avoid excessive responses that result in the disruption of tissue barrier integrity or inefficient responses that allow for pathogen escape. Here we examine the contribution of Mitogen Activated Protein Kinase (MAPK) signaling on IFN{lambda}-mediated antiviral activity. We find that extracellular-signal-regulated kinase 5 (ERK5), a poorly characterized member of the conventional MAPK family, potentiates the antiviral efficacy of IFN{lambda}. Chemical inhibition and genetic targeting of ERK5 during IFN{lambda} treatment of cells results in a decrease in ISG induction and impaired control of viral infections. This decrease in IFN{lambda} antiviral efficacy in the absence of ERK5 kinase activity corresponded to lowered STAT1 phosphorylation, revealing a noncanonical role for ERK5 in STAT1 activation downstream of IFN{lambda}. In contrast, type I IFN antiviral signaling is largely resistant to ERK5 modulation. Altogether, we identify ERK5 as a potentiator of STAT1 activation, ISG expression, and antiviral activity following type III IFN stimulation. SIGNIFICANCERegulation of type III interferons (IFN{lambda}) at mucosal barriers in response infection to mitigate viral replication and support barrier integrity. The specific mechanistic requirements for MAPK signaling to sustain IFN{lambda}-mediated gene expression have remained elusive. Amongt the least characterized members of the MAPK family, the role of ERK5 in regulating host inflammatory responses has been hampered by off-target effects of kinase inhibitors. Here, we combine pharmacological and genetic approaches to specifically demonstrate that ERK5 promotes antiviral immunity in epithelial cells. Mechanistically, ERK5 enhances the activation of STAT1 in response to IFN stimulation to augment the transcription of IFN-stimulated genes. Our work demonstrates that therapeutic modulation of MAPK and IFN signaling pathway co-integration could distinguish between the protective and deleterious outcomes of IFN expression. One-sentence summaryERK5 potentiates IFN lambda responses.

immunology↗

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↗

bioRxiv2024

Experimental evolution for improved post-infection survival selects for increased disease resistance in Drosophila melanogaster

Disease resistance (defined as the host capacity to limit systemic infection intensity) and disease tolerance (defined as the host capacity to limit infection-induced damage) are two complementary defense strategies that help the hosts maximize their survival and fitness when infected with pathogens and parasites. In addition to the underlying physiological mechanisms, existing theory postulates that these two strategies differ in terms of the conditions under which each strategy evolves in host populations, their evolutionary dynamics, and the ecological and epidemiological consequences of their evolution. Here we explored if one or both of these strategies evolve when host populations are subjected to selection for increased post-infection survival. We experimentally evolved Drosophila melanogaster populations, selecting for the flies that survived an infection with the entomopathogen Enterococcus faecalis, and found that the host populations evolved increased disease resistance in response. This was despite the physiological costs associated with increased resistance. We did not find evidence of any change in disease tolerance in the host populations. We have therefore demonstrated that in an experimental evolution set-up, where insect hosts must survive an infection with a pathogenic bacterium, the hosts evolve improved disease resistance but not disease tolerance.

evolutionary biology↗

bioRxiv2023

Proximity labeling reveals dynamic changes in the SQSTM1 protein network

Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.

cell biology↗