Biology subjects

Saha, J.

Publications and source records attributed to Saha, J..

At least 19 recordsLinked to original sources

bioRxiv2026

FAIM Inhibits Insulin Amyloidogenesis through a Noncanonical Aggregation Pathway

Insulin can misfold and assemble into amyloid fibrils, a process linked not only to complications of insulin therapy but also to proteotoxic stress in pancreatic {beta}-cells. Despite growing interest in the pathological consequences of insulin aggregation, prevention efforts are limited by an incomplete understanding of the endogenous mechanisms that counteract it. Here, we identify Fas apoptosis inhibitory molecule (FAIM) as an endogenous suppressor of insulin amyloid formation. FAIM reduces {beta}-sheet formation and redirects insulin toward disordered, growth-incompetent assemblies. Further, FAIM attenuates the cytotoxicity of insulin aggregates in vitro. We hypothesize that this effect arises from masking aggregation-prone regions of insulin and show through structural modeling that FAIM interacts with both insulin chains. These findings extend the anti-aggregation function of FAIM to insulin and suggest a mechanism for endogenous suppression of insulin amyloid formation. More broadly, our results provide insight into the regulation of insulin assembly and highlight FAIM as a candidate modulator of proteostasis in metabolic disease. Statement for a broader audienceInsulin can clump together into harmful aggregates, contributing to complications of insulin therapy and potentially damaging the insulin-producing cells of the pancreas. This study identifies the naturally occurring protein FAIM as a protective factor that inhibits the formation of these harmful aggregates and reduces their toxicity. These findings improve our understanding of how cells protect insulin from harmful aggregation and may open new avenues for developing therapies to combat diabetes-related protein aggregation.

biochemistry↗

bioRxiv2026

SEC Purified Monomeric Aβ42 Produces Reproducible and Reliable Ag-gregation Measurements

The accumulation of amyloid-beta (A{beta}) plaques is a hallmark of Alzheimers disease (AD), with A{beta}42 representing the predominant and most aggregation-prone isoform. Reliable preparation of monomeric A{beta}42 is essential for investigating the kinetics and mechanisms of its aggregation into oligomers and fibrils. This study provides a direct comparison of two monomerization protocols for recombinantly expressed A{beta}42: one incorporating size-exclusion chromatography (SEC) and the other relying solely on chemical denaturation, using agents such as NaOH and NH4OH. A{beta}42 was produced in E. coli, purified through urea solubilization followed by HPLC, and subjected to monomerization via the respective methods. Monomeric preparations were evaluated using Thioflavin T (ThT) fluorescence to assess aggregation kinetics, TEM to detect fibrils and preformed aggregates, and NMR spectroscopy. SEC-isolated monomers displayed sigmoidal aggregation profiles in ThT assays, featuring distinct lag, growth, and plateau phases consistent with secondary nucleation-dominated models as determined by AmyloFit analysis. Increasing the initial peptide concentration resulted in higher fibril yields, which was further supported by TEM images showing extensive fibrillization following incubation. In contrast, non-SEC preparations containing pre-existing aggregates detectable by TEM and showed attenuated NMR signals, leading to impaired aggregation behavior. NaOH-denatured samples predominantly exhibited flat ThT curves, whereas NH4OH-denatured samples displayed extended lag phases. NH4OH performance better than NaOH, likely because its gradual pH neutralization reduced peptide structural perturbation. Overall, these findings demonstrate that SEC is critical for obtaining highly pure monomeric A{beta}42 and improving the reproducibility of aggregation assays, highlighting the importance of standardized monomer preparation protocols in AD research. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=49 SRC="FIGDIR/small/724608v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1a3b9caorg.highwire.dtl.DTLVardef@1fa85d2org.highwire.dtl.DTLVardef@67a83dorg.highwire.dtl.DTLVardef@1564f77_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Higher Magnetic Field NMR Renders Resolution Enhancement on Ganglioside GD3 Catalyzed Abeta42 Aggregates

Magic-angle spinning (MAS) solid-state NMR (SSNMR) has been widely used to determine amyloid fibril structures at atomic resolution. Such studies typically rely on homogeneous fibril preparations that produce narrow linewidths and high spectral resolution, enabling reliable resonance assignment and structural analysis. However, many biologically relevant amyloid aggregates are structurally heterogeneous, resulting in spectral broadening and reduced sensitivity that hinder atomic-resolution characterization. Lipids are known to modulate amyloid aggregation pathways and promote the formation of toxic species that are often less homogeneous, further complicating NMR-based investigations. Here, we evaluate the feasibility of utilizing the benefits associated with high-field (1.1 GHz) SSNMR for studying ganglioside GD3-catalyzed A{beta}42 aggregates. Uniformly-13C,15N-labeled A{beta}42 was incubated with GD3 to generate lipid-associated aggregates and analyzed under MAS conditions. 13C cross-polarization magic-angle spinning (CPMAS) spectra and 2D 13C-13C chemical shift correlation experiments using CORD (COmbined R2nv-Driven) mixing were acquired and compared with data collected at 600 MHz. Despite the heterogeneous nature of the GM1-associated assemblies, the 1.1 GHz spectra exhibit enhanced sensitivity and improved spectral resolution. Better resolved resonances corresponding to selectively structured regions of A{beta}42 are observed, indicating the presence of an ordered core within the lipid-associated aggregates. These results demonstrate that ultrahigh-field SSNMR significantly improves the characterization of heterogeneous amyloid assemblies and provides a promising approach for atomic-level investigation of biologically relevant, lipid-modulated A{beta} aggregates.

biophysics↗

bioRxiv2026

Gangliosides GM3 And GD3 Modulate Insulin Aggregation Pathways and Reduce Cytotoxicity Through Structural Remodeling

Insulin amyloid aggregation is a key pathological and pharmaceutical concern, particularly in the context of Type-2 Diabetes (T2D), where amyloid deposition of protein can impair therapeutic efficacy and contribute to cell death leading to local tissue damage. Although gangliosides--glycosphingolipids containing sialic acid residues--are known to modulate amyloid formation in neurodegenerative disorders, their influence on insulin aggregation remains largely unexplored. In this study, we investigate the effects of gangliosides GM3 and GD3 on insulin aggregation. Using Thioflavin-T (ThT) based fluorescence kinetics, Fourier Transform Infrared (FTIR) spectroscopy, Circular Dichroism (CD) spectroscopy, Small Angle X-ray Scattering (SAXS), Nuclear Magnetic Resonance (NMR) spectroscopy, and Transmission Electron Microscopy (TEM), the aggregation pathway, changes in the secondary structure and morphology of insulin aggregates have been characterized. Our results show that both GM3 and GD3 lipids accelerated insulin aggregation in a concentration-dependent manner while steering the pathway away from classical fibril formation, producing short, beaded structures distinct from the extended fibrils observed under lipid-free conditions. CD and FTIR data analyses revealed that insulin in the presence of gangliosides formed non-fibrillar intermediates with distinct secondary structures: {beta}-sheet-rich globular clusters in presence of GD3 and -helical intermediates in GM3-treated samples. Cytotoxicity assays further demonstrated that ganglioside-induced aggregates are significantly less toxic to cells when compared to insulin-only aggregates. Furthermore, ganglioside-bound insulin oligomers retain seeding capacity, suggesting that they can nucleate further aggregation despite their non-fibrillar morphology. These findings underscore the role of gangliosides in modulating insulin amyloid polymorphism and toxicity, offering new insights into their potential impact on the pathology of T2D and treatment strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/703542v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@5bf40eorg.highwire.dtl.DTLVardef@f400ddorg.highwire.dtl.DTLVardef@164dcd8org.highwire.dtl.DTLVardef@def4e7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGangliosides GD3 and GM3 accelerate insulin aggregation, forming non-fibrillar assemblies. C_LIO_LIGanglioside-bound insulin aggregates are less cytotoxic than fibrillar aggregates. C_LIO_LIDespite altered morphology, ganglioside-bound aggregates retain seeding ability. C_LI

biophysics↗

bioRxiv2025

MAS cryoprobe enhances solid-state NMR signals of α-synuclein fibrils

Solid-state NMR spectroscopy is increasingly applied to structural and dynamics studies across a broad range of chemical, material, and biological systems. Although sensitivity has traditionally been a major limitation, the recently developed MAS cryoprobe has been shown to substantially overcome this challenge. Its ability to enhance the signal-to-noise (S/N) ratio without requiring sample freezing makes it particularly attractive for investigating non-isotropic systems, including soft materials (e.g., hydrogels), semi-solids (e.g., membrane mimetics) and rigid solids (e.g., amyloid fibrils). In this study, we report on the enhanced sensitivity of solid-state NMR experiments on -synuclein fibrils using a MAS cryoprobe. Nearly an order-of-magnitude improvement in S/N was observed in CPMAS, refocused-INEPT and 2D 13C-13C chemical shift correlation spectra of -synuclein fibrils compared with data collected on a conventional MAS probe. The improved S/N enables the acquisition of slowly decaying signals in the indirect dimension, facilitating faster, high-resolution multidimensional solid-state NMR spectroscopy. We therefore anticipate that MAS cryoprobe will become increasingly valuable for structural studies a wide range of samples that are less abundant, less stable, or transient, such as amyloid intermediates.

biophysics↗

bioRxiv2025

A Simple Algorithm to Suppress Diagonal Peaks in High-Resolution Homonuclear Chemical Shift Correlation NMR Spectra

Previous experimental strategies aimed at completely suppressing diagonal peaks in NMR homonuclear correlation spectra often resulted in reduced sensitivity for cross peaks. In this work, we report a spectral shearing approach that transforms diagonal peaks along the diagonal axis of a homonuclear correlation spectrum into a zero-frequency line in the indirect dimension. This allows for effective extraction and substantial suppression of diagonal peaks using a recently proposed data processing algorithm based on quadrature-detected spin-echo diagonal peak suppression. Since the shearing process only rearranges the positions of cross peaks without affecting their intensities, the sensitivity of cross peaks is fully preserved while diagonal peaks are significantly reduced. The effectiveness of this method is demonstrated using uniformly 13C&15N labeled -synuclein amyloid fibril and aquaporin Z membrane protein samples.

biophysics↗

bioRxiv2025

A Software for Identification and Characterization of Theta Rhythms in the Hippocampus

Characterizing theta rhythms in the hippocampus provides a window into understanding memory processing. An inquiry that arises when an animal sustains a pathological state is how theta rhythms are affected. In pathological states like epilepsy or Alzheimers, these rhythms change in specific ways. Statistically robust changes in these rhythms could serve as potential biomarkers, indicating the severity of the animals condition and the effectiveness of a drug. However, this understanding depends on how the data is analyzed. There are currently no standard criteria for recognizing theta dominance in experimental recordings. To address this, we have developed novel MATLAB-based software with an easy-to-use graphical user interface which enables identifying and analyzing theta rhythms in a standard way. We discuss the softwares functionality and its underlying algorithms. The algorithms were developed using previously acquired EEG/LFP data recorded from the hippocampus of a mouse kindling model of epilepsy. Two primary analyses were conducted to test the softwares functionality: first, comparing theta rhythms during the baseline period versus during spontaneous recurrent seizures; second, analyzing the timing of theta rhythms relative to the seizure event. Our illustrative results indicate that our developed software can robustly identify theta events with statistically significant feature differences. Further, the examination presented here with two mice shows that while theta events can occur just before seizures, it takes tens of minutes post-seizure before theta rhythms occur again. Our software thus provides the user with the ability to robustly identify and characterize theta rhythms and their feature changes. Significance StatementTheta rhythms in the hippocampus are fundamental for spatial navigation and memory formation. Their observed changes during several pathological states such as epilepsy and Alzheimers make them highly interesting to be able to serve as biomarkers. However, their variability (in terms of the time of occurrence, duration, and frequency range) makes them challenging to quantify. The absence of available tools for the automatic extraction of these rhythms from extended datasets significantly hampers processing efficiency and reduces accuracy and consistency. Clinicians and researchers often manually inspect their data to identify these rhythms, a process that is not only time-consuming but also inherently subjective. We have thus developed a MATLAB software for precise, automatic analysis of theta rhythms in EEG/LFP recordings.

neuroscience↗

bioRxiv2025

Anionic lipid catalyzes the generation of cytotoxic insulin oligomers

Misfolding and aggregation of proteins into amyloidogenic assemblies are key features of several metabolic and neurodegenerative diseases. Human insulin has long been known to form amyloid fibrils under various conditions, which affects its bioavailability and function. Clinically, insulin aggregation at recurrent injection sites poses a challenge for diabetic patients who rely on insulin therapy. Furthermore, decreased responsiveness to insulin in type 2 diabetic (T2D) patients may lead to its overproduction and accumulation as aggregates. Earlier reports have reported that various factors such as pH, temperature, agitation, and the presence of lipids or other proteins influence insulin aggregation. Our present study aims to elucidate the effects of non-micellar anionic DMPG (1,2-dimyristoyl-sn-glycero-3-phosphoglycerol) lipids on insulin aggregation. Distinct pathways of insulin aggregation and intermediate formation were observed in the presence of DMPG using a ThT fluorescence assay. The formation of soluble intermediates, alongside large insulin fibrils, was observed in insulin incubated with DMPG via TEM, DLS and NMR, as opposed to insulin aggregates generated without lipids. 13C magic angle spinning solid-state NMR and FTIR experiments indicated that lipids do not alter the conformation of insulin fibrils but do alter the time scale of motion of aromatic and aliphatic sidechains. Furthermore, the soluble intermediates were found to be more cytotoxic as compared to fibrils generated with or without lipids. Overall, our study elucidates the importance of anionic lipids in dictating the pathways and intermediates associated with insulin aggregation. These findings could be useful in determining various approaches to avoid toxicity and enhance the effectiveness of insulin in therapeutic applications.

biophysics↗

bioRxiv2024

Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation

Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large inversions segregating in the benthic subradiation that each suppress recombination over more than half a chromosome. Two inversions were transferred from deepwater pelagic Diplotaxodon via admixture, while the others established early in the deep benthic clade. Introgression of haplotypes from lineages inside and outside the Malawi radiation coincided with bursts of species diversification. Inversions show evidence for transient sex linkage and a striking excess of protein changing substitutions points towards selection on neuro-sensory, physiological and reproductive genes. We conclude that repeated interplay between depth adaptation and sex-specific selection on large inversions has been central to the evolution of this iconic system.

evolutionary biology↗

bioRxiv2024

Defective Homologous Recombination and Genomic Instability Predict Increased Responsiveness to Carbon Ion Radiotherapy in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is inherently resistant to conventional chemo-and radiation-therapy. However, clinical trials showed that carbon ion radiotherapy (CIRT) with concurrent gemcitabine can be effective for treating unresectable locally advanced PDAC. In this study, we aimed to determine features that could identify patients who would benefit most from CIRT. A panel of human PDAC cell lines with various genetic backgrounds was leveraged to determine whether a subset could be identified that preferentially responds to CIRT. The cell lines displayed a differential response to CIRT as compared to {gamma}-rays as measured by relative biological effectiveness (RBE) calculated at 10% survival, which ranged from 1.96 to 3.04. Increased radiosensitivity correlated with decreased DNA double strand break (DSB) repair as measured by {gamma}H2AX foci resolution. We determined that the cell lines most sensitive to CIRT are defective in the homologous recombination (HR) DSB repair pathway and/or have high genomic instability due to elevated replication stress. Next, this knowledge was utilized to assess whether the HR pathway could be targeted to potentiate CIRT in vitro. It was determined that pretreating a radioresistant PDAC cell line with the HR inhibitor, B02, resulted in a marked increase in sensitivity to CIRT when treated with high linear energy transfer (LET) radiation in the spread-out Bragg peak (74.1-89.3 keV/m) but not at the entry LET (13.0-16.4 keV/m) in vitro as opposed to that seen with a NHEJ inhibitor. These data suggest a greater therapeutic index with the combination therapy in the tumor over normal tissues based on LET distribution. These data support the notion that PDAC tumors with defects in HR and/or those with high inherent replication stress respond to CIRT without the concern for excessive normal tissue toxicity. With the advent of agents targeting HR, the difference in tumor cell response in the entry region vs within the SOBP based upon the respective LETs of those regions of the beam profile, will be superior to agents that target NHEJ.

cancer biology↗

bioRxiv2023

Probabilistic clustering of cells using single-cell RNA-seq data

Single-cell RNA sequencing is a modern technology for analyzing cellular heterogeneity. A key challenge is to cluster a heterogeneous sample of different cell types into multiple different homogeneous groups. Although there exist a number of clustering methods, they do not perform well consistently across various datasets. Moreover, most of them are not based on probabilistic approaches making it difficult to assess uncertainties in their results. Therefore, in spite of having large cell atlases, it is often quite difficult to map cells to types. In addition, many of the methods require prior knowledge such as marker gene information for each type. Also due to technological limitations, dropouts of gene expressions may occur in the data which is not taken into account in other methods. Here we present a probabilistic method named CellHorizon for clustering scRNA-seq data that is based on a generative model, handles dropouts and works without any prior marker gene information. Experiments reveal that our method outperforms current state-of-the-art methods overall on six gold standard datasets.

bioinformatics↗

bioRxiv2023

Novel carbon nanoparticles derived from Bougainvillea modulate vegetative growth in Arabidopsis

We present a green synthesis method of producing blue fluorescence emitting carbon nanoparticles (CNPs) through a simple and cost-effective single-step hydrothermal reaction. The synthesis utilized bract extracts and pollen grains from three Bougainvillea species: B. spectabilis, B. alba, and B. buttiana. The CNPs exhibited photoluminescence, with the highest emission observed in the ultraviolet region. Atomic force microscopy analysis revealed that the size of synthesized CNPs ranged from 23 nm to 83 nm. Fourier transform infrared analysis provided a comprehensive understanding of the CNPs surface functional groups, with carbon being the predominant group. X-ray diffraction analysis confirmed the amorphous nature of the synthesized CNPs. Zeta potential measurements indicated that the particles carried a negative charge, suggesting their colloidal stability. In experiments conducted with Arabidopsis thaliana seedlings, CNPs derived from B. alba pollen grains were found to promote leaf area expansion while simultaneously inhibiting primary root growth. Conversely, other CNPs demonstrated detrimental effects on vegetative growth. These findings underscore the potential application of these novel CNPs in agriculture.

plant biology↗

bioRxiv2023

Sugar distributions on gangliosides guide the formation and stability of amyloid-β oligomers

Aggregation of A{beta} peptides has been known as a key contributor to the etiology of Alzheimers disease. Being intrinsically disordered, the monomeric A{beta} is susceptible to conformational excursions, especially in the presence of key interacting partners such as membrane lipids, to adopt specific aggregation pathways. Furthermore, key components such as gangliosides in membranes and lipid rafts are known to play important roles in the adoption of pathways and the generation of discrete neurotoxic oligomers. Yet, what roles the carbohydrates on gangliosides play in this process remains unknown. Here, using GM1, GM3, and GD3 ganglioside micelles as models, we show that the sugar distributions and cationic amino acids within A{beta} N-terminal region modulate oligomerization of A{beta} temporally, and dictate the stability and maturation of oligomers.

biophysics↗

bioRxiv2023

De novo amyloid peptides with subtle sequence variations differ in their self-assembly and nanomechanical properties

Proteinaceous amyloids are well known for their widespread pathological roles but lately have emerged also as key components in several biological functions. The remarkable ability of amyloid fibers to form tightly packed conformations in a cross {beta}-sheet arrangement manifests in their robust enzymatic and structural stabilities. These characteristics of amyloids make them attractive for designing proteinaceous biomaterials for various biomedical and pharmaceutical applications. In order to design customizable and tunable amyloid nanomaterials, it is imperative to understand the sensitivity of the peptide sequence for subtle changes based on amino acid position and chemistry. Here we report our results from four rationally-designed amyloidogenic decapeptides that subtly differ in hydrophobicity and polarity at positions 5 and 6. We show that making the two positions hydrophobic renders the peptide with enhanced aggregation and material properties while the introduction of polar residues in position 5 dramatically changes the structure and nanomechanical properties of the fibrils formed. A charged residue at position 6, however, completely abrogates amyloid formation. In sum, we show that subtle changes in the sequence do not make the peptide innocuous but rather sensitive to aggregation, reflected in the biophysical and nanomechanical properties of the fibrils. We conclude that tolerance of peptide amyloid for subtle changes in the sequence should not be neglected for the effective design of customizable amyloid nanomaterials.

biophysics↗

bioRxiv2023

Robust Removal of Slow Artifactual Dynamics Induced by Deep Brain Stimulation in Local Field Potential Recordings using SVD-based Adaptive Filtering

Deep brain stimulation (DBS) is widely used as a treatment option for patients with movement disorders. In addition to its clinical impact, DBS has been utilized in the field of cognitive neuroscience wherein the answers to several fundamental questions underpinning the mechanisms of neuromodulation in decision making rely on how a burst of DBS pulses, usually delivered at clinical frequency, i.e., 130 Hz, perturb participants choices. It was observed that neural activities recorded during DBS were contaminated with stereotype large artifacts, which lasts for a few milliseconds, as well as a low-frequency (slow) signal ([~]1-2 Hz) that can persist for hundreds of milliseconds. While the focus of the most of methods for removing DBS artifact was on the former, the artifact removal of the slow signal has not been addressed. In this work, we propose a new method based on combining singular value decomposition (SVD) and normalized adaptive filtering to remove both large (fast) and slow artifacts in local field potentials recorded during a cognitive task in which bursts of DBS were utilized. Using synthetic data, we show that our proposed algorithm outperforms four commonly used techniques in the literature, namely, (1) Normalized least mean square adaptive filtering, (2) Optimal FIR Wiener filtering, (3) Gaussian model matching, and (4) Moving average. The algorithms capabilities are further demonstrated by its ability to effectively remove DBS artifacts in local field potentials recorded from the subthalamic nucleus during a verbal Stroop task, highlighting its utility in real-world applications.

neuroscience↗

bioRxiv2022

Ganglioside enriched phospholipid vesicles induce cooperative Aβ oligomerization and membrane disruption

A major hallmark of Alzheimer disease (AD) is the accumulation of extracellular aggregates of amyloid-{beta} (A{beta}). Structural polymorphism observed among A{beta} fibrils in AD brains seem to correlate with the clinical sub-types suggesting a link between fibril polymorphism and pathology. Since fibrils emerge from a templated growth of low-molecular weight oligomers, understanding the factors affecting oligomer generation is important. The membrane lipids are key factors that influence early stages of A{beta} aggregation and oligomer generation, and cause membrane disruption. We have previously demonstrated that conformationally discrete A{beta} oligomers can be generated by modulating the charge, composition, chain length of lipids and surfactants. Here, we extend our studies into liposomal models by investigating A{beta} oligomerization on large unilamellar vesicles (LUVs) of total brain extracts (TBE), reconstituted lipid rafts (LRs) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Specifically, we varied the vesicle composition by varying the amount of GM1 gangliosides added as a constituent. We found that liposomes enriched in GM1 induce the formation of toxic, low-molecular weight oligomers that are isolable in a lipid-complexed form. Importantly, the data indicate that oligomer formation and membrane disruption are highly cooperative processes. Numerical simulations on the experimental data confirm cooperativity and reveal that GM1-enriched liposomes form twice as many numbers of pores as those without GM1. Overall, this study uncovers mechanisms of cooperativity between oligomerization and membrane disruption under controlled lipid compositional bias, and refocuses the significance of the early stages of A{beta} aggregation in polymorphism, propagation, and toxicity in AD. TOC figure O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

biophysics↗

bioRxiv2021

αS oligomers generated from polyunsaturated fatty acid and dopamine metabolite differentially interact with Aβ to enhance neurotoxicity

It is increasingly becoming clear that neurodegenerative diseases are not as discrete as originally thought to be but rather display significant overlap in histopathological and clinical presentations. For example, nearly half of the patients with Alzheimer disease (AD) and synucleinopathies such as Parkinson disease (PD) show symptoms and pathological features of one another. Yet, the molecular events and features that underlie such comorbidities in neurodegenerative diseases remain poorly understood. Here, inspired to uncover the molecular underpinnings of the overlap between AD and PD, we investigated the interactions between amyloid-{beta} (A{beta}) and -synuclein (S), aggregates of which form the major components of amyloid plaques and Lewy bodies, respectively. Specifically, we focused on S oligomers generated from the dopamine metabolite called dihydroxyphenylacetaldehyde (DOPAL), and a polyunsaturated fatty acid docosahexaenoic acid (DHA). Both S oligomers showed structural and conformational differences confirmed by their disparity in size, secondary structure, susceptibility to proteinase K digestion and cytotoxicity. More importantly, the two oligomers differentially modulated A{beta} aggregation. While both oligomers inhibited A{beta} aggregation to varying extents, they induced structurally different A{beta} assemblies. Furthermore, A{beta} seeded with DHA-derived S oligomers showed greater toxicity than DOPAL-derived S oligomers in SH-SY5Y neuroblastoma cells. These results provide insights into the interactions between two amyloid proteins with empirically distinctive biophysical and cellular manifestations, enunciating a basis for potentially ubiquitous cross-amyloid interactions across many neurodegenerative diseases.

biophysics↗

bioRxiv2021

Ablating Ku70 phosphorylation results in defective DNA damage repair and spontaneous induction of hepatocellular carcinoma

Multiple pathways mediate the repair of DNA double-strand break (DSB), with numerous mechanisms responsible for driving choice between the pathways. Previously, we reported that phosphorylation of the non-homologous end joining (NHEJ) factor, Ku70, is required for the dissociation of the Ku heterodimer from DNA ends to allow DSB repair via homologous recombination (HR). A knock-in mouse, in which phosphorylation is ablated in the three conserved sites of Ku70 (Ku703A/3A), was generated in order to test the hypothesis that Ku70 phosphorylation is required for initiation of HR and that blocking this process results in enhanced genomic instability and tumorigenesis. Here, we show that Ku703A/3A mice develop spontaneous and have accelerated chemical-induced hepatocellular carcinoma (HCC) compared to wild-type (Ku70+/+) littermates. The HCC tumors from the Ku703A/3A mice have increased {gamma}H2AX and 8-oxo-G staining, suggesting DNA repair is decreased in these mice. Spontaneous transformed cell lines from Ku703A/3A mice are more radiosensitive, have a significant decrease in DNA end resection, and are more sensitive to the DNA cross-linking agent mitomycin C compared to cells from Ku70+/+ littermates. Collectively, these findings demonstrate that phosphorylation-mediated dissociation of Ku heterodimer from DNA ends is required for efficient DNA damage repair and disruption of this process results in genomic instability and accelerated development of HCC.

cancer biology↗