Biology subjects

Pillai, J.

Publications and source records attributed to Pillai, J..

5 recordsLinked to original sources

bioRxiv2026

Association of object mnemonic discrimination deficit with age and AD biomarkers in older adults

Background Blood-based Alzheimers disease (AD) biomarkers provide scalable detection of AD pathology, yet their relationships with hippocampal-dependent mnemonic discrimination remain unclear. This study examined how object mnemonic discrimination relates to age, hippocampal structure, and plasma AD biomarkers in cognitively normal (CN) older adults and individuals with amnestic mild cognitive impairment (aMCI). Methods Forty-six CN and forty-one aMCI participants completed an object mnemonic similarity task (MST). Mnemonic discrimination was quantified using the overall lure discrimination index (LDI) and similarity-specific LDIs. Plasma pTau181, pTau217, pTau231, and GFAP were assayed, and hippocampal volumes were derived from 7T MR scanner. Multiple linear regression models assessed associations between LDI and biomarkers, controlling for age, sex, education, APOE4 status, and diagnosis. Repeated-measures ANCOVA and linear mixed-effects models evaluated similarity-dependent age effects. ROC analyses and stepwise logistic regression quantified diagnostic classification performance. Results LDI was significantly reduced in aMCI compared to CN. Total hippocampal volume and plasma pTau217 showed the strongest associations with LDI, exceeding those of pTau181, pTau231, and GFAP. LDI discriminated aMCI from CN with high accuracy (AUC = 0.836), comparable to hippocampal volume and plasma biomarkers. A combined model including LDI, pTau181, pTau217, and hippocampal volume achieved the highest diagnostic accuracy (AUC = 0.931). Age effects were similarity-dependent: discrimination declined with age only for low-similarity lures, independent of diagnosis. Sex differences emerged within aMCI, with females showing lower LDI than males. Conclusions Object mnemonic discrimination provides a sensitive behavioral marker linked to hippocampal volume and plasma pTau217, showing discriminative power comparable to established AD biomarkers in separating aMCI from CN participants. Similarity-dependent age effects highlight age-related deficits are not universal for lures with varying similarity levels.

neuroscience↗

bioRxiv2026

Correlations of 276 missense variants of PSEN1, PSEN2, and APP on the production of Aβ peptides against variant effect predictors and biophysical structures

INTRODUCTIONEarly-onset Alzheimers disease (EOAD) is mostly caused by mutations in Presenilin-1,2 (PSEN1, PSEN2), and amyloid precursor protein (APP) genes. Both genetic and experimental evidence has supported the PSEN-APP amyloid hypothesis as the leading pathogenesis of AD. Thus far, 276 missense variants from PSEN1,2, and APP have been identified. Herein, we report the development of algorithm platforms for predicting the degrees of pathogenic potentials of these various missense mutations in AD. METHODSWe performed extensive pairwise correlations between 276 in vitro functional assays of missense variants from PSEN1, PSEN2, and APP and clinical data among EOAD patients against 37 variant effect predictors (VEPs). Furthermore, we used the structural models of all three proteins to refine understanding of the molecular basis of missense variants in dominant negative (DN) or loss-of-function (LoF) effects. RESULTSWe found that VEPs were consistently correlated with age of onset (AAO) among EOAD patients and the A{beta}42/A{beta}40 ratio biomarker. This study also identified discrepancies in the predictor variable leading to an increase in the A{beta}42/A{beta}40 ratio; The increased A{beta}42/A{beta}40 ratio was due to decreased A{beta}40 levels by Sun et al., (2016), while Petit et al., (2022) argued that increased A{beta}42 level was the culprit. We also identified that with increased predicted pathogenicity, there were decreased A{beta}38 levels. Conversely, this study found no direct correlations with A{beta}37 and A{beta}43. Lastly, structural studies show characteristics of either DN and LoF mechanisms, as there were numerous variants located in buried hydrophobic domains and those on charged surfaces of the proteins. DISCUSSIONCurrently, a major limitation in the field is the lack of reliable approaches for predicting the pathogenicity of variants in EOAD. We show that VEPs are promising in deciphering the effects of variants in PSEN1, PSEN2, and APP genes, especially between multiple pathogenic mutations. Our study also illuminates the need for experimental studies to identify the predictor variable causing the increased A{beta}42/A{beta}40 biomarker. Our biophysical studies also identify the need to characterize whether the mechanism of pathogenesis caused by DN or LoF effects is in scope of the presenilin hypothesis. Research in ContextO_LISystematic review: The authors reviewed experimental evidence of pathogenic PSEN1, PSEN2, and APP variants in scope of the presenilin hypothesis. To our knowledge, the pathogenesis of EOAD remains incompletely understood. There are also no predictive tools/models available for informing clinical translation. C_LIO_LIInterpretation: VEPs demonstrate strong correlations with AAO and A{beta} levels from pairwise correlations with 276 missense variants. Structurally, it appears that mutations demonstrate characteristics of dominant negative and loss-of-function effects. C_LIO_LIFuture Direction: Larger studies are necessary of VEPs for realistic clinical usage. C_LI HighlightsO_LIWe performed correlations of 37 VEPs against in vitro data of EOAD variants. C_LIO_LIVEPs demonstrate potential as diagnostic tools for early onset Alzheimers disease. C_LIO_LIPathogenic missense variants show characteristics of DN and LoF effects. C_LI

neuroscience↗

bioRxiv2025

Deciphering gain-of-function from loss-of-function variants with AlphaMissense: A case study with the mechanosensitive PIEZO1 ion channel protein

Pathogenic missense mutations are commonly found in protein-coding regions of DNA, and often alter protein function. In the past decade, enormous experimental efforts have been undertaken through the development of functional assays, mutagenesis screenings, and computational prediction algorithms to characterize these variants. Indeed, most efforts have been focused towards identifying degrees of loss-of-function (LoF) effects on the three-dimensional structures of proteins, but gain-of-function (GoF) mutations remain poorly understood. Herein, we performed a case study of the PIEZO1 mechanosensitive ion channel protein whose GoF variants (n = 56) are implicated in hereditary xerocytosis (HX) and LoF variants (n = 6) in lymphatic dysplasia (LD), respectively. This study evaluated the abilities of AlphaMissense (AM) to decipher both mutation types, and benchmarked its performance against other algorithmic approaches, including Combined Annotation Dependent Depletion (CADD) v1.7, evolutionary model of variant effect (EVE), and Evolutionary Scale Modeling-1b (ESM-1B). We found that all approaches excelled in identifying LoF variants but were often ambiguous in their predictions for GoF PIEZO1 variants. ESM-1b was a notable exception that demonstrated balance sensitivity to both GoF and LoF variants as it likely identified certain sequential features not utilized in other approaches. Secondly, our findings suggest that GoF variants of HX do not significantly destabilize the PIEZO1 structure and are not generally identified by conventional signatures of damage from these algorithms. GoF variants are not synonymous with direct changes in changes in free energy upon mutations. Furthermore, we validated computational structure predictions of PIEZO1 against resolved cryo-EM structures, and provided biophysical data for variants located on unresolved residues of this ion channel. We formulated a weighted ensemble model that performed similarly to AM and outperformed all other traditional approaches evaluated in this study. Overall, this is the first study to directly evaluate the capabilities of pathogenicity prediction algorithms for deciphering GoF and LoF variants, and underscores the limitations present in current approaches.

biophysics↗

bioRxiv2025

Evaluating the pathogenicity, stability, and stereochemical effects of variants of unknown significance in TREM2 using orthogonal structural analyses

Triggering receptor expressed on myeloid cells 2 (TREM2), an immune receptor expressed on the surface of microglia, has been identified through genome-wide association studies to be one of the risk factors in Alzheimers disease (AD). Several studies have also identified missense variants of TREM2 to be associated with frontotemporal dementia and Nasu-Hakola disease (NHD). To date, 51 novel missense variants of TREM2 have been identified in the literature, with the disease risk profiles of most variants still unknown. Assessing and classifying the pathogenicity of these variants is essential to investigate the disease mechanisms and develop effective treatments. Herein, we classified 32 missense variants involved in TREM2 using structural bioinformatic data with AlphaFold2. Using the protocol described in our previous work (Pillai et al., 2025), we determined the structural, stability, and potential functional effects of these variants. Our evaluations of the mutations were divided into those (i) implicated in NHD, (ii) located on the transmembrane domain, (iii) surface of the IgV-like domain, and (iii) buried in the receptor. Our analysis of variants involved in NHD suggests that, while V126G imposes the greatest effects, the T66M variant exerts significantly less effects on the TREM2 structures compared to the other remaining variants. Variants in the transmembrane domain of TREM2 did not impose significant alterations to the three-dimensional structure. Outside of known variants in the IgV-like domain, we identified 10 variants that imposed significant destabilizing effects to the structure and are of potential interest. Overall, the baseline biochemical data provided from this study may be informative to experimental efforts to better classify rare coding variants of TREM2 that are of unknown biological and clinical significance. HighlightsUsing our previously published protocol, we characterized the structure, stability, and functional effects of 27 unique variants of unknown biological significance in TREM2. Our analysis was divided into variants located on the transmembrane domain, surface of the IgV-like domain, buried in the IgV-like domain, and those leading to Nasu-Hakola disease. Excluding AD- and NHD-causing variants, we identified 10 TREM2 variants that cause significant destabilizing effects to the receptor. The in-silico data provided from this study serve as a baseline, and can guide future experimental efforts involving TREM2 variants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/656054v1_ufig1.gif" ALT="Figure 1000"> View larger version (35K): org.highwire.dtl.DTLVardef@c426b1org.highwire.dtl.DTLVardef@1c859f1org.highwire.dtl.DTLVardef@88ea70org.highwire.dtl.DTLVardef@d777f4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

Peripheral sTREM2-related inflammatory activity alterations in early stage Alzheimer's disease

Alzheimers disease (AD) has been linked to multiple immune system genetic variants, implicating potential broad alterations in inflammatory profiles in the disease. Triggering receptor expressed on myeloid cells 2 (TREM2) genetic variants are risk factors for AD and other neurodegenerative diseases. A soluble TREM2 isoform (sTREM2) is elevated in cerebrospinal fluid in the early stages of AD suggesting it may be a biomarker of progressive alterations in immune response to AD-related pathology. Multiple studies have reported an altered peripheral immune response in AD. However, less is known about the relationship between plasma sTREM2 and the altered peripheral immune response in AD. The objective of this exploratory study was to examine the relationship between sTREM2 and inflammatory activity in human participants defined by clinically characterized cognitive symptoms and groups defined by the cerebrospinal fluid biomarkers amyloid beta, phosphorylated tau, and neurodegeneration (NIA-AA Research Framework: "ATN continuum".) The hypothesis of this exploratory study was that sTREM2 related inflammatory activity differs by AD stage. We observed different patterns of inflammatory activity across disease groups and ATN categories that implicates peripheral sTREM2 related inflammatory activity as altered in the early stages of AD. Notably, fractalkine showed a significant relationship with sTREM2 across different analyses in the control groups that was lost as disease progressed, and fractalkine, IL-5 and IL-17A were decreased in AD. These preliminary data provide important support to the hypothesis that sTREM2-related inflammatory activity is a stage-specific biomarker of AD progression, providing the groundwork for future studies and therapeutic strategies.

neuroscience↗