Carrasquillo, Minerva M.

AbstractBackgroundAlzheimer’s disease (AD) patients have decline in cognitive domains including memory, language, visuospatial, and/or executive function and brain pathology including amyloid‐β and tau deposition, neurodegeneration, and frequent vascular co‐pathologies detectable by neuroimaging and/or cerebrospinal fluid biomarkers. However, molecular disease mechanisms are complex and heterogeneous. It is necessary to develop cost‐effective blood‐based biomarkers reflecting brain molecular perturbations in AD. We identified blood‐based gene and co‐expression network level changes associated with AD/mild cognitive impairment (MCI) diagnosis and AD‐related phenotypes.MethodWe performed differential gene expression and weighted gene co‐expression network analysis, followed by meta‐analysis, using blood transcriptome data of 391 participants from the Mayo Clinic Study of Aging and 654 participants from the Alzheimer's Disease Neuroimaging Initiative. The neuroimaging phenotypes include microhemorrhages, infarcts, amyloid burden, hippocampal volume, and white matter hyperintensities. The cognitive phenotypes include standardized cognitive subtest scores and composite scores for memory, language, visuospatial, and executive function.ResultFive out of 18 modules(M) are significantly associated with diagnosis or cognition (FDR‐adjusted p<0.05). M1 and M15 both positively associates with memory, M1 positively associated with language and M15 with visuospatial function. M1 and M15 are enriched in differentially expressed genes (DEGs) associated with language and executive function, respectively. M2 negatively associates with logical memory delayed recall scores(LMDR), memory, executive, and language functions and is enriched in DEGs for these phenotypes. M8 negatively associates with memory, language and executive functions and is enriched in DEGs for memory and language. M12 positively associates with LMDR. M1 and M15 are down‐regulated while M2 and M8 are up‐regulated in AD/MCI patients. Cell‐type enrichment analysis showed M2 is enriched in monocytes and neutrophils; M8 in monocytes; M15 in B cells (FDR <0.05). Gene ontology terms enriched in these modules indicated broad consistency with their cell types.ConclusionWe identified five modules significantly associated with AD/MCI or cognitive phenotypes using blood transcriptome data. These findings nominate blood transcriptome changes and their enriched biological processes as potential pathomechanisms in cognitive decline and AD/MCI development. We aim to investigate these blood transcripts as potential biomarkers for AD or AD‐related phenotypes and therapeutic targets through additional replication and experimental validation studies.

AbstractBackgroundThe prevalence of dementia in populations that are underrepresented in research is projected to increase with population aging. Latino and Black individuals, the largest underrepresented populations in the US, experience a higher dementia burden than non‐Hispanic White individuals, which is not explained by ethnoracial biological factors. Disparities in structural and social determinants of health may contribute to the preponderance of medical conditions known to increase dementia risk, including potentially modifiable factors in Latino and Black communities. To assess the scope of this problem, we measured the frequency of common modifiable dementia risk factors in community‐dwelling, cognitively normal, Latino and Black adults.MethodCognitively normal community‐dwelling Latino and Black adults, ≥45‐years‐old, were enrolled within our longitudinal study of memory and aging at Mayo Clinic in Florida (Jacksonville, FL) and completed a baseline assessment between 3/2022 and 10/2023. Demographics, and self‐reported race/ethnicity and history of dementia risk factors were recorded. Dementia risk factors were objectively sampled through clinical interview (depression: Geriatric Depression Scale ≥5), examination (hypertension: BP >130/80 mmHg; obesity: BMI≥30), and serum analyses (hyperlipidemia: total cholesterol<200mg/dL, HDL>50mg/dL, LDL<100mg/dL, Triglycerides<150mg/dL; diabetes: HbA1C >5.6%, vitamin B12 deficiency: <350 ng/dL).Result86 participants (43 Latino, 43 Black), 65.8 (8.8) years‐old, female (62.8%), with 16 (2.4) years of education were assessed. Dementia risk factors were frequent in Latino and Black participants, including hypertension (63%, 90%; p = 0.005), hyperlipidemia (93%, 89%; p = 0.702), obesity (33%, 44%; p = 0.370), diabetes (60%, 47%; p = 0.370), vitamin B12 deficiency (21%, 21%; p = 0.989), and depression (5%, 24%; p = 0.781). These risk factors were unrecognized or suboptimally managed in a substantial proportion of Latino and Black participants: hypertension (56%, 73%; p = 0.170), hyperlipidemia (80%, 73%; p = 0.591), diabetes (57%, 47%; p = 0.502), vitamin B12 deficiency (21%, 21%; p = 0.789), and depression (5%, 3%; p>0.99).ConclusionPotentially modifiable dementia risk factors were detected in the majority of community‐dwelling Latino and Black cognitively normal older‐adults and were frequently unrecognized or suboptimally managed. Proactive screening for known dementia risk factors may provide opportunities for targeted interventions to improve brain health and decrease dementia disparities in underrepresented populations.

AbstractBackgroundAfrican Americans (AA) and Latin Americans (LA) are at a higher risk of developing AD compared to non‐Hispanic whites (NHW) but are traditionally underrepresented in AD research. The disproportionate risk is likely multifactorial including differences in co‐morbidities and structural and social determinants of health (SSDoH). AD risk is thought to result from multiple genetic and environmental factors, and their interactions (GxE). However, the molecular mechanisms underlying these interactions are largely unknown. The best‐established genetic risk factor for AD is APOE‐ε4, while APOE‐ε2 is protective. Environmental factors, such as living in neighborhoods with greater socioeconomic disadvantage, have been associated with greater AD neuropathology and worse cognitive function. Studying the potential modifying role of neighborhood disadvantage regarding associations of APOE‐ε4 and APOE‐ε2 with AD risk using a socioeconomic metric like the Area Deprivation Index (ADI) in a multiethnic post‐mortem cohort could offer valuable insights for precision medicine.MethodWe analyzed a post‐mortem cohort of 421 multi‐ethnic donors (NHW: N = 234, AD = 70, non‐AD = 164; LA: N = 145, AD = 102, non‐AD = 43; AA: N = 42, AD = 24, non‐AD = 18), from Mayo Clinic Florida, Banner Sun Health Research Institute, and the University of Florida Brain Banks as part of the AMP AD Diversity initiative. This study used the same neuropathological criteria to categorize AD vs. non‐AD as in the MayoRNAseq study (syn5550404). ADI from the Neighborhood Atlas® was obtained from de‐identified addresses. Associations of APOE‐ε4, APOE‐ε2, and ADI with AD risk were examined using logistic regression models adjusted for age‐at‐death, sex, and ethnic group; interactions of APOE genotype with ADI were also assessed.ResultAPOE‐ε4 and APOE‐ε2 showed a significant association with AD diagnosis (APOE‐ε4combined cohort OR = 3.23, P = 3.14E‐08; APOE‐ε2combined cohort OR = 0.30, P = 0.003). However, contrary to prior findings, our study found no association between ADI and AD diagnosis [OR = 1.023 (per each 10 unit increase in ADI), P = 0.629]. No significant interactions of ADI with APOE‐ε4 or APOE‐ε2 regarding association with AD diagnosis were identified (P = 0.083, P = 0.781).ConclusionThis is the first study evaluating the potential interaction of neighborhood disadvantage with APOE on AD risk in a multi‐ethnic autopsy cohort. However, these findings require further investigation in larger, more well‐powered cohorts for validation.

AbstractBackgroundSystemic inflammation plays a pivotal role in many chronic diseases including Alzheimer’s disease (AD). Assessing the composition of immune pathways in neurodegenerative diseases can contribute to precision medicine. Using publicly available transcriptomic data, we sought to elucidate transcriptional networks pertinent to inflammatory pathways across brain regions and peripheral blood in AD/mild cognitive impairment (MCI) and peripheral blood in Parkinson’s disease (PD).MethodFor the AD/MCI vs. control dataset, we analyzed bulk‐RNAseq collected from 6 brain regions of donors from ROSMAP, Mayo Clinic, and Mount Sinai School of Medicine (MSSM) brain banks available from the AMP‐AD consortium. Ante‐mortem, blood RNAseq expression data was retrieved from the AMP‐AD Emory Vascular cohort and Mayo Clinic Study of Aging (MCSA). We also collected blood‐derived microarray expression data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). For the PD vs Control dataset, blood‐derived bulk‐RNAseq from the PDBP and PPMI cohorts were available through the AMP‐PD consortium. Following quality control, normalization, and residual generation to account for biological and technical variables, co‐expression network modules and their enriched pathways were identified using WGCNA within each dataset. Module/trait correlation tests for aging and diagnosis (cases [AD/MCI or PD] vs control) phenotypes were evaluated. Gene Ontology enrichment analyses were executed to identify enriched pathways and brain or blood cell types within the modules. Modules were tested for preservation across cohorts.ResultWe identified conserved immune signatures across brain regions and cohorts. Modules involved in immune response were preserved across all cohorts. Blood consensus modules involved in immune response were preserved in the brain and vice versa. Some immune modules were associated with AD/MCI, PD, and/or aging. Brain immune modules are significantly associated with aging and/or AD. Significant correlations (q<0.05) with PD diagnosis were present. In the MCSA and Emory vascular cohorts, there were no significant (q<0.05) associations between modules and diagnosis, while in ADNI there were nominal (p<0.05) associations.ConclusionPreserved transcriptional immune networks were identified across blood and brain and across two neurodegenerative diseases. Expanding gene co‐expression network analyses to other diseases and integrating additional omics measures and phenotypes can further strengthen these findings to unravel the immune signatures across complex diseases.

AbstractBackgroundAlzheimer’s disease (AD) is a devastating neurodegenerative disorder with few therapies to treat, mitigate or prevent its onset. Understanding of this disease is predominantly based on research in non‐Hispanic Whites (NHW) although AD disproportionately affects African Americans (AA) and Latin Americans (LA), underrepresented in AD research. To address this knowledge gap, the Accelerating Medicine Partnership for Alzheimer’s Disease (AMP‐AD) Diversity Working Group was launched to generate multi‐omics data from post‐mortem brain tissue from donors of predominantly AA and LA descent. Here, we focus on genomic and transcriptomics measures, made available through the AD Knowledge Portal (ADKP).MethodBrain tissue from dorsolateral prefrontal cortex (DLPFC), caudate nucleus (CN), superior temporal gyrus (STG) and temporal pole (TP) regions of AA (N = 299), LA (N = 344) and NHW (N = 532) donors was obtained through Mayo Clinic, Mt. Sinai School of Medicine, Emory, Columbia, Rush Alzheimer’s Disease Center, Banner Sun Health, and 1Florida. DNA extracted from DLPFC tissue samples (n = 641) was utilized for whole genome sequencing (WGS) at New York Genome Center (NYGC). RNAseq of 2,224 samples was conducted either at Mayo, Rush or NYGC. Sequencing reads were processed through GenomeGPS and MAPRseq pipelines for WGS and RNAseq data, respectively. Following quality control (QC), RNAseq data was normalized and assessed for sources of variation (SOV). Integration of WGS and RNAseq data to perform comparative eQTL analysis across multi‐ethnic populations and brain regions is ongoing.ResultWGS data for 621 donors, and RNAseq data generated at Mayo (n = 1,136 samples), Rush (n = 627), and NYGC (n = 779) sequencing centers, were deposited to the ADKP. Consensus processing of RNAseq data revealed site, sex, race/ethnicity, RIN, AD diagnosis, age at death and/or library batch as SOV across various sites and brain regions. Principal component analysis of gene expression measures revealed no major stratification by disease or brain region. Accompanying clinical metadata of donors have been distributed through ADKP.ConclusionThese multi‐omics data made available to the research community is expected to be an initial step towards bridging our data and knowledge gap to elucidate conserved and distinct AD related pathways across these underrepresented at‐risk populations.

AbstractBackgroundAlzheimer’s disease (AD) is neuropathologically characterized by amyloid‐β (Aβ) plaques and tau neurofibrillary tangles often quantified by Thal phase and Braak stage, respectively. Aβ also frequently deposits in the cerebrovasculature with severity categorized by a cerebral amyloid angiopathy (CAA) score. These and related measures often show high variability within AD suggesting distinct underlying mechanisms. We hypothesize that, within the AD brain, neuropathology and levels of core AD‐related proteins are influenced by variations in DNA methylation (DNAm). To test this, we performed epigenome‐wide association studies (EWAS) using DNAm measures from the temporal cortex (TCX) and cerebellum (CER) with AD‐related neuropathologic measures (Braak, Thal, CAA) and brain biochemical levels of five proteins (apoE, Aβ40, Aβ42, tau, p‐tau).MethodsDNAm from neuropathologically‐confirmed AD cases was measured by reduced representation bisulfite sequencing (RRBS) from 471 TCX samples, 200 of which also had CER RRBS. TCX levels of five AD‐related proteins from three tissue fractions (buffer‐, detergent‐, and in‐soluble) were measured previously by ELISA (Liu 2020). CpG methylation (CpGm) was binned by a 15‐state chromatin model (Kundaje 2015) and averaged into CpGm clusters (rCpGm). rCpGms were tested for association with each AD endophenotype and expression levels of nearby genes through multi‐variable linear regression. Replication of significant rCpGms was performed in two independent datasets with AD‐related endophenotypes (Shireby 2022, De Jager 2014).ResultsOur innovative binning method demonstrated biologically relevant CpGm patterns. We found epigenome‐wide significant associations primarily with tau‐related endophenotypes including 93 that had significant and concordant associations in the replication datasets. These rCpGms also significantly associated with expression of nearby genes showing enrichment in oligodendrocyte marker genes including those related to myelination. In vitro validation of tau effects on oligodendrocyte gene expression through DNAm is ongoing.ConclusionsAlthough all endophenotypes tested are core to AD pathophysiology, our results suggest each has a distinct epigenetic architecture underlying their variability in the AD brain. In particular, we found evidence of DNAm variability associating with brain oligodendrocyte gene expression and TCX tau levels. By discovering AD brain endophenotype‐specific DNAm changes, we can identify core components of complex mechanisms revealing important biological insights into AD pathophysiology.

Abstract INTRODUCTION Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, yet our comprehension predominantly relies on studies within non‐Hispanic White (NHW) populations. Here we provide an extensive survey of the proteomic landscape of AD across diverse racial/ethnic groups. METHODS Two cortical regions, from multiple centers, were harmonized by uniform neuropathological diagnosis. Among 998 unique donors, 273 donors self‐identified as African American, 229 as Latino American, and 434 as NHW. RESULTS While amyloid precursor protein and the microtubule‐associated protein tau demonstrated higher abundance in AD brains, no significant race‐related differences were observed. Further proteome‐wide and focused analyses (specific amyloid beta [Aβ] species and the tau domains) supported the absence of racial differences in these AD pathologies within the brain proteome. DISCUSSION Our findings indicate that the racial differences in AD risk and clinical presentation are not underpinned by dramatically divergent patterns in the brain proteome, suggesting that other determinants account for these clinical disparities. Highlights We present a large‐scale proteome (∼10,000 proteins) of DLPFC (998) and STG (244) across AD cases. About 50% of samples were from racially and ethnically diverse brain donors. Key AD proteins (amyloid and tau) correlated with CERAD and Braak stages. No significant race‐related differences in amyloid and tau protein levels were observed in AD brains. AD‐associated protein changes showed a strong correlation between the brain proteomes of African American and White individuals. This dataset advances understanding of ethnoracial‐specific AD pathways and potential therapies.

Abstract INTRODUCTION Multi‐omics studies in Alzheimer's disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked Black Americans (BA) and Latin Americans (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership in Alzheimer's Disease (AMP‐AD) expanded brain multi‐omics profiling to multi‐ethnic donors. RESULTS We generated multi‐omics data and curated and harmonized phenotypic data from BA ( n = 306), LA ( n = 326), or BA and LA ( n = 4) brain donors plus non‐Hispanic White ( n = 252) and other ( n = 20) ethnic groups, to establish a foundational dataset enriched for BA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSION The inclusion of traditionally underrepresented groups in multi‐omics studies is essential to discovering the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD. Highlights Accelerating Medicines Partnership in Alzheimer's Disease Diversity Initiative led brain tissue profiling in multi‐ethnic populations. Brain multi‐omics data is generated from Black American, Latin American, and non‐Hispanic White donors. RNA, whole genome sequencing and tandem mass tag proteomicsis completed and shared. Multiple brain regions including caudate, temporal and dorsolateral prefrontal cortex were profiled.

AbstractBackgroundA hallmark of Alzheimer’s disease is amyloid‐β (Aβ) deposition in the brain parenchyma as senile plaques which Aß frequently accompanies in the cerebral vasculature as cerebral amyloid angiopathy (CAA). Previous studies demonstrated that the cerebrovascular system is essential for Aβ clearance and interactions exist between cerebrovascular disease and AD. Neuroimaging data, including measures on small vessel disease, amyloid deposits, and microhemorrhages (MCH), can reflect both cerebrovascular disease and AD pathology, thereby serving as intermediate phenotypes of both conditions. We aim to identify genes and co‐expression networks in blood associated with these neuroimaging endophenotypes and the biological pathways enriched in these perturbed transcriptional networks.MethodWe conducted differential gene expression and Weighted Gene Co‐Expression Network analyses (WGCNA) on blood RNA sequencing data of 407 participants from the longitudinally followed Mayo Clinic Study of Aging cohort. The neuroimaging phenotypes include MCH, infarction, and amyloid deposits measured by Pittsburgh compound B positron emission tomography (PiB PET).ResultWGCNA analysis showed a nominally significant association (p<0.05) between several module eigengenes (MEs) and MCH and PiB PET. One module, M42, remained significantly associated with PiB PET after Bonferroni correction for all 43 modules tested. Pathway enrichment analysis of M42 identified two significant pathways (FDR‐adjusted p<0.05) including phosphodiesterase I activity and IgE binding. These pathways contain genes such as MS4A2 encoding the high‐affinity IgE receptor involved in the immune response. Similarly, ENPP2 in the phosphodiesterase I activity pathway represents an additional candidate gene previously implicated in Alzheimer’s disease.ConclusionWe generated co‐expression networks and identified one network module with a statistically significant association between brain amyloid deposits and blood transcriptome data. Further investigations of this network and its enriched pathways are necessary to understand their roles in amyloidosis, CAA, and neurodegeneration. Future studies will include seeking replication of these results in other datasets. Such studies can help elucidate the biological mechanisms of pathogenesis of cerebrovascular damage and amyloid deposits. In addition, in a clinical setting, blood levels of transcripts discovered in this study may serve as predictive or diagnostic biomarkers with mechanistic implications.

AbstractBackgroundFor blood‐based biomarkers to fulfill their potential to revolutionize diagnosis and management of Alzheimer’s disease (AD), additional research in diverse populations remains critical. Here, we analyzed a biracial sample to assess the profiles of blood‐based AD biomarkers and their relationships to cognition and medical comorbidities.MethodsSelf‐reported African‐American (AA; n = 267) and non‐Hispanic White (NHW; n = 268) participants evaluated through the Mayo Jacksonville Alzheimer’s Disease Research Center were matched on age, sex, and clinical diagnosis. Plasma AD biomarkers (Aβ42/40, p‐tau181, GFAP, NfL) were measured using the Quanterix SiMoA HD‐X analyzer. Cognition was assessed with the Mini Mental State Examination. Wilcoxon rank sum tests were used to assess for differences in plasma biomarker levels by sex. Linear models tested for associations of race, chronic kidney disease (CKD), and vascular risk factors with plasma AD biomarker levels, covarying for age and sex. Additional models assessed for interactions between race and plasma biomarkers in predicting cognition, further covarying for education.ResultsThe sample included adults aged 43‐100 years, with 69% women. Education was higher in NHW participants (median 16 vs. 12 years, p<0.001). APOE (apolipoprotein E) ε4 positivity was higher in AA participants (43% vs. 34%; p = 0.04). There were no differences in plasma AD biomarker levels between AA and NHW participants. These findings were unchanged after stratifying by cognitive status (unimpaired versus impaired). Although the association between p‐tau181 and cognition appeared stronger in NHW participants while the association between Aβ42/40 and cognition appeared stronger in AA participants, these findings did not survive after excluding individuals with CKD. Women displayed higher GFAP (p = 0.002) and lower p‐tau181 (p = 0.001) levels than men. Diabetes was inversely associated with GFAP levels (p<0.001).ConclusionsIn a biracial, community‐based sample, we observed that sex differences, CKD, and vascular risk factors contributed to variation in plasma AD biomarkers, while self‐reported race did not. Our results reinforce the critical need to account for sex and systemic medical comorbidities in equitably deploying blood‐based AD biomarkers in the general population.