Batra, Richa

Abstract Background Mitochondrial dysfunction in Alzheimer's Disease (AD) is characterized by impaired energy production, oxidative stress, and disrupted calcium homeostasis, which collectively contribute to neuronal damage, synaptic dysfunction, and the progression of AD pathology. A significant knowledge gap in studying mitochondrial dysfunction in Alzheimer's Disease (AD) lies in understanding the precise molecular mechanisms linking mitochondrial metabolic alterations to neuronal damage, particularly how sex‐specific and cell‐type‐specific mitochondrial processes contribute to the progression of AD pathology. Method This study integrates multiple datasets, post‐mortem brain RNAseq from ROSMAP, Mayo Clinic brain bank and Mount Sinai Brain Bank cohort data available via AD Knowledge Portal hosted by Sage Bionetworks), Human Protein Atlas (HPA), MitoCarta3, genome‐scale human metabolic reconstruction, mitochondriome analysis, and brain & blood metabolomics data (data generated by the Alzheimer's Disease Metabolomics Consortium (ADMC)) to identify mitochondrial genes associated with disrupted metabolism in AD. Additionally, biodomain analysis was used to identify key processes associated with pathology. Result A total of 62 common genes were identified across these approaches, highlighting their potential significance in mitochondrial processes. We also developed the framework to perform metabolite‐gene correlation analyses revealing key mitochondrial‐metabolic interactions (eg. homocysteine and MTHFR gene; acetyl‐CoA and PDHA1 gene). Integrated in silico metabolic analysis identified reaction fluxes, uncovering sex‐specific differences in mitochondrial transport and tricarboxylic acid (TCA) cycle subsystems, with notable alterations in females. Biodomain enrichment analysis focused on mitochondrial processes, identifying disruptions in pathways critical for energy production and redox homeostasis. Additionally, we analyzed datasets related to metformin and complex I inhibitors, linking mitochondrial complex I modulation with metabolic alterations in AD. This analysis identified druggable targets and potential therapeutic candidates for mitochondrial metabolic pathways. Conclusion Our findings integrate multiple data sources to provide a systems‐level understanding of mitochondrial metabolism in AD. Sex‐specific differences associated with mitochondrial dysfunction in AD were identified. We identify important mitochondrial transport proteins and metabolites that could potentially be used as druggable targets in AD.

AbstractBackgroundOur Alzheimer Disease Metabolomics Consortium (ADMC), part of the Accelerating Medicines Partnership for AD (AMP‐AD) and in partnership with AD Neuroimaging Initiative (ADNI), applied state‐of‐the‐art metabolomics and lipidomics technologies combined with genomic and imaging data to map metabolic failures across the trajectory of the disease. Our studies confirmed that peripheral metabolic changes influenced by the exposome inform about cognitive changes, brain imaging changes, and ATN markers for disease confirming that peripheral and central changes are connected, in part through the metabolome.MethodsTo map the biochemical changes in AD, we used various targeted and untargeted metabolic platforms to profile ∼800 postmortem brain tissue, and ∼ 5000 blood samples.ResultsRecently, we built a comprehensive reference map of extensive AD‐related metabolic changes in brain, spanning multiple AD‐related traits, including neuropathological b‐amyloid and tau tangle burden, as well as late‐life cognitive performance. Using this resource, we extracted novel metabolic including bioenergetic pathways, cholesterol metabolism, neuroinflammation, broad impairment of osmoregulation, an imbalance between excitatory/inhibitory neurotransmitter ratios and identification of tau load as a potential driver of metabolic dysfunction in the AD brain, with minimal contributions from b‐amyloid load. As AD and progressive supranuclear palsy (PSP) share the pathological feature of tauopathy and metabolic alterations, we compared their metabolomic profiles to identify shared biological pathways that could be targeted for therapeutic interventions. Our findings indicate that both diseases display oxidative stress, mitochondrial dysfunction, and tau‐induced polyamine stress response.ConclusionOverall, through our studies, (1) We identified biochemical processes altered in AD, with findings supported across both metabolomic and proteomic data, indicating multimodal deregulation. (2) Our research pinpointed widespread AD‐related biochemical changes across various brain regions with differing levels of neuropathology. While there are many overlapping changes across the brain regions, each region also has its distinct metabolic alterations. (3) We identified biochemical processes disrupted by AD, with parallel findings in other neurodegenerative diseases, hinting at broader implications in neurodegenerative research. Currently, we are working on mapping widespread connections of the brain metabolome with various determinants of AD namely genome, gut microbiome, exposome, and linking with peripheral metabolic alterations in AD.

AbstractBackgroundAlzheimer’s disease (AD) is a neurodegenerative disorder with significant environmental factors, including diet, that influence its onset and progression. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have explored the KD’s molecular impact for markers of AD therapeutic potential. The BEAM diet study simultaneously profiled the KD’s effect on the lipidome, blood and cerebrospinal metabolome, and microbiome of both cognitively impaired and cognitively normal individuals. The findings summarized here assess the biological impact of a Modified Mediterranean KD in the context of Alzheimer’s disease treatment and prevention.MethodBEAM involved participants at risk for AD, either cognitively normal or with mild cognitive impairment. The participants consumed both a modified Mediterranean‐ketogenic diet (MMKD) and the American Heart Association diet (AHAD) for 6 weeks each, separated by a 6‐week washout period. We employed HPLC‐MS/MS lipidomics profiling in plasma, nuclear magnetic resonance (NMR)‐based metabolomics to profile serum and CSF, and metagenomics profiling on fecal samples before and after each diet to assess dietary‐induced changes.ResultThe MMKD led to significant alterations in the blood, CSF, and microbiome. These changes included a global elevation across all plasmanyl and plasmenyl ether lipid species, improved modifiable risk factors, like increased HDL‐C and reduced BMI, the reversal of serum metabolic disturbances linked to AD such as an increase in valine levels, and a reduction in systemic inflammation. Leveraging prior clinical studies on AD (n = 1,912), we found that MMKD was inversely associated with the peripheral lipidomic signature of prevalent and incident AD. In the CSF, the MMKD was linked to modified amino acid levels and the breakdown of branched‐chain amino acids (BCAAs). Importantly, we observed a strong correlation between metabolic changes in the CSF and serum, suggesting a systemic regulation of metabolism. In addition, participants with MCI on the MMKD had lower levels of GABA‐producing microbes and GABA, and higher levels of GABA‐regulating microbes.ConclusionOur findings highlight that MMKD can improve AD‐related risk factors, reverse some metabolic disturbances associated with AD, and align metabolic changes across the blood‐CSF barrier.Funding: Alzheimer’s Gut Microbiome Project, NIA U19AG063744

Abstract BACKGROUND Metabolic dysregulation is a hallmark of neurodegenerative diseases, including Alzheimer's disease (AD) and progressive supranuclear palsy (PSP). Although metabolic dysregulation is a common link between these two tauopathies, a comprehensive brain metabolic comparison of the diseases has not yet been performed. METHODS We analyzed 342 postmortem brain samples from the Mayo Clinic Brain Bank and examined 658 metabolites in the cerebellar cortex and the temporal cortex between the two tauopathies. RESULTS Our findings indicate that both diseases display oxidative stress associated with lipid metabolism, mitochondrial dysfunction linked to lysine metabolism, and an indication of tau‐induced polyamine stress response. However, specific to AD, we detected glutathione‐related neuroinflammation, deregulations of enzymes tied to purines, and cognitive deficits associated with vitamin B. DISCUSSION Our findings underscore vast alterations in the brain's metabolome, illuminating shared neurodegenerative pathways and disease‐specific traits in AD and PSP. Highlights First high‐throughput metabolic comparison of Alzheimer's diesease (AD) versus progressive supranuclear palsy (PSP) in brain tissue. Cerebellar cortex (CER) shows substantial AD‐related metabolic changes, despite limited proteinopathy. AD impacts both CER and temporal cortex (TCX); PSP's changes are primarily in CER. AD and PSP share metabolic alterations despite major pathological differences.

AbstractBackgroundImpaired glucose utilization is central to the pathogenesis of Alzheimer’s disease. In a hypometabolic state, the brain depends on alternative sources of energy, including amino acids, fatty acids, and ketone bodies (KBs). As KBs can cross the blood‐brain barrier, it is considered that a ketogenic diet could augment the high energetic demand of the central nervous system (CNS). A ketogenic diet is already a part of clinical care in epilepsy a CNS disorder. However, the holistic benefits of this diet for Alzheimer’s remain to be determined.MethodsA randomized crossover pilot trial was conducted where participants consumed either the Modified Mediterranean‐Ketogenic Diet (MMKD) or the American Heart Association Diet (AHAD) for 6 weeks, followed by a 6‐week washout, after which the respective other diet was consumed for 6 weeks. The cohort included both mild cognitively impaired (MCI) and cognitively normal (CN) individuals. Serum and cerebrospinal fluid (CSF) samples of these individuals were profiled using two metabolic platforms: MS‐based and NMR‐based metabolomics. Diet‐related changes in levels of metabolites were determined using linear‐mixed effect models with age and sex as confounders.ResultsWe identified post‐diet changes in the two diet groups (AHAD and MMKD), two cognitive groups (MCI and CN), and two fluids (serum and CSF). AHAD was associated with a decrease in serum levels of only a single metabolite, glutamine. MMKD led to widespread lipidomic and metabolic changes in the serum of mild cognitively impaired individuals. Remarkably, MMKD was associated with the reversal of AD‐related metabolic alterations identified in large cohorts like ADNI, AIBL, ROS/MAP, and signature for incident dementia in large epidemiological studies. The post‐MMKD changes include correcting metabolic dysregulation in branched‐chain amino acids, triglycerides, and plasmalogens a class of lipids implicated in membrane structure and function. Peripheral‐central metabolic correlations will be shared.ConclusionOur findings highlight the potential of dietary interventions, specifically the MMKD, in improving the cognitive and metabolic state of individuals with MCI. Further investigation is needed to capture the entirety of MMKD‐related modulation in metabolic profiles and the resulting benefit for AD.

AbstractBackgroundMetabolic dysregulation is one of the hallmarks of Alzheimer’s disease (AD). Alterations in metabolism have been associated with AD‐related comorbidities, cognitive decline, and AD brain pathology. Brain regions are differentially affected with AD neuropathology and exhibit metabolic heterogeneity. Therefore, to build a more comprehensive picture of metabolic impact of AD, region‐specific AD‐associated metabolic changes need to be determined.MethodWe profiled 344 brain samples from the Mayo Clinic brain bank using Metabolon’s untargeted metabolomics platform, covering 182 samples from the cerebellum (CER) and 162 samples from the temporal cortex (TCX). Generalized linear models were used to assess the association of metabolic profiles with AD. Models included confounder correction for age at death, sex, and number of APOE‐ε4 alleles. To extend this study to four more brain regions, we included results from previously published brain metabolomics studies based on samples from three independent cohorts, including dorsolateral prefrontal cortex (DLPFC) from ROS/MAP, parietal lobe (PTL) from Washington University School of Medicine (WUSM), inferior temporal gyrus (ITG) and middle frontal gyrus (MFG) from Baltimore Longitudinal Study of Aging (BLSA).ResultIn the Mayo cohort, a total of 190 out of the 658 metabolites were significantly associated with AD. Out of the 190, 127 metabolites associated only in the CER region, 37 metabolites associated only in the TCX region, and 26 metabolites were associated in both brain regions. There were no metabolites commonly regulated in all the 6 brain regions under investigation. DLPFC and CER had the highest overlap of 70 metabolites, followed by DLPFC and PTL with 64 metabolites, and CER and PTL with 47 metabolites. For functional interpretation of our findings, each metabolite was further categorized with a sub‐pathway annotation provided by Metabolon. 3 of the 88 pathways including methionine cycle, phospholipid metabolism, and glutathione metabolism, were commonly regulated in the six brain regions under investigation.ConclusionWe present a first global perspective on AD‐associated metabolic alterations across six brain regions. This study will pave the way to fill the gap in our understanding of region‐specific metabolic deregulations associated with AD pathophysiology.

Abstract Introduction Alzheimer's disease (AD) is accompanied by metabolic alterations both in the periphery and the central nervous system. However, so far, a global view of AD‐associated metabolic changes in the brain has been missing. Methods We metabolically profiled 500 samples from the dorsolateral prefrontal cortex. Metabolite levels were correlated with eight clinical parameters, covering both late‐life cognitive performance and AD neuropathology measures. Results We observed widespread metabolic dysregulation associated with AD, spanning 298 metabolites from various AD‐relevant pathways. These included alterations to bioenergetics, cholesterol metabolism, neuroinflammation, and metabolic consequences of neurotransmitter ratio imbalances. Our findings further suggest impaired osmoregulation as a potential pathomechanism in AD. Finally, inspecting the interplay of proteinopathies provided evidence that metabolic associations were largely driven by tau pathology rather than amyloid beta pathology. Discussion This work provides a comprehensive reference map of metabolic brain changes in AD that lays the foundation for future mechanistic follow‐up studies.