Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age

In the paper

“For instance, of the 157 proteins designated as mitochondrial, 112 were presynaptic, 10 postsynaptic, and 35 were other (Supplementary Data 3).”

In the paper

“For the 569 unique proteins, 484 had at least one PPI, and there were a total of 2587 PPIs among these 484 proteins (Supplementary Data 3; Supplementary Fig. 4).”

In the paper

“Regarding the direction of association, 350 proteins had increased abundance while 229 had decreased abundance in cognitive stability.”

In the paper

“The 569 unique proteins among these 579 proteins (10 had isoforms) were categorized into presynaptic (N = 159), postsynaptic (N = 150), both (present in both presynaptic and postsynaptic density; N = 20), or other (N = 240) using Boyken et. al. presynaptic list16 and Bayes et. al. postsynaptic density list17 (Supplementary Data 3).”

What the sources say

• Not checked yetcites [16] Boyken, J. et al. Molecular profiling of synaptic vesicle docking sites reveals novel proteins but few differences between glutamatergic and GABAergic synapses. Neuron 78, 285–297 (2013). source
• Not checked yetcites [17] Bayes, A. et al. Characterization of the proteome, diseases and evolution of the human postsynaptic density. Nat. Neurosci. 14, 19–21 (2011). source

In the paper

“The median rate of cognitive change was −0.3 unit of MMSE score per year for Banner participants and −0.1 unit of MMSE per year for BLSA participants (Table 1).”

In the paper

“The meta-analysis showed 579 proteins associated with cognitive trajectory in the same directions in both the discovery and replication cohorts and at FDR < 0.05 among the 2752 protein isoforms commonly detected in both cohorts (N = 143 individuals; Fig. 3a, Supplementary Data 2).”

• Also stated in: § Abstract · plain

  “We find 579 proteins associated with cognitive trajectory after meta-analysis.”

In the paper

“Focusing on PPIs emanating from presynaptic proteins, we found 374 proteins with interactions (nodes) and 1745 PPIs (edges) (Supplementary Fig. 5A).”

In the paper

“Lower-abundance proteins were enriched for the processes of glycolysis, assembly of neurofilament bundle, cell–cell adhesion, and RNA binding, and for oligodendrocyte, astrocyte, and microglia (Table 3; Supplementary Data 6).”

In the paper

“In Banner, these seven modules had 123 hub proteins, of which 102 (83%) were associated with cognitive trajectory (Supplementary Data 8).”

In the paper

“After adjusting for β-amyloid plaques and neurofibrillary tangles, there were 232 cognitive trajectory-associated proteins, and enrichment was performed separately for lower-abundance proteins in cognitive stability (81 proteins, colored in salmon) and higher-abundance proteins in cognitive stability (151 proteins, colored in turquoise), respectively.”

In the paper

“Notably, these 38 proteins were associated with cognitive trajectory independently of β-amyloid plaques and neurofibrillary tangles in both Banner and BLSA, and were also hub”

• Also stated in: § Discussion · plain

  “The next notable finding is the 38 proteins that were associated with cognitive trajectory independently of typical AD neuropathologies and were also hub proteins in both Banner and BLSA protein networks.”

In the paper

“There are 579 cognitive trajectory-associated proteins in Banner and BLSA cohorts, which were divided into lower-abundance proteins in cognitive stability (229 proteins, colored in salmon) and higher-abundance proteins in cognitive stability (350 proteins, colored in turquoise), respectively.”

In the paper

“particularly the 38 proteins that act independently of neuropathologies and are also hub proteins of protein co-expression networks”

In the paper

“This is consistent with our finding that 157 proteins of the 579 cognitive trajectory-associated proteins are mitochondrial proteins and of these, 122 are located in the mitochondria either in the pre- or postsynaptic density.”

In the paper

“Among these proteins, only GRIA3 was detected in our datasets and had lower-abundance in faster cognitive decline in both Banner and BLSA, consistent with Bereczki and colleagues’ finding.”

In the paper

“Among these 38 proteins, those that are higher-abundance in cognitive stability are involved in either mitochondrial activities or synaptic function, and those with lower-abundance in cognitive stability are involved in myelination or apoptosis.”

In the paper

“After label-free quantification, 3710 protein groups in Banner and 3933 protein groups in BLSA cohorts were detected, and 2752 protein isoforms were detected in both Banner and BLSA cohorts.”

In the paper

“For instance, in the Banner cohort, batch and sex explained substantial proportions while age at death and PMI explained some proportions of variance of the proteomic profile (Supplementary Fig. 2).”

In the paper

“A stable cognitive trajectory in advanced age is desirable and may reflect cognitive resilience, while decline in cognitive performance may be the earliest manifestation of a serious neurodegenerative disease1,3.”

What the sources say

• Not checked yetcites [1] Zaninotto, P., Batty, G. D., Allerhand, M. & Deary, I. J. Cognitive function trajectories and their determinants in older people: 8 years of follow-up in the English Longitudinal Study of Ageing. J. Epidemio.l Community Health 72, 685–694 (2018). source
• Not checked yetcites [3] Rajan, K. B., Wilson, R. S., Weuve, J., Barnes, L. L. & Evans, D. A. Cognitive impairment 18 years before clinical diagnosis of Alzheimer disease dementia. Neurology 85, 898–904 (2015). source

In the paper

“Like all complex human traits, cognitive trajectory varies from person to person and is determined by a combination of genetic and environmental factors including premorbid cognitive abilities, educational attainment, lifestyle choices, and environmental exposures1,2.”

What the sources say

• Not checked yetcites [1] Zaninotto, P., Batty, G. D., Allerhand, M. & Deary, I. J. Cognitive function trajectories and their determinants in older people: 8 years of follow-up in the English Longitudinal Study of Ageing. J. Epidemio.l Community Health 72, 685–694 (2018). source
• Not checked yetcites [2] Plassman, B. L., Williams, J. W. Jr., Burke, J. R., Holsinger, T. & Benjamin, S. Systematic review: factors associated with risk for and possible prevention of cognitive decline in later life. Ann. Intern. Med. 153, 182–193 (2010). source

In the paper

“Hence, variation in cognitive trajectory can influence onset age for MCI or dementia.”

In the paper

“and aggregation of hyperphosphorylated tau proteins can lead to the formation of neurofibrillary tangles and Alzheimer’s dementia14.”

What the sources say

• Not checked yetcites [14] Ballatore, C., Lee, V. M. & Trojanowski, J. Q. Tau-mediated neurodegeneration in Alzheimer's disease and related disorders. Nat. Rev. Neurosci. 8, 663–672 (2007). source

In the paper

“Thus there is ample evidence that the proteins associated with cognitive trajectory interact with each other and reveal many PPIs within and between presynaptic and postsynaptic proteins associated with cognitive trajectory.”

In the paper

“MAPT (microtubule-associated protein tau) is involved in axonal transport, synaptic plasticity, and synaptic function13,”

What the sources say

• Not checked yetcites [13] Caillet-Boudin, M. L., Buee, L., Sergeant, N. & Lefebvre, B. Regulation of human MAPT gene expression. Mol. Neurodegener. 10, 28 (2015). source

In the paper

“In addition, the proteins with decreased abundance in cognitive stability were involved in inflammatory response, apoptosis, and endothelial function in glial cells, likely acting via β-amyloid plaques and neurofibrillary tangles.”

In the paper

“VGF is a neuropeptide that regulates synaptic function10, synaptic plasticity11, and hippocampal memory consolidation12.”

What the sources say

• Not checked yetcites [10] Alder, J. et al. Brain-derived neurotrophic factor-induced gene expression reveals novel actions of VGF in hippocampal synaptic plasticity. J. Neurosci. 23, 10800–10808 (2003). source
• Not checked yetcites [11] Bozdagi, O. et al. The neurotrophin-inducible gene Vgf regulates hippocampal function and behavior through a brain-derived neurotrophic factor-dependent mechanism. J. Neurosci. 28, 9857–9869 (2008). source
• Not checked yetcites [12] Lin, W. J. et al. VGF and Its C-terminal peptide TLQP-62 regulate memory formation in hippocampus via a BDNF-TrkB-dependent mechanism. J. Neurosci. 35, 10343–10356 (2015). source

In the paper

“Furthermore, we provide additional evidence for increased synaptic abundance and decreased inflammation and apoptosis in cognitive stability.”

In the paper

“Mitochondria in neurons are crucial for maintaining synaptic function, and most of the mitochondrial proteins are encoded in the nuclear genome29.”

What the sources say

• Not checked yetcites [29] Devine, M. J. & Kittler, J. T. Mitochondria at the neuronal presynapse in health and disease. Nat. Rev. Neurosci. 19, 63–80 (2018). source

In the paper

“Synaptic mitochondria, therefore, are vital for the maintenance of synaptic function and transmission29–31.”

What the sources say

• Not checked yetcites [29] Devine, M. J. & Kittler, J. T. Mitochondria at the neuronal presynapse in health and disease. Nat. Rev. Neurosci. 19, 63–80 (2018). source
• Not checked yetcites [30] Du, H. et al. Early deficits in synaptic mitochondria in an Alzheimer's disease mouse model. Proc. Natl Acad. Sci. USA 107, 18670–18675 (2010). source
• Not checked yetcites [31] Reddy, P. H. et al. Amyloid-beta and mitochondria in aging and Alzheimer's disease: implications for synaptic damage and cognitive decline. J. Alzheimers. Dis. 20(Suppl 2), S499–S512 (2010). source

In the paper

“In the brain, mitochondria regulate synaptic transmission by generating ATP to power the process and by modulating presynaptic calcium level, which in turn determines the release of neurotransmitters29.”

What the sources say

• Not checked yetcites [29] Devine, M. J. & Kittler, J. T. Mitochondria at the neuronal presynapse in health and disease. Nat. Rev. Neurosci. 19, 63–80 (2018). source

In the paper

“likely due to small sample size and thus lower power”

In the paper

“Mitochondrial dysfunction has been suggested to occur early in the progression to AD and continues into later stages of AD31–34.”

What the sources say

• Not checked yetcites [31] Reddy, P. H. et al. Amyloid-beta and mitochondria in aging and Alzheimer's disease: implications for synaptic damage and cognitive decline. J. Alzheimers. Dis. 20(Suppl 2), S499–S512 (2010). source
• Not checked yetcites [32] Valla, J. et al. Reduced posterior cingulate mitochondrial activity in expired young adult carriers of the APOE epsilon4 allele, the major late-onset Alzheimer's susceptibility gene. J. Alzheimers. Dis. 22, 307–313 (2010). source
• Not checked yetcites [33] Liang, W. S. et al. Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc. Natl Acad. Sci. USA 105, 4441–4446 (2008). source
• Not checked yetcites [34] Mastroeni, D. et al. Nuclear but not mitochondrial-encoded oxidative phosphorylation genes are altered in aging, mild cognitive impairment, and Alzheimer's disease. Alzheimers Dement. 13, 510–519 (2017). source

In the paper

“which is one of the most abundant scaffold proteins at the excitatory brain synapses and known to affect brain development, neuronal plasticity, memory and learning, and overall cognitive function24–28.”

What the sources say

• Not checked yetcites [24] Fernandez, E. et al. Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins. Mol. Syst. Biol. 5, 269 (2009). source
• Not checked yetcites [25] Fernandez, E. et al. Arc Requires PSD95 for Assembly into Postsynaptic Complexes Involved with Neural Dysfunction and Intelligence. Cell Rep 21, 679–691 (2017). source
• Not checked yetcites [26] Krishnan, M. L. et al. Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants. Nat. Commun. 8, 428 (2017). source
• Not checked yetcites [27] Migaud, M. et al. Enhanced long-term potentiation and impaired learning in mice with mutant postsynaptic density-95 protein. Nature 396, 433–439 (1998). source
• Not checked yetcites [28] Nithianantharajah, J. et al. Synaptic scaffold evolution generated components of vertebrate cognitive complexity. Nat. Neurosci. 16, 16–24 (2013). source

In the paper

“PSD-95 is a major scaffold protein of the dendritic spines and its expression level has been shown to be altered in aging, AD, and several psychiatric disorders37.”

What the sources say

• Not checked yetcites [37] Savioz, A., Leuba, G. & Vallet, P. G. A framework to understand the variations of PSD-95 expression in brain aging and in Alzheimer's disease. Ageing Res. Rev. 18, 86–94 (2014). source

In the paper

“A notable theme among the proteins participating in synaptic function on this list of 38 proteins is that they are important for neuronal plasticity and memory consolidation and their overexpression is associated with cognitive”

In the paper

“Furthermore, a transgenic mouse model showed that amyloid pathology, even at a low level, can induce deficits in the functioning of synaptic mitochondria leading to synaptic degeneration30.”

What the sources say

• Not checked yetcites [30] Du, H. et al. Early deficits in synaptic mitochondria in an Alzheimer's disease mouse model. Proc. Natl Acad. Sci. USA 107, 18670–18675 (2010). source

In the paper

“In that study, young-adult participants in both groups did not have amyloid or tangle deposition in the posterior cingulate cortex (PCC); yet, APOE4 carriers, i.e., those at greater risk for developing AD, showed reduced mitochondrial activity in PCC neurons, as measured by cytochrome oxidase levels”

What the sources say

• Not checked yetcites [32] Valla, J. et al. Reduced posterior cingulate mitochondrial activity in expired young adult carriers of the APOE epsilon4 allele, the major late-onset Alzheimer's susceptibility gene. J. Alzheimers. Dis. 22, 307–313 (2010). source

In the paper

“Decreased abundance of this protein can lead to susceptibility to neuroinflammation and disruption of synaptic plasticity42.”

What the sources say

• Not checked yetcites [42] Rodriguez-Perdigon, M. et al. Down-regulation of glutamatergic terminals (VGLUT1) driven by Abeta in Alzheimer's disease. Hippocampus 26, 1303–1312 (2016). source

In the paper

“PSD-95 is important for neuronal plasticity and memory consolidation via its regulation of synaptic glutamate receptors, signaling proteins, adhesion molecules, and cytoskeletal proteins37,38.”

What the sources say

• Not checked yetcites [37] Savioz, A., Leuba, G. & Vallet, P. G. A framework to understand the variations of PSD-95 expression in brain aging and in Alzheimer's disease. Ageing Res. Rev. 18, 86–94 (2014). source
• Not checked yetcites [38] Bustos, F. J. et al. Epigenetic editing of the Dlg4/PSD95 gene improves cognition in aged and Alzheimer's disease mice. Brain 140, 3252–3268 (2017). source

In the paper

“This study found that the nuclear genes encoding the mitochondrial electron transport chain subunits had decreased expression in AD cases compared to controls in PCC and other brain regions33.”

What the sources say

• Not checked yetcites [33] Liang, W. S. et al. Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc. Natl Acad. Sci. USA 105, 4441–4446 (2008). source

In the paper

“SLC30A3, aka ZNT3, is a synapse-specific vesicular zinc transporter that is important for zinc homeostasis and required for hippocampus-dependent memory41.”

What the sources say

• Not checked yetcites [41] Sindreu, C., Palmiter, R. D. & Storm, D. R. Zinc transporter ZnT-3 regulates presynaptic Erk1/2 signaling and hippocampus-dependent memory. Proc. Natl.Acad. Sci. USA 108, 3366–3370 (2011). source

In the paper

“Along the same theme, SYNPO has been found to be important for synaptic plasticity43,44.”

What the sources say

• Not checked yetcites [43] Deller, T. et al. Synaptopodin-deficient mice lack a spine apparatus and show deficits in synaptic plasticity. Proc. Natl Acad. Sci. USA 100, 10494–10499 (2003). source
• Not checked yetcites [44] Vlachos, A. et al. Synaptopodin regulates denervation-induced homeostatic synaptic plasticity. Proc. Natl Acad. Sci. USA 110, 8242–8247 (2013). source

In the paper

“Synaptic degeneration has been suggested to be one of the earliest cellular event in AD pathogenesis, and synaptic loss to be the best correlate of cognitive impairment in AD (see review by Reddy et al.31).”

What the sources say

• Not checked yetcites [31] Reddy, P. H. et al. Amyloid-beta and mitochondria in aging and Alzheimer's disease: implications for synaptic damage and cognitive decline. J. Alzheimers. Dis. 20(Suppl 2), S499–S512 (2010). source

In the paper

“Overexpression of Syt1 in mouse hippocampi was found to promote protective presenilin-1 conformation39”

What the sources say

• Not checked yetcites [39] Zoltowska, K. M. et al. Dynamic presenilin 1 and synaptotagmin 1 interaction modulates exocytosis and amyloid beta production. Mol. Neurodegener. 12, 15 (2017). source

In the paper

“SLC17A7, aka VGLUT1, is a sodium-dependent phosphate transporter that is specifically expressed in the neuron-rich regions of the brain and transports glutamate.”

What the sources say

• Not checked yetcites [42] Rodriguez-Perdigon, M. et al. Down-regulation of glutamatergic terminals (VGLUT1) driven by Abeta in Alzheimer's disease. Hippocampus 26, 1303–1312 (2016). source

In the paper

“VGF is induced by BDNF and serotonin and is upregulated by antidepressants, exercise, and is reduced in animal models of depression51.”

What the sources say

• Not checked yetcites [51] Thakker-Varia, S. & Alder, J. Neuropeptides in depression: role of VGF. Behav. Brain. Res. 197, 262–278 (2009). source

In the paper

“Second, our label-free proteomic method yielded approximately 3900 proteins in the proteome, which is not as comprehensive of a proteomic profile as would be ideal”

In the paper

“First, this is an association study and thus it precludes causal inference.”

In the paper

“Myelination refers to the formation of a membranous sheath surrounding axons to increase signal transmitting speed between neurons and is not limited to early development but occurs throughout adulthood45.”

What the sources say

• Not checked yetcites [45] Snaidero, N. & Simons, M. Myelination at a glance. J. Cell Sci. 127, 2999 (2014). source

In the paper

“Beach et al. described in detail how these measures were derived for the Banner cohort56.”

What the sources say

• Not checked yetcites [56] Beach, T. G. et al. Arizona Study of Aging and Neurodegenerative Disorders and Brain and Body Donation Program. Neuropathology 35, 354–389 (2015). source

In the paper

“Our findings may reflect the two types of astrocytes as described in the literature—reactive astrocytes that lose the ability to promote neuronal survival, outgrowth, and synaptogenesis, and induce death of neurons and oligodendrocytes, and homeostatic astrocytes that promote neural functioning54.”

What the sources say

• Not checked yetcites [54] Liddelow, S. A. et al. Neurotoxic reactive astrocytes are induced by activated microglia. Nature 541, 481–487 (2017). source

In the paper

“suggesting that some networks act through pathology while others act independently of pathology to contribute to variation in cognitive trajectory.”

In the paper

“Proteomic quantification for both cohorts used the approach described in detail in Seyfried et al.23 and enumerated below.”

What the sources say

• Not checked yetcites [23] Wingo, T. S. et al. Integrating next-generation genomic sequencing and mass spectrometry to estimate allele-specific protein abundance in human brain. J. Proteome. Res. 16, 3336–3347 (2017). source

In the paper

“In the BLSA cohort, O'Brien et al. described how estimates of β-amyloid positive plaques and neurofibrillary tangles were derived62.”

What the sources say

• Not checked yetcites [62] O'Brien, R. J. et al. Neuropathologic studies of the Baltimore Longitudinal Study of Aging (BLSA). J Alzheimers Dis 18, 665–675 (2009). source

In the paper

“From a genome-wide screen, a prominent observation after genetic ablation of IGF1 receptor in AD mice is the reduction in expression level of NEFM, down to control level, suggesting that lower-abundance of NEFM is protective46.”

What the sources say

• Not checked yetcites [46] George, C. et al. The Alzheimer's disease transcriptome mimics the neuroprotective signature of IGF-1 receptor-deficient neurons. Brain 140, 2012–2027 (2017). source

In the paper

“NEFM was shown to accumulate in the hippocampus in the presence of amyloid pathology46.”

What the sources say

• Not checked yetcites [46] George, C. et al. The Alzheimer's disease transcriptome mimics the neuroprotective signature of IGF-1 receptor-deficient neurons. Brain 140, 2012–2027 (2017). source

In the paper

“We also note that the published BLSA protein co-expression modules used here were constructed using the protein expression levels from both the dorsolateral prefrontal cortex (dPFC) and precuneus so the module memberships might be slightly different than those from the dPFC alone.”

In the paper

“These subjects were followed for a total of 887 person-years over 676 visits.”

In the paper

“We also employed a discovery and replication cohort design followed by meta-analysis to reduce false positive findings.”

In the paper

“Astrocytes provide neurotrophic support to promote neuronal survival, are important in the formation and maturation of synapses, help control neurotransmitter concentrations, and play a role in maintaining the blood-brain barrier53.”

What the sources say

• Not checked yetcites [53] Liddelow, S. & Barres, B. SnapShot: astrocytes in health and disease. Cell 162, 1170–1170 (2015). e1171. source

In the paper

“BLSA is a prospective cohort study of aging in community-dwelling individuals59,60.”

What the sources say

• Not checked yetcites [59] Seddighi, S. et al. SPARCL1 Accelerates symptom onset in Alzheimer's disease and influences brain structure and function during aging. J. Alzheimers. Dis. 61, 401–414 (2018). source
• Not checked yetcites [60] Simpson, B. N. et al. Blood metabolite markers of cognitive performance and brain function in aging. J. Cereb. Blood Flow Metab. 36, 1212–1223 (2016). source

In the paper

“VGF is a neuropeptide that promotes hippocampal neurogenesis, dendritic maturation, and synaptic activity50.”

What the sources say

• Not checked yetcites [50] Behnke, J. et al. Neuropeptide VGF promotes maturation of hippocampal dendrites that is reduced by single nucleotide polymorphisms. Int. J. Mol. Sci. 18, pii: E612 (2017). source

In the paper

“Fourth, our sample sizes are relatively small (n = 104 and n = 39) and exclusively Caucasians, which may limit the generalizability of our findings and power.”

In the paper

“Third, the available cognitive data was from the MMSE, a widely used screening tool that provides a coarse gauge of cognitive performance.”

In the paper

“Despite this, ours is the largest brain proteomic study of cognitive trajectory to our knowledge.”

In the paper

“Finally, our findings establish a framework for understanding mechanisms underlying cognitive trajectory and nominate a list of highly promising targets for future mechanistic studies of cognitive stability.”

In the paper

“Measures of AD pathology, i.e., β-amyloid plaques and neurofibrillary tangles, were used as covariates to adjust for the degree of AD pathology in each sample.”

In the paper

“The false discovery rate (FDR) for peptide spectral matches, proteins, and site decoy fraction were all set to 1 percent.”

In the paper

“We removed these technical (batch and PMI) and biological effects (sex and age at death) because they may confound our association analyses between cognitive trajectory and protein levels.”

In the paper

“The BLSA study was approved by the Institutional Review Board and the National Institute on Aging.”

In the paper

“For enrichment analysis, we used a modified version of the GeneOverlap function (from package of the same name) in R and Fisher’s exact test so that all pair-wise tests were adjusted for multiple testing using BH method to control the FDR67.”

What the sources say

• Not checked yetcites [67] Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Statist. 29, 1165–1188 (2001). source

In the paper

“For all analyses, we used Benjamini–Hochberg (BH) method to control the false discovery rate (FDR)67, and declared significantly associated proteins as those with BH FDR p < 0.05.”

What the sources say

• Not checked yetcites [67] Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Statist. 29, 1165–1188 (2001). source

In the paper

“Only proteins quantified in at least 90% of the samples were included in the analysis.”

In the paper

“All BLSA participants provided written informed consent at each visit61.”

What the sources say

• Not checked yetcites [61] Ferrucci, L. The Baltimore Longitudinal Study of Aging (BLSA): a 50-year-long journey and plans for the future. J Gerontol A Biol Sci Med Sci 63, 1416–1419 (2008). source

In the paper

“For BLSA, we used the BLSA networks from Seyfried et al.23, which were previously built using proteins measured from the precuneus and prefrontal cortex in the same individual.”

What the sources say

• Not checked yetcites [23] Wingo, T. S. et al. Integrating next-generation genomic sequencing and mass spectrometry to estimate allele-specific protein abundance in human brain. J. Proteome. Res. 16, 3336–3347 (2017). source

In the paper

“Therefore, within each cohort, effect of batch was removed using Combat64, and effects of sex, age at death, and PMI were removed using bootstrap regression.”

What the sources say

• Not checked yetcites [64] Johnson, W. E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127 (2007). source

In the paper

“Then, batch effects were removed using Combat64, and age at death, sex, and PMI were regressed from the proteomic profiles using Bootstrap regression.”

What the sources say

• Not checked yetcites [64] Johnson, W. E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127 (2007). source