Analysis of genes (TMEM106B, GRN, ABCC9, KCNMB2, and APOE) implicated in risk for LATE-NC and hippocampal sclerosis provides pathogenetic insights: a retrospective genetic association study

Abstract

Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is the most prevalent subtype of TDP-43 proteinopathy, affecting up to 1/3rd of aged persons. LATE-NC often co-occurs with hippocampal sclerosis (HS) pathology. It is currently unknown why some individuals with LATE-NC develop HS while others do not, but genetics may play a role. Previous studies found associations between LATE-NC phenotypes and specific genes: TMEM106B, GRN, ABCC9, KCNMB2, and APOE. Data from research participants with genomic and autopsy measures from the National Alzheimer's Coordinating Center (NACC; n = 631 subjects included) and the Religious Orders Study and Memory and the Rush Aging Project (ROSMAP; n = 780 included) were analyzed in the current study. Our goals were to reevaluate disease-associated genetic variants using newly collected data and to query whether the specific genotype/phenotype associations could provide new insights into disease-driving pathways. Research subjects included in prior LATE/HS genome-wide association studies (GWAS) were excluded. Single nucleotide variants (SNVs) within 10 kb of TMEM106B, GRN, ABCC9, KCNMB2, and APOE were tested for association with HS and LATE-NC, and separately for Alzheimer's pathologies, i.e. amyloid plaques and neurofibrillary tangles. Significantly associated SNVs were identified. When results were meta-analyzed, TMEM106B, GRN, and APOE had significant gene-based associations with both LATE and HS, whereas ABCC9 had significant associations with HS only. In a sensitivity analysis limited to LATE-NC + cases, ABCC9 variants were again associated with HS. By contrast, the associations of TMEM106B, GRN, and APOE with HS were attenuated when adjusting for TDP-43 proteinopathy, indicating that these genes may be associated primarily with TDP-43 proteinopathy. None of these genes except APOE appeared to be associated with Alzheimer's-type pathology. In summary, using data not included in prior studies of LATE or HS genomics, we replicated several previously reported gene-based associations and found novel evidence that specific risk alleles can differentially affect LATE-NC and HS.

Keywords: Arteriolosclerosis; Dementia; Mixed pathology; Pleiotropy; Proteinopathy; SNP.

Fig. 1

Photomicrographs of human hippocampi depict the main neuropathologic endophenotypes analyzed in the current study. Hippocampal sclerosis (HS) is evaluated with H&E stain (panels A, C, E), whereas LATE-NC is operationalized with phospho-TDP-43 immunohistochemistry (IHC; panels B, D, and F). All photomicrographs depict mid-level hippocampal sections dissected in the coronal plane. Panels A and B show stained brain sections from a woman (APOE e3/e4) who died at age 83; autopsy revealed neither LATE-NC nor HS. Panels C and D are from a man (APOE e3/e4) who died at age 93 with LATE-NC Stage 2. Panels E and F are from a woman (APOE e3/e3) who died at age 95 with LATE-NC Stage 2 and comorbid HS. Note the relatively atrophic hippocampal profile in Panel E in comparison to a or c (same scale bar); the HS + profile in panel E also demonstrates parenchymal rarefaction which can be appreciated even at low magnification. Phospho-TDP-43 immunoreactive intraneuronal inclusions are highlighted with arrows in panels D and F. The representative photomicrographs were from research participants of the University of Kentucky AD Research Center. Scale bar = 2 mm in A, C, and E, 75 microns in A, D, and F

Fig. 2

Included and excluded research participants, along with criteria for exclusion. A flowchart summarizing inclusions and exclusions for National Alzheimer's Coordinating Center (NACC) and Religious Orders Study and Rush Memory and Aging Project (ROSMAP) participants

Fig. 3

Venn diagrams of the overlap between endophenotypes across studies. Venn diagrams of the overlap between limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) and hippocampal sclerosis (HS) cases in A. National Alzheimer's Coordinating Center (NACC) and B. Religious Orders Study and Rush Memory and Aging Project (ROSMAP). LATE-NC = limbic-predominant age-related TDP-43 encephalopathy neuropathological change; HS = hippocampal sclerosis; NACC = National Alzheimer's Coordinating Center; ROSMAP = Religious Orders Study and Rush Memory and Aging Project

Fig. 4

Variant-level results for TMEM106B and GRN. Adjusted, meta-analytic, single nucleotide variant (SNV)-level p-values for hippocampal sclerosis (HS) and limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) across A. TMEM106B ± 10 kb and B. GRN ± 10 kb. All analyses were adjusted for sex, age at death, cohort/study, and the first three genetic principal components. Horizontal dashed lines represent the Bonferroni-corrected thresholds for significance that account for the number of independent tests in each genomic region. A diamond represents the SNV with the smallest p-value. The previously identified TMEM106B SNV (Rutherford et al. [62]) is labeled and identified with an arrow. MOI = mode of inheritance; LATE-NC = limbic-predominant age-related TDP-43 encephalopathy neuropathological change; HS = hippocampal sclerosis

Fig. 5

Variant-level results for APOE. Adjusted, meta-analytic, single nucleotide variant (SNV)-level p-values for hippocampal sclerosis (HS) and limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) across APOE ± 10 kb. All analyses were adjusted for sex, age at death, cohort/study, and the first three genetic principal components. The horizontal dashed line represents the Bonferroni-corrected threshold for significance that accounts for the number of independent tests in the APOE ± 10 kb region. A diamond represents the SNV with the smallest p-value. MOI = mode of inheritance; LATE-NC = limbic-predominant age-related TDP-43 encephalopathy neuropathological change; HS = hippocampal sclerosis

Fig. 6

Variant-level results for ABCC9. Adjusted, meta-analytic, single nucleotide variant (SNV)-level p-values for hippocampal sclerosis (HS) and limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) across ABCC9 ± 10 kb assuming a recessive mode of inheritance (MOI). A recessive MOI was assumed for ABCC9 since it has consistently been the MOI with the strongest HS association for ABCC9 [43, 48, 29]. All analyses were for sex, age at death, cohort/study, and the first three genetic principal components. The horizontal dashed line represents the Bonferroni-corrected threshold for significance that accounts for the number of independent tests in the ABCC9 ± 10 kb region. A diamond represents the SNV with the smallest p-value. The previously identified ABCC9 SNV [43] is labeled and identified with an arrow. MOI = mode of inheritance; LATE-NC = limbic-predominant age-related TDP-43 encephalopathy neuropathological change; HS = hippocampal sclerosis

Fig. 7

Expression quantitative trait loci (eQTL) analyses for rs1914361 and ABCC9 across tissue types. Expression quantitative trait loci (eQTL) analyses for rs1914361 and ABCC9 gene expression across human tissues in the Genotype-Tissue Expression (GTEx) database. a Multi-tissue eQTL plot of rs1914361 and ABCC9 gene expression; b ABCC9 normalized gene expression stratified by rs1914361 minor alleles in the nucleus acumbens region of the brain; and c ABCC9 normalized gene expression stratified by rs1914361 minor alleles in the aorta region of the artery. GTEx = Genotype-Tissue Expression; NES = normalize effect size; eQTL = expression quantitative trait loci

Fig. 8

Adjusted odds ratios for hippocampal sclerosis (HS) across variants. Adjusted odds ratio estimates and 95% confidence intervals for genetic single nucleotide variants (SNV) and APOE ε4 carrier status from separate regression models of hippocampal sclerosis (HS) fit using data from the National Alzheimer's Coordinating Center (NACC), the Religious Orders Study and Rush Memory and Aging Project (ROSMAP), and the meta-analysis of NACC and ROSMAP. All regression models were adjusted for sex, age at death, cohort/study, and the first three genetic principal components. Regression models were also adjusted for limbic-predominant age-related TDP-43 encephalopathy neuropathological change (LATE-NC) case status by the including LATE-NC status as an additional predictor variable and these odds ratio estimates are represented by triangles. For each variant, the effect allele is defined as the HS risk-causing allele (HA odds ratio estimates > 1.0), and not necessarily the minor allele. An additive mode of inheritance (MOI) is assumed for all variants except for rs704178 where a dominant MOI was assumed (since a recessive MOI resulted in a significant protective effect for HS). HS = hippocampal sclerosis; LATE-NC = limbic-predominant age-related TDP-43 encephalopathy neuropathological change; NACC = National Alzheimer's Coordinating Center; ROSMAP = Religious Orders Study and Rush Memory and Aging Project

Fig. 9

ABCC8 and ABCC9 gene expression across tissue types. ABCC8 and ABCC9 gene expression in various human tissues in the a Genotype-Tissue Expression (GTEx) and b Functional Annotation of Human Long Noncoding RNAs via Molecular Mapping (FANTOM5) databases. In GTEx, central nervous system (CNS) tissues included Brodmann (1909) area 24, Brodmann (1909) area 9, C1 segment of cervical spinal cord, amygdala, caudate nucleus, cerebellar hemisphere, cerebellum, cerebral cortex, hippocampus proper, hypothalamus, nucleus accumbens, pituitary gland, and substantia nigra; vascular/smooth muscle tissues included aorta, atrium auricular region, coronary artery, tibial artery, endocervix, esophagus muscularis mucosa, urinary bladder, and uterus; and other tissues included all other tissue types. In FANTOM5, CNS tissues included amygdala, brain, caudate nucleus, cerebellum, diencephalon, dorsal thalamus, globus pallidus, hippocampal formation, locus ceruleus, medulla oblongata, middle frontal gyrus, middle temporal gyrus, occipital cortex, occipital lobe, olfactory apparatus, parietal lobe, pituitary gland, putamen, spinal cord, and substantia nigra; vascular/smooth muscle tissue included artery, heart, heart left ventricle, left cardiac atrium, mitral valve, smooth muscle, tricuspid valve, and uterus; and other tissues included all other tissue types. GTEx = Genotype-Tissue Expression; FANTOM5 = Functional Annotation of Human Long Noncoding RNAs via Molecular Mapping; TPM = transcripts per million; CNS = central nervous system

Fig. 10

Diagrams depicting potential causal relationships between the genes under study with positive findings. Diagrams depicting potential causal relationships between the genes under study with positive findings (TMEM106B, ABCC9, GRN, and APOE) and TDP-43 proteinopathy/limbic-predominant age-related TDP-43 encephalopathy (LATE), hippocampal sclerosis (HS), and Alzheimer’s disease (AD). a The candidate genes and their corresponding colors in the diagrams, b a diagram of the current study’s prima facie results, and c a diagram showing hypothetical mechanistic pathways that are compatible with the findings of the current study, including how AD neuropathologic changes (often linked to the APOE risk allele) may fit in with the current study’s results. LATE = limbic-predominant age-related TDP-43 encephalopathy; HS = hippocampal sclerosis; AD = Alzheimer’s disease