IU Indianapolis ScholarWorks :: Browsing by Author "Foroud, Tatiana M."

Browsing by Author "Foroud, Tatiana M."

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A multiethnic transcriptome for Alzheimer Disease identifies cross‐ancestry and ancestry‐specific expression profiles
(Wiley, 2025-01-03) Yang, Zikun; Cieza, Basilio; Reyes-Dumeyer, Dolly; Lee, Annie J.; Dugger, Brittany N.; Jin, Lee-Way; Murray, Melissa E.; Dickson, Dennis W.; Pericak-Vance, Margaret A.; Vance, Jeffery M.; Foroud, Tatiana M.; Teich, Andrew F.; Mayeux, Richard; Tosto, Giuseppe; Neurology, School of Medicine
Background: Alzheimer’s Disease (AD) presents complex molecular heterogeneity, influenced by a variety of factors including heterogeneous phenotypic, genetic, and neuropathologic presentations. Regulation of gene expression mechanisms is a primary interest of investigations aiming to uncover the underlying disease mechanisms and progression. Method: We generated bulk RNA‐sequencing in prefrontal cortex from 565 AD brain samples (non‐Hispanic Whites, n = 399; Hispanics, n = 113; African American, n = 12) across six U.S. brain banks, and conducted differential gene expression and enrichment analyses. We sought to identify cross‐ancestry and ancestry‐specific differentially expressed genes (DEG) and pathways across Braak stages, adjusting for sex, age at death, and RNA quality metrics. We validated our findings using the Religious Orders Study/Memory and Aging Project study (ROS/MAP, n = 1,095). Lastly, we validated top DEG using publically‐available human single‐nucleus RNA sequencing (snRNAseq) data. Result: AD‐known genes VGF (LFC = ‐0.661, padj = 3.78) and ADAMTS2 (padj = 1.21) were consistently differentially expressed across statistical models, ethnic groups, and replicated in ROS/MAP (Figure 1). Genes from the heat shock protein (HSP) family, e.g. HSPB7 (padj = 3.78), were the top DEG, also replicated in ROS/MAP. Ethnic‐stratified analyses prioritized TNFSF14 and SPOCD1 as top DEG in Hispanic samples. Gene set enrichment analysis highlighted several significantly pathways, including “TYROBP causal network in microglia” (WP3945; padj = 1.68) and “Alzheimer Disease” (WP5124; padj = 4.24). snRNAseq validated several DEG, including VGF downregulated in neurons (padj = 1.1). Conclusion: To our knowledge, this is the largest diverse transcriptome study for AD in post‐mortem tissue. We identified perturbated genes and pathways resulting in cross‐ethnic and ethnic‐specific findings, ultimately highlighting the importance of diversity in AD investigations.
Absence of C9ORF72 expanded or intermediate repeats in autopsy-confirmed Parkinson's disease
(Wiley, 2014-05) Nuytemans, Karen; Inchausti, Vanessa; Beecham, Gary W.; Wang, Liyong; Dickson, Dennis W.; Trojanowski, John Q.; Lee, Virginia M.-Y.; Mash, Deborah C.; Frosch, Matthew P.; Foroud, Tatiana M.; Honig, Lawrence S.; Montine, Thomas J.; Dawson, Ted M.; Martin, Eden R.; Scott, William K.; Vance, Jeffery M.; Medical & Molecular Genetics, School of Medicine
BACKGROUND: We have reported that intermediate repeat lengths of the C9ORF72 repeat are a risk factor for Parkinson's disease (PD) in a clinically diagnosed data set. Because 10% to 25% of clinically diagnosed PD have different diagnoses upon autopsy, we hypothesized that this may reflect phenotypic heterogeneity or concomitant pathology of other neurodegenerative disorders. METHODS: We screened 488 autopsy-confirmed PD cases for expansion haplotype tag rs3849942T. In 196 identified haplotype carriers, the C9ORF72 repeat was genotyped using the repeat-primed polymerase chain reaction assay. RESULTS: No larger (intermediate or expanded) repeats were found in these autopsy-confirmed PD samples. This absence of larger repeats is significantly different from the frequency in clinically diagnosed datasets (P = 0.002). CONCLUSIONS: Our results suggest that expanded or intermediate C9ORF72 repeats in clinically diagnosed PD or parkinsonism might be an indication of heterogeneity in clinically diagnosed PD cases. Further studies are needed to elucidate the potential contribution of the C9ORF72 repeat to autopsy-confirmed PD.
Adaptation of Subjective Responses to Alcohol is Affected by an Interaction of GABRA2 Genotype and Recent Drinking
(Wiley Blackwell (Blackwell Publishing), 2015-07) Kosobud, Ann E. K.; Wetherill, Leah; Plawecki, Martin H.; Kareken, David A.; Liang, Tiebing; Nurnberger, John L.; Windisch, Kyle; Xuei, Xiaoling; Edenberg, Howard J.; Foroud, Tatiana M.; O’Connor, Sean J.; Department of Psychiatry, IU School of Medicine
BACKGROUND: Subjective perceptions of alcohol intoxication are associated with altered risk for alcohol abuse and dependence. Acute adaptation of these perceptions may influence such risk and may involve genes associated with pleasant perceptions or the relief of anxiety. This study assessed the effect of variation in the GABAA receptor genes GABRG1 and GABRA2 and recent drinking history on the acute adaptation of subjective responses to alcohol. METHODS: One hundred and thirty-two nondependent moderate to heavy drinkers, aged 21 to 27, participated in 2 single-blind, counterbalanced sessions, approximately 1 week apart. One session was an intravenous alcohol "clamp," during which breath alcohol concentration was held steady at 60 mg/dl (60 mg%) for 3 hours, and the other an identical session using saline infusion. Subjective perceptions of Intoxication, Enjoyment, Stimulation, Relaxation, Anxiety, Tiredness, and Estimated Number of Drinks were acquired before (baseline), and during the first and final 45 minutes of the clamp. A placebo-adjusted index of the subject's acute adaptation to alcohol was calculated for each of the 7 subjective measures and used in a principal component analysis to create a single aggregate estimate for each subject's adaptive response to alcohol. Analysis of covariance tested whether GABRA2 and GABRG1 single nucleotide polymorphism (SNP) genotypes, gender, placebo session, family history of alcoholism, recent drinking history, and the genotype × recent drinking history interaction significantly predicted the adaptive response. RESULTS: Recent drinking history (p = 0.01), and recent drinking history × genotype interaction (p = 0.01) were significantly associated with acute adaptation of the subjective responses to alcohol for the GABRA2 SNP rs279858. CONCLUSIONS: Higher recent drinking was found to be associated with reduced acute tolerance to positive, stimulating effects of alcohol in carriers of the rs279858 risk allele. We postulate that the GABRA2 effect on alcohol dependence may, in part, be due to its effect on subjective responses to alcohol.
An ADH1B variant and peer drinking in progression to adolescent drinking milestones: Evidence of a gene-by-environment interaction
(Wiley Online Library, 2014-10) Olfson, Emily; Edenberg, Howard J.; Nurnberger Jr., John; Agrawal, Arpana; Bucholz, Kathleen K.; Almasy, Laura A.; Chorlian, David; Dick, Danielle M.; Hesselbrock, Victor M.; Kramer, John R.; Kuperman, Samuel; Porjesz, Bernice; Schuckit, Marc A.; Tischfield, Jay A.; Wang, Jen-Chyong; Wetherill, Leah; Foroud, Tatiana M.; Rice, John; Goate, Alison; Bierut, Laura J.; Department of Biochemistry & Molecular Biology, IU School of Medicine
BACKGROUND: Adolescent drinking is an important public health concern, one that is influenced by both genetic and environmental factors. The functional variant rs1229984 in alcohol dehydrogenase 1B (ADH1B) has been associated at a genome-wide level with alcohol use disorders in diverse adult populations. However, few data are available regarding whether this variant influences early drinking behaviors and whether social context moderates this effect. This study examines the interplay between rs1229984 and peer drinking in the development of adolescent drinking milestones. METHODS: One thousand five hundred and fifty European and African American individuals who had a full drink of alcohol before age 18 were selected from a longitudinal study of youth as part of the Collaborative Study on the Genetics of Alcoholism (COGA). Cox proportional hazards regression, with G × E product terms in the final models, was used to study 2 primary outcomes during adolescence: age of first intoxication and age of first DSM-5 alcohol use disorder symptom. RESULTS: The minor A allele of rs1229984 was associated with a protective effect for first intoxication (HR = 0.56, 95% CI 0.41 to 0.76) and first DSM-5 symptom (HR = 0.45, 95% CI 0.26 to 0.77) in the final models. Reporting that most or all best friends drink was associated with a hazardous effect for first intoxication (HR = 1.81, 95% CI 1.62 to 2.01) and first DSM-5 symptom (HR = 2.17, 95% 1.88 to 2.50) in the final models. Furthermore, there was a significant G × E interaction for first intoxication (p = 0.002) and first DSM-5 symptom (p = 0.01). Among individuals reporting none or few best friends drinking, the ADH1B variant had a protective effect for adolescent drinking milestones, but for those reporting most or all best friends drinking, this effect was greatly reduced. CONCLUSIONS: Our results suggest that the risk factor of best friends drinking attenuates the protective effect of a well-established ADH1B variant for 2 adolescent drinking behaviors. These findings illustrate the interplay between genetic and environmental factors in the development of drinking milestones during adolescence.
AluY-mediated germline deletion, duplication and somatic stem cell reversion in UBE2T defines a new subtype of Fanconi anemia
(Oxford University Press, 2015-09-15) Virts, Elizabeth L.; Jankowska, Anna; Mackay, Craig; Glaas, Marcel F.; Wiek, Constanze; Kelich, Stephanie L.; Lottmann, Nadine; Kennedy, Felicia M.; Marchal, Christophe; Lehnert, Erik; Scharf, Rüdiger E.; Dufour, Carlo; Lanciotti, Marina; Farruggia, Piero; Santoro, Alessandra; Savasan, Süreyya; Scheckenbach, Kathrin; Schipper, Jörg; Wagenmann, Martin; Lewis, Todd; Leffak, Michael; Farlow, Janice L.; Foroud, Tatiana M.; Honisch, Ellen; Niederacher, Dieter; Chakraborty, Sujata C.; Vance, Gail H.; Pruss, Dmitry; Timms, Kirsten M.; Lanchbury, Jerry S.; Alpi, Arno F.; Hanenberg, Helmut; Department of Pediatrics, IU School of Medicine
Fanconi anemia (FA) is a rare inherited disorder clinically characterized by congenital malformations, progressive bone marrow failure and cancer susceptibility. At the cellular level, FA is associated with hypersensitivity to DNA-crosslinking genotoxins. Eight of 17 known FA genes assemble the FA E3 ligase complex, which catalyzes monoubiquitination of FANCD2 and is essential for replicative DNA crosslink repair. Here, we identify the first FA patient with biallelic germline mutations in the ubiquitin E2 conjugase UBE2T. Both mutations were aluY-mediated: a paternal deletion and maternal duplication of exons 2–6. These loss-of-function mutations in UBE2T induced a cellular phenotype similar to biallelic defects in early FA genes with the absence of FANCD2 monoubiquitination. The maternal duplication produced a mutant mRNA that could encode a functional protein but was degraded by nonsense-mediated mRNA decay. In the patient's hematopoietic stem cells, the maternal allele with the duplication of exons 2–6 spontaneously reverted to a wild-type allele by monoallelic recombination at the duplicated aluY repeat, thereby preventing bone marrow failure. Analysis of germline DNA of 814 normal individuals and 850 breast cancer patients for deletion or duplication of UBE2T exons 2–6 identified the deletion in only two controls, suggesting aluY-mediated recombinations within the UBE2T locus are rare and not associated with an increased breast cancer risk. Finally, a loss-of-function germline mutation in UBE2T was detected in a high-risk breast cancer patient with wild-type BRCA1/2. Cumulatively, we identified UBE2T as a bona fide FA gene (FANCT) that also may be a rare cancer susceptibility gene.
Alzheimer’s Disease Plasma Biomarker Results from across 14 Alzheimer’s Disease Research Centers
(Wiley, 2025-01-09) Russ, Kristen A.; Asthana, Sanjay; Johnson, Sterling C.; Wilson, Rachael E.; Craft, Suzanne; Register, Thomas C.; Lockhart, Samuel N.; Nairn, Angus C.; Strittmatter, Stephen M.; van Dyck, Christopher H.; Foroud, Tatiana M.; Dage, Jeffrey L.; Neurology, School of Medicine
Background: The Alzheimer’s Disease Center Fluid Biomarker (ADCFB) Initiative samples are analyzed centrally at NCRAD for AD plasma biomarkers. When combining NACC accessible data from across centers, biofluid biomarker data must be evaluated carefully. This will become more critical with the implementation of disease modifying therapies. Methods: Beta amyloid 1‐42 (Aβ42) and beta amyloid 1‐40 (Aβ40) were analyzed utilizing the Neurology 4‐Plex E kits on a Quanterix Simoa HD‐X. All assays were performed according to manufacturer’s instructions. NACC data from participants 65 or older was combined with biomarker results into one data set. Samples with PET results from the same visit as the blood collection were utilized for this analysis (n=114). Results: Data for amyloid and tau PET was used along with Aβ42/40 ratios to assess the area under the curve (AUC) for this data set (Figure 1). Amyloid PET and Tau PET by Aβ42/40 ROC analysis including age and APOE4 carrier status showed lower than expected AUCs (both 0.72). A subset of data (n=90) was analyzed using participants that were not on any FDA‐approved drugs for AD. This had no effect on AUCs for amyloid or tau PET by Aβ42/40 ratios. Distribution of Aβ42/40 ratios across sites showed a single site had a subset of very high Aβ42/40 ratios (n=8) in comparison to other sites. After removal of the Aβ42/40 outliers from the specific site from the data set, diagnostic accuracies of Aβ42/40 for both Amyloid PET (AUC=0.77) and Tau PET (AUC=0.76) were increased. More investigation into the exact cause of the outliers is necessary, but Aβ42/40 elevations independent from other biomarkers have been seen in clinical trials of Solanezumab and some other Aβ targeting antibodies. Conclusion: To avoid errors in data analysis when using shared data, it is important to track clinical trial co‐enrollment and drug type within ADCs at NACC. As FDA‐approved treatments become available or co‐enrollment of AD drug trials at centers occurs, it is critical to carefully track participant variables and review biofluid biomarker data when it is being combined across centers or studies.
Alzheimer’s Disease Polygenic Risk in the LEADS Cohort
(Wiley, 2025-01-03) Nudelman, Kelly N.; Pentchev, Julian V.; Jackson, Trever; Eloyan, Ani; Dage, Jeffrey L.; Foroud, Tatiana M.; Hammers, Dustin B.; Carrillo, Maria C.; Dickerson, Bradford C.; Rabinovici, Gil D.; Apostolova, Liana G.; LEADS Consortium; Medical and Molecular Genetics, School of Medicine
Background: Currently, it is unclear to what extent late‐onset Alzheimer’s disease (AD) risk variants contribute to early‐onset AD (EOAD). One method to clarify the contribution of late‐onset AD genetic risk to EOAD is to investigate the association of AD polygenic risk scores (PRS) with EOAD. We hypothesize that in the Longitudinal Early‐Onset Alzheimer’s Disease Study (LEADS), EOAD participants will have greater PRS than early‐onset amyloid‐negative cognitively‐impaired participants (EOnonAD) and controls, and investigate the association of AD PRS with age of disease onset (AoO) and cognitive performance. Methods: GWAS data was generated for LEADS participants, including those with EOAD, EOnonAD, and controls, with the Illumina Global Screening Array. A PRS was calculated using the 31 SNPs and weights published previously by Desikan et al. (2017) for LEADS participants with imputed GWAS data (N = 369). Logistic regression models including age, sex, PRS, and genetic ancestry principal components were tested to identify predictors of EOAD (N = 210) vs. EOnonAD (N = 69) and controls (N = 89). ANCOVA models were used to assess group differences in PRS scores. Kaplan‐Meier regression was used to assess differences in EOAD AoO for tertile‐binned PRS groups. Within EOAD, pre‐calculated cognitive domain scores for speed and attention, working memory, episodic memory, language, and visuospatial performance were assessed for correlation with PRS. Results: The AD PRS was a predictor of EOAD (p = 0.014), with the model explaining 10.5% of variance (X2 = 40.971, p<0.001). EOAD participants had higher PRS scores (mean = 0.0012, standard deviation (SD) = 0.015) compared to EOnonAD and controls (mean = ‐0.0018, SD = 0.015) (F = 6.602, p = 0.011). Survival analysis indicated no significant differences in EOAD AoO between PRS groups (X2 = 3.396, p = 0.183). In the EOAD group, PRS was associated with cognitive scores for speed and attention (r = 0.204, p = 0.007), language (r = 0.230, p = 0.002), and visuospatial performance (r = 0.166, p = 0.037). Conclusions: In the LEADS cohort, AD PRS is a predictor for EOAD, and is associated with cognitive performance, but does not predict EOAD AoO. This suggests that while late onset AD‐associated genetic variants contribute to disease risk and processes, they do not account for a large portion of disease risk, and do not explain differences in disease AoO in the LEADS cohort.
Analysis of a TNFRSF11A Gene Polymorphism and External Apical Root Resorption During Orthodontic Treatment
(2005-07) French, Michael; Hartsfield, James K., Jr.; Al-Qawasmi, Riyad A.; Foroud, Tatiana M.; Roberts, W. Eugene; Shanks, James
External Apical Root Resorption (EARR) can be an undesirable side effect of orthodontic treatment. Several studies have already recognized a genetic predisposition to EARR, and some have suggested possible candidate genes that may be involved. The objective of this prospective study was to explore one possible candidate gene that may predispose individuals to EARR during orthodontic treatment. The TNFRSF11A gene encodes the receptor activator of nuclear factor-kappa β (RANK). Together with the RANK ligand, RANK mediates cell signaling that leads to osteoclastogenesis. A diallelic marker was used to investigate the possible relationship between a nonsynonymous TNFRSF11A (RANK) polymorphism and the individuals' development of EARR concurrent with orthodontic treatment. Buccal swab cells of 112 patients who had completed orthodontic treatment were collected for DNA isolation and analysis. EARR of the maxillary central incisors was calculated based on measurements from pre and post treatment occlusal radiographs. Linear regression analysis indicated that length of treatment, overjet, and molar classification are significant predictors of EARR (p=0.05). Other factors, including age, gender, and overbite, were not found to be significantly associated with EARR. An ANOVA was performed to examine the relationship of the genotyped TNFRSF11A marker with the dependent variable EARR. When individuals having at least one copy of allele 2 (1,2 and 2,3 genotypes) were pooled together, a marginally significant association was found between EARR and the marker. Further analysis using logistic regression revealed that individuals with a (1,1) genotype are 4.3 times more likely to be affected by EARR than a person with a (1,2) or (2,2) genotype. From these findings it was concluded that EARR is a complex condition influenced by several treatment variables with the TNFRSF11A gene and its product (RANK) contributing to the individuals' predisposition.
Analysis of the Inverse Association between Cancer and Alzheimer’s Disease: Results from the Alzheimer’s Disease Neuroimaging Initiative Cohort
(Office of the Vice Chancellor for Research, 2014-04-11) Nudelman, Kelly N. H.; Risacher, Shannon L.; West, John D.; Nho, Kwangsik; Ramanan, Vijay K.; McDonald, Brenna C.; Shen, Li; Foroud, Tatiana M.; Schneider, Bryan P.; Saykin, Andrew J.
Although a number of studies support a reciprocal inverse association between diagnoses of cancer and Alzheimer’s disease (AD), to date there has not been any systemic investigation of the neurobiological impact of or genetic risk factors underlying this effect. To facilitate this goal, this study aimed to replicate the inverse association of cancer and AD using data from the NIA Alzheimer’s Disease Neuroimaging Initiative, which includes age-matched cases and controls with information on cancer history, AD progression, neuroimaging, and genomic data. Subjects included individuals with AD (n=234), mild cognitive impairment (MCI, n=542), and healthy controls (HC, n=293). After controlling for sex, education, race/ethnicity, smoking, and apolipoprotein E (APOE) e2/3/4 allele groups, cancer history was protective against baseline AD diagnosis (p=0.042), and was associated with later age of AD onset (p=0.001). Cancer history appears to result in a cumulative protective effect; individuals with more than one cancer had a later age of AD onset compared to those with only one cancer (p=0.001). Finally, a protective effect of AD was also observed in individuals who developed incident cancer after enrolling (post-baseline visit); 20 individuals with MCI and 9 HC developed cancer, while no AD patients had subsequent cancer diagnoses (p=0.013). This supports previous research on the inverse association of cancer and AD, and importantly provides novel evidence that this effect appears to be independent of APOE, the major known genetic risk factor for AD. Future analyses will investigate the neurobiological and genetic basis of this effect.
Analysis of the Relationship Between Growth Hormone Receptor Polymorphism rs6180 and Craniofacial Morphological Changes Associated with Herbst Appliance Therapy
(2007) Ellis, Lawrence Charles; Hartsfield, James K., Jr.; Baldwin, James J.; Foroud, Tatiana M.; Roberts, W. Eugene; Shanks, James C.
Craniofacial growth results from both environmental and genetic factors over time. It would be exciting to isolate genetic factors that influence treatment responses from patients undergoing orthodontic treatment. Genetic genotyping and analysis of orthodontic patients is a new technologic advancement. The aim of this retrospective study is to examine the relationship of a specific single nucleotide polymorphism (SNP), rs6180, of the Growth Hormone Receptor (GHR) gene with various craniofacial length parameters in patients who have received Herbst appliance therapy as part of orthodontic treatment. An initial lateral cephalometric radiograph was taken along with two buccal cheek swabs. The cells obtained have undergone DNA isolation with the Puregene method in microcentrifuge tubes (Gentra Systems, Minneapolis, MN). Upon termination of functional appliance therapy (post-Herbst), a final lateral cephalometric radiograph was taken. To analyze the genetic polymorphism and determine genotype, polymerase chain reaction (PCR) and allelic discrimination were done using the 7000 Sequence Detection System (Applied Biosystems). Lateral cephalometric radiographs (initial, post-Herbst) of 25 patients were digitized and measured using the Dolphin Imaging program. Cephalometric measurements (S-N, S-A, Co-Go, Go-Gn, Ar-Gn, Go-Gn) were used to identify mandibular and craniofacial morphologic changes. Changes in Z-scores based on standards from the Michigan Growth Study were then converted to slow or normal growth status by slow being when the Z-score difference between the initial and final measurements is less than zero. The number of subjects with a slow versus normal growth status was compared to GHR polymorphism genotype. Statistical analysis of Hardy-Weinberg equilibrium and the changes in craniofacial length Z-scores in relation to a patient's genotype were performed using chi-square analysis. Results: The genotype frequencies were in Hardy-Weinberg equilibrium. Z-score differences for the S-A measurement was the only one found to be significant (p=0.005).

Browsing by Author "Foroud, Tatiana M."

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