Mapping human tissues with highly multiplexed RNA in situ hybridization
(2024) Nature Communications, 15 (1), art. no. 2511, .
Kalhor, K.a , Chen, C.-J.a b , Lee, H.S.a c , Cai, M.a , Nafisi, M.a , Que, R.a , Palmer, C.R.d e , Yuan, Y.a , Zhang, Y.f , Li, X.g , Song, J.a , Knoten, A.h , Lake, B.B.a g , Gaut, J.P.i , Keene, C.D.j , Lein, E.k , Kharchenko, P.V.f g , Chun, J.d , Jain, S.h i , Fan, J.-B.l , Zhang, K.a g
a Department of Bioengineering, University of California San Diego, La JollaCA, United States
b Program in Bioinformatics and Systems Biology, University of California San Diego, La JollaCA, United States
c Department of Electrical Engineering, University of California San Diego, La JollaCA, United States
d Sanford Burnham Prebys Medical Discovery Institute, La JollaCA, United States
e Program in Biomedical Sciences, University of California San Diego, La JollaCA, United States
f Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
g Altos Labs, San Diego, CA, United States
h Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
i Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, United States
j Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
k Allen Institute for Brain Science, Seattle, WA 98103, United States
l Illumina, San Diego, CA, United States
Abstract
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in <10 h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts. © The Author(s) 2024.
Document Type: Article
Publication Stage: Final
Source: Scopus
Longitudinal analysis of CSF HIV RNA in untreated people with HIV: Identification of CSF controllers
(2024) Journal of Medical Virology, 96 (3), art. no. e29550, .
Trunfio, M.a b , Tang, B.a , Okwuegbuna, O.a , Iudicello, J.E.a , Bharti, A.c , Moore, D.J.a , Gelman, B.B.d , Morgello, S.e , Patel, P.B.f , Rubin, L.H.g h , Ances, B.M.i , Gianella, S.c , Heaton, R.K.a , Ellis, R.J.a , Letendre, S.L.a
a HIV Neurobehavioral Research Program, Departments of Neurosciences and Psychiatry, University of California San Diego, San Diego, CA, United States
b Department of Medical Sciences, University of Turin, Turin, Italy
c Division of Infectious Diseases and Global Health, University of California San Diego, San Diego, CA, United States
d Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
e Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
f Department of Neurology, University of Washington, Seattle, WA, United States
g Department of Neurology, Psychiatry and Behavioral Sciences, Molecular and Cellular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
h Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
i Department of Neurology, Washington University, St Louis, MO, United States
Abstract
Interindividual variation of human immunodeficiency virus (HIV) RNA setpoint in cerebrospinal fluid (CSF) and its determinants are poorly understood, but relevant for HIV neuropathology, brain reservoirs, viral escape, and reseeding after antiretroviral interruptions. Longitudinal multicentric study on demographic, clinical, and laboratory correlates of CSF HIV RNA in 2000 follow-up visits from 597 people with HIV (PWH) off antiretroviral therapy (ART) and with plasma HIV RNA > the lower limit of quantification (LLQ). Factors associated with CSF control (CSFC; CSF HIV RNA < LLQ while plasma HIV RNA > LLQ) and with CSF/plasma discordance (CSF > plasma HIV RNA > LLQ) were also assessed through mixed-effects models. Posthoc and sensitivity analyses were performed for persistent CSFC and ART-naïve participants, respectively. Over a median follow-up of 2.1 years, CSF HIV RNA was associated with CD4+ and CD8+ T cells, CSF leukocytes, blood–brain barrier (BBB) integrity, biomarkers of iron and lipid metabolism, serum globulins, past exposure to lamivudine, and plasma HIV RNA (model p < 0.0001). CSFC (persistent in 7.7% over 3 years) and CSF/plasma discordance (persistent in <0.01% over 1 year) were variably associated with the same parameters (model p < 0.001). Sensitivity analyses confirmed most of the previous associations in participants never exposed to ART. Persistent CSFC was associated with higher CD4+ T-cell count nadir (p < 0.001), lower serum globulins (p = 0.003), and lower CSF leukocytes (p < 0.001). Without ART, one in 13 PWH had persistently undetectable CSF HIV RNA, while persistent CSF/plasma discordance was extremely rare over years. Immune responses, inflammation, BBB permeability, and iron and lipid metabolism were all associated with HIV replication in CSF. © 2024 Wiley Periodicals LLC.
Author Keywords
antiretroviral naïve; blood–brain barrier; central nervous system; CSF control; CSF/plasma discordance; HIV viral load
Document Type: Article
Publication Stage: Final
Source: Scopus
Migraine is a risk factor for pseudophakic positive dysphotopsia following monofocal lens implantation
(2024) Canadian Journal of Ophthalmology, .
Xing, M.J.a , Moulin, T.A.a , Suresh, T.a , Gira, J.P.b , Sheybani, A.a , Van Stavern, G.P.a
a Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, United States
b Ophthalmology Consultants, St. Louis, MO, United States
Abstract
Objective: To identify neuroadaptation-related risk factors for persistent positive dysphotopsia (>6 months) following monofocal lens implantation. Design: Retrospective cohort study. Participants: Patients of an academic institution and a private practice in Saint Louis, Missouri. Inclusion criteria were adults with cataract extraction between January 2010 and April 2021 with monofocal intraocular lens implantation. Exclusion criteria included dementia, <20/40 acuity, visual pathway damage, visual field loss, and significant pathology causing photopsia. Methods: Participants were surveyed via telephone. Results: There were 385 participants (385 eyes), of whom 66 had persistent dysphotopsia (58 positive), 298 had none, and 21 had nonpersistent dysphotopsia. Among the 58 who had positive persistent dysphotopsia, mean Pseudophakic Dysphotopsia Questionnaire 6 (PDQ-6) score was 14.11 (SD, 8.46). There were no significant differences in sex or race. Migraine prevalence was greater among those with dysphotopsia (21.2%) than among those without (11.4%; p = 0.054). History of migraine was associated with an increase in PDQ-6 score of 2.76 points (p = 0.006). Six people in each group had Visual Aura Rating Scale (VARS) scores greater than zero. Mean VARS score was 0.48 for those with dysphotopsia and 0.14 for those without (p = 0.03). History of migraine or increased VARS score, younger age, and female sex were associated with lower satisfaction. Conclusion: History of migraine was associated with increased dysphotopsia severity and decreased patient satisfaction. Although further study with a larger sample size is warranted, these preliminary results highlight the potential of simple questions to individualize lens choice, reduce the risk of dysphotopsia, and improve patient satisfaction. © 2024
Document Type: Article
Publication Stage: Article in Press
Source: Scopus
Clinical validation of the PrecivityAD2 blood test: A mass spectrometry-based test with algorithm combining %p-tau217 and Aβ42/40 ratio to identify presence of brain amyloid
(2024) Alzheimer’s and Dementia, .
Meyer, M.R.a , Kirmess, K.M.a , Eastwood, S.a , Wente-Roth, T.L.a , Irvin, F.a , Holubasch, M.S.a , Venkatesh, V.a , Fogelman, I.a , Monane, M.a , Hanna, L.b , Rabinovici, G.D.c , Siegel, B.A.d , Whitmer, R.A.e , Apgar, C.f , Bateman, R.J.d , Holtzman, D.M.d , Irizarry, M.g , Verbel, D.g , Sachdev, P.g , Ito, S.h , Contois, J.a , Yarasheski, K.E.a , Braunstein, J.B.a , Verghese, P.B.a , West, T.a
a C2N Diagnostics, St. Louis, MO, United States
b Center for Statistical Sciences, Brown University School of Public Health, Providence, RI, United States
c UCSF, San Francisco, CA, United States
d School of Medicine, Washington University, St. Louis, MO, United States
e UC Davis, Sacramento, CA, United States
f American College of Radiology, Philadelphia, PA, United States
g Eisai Inc., Nutley, NJ, United States
h Eisai Co., Ltd., Tokyo, Japan
Abstract
BACKGROUND: With the availability of disease-modifying therapies for Alzheimer’s disease (AD), it is important for clinicians to have tests to aid in AD diagnosis, especially when the presence of amyloid pathology is a criterion for receiving treatment. METHODS: High-throughput, mass spectrometry-based assays were used to measure %p-tau217 and amyloid beta (Aβ)42/40 ratio in blood samples from 583 individuals with suspected AD (53% positron emission tomography [PET] positive by Centiloid > 25). An algorithm (PrecivityAD2 test) was developed using these plasma biomarkers to identify brain amyloidosis by PET. RESULTS: The area under the receiver operating characteristic curve (AUC-ROC) for %p-tau217 (0.94) was statistically significantly higher than that for p-tau217 concentration (0.91). The AUC-ROC for the PrecivityAD2 test output, the Amyloid Probability Score 2, was 0.94, yielding 88% agreement with amyloid PET. Diagnostic performance of the APS2 was similar by ethnicity, sex, age, and apoE4 status. DISCUSSION: The PrecivityAD2 blood test showed strong clinical validity, with excellent agreement with brain amyloidosis by PET. © 2024 C2N Diagnostics LLC. Alzheimer’s & Dementia published by Wiley Periodicals LLC on behalf of Alzheimer’s Association.
Author Keywords
Alzheimer’s; amyloid beta; blood biomarker; clinical validity; diagnostic; p-tau217
Document Type: Article
Publication Stage: Article in Press
Source: Scopus
Comparison of cerebrospinal fluid, plasma and neuroimaging biomarker utility in Alzheimer’s disease
(2024) Brain Communications, 6 (2), .
Meeker, K.L.a , Luckett, P.H.b , Barthélemy, N.R.a , Hobbs, D.A.c , Chen, C.c , Bollinger, J.a , Ovod, V.a , Flores, S.c , Keefe, S.c , Henson, R.L.a , Herries, E.M.a , McDade, E.a , Hassenstab, J.J.a d , Xiong, C.d e , Cruchaga, C.d f , Benzinger, T.L.S.c d , Holtzman, D.M.a d , Schindler, S.E.a d , Bateman, R.J.a , Morris, J.C.a d , Gordon, B.A.c d , Ances, B.M.a c d
a Department of Neurology, Washington University in St Louis, St Louis, MO 63110, United States
b Department of Neurosurgery, Washington University in St Louis, St Louis, MO 63110, United States
c Department of Radiology, Washington University in St Louis, St Louis, MO 63110, United States
d Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO 63110, United States
e Division of Biostatistics, Washington University in St Louis, St Louis, MO 63110, United States
f Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, United States
Abstract
Alzheimer’s disease biomarkers are crucial to understanding disease pathophysiology, aiding accurate diagnosis and identifying target treatments. Although the number of biomarkers continues to grow, the relative utility and uniqueness of each is poorly understood as prior work has typically calculated serial pairwise relationships on only a handful of markers at a time. The present study assessed the cross-sectional relationships among 27 Alzheimer’s disease biomarkers simultaneously and determined their ability to predict meaningful clinical outcomes using machine learning. Data were obtained from 527 community-dwelling volunteers enrolled in studies at the Charles F. and Joanne Knight Alzheimer Disease Research Center at Washington University in St Louis. We used hierarchical clustering to group 27 imaging, CSF and plasma measures of amyloid beta, tau [phosphorylated tau (p-tau), total tau t-tau)], neuronal injury and inflammation drawn from MRI, PET, mass-spectrometry assays and immunoassays. Neuropsychological and genetic measures were also included. Random forest-based feature selection identified the strongest predictors of amyloid PET positivity across the entire cohort. Models also predicted cognitive impairment across the entire cohort and in amyloid PET-positive individuals. Four clusters emerged reflecting: core Alzheimer’s disease pathology (amyloid and tau), neurodegeneration, AT8 antibody-associated phosphorylated tau sites and neuronal dysfunction. In the entire cohort, CSF p-tau181/Aβ40lumi and Aβ42/Aβ40lumi and mass spectrometry measurements for CSF pT217/T217, pT111/T111, pT231/T231 were the strongest predictors of amyloid PET status. Given their ability to denote individuals on an Alzheimer’s disease pathological trajectory, these same markers (CSF pT217/T217, pT111/T111, p-tau/Aβ40lumi and t-tau/Aβ40lumi) were largely the best predictors of worse cognition in the entire cohort. When restricting analyses to amyloid-positive individuals, the strongest predictors of impaired cognition were tau PET, CSF t-tau/Aβ40lumi, p-tau181/Aβ40lumi, CSF pT217/217 and pT205/T205. Non-specific CSF measures of neuronal dysfunction and inflammation were poor predictors of amyloid PET and cognitive status. The current work utilized machine learning to understand the interrelationship structure and utility of a large number of biomarkers. The results demonstrate that, although the number of biomarkers has rapidly expanded, many are interrelated and few strongly predict clinical outcomes. Examining the entire corpus of available biomarkers simultaneously provides a meaningful framework to understand Alzheimer’s disease pathobiological change as well as insight into which biomarkers may be most useful in Alzheimer’s disease clinical practice and trials. © The Author(s) 2024.
Author Keywords
Alzheimer’s disease; biomarkers; machine learning
Document Type: Article
Publication Stage: Final
Source: Scopus
Discrimination and sense of purpose: Taking an intergenerational lens
(2024) International Journal of Behavioral Development, .
Wolk, M.W., Bogdan, R., Oltmanns, T.F., Hill, P.L.
Washington University, St. Louis, United States
Abstract
Given the developmental benefits associated with higher sense of purpose, past work has aimed to understand how experiences of adversity relate to sense of purpose. With a specific focus on experiences of adversity that may impact individuals from marginalized groups, past work has found that discrimination is related to lower sense of purpose in life, but that these effects are weaker for Black adults relative to White adults. The current research aims to extend past work by examining how and for whom discrimination is related to sense of purpose in life. Moreover, the current work also aimed to understand the extent to which sense of purpose spans across generations and whether there are generational differences in the relationship between discrimination and sense of purpose. Using data from the St. Louis Personality and Aging Network study, 822 parents (G1 participants) and 654 children (G2 participants) completed measures for sense of purpose, major experiences of discrimination, and personality traits. Results found mixed evidence for a relationship between discrimination and sense of purpose, with little evidence for consistent moderators. In addition, while the current work found no evidence of intergenerational associations for sense of purpose, results showed that discrimination was positively associated across generations, suggesting a potential for an intergenerational cycle of marginalization. © The Author(s) 2024.
Author Keywords
Discrimination; intergenerational; sense of purpose
Document Type: Article
Publication Stage: Article in Press
Source: Scopus
Disease staging of Alzheimer’s disease using a CSF-based biomarker model
(2024) Nature Aging, .
Salvadó, G.a , Horie, K.b c d , Barthélemy, N.R.b c , Vogel, J.W.a e , Pichet Binette, A.a , Chen, C.D.f , Aschenbrenner, A.J.c g , Gordon, B.A.f , Benzinger, T.L.S.f g , Holtzman, D.M.c g , Morris, J.C.c g , Palmqvist, S.a h , Stomrud, E.a h , Janelidze, S.a , Ossenkoppele, R.a i j , Schindler, S.E.c g , Bateman, R.J.b c g , Hansson, O.a h
a Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
b Tracy Family Stable Isotope Labeling Quantitation (SILQ) Center, Washington University School of Medicine, St. Louis, MO, United States
c Department of Neurology, Washington University School of Medicine, St. Louis, MO, United States
d Eisai, Inc., Nutley, NJ, United States
e Department of Clinical Science, Malmö, SciLifeLab, Lund University, Lund, Sweden
f Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States
g Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, United States
h Memory Clinic, Skåne University Hospital, Malmö, Sweden
i Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, Netherlands
j Amsterdam Neuroscience, Neurodegeneration, Amsterdam, Netherlands
Abstract
Biological staging of individuals with Alzheimer’s disease (AD) may improve diagnostic and prognostic workup of dementia in clinical practice and the design of clinical trials. In this study, we used the Subtype and Stage Inference (SuStaIn) algorithm to establish a robust biological staging model for AD using cerebrospinal fluid (CSF) biomarkers. Our analysis involved 426 participants from BioFINDER-2 and was validated in 222 participants from the Knight Alzheimer Disease Research Center cohort. SuStaIn identified a singular biomarker sequence and revealed that five CSF biomarkers effectively constituted a reliable staging model (ordered: Aβ42/40, pT217/T217, pT205/T205, MTBR-tau243 and non-phosphorylated mid-region tau). The CSF stages (0–5) demonstrated a correlation with increased abnormalities in other AD-related biomarkers, such as Aβ-PET and tau-PET, and aligned with longitudinal biomarker changes reflective of AD progression. Higher CSF stages at baseline were associated with an elevated hazard ratio of clinical decline. This study highlights a common molecular pathway underlying AD pathophysiology across all patients, suggesting that a single CSF collection can accurately indicate the presence of AD pathologies and characterize the stage of disease progression. The proposed staging model has implications for enhancing diagnostic and prognostic assessments in both clinical practice and the design of clinical trials. © The Author(s) 2024.
Document Type: Article
Publication Stage: Article in Press
Source: Scopus