MSTPublications: July 2021
MASiVar: Multisite, multiscanner, and multisubject acquisitions for studying variability in diffusion weighted MRI.
Cai LY, Yang Q, Kanakaraj P, Nath V, Newton AT, Edmonson HA, Luci J, Conrad BN, Price GR, Hansen CB, Kerley CI, Ramadass K, Yeh FC, Kang H, Garyfallidis E, Descoteaux M, Rheault F, Schilling KG, Landman BA.
Magn Reson Med. 2021 Jul 16. doi: 10.1002/mrm.28926. Online ahead of print.
Purpose: Diffusion-weighted imaging allows investigators to identify structural, microstructural, and connectivity-based differences between subjects, but variability due to session and scanner biases is a challenge.
Methods: To investigate DWI variability, we present MASiVar, a multisite data set consisting of 319 diffusion scans acquired at 3 T from b = 1000 to 3000 s/mm2 across 14 healthy adults, 83 healthy children (5 to 8 years), three sites, and four scanners as a publicly available, preprocessed, and de-identified data set. With the adult data, we demonstrate the capacity of MASiVar to simultaneously quantify the intrasession, intersession, interscanner, and intersubject variability of four common DWI processing approaches: (1) a tensor signal representation, (2) a multi-compartment neurite orientation dispersion and density model, (3) white-matter bundle segmentation, and (4) structural connectomics. Respectively, we evaluate region-wise fractional anisotropy, mean diffusivity, and principal eigenvector; region-wise CSF volume fraction, intracellular volume fraction, and orientation dispersion index; bundle-wise shape, volume, fractional anisotropy, and length; and whole connectome correlation and maximized modularity, global efficiency, and characteristic path length.
Results: We plot the variability in these measures at each level and find that it consistently increases with intrasession to intersession to interscanner to intersubject effects across all processing approaches and that sometimes interscanner variability can approach intersubject variability.
Conclusions: This study demonstrates the potential of MASiVar to more globally investigate DWI variability across multiple levels and processing approaches simultaneously and suggests harmonization between scanners for multisite analyses should be considered before inference of group differences on subjects.
Sulfation of glycosaminoglycans depends on catalytic activity of a lithium-inhibited phosphatase
Eisele BS, Luka ZA, Wu AJ, Yang F, Hale AT, York JD
bioRxiv 2021.06.24.449779; doi: https://doi.org/10.1101/2021.06.24.449779
Golgi-resident bisphosphate nucleotidase 2 (BPNT2) is a member of a family of magnesium-dependent/lithium-inhibited phosphatases that share a three-dimensional structural motif that directly coordinates metal binding to effect phosphate hydrolysis. BPNT2 is responsible for the breakdown of 3’-phosphoadenosine-5’-phosphate (PAP), a by-product of glycosaminoglycan (GAG) sulfation. Disruption of BPNT2 in mice leads to skeletal abnormalities due to impaired GAG sulfation, especially chondroitin-4-sulfation. Mutations in BPNT2 have also been found to underlie a chondrodysplastic disorder in humans. The precise mechanism by which loss of BPNT2 impairs sulfation remains unclear. Here, we utilize an in vitro approach using mouse embryonic fibroblasts (MEFs) to test the hypothesis that catalytic activity of BPNT2 is required for GAG sulfation. We show that a catalytic-dead Bpnt2 construct (D108A) does not rescue impairments in intracellular or secreted sulfated GAG, including decreased chondroitin-4-sulfate, present in Bpnt2-knockout MEFs. We also demonstrate that missense mutations in Bpnt2 which are adjacent to the catalytic site (and known to cause chondrodysplasia in humans) recapitulate defects in overall GAG sulfation and chondroitin-4-sulfation in MEF cultures. We further show that treatment of MEFs with lithium inhibits GAG sulfation, and that this effect depends on the presence of BPNT2. This work demonstrates that the catalytic activity of an enzyme potently inhibited by lithium can modulate GAG sulfation and therefore extracellular matrix composition, revealing new insights into lithium pharmacology and the pathophysiology of psychiatric disorders responsive to lithium.
IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues
Radtke AJ*, Kandov E*, Lowekamp B, Speranza E, Chu CJ, Gola A, , , , , , , , , , .
Proc Natl Acad Sci. 2020 Dec 29;117(52):33455-33465. doi: 10.1073/pnas.2018488117. Epub 2020 Dec 21.
The diverse composition of mammalian tissues poses challenges for understanding the cell-cell interactions required for organ homeostasis and how spatial relationships are perturbed during disease. Existing methods such as single-cell genomics, lacking a spatial context, and traditional immunofluorescence, capturing only two to six molecular features, cannot resolve these issues. Imaging technologies have been developed to address these problems, but each possesses limitations that constrain widespread use. Here we report a method that overcomes major impediments to highly multiplex tissue imaging. “Iterative bleaching extends multiplexity” (IBEX) uses an iterative staining and chemical bleaching method to enable high-resolution imaging of >65 parameters in the same tissue section without physical degradation. IBEX can be employed with various types of conventional microscopes and permits use of both commercially available and user-generated antibodies in an “open” system to allow easy adjustment of staining panels based on ongoing marker discovery efforts. We show how IBEX can also be used with amplified staining methods for imaging strongly fixed tissues with limited epitope retention and with oligonucleotide-based staining, allowing potential cross-referencing between flow cytometry, cellular indexing of transcriptomes and epitopes by sequencing, and IBEX analysis of the same tissue. To facilitate data processing, we provide an open-source platform for automated registration of iterative images. IBEX thus represents a technology that can be rapidly integrated into most current laboratory workflows to achieve high-content imaging to reveal the complex cellular landscape of diverse organs and tissues.
Estimating the Post-Test Probability of Long QT Syndrome Diagnosis for Rare KCNH2Variants.
Kozek K, Wada Y, Sala L, Denjoy I, Egly C, O’Neill MJ, Aiba T, Shimizu W, Makita N, Ishikawa T, Crotti L, Spazzolini C, Kotta MC, Dagradi F, Castelletti S, Pedrazzini M, Gnecchi M, Leenhardt A, Salem JE, Ohno S, Zuo Y, Glazer AM, Mosley JD, Roden DM, Knollmann BC, Blume JD, Extramiana F, Schwartz PJ, Horie M, Kroncke BM.
Circ Genom Precis Med. 2021 Jul 26. doi: 10.1161/CIRCGEN.120.003289. Online ahead of print.
Background – The proliferation of genetic profiling has revealed many associations between genetic variations and disease. However, large-scale phenotyping efforts in largely healthy populations, coupled with DNA sequencing, suggest variants currently annotated as pathogenic are more common in healthy populations than previously thought. In addition, novel and rare variants are frequently observed in genes associated with disease both in healthy individuals and those under suspicion of disease. This raises the question of whether these variants can be useful predictors of disease. To answer this question, we assessed the degree to which the presence of a variant in the cardiac potassium channel gene KCNH2 was diagnostically predictive for the autosomal dominant long QT syndrome. Methods – We estimated the probability of a long QT diagnosis given the presence of each KCNH2 variant using Bayesian methods that incorporated variant features such as changes in variant function, protein structure, and in silico predictions. We call this estimate the post-test probability of disease. Our method was applied to over 4,000 individuals heterozygous for 871 missense or in-frame insertion/deletion variants in KCNH2 and validated against a separate international cohort of 933 individuals heterozygous for 266 missense or in-frame insertion/deletion variants. Results – Our method was well-calibrated for the observed fraction of heterozygotes diagnosed with Long QT. Heuristically, we found that the innate diagnostic information one learns about a variant from three-dimensional variant location, in vitro functional data, and in silico predictors is equivalent to the diagnostic information one learns about that same variant by clinically phenotyping 10 heterozygotes. Most importantly, these data can be obtained in the absence of any clinical observations. Conclusions – We show how variant-specific features can inform a prior probability of disease for rare variants even in the absence of clinically-phenotyped heterozygotes.
Quantifying the contribution of Neanderthal introgression to the heritability of complex traits.
McArthur E, Rinker DC, Capra JA.
Nat Commun. 2021 Jul 22;12(1):4481. doi: 10.1038/s41467-021-24582-y.
Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects.
A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia
Reisman BJ, Guo H, Ramsey HE, Wright MT, Reinfeld BI, Ferrell PB, Sulikowski GA, Rathmell WK, Savona MR, Plate L, Rubinstein JL, Bachmann BO
bioRxiv 2021.05.31.445492; doi: https://doi.org/10.1101/2021.05.31.445492
Cancer cells have long been recognized to exhibit unique bioenergetic requirements. The apoptolidin family of glycomacrolides are distinguished by their selective cytotoxicity towards oncogene transformed cells, yet their molecular mechanism remains uncertain. We used photoaffinity analogs of the apoptolidins to identify the F1 subcomplex of mitochondrial ATP synthase as the target of apoptolidin A. CryoEM of apoptolidin and ammocidin-ATP synthase complexes revealed a novel shared mode of inhibition that was confirmed by deep mutational scanning of the binding interface to reveal resistance mutations which were confirmed using CRISPR-Cas9. Ammocidin A was found to suppress leukemia progression in vivo at doses that were tolerated with minimal toxicity. The combination of cellular, structural, mutagenesis, and in vivo evidence define the mechanism of action of apoptolidin family glycomacrolides and establish a path to address OXPHOS-dependent cancers.
Pre-exposure prophylaxis use among HIV serodiscordant couples: a qualitative study in Mozambique.
Sack DE, De Schacht C, Paulo P, Graves E, Emílio AM, Matino A, Fonseca CL, Aboobacar AU, Van Rompaey S, Audet CM.
Glob Health Action. 2021 Jan 1;14(1):1940764. doi: 10.1080/16549716.2021.1940764.
Background: Pre-exposure prophylaxis (PrEP) has the potential to reduce HIV transmission and stem the HIV epidemic. Unfortunately, PrEP uptake in rural sub-Saharan Africa has been slow and medication adherence has been suboptimal.
Objective: To explore the perspectives, attitudes, and experiences of HIV serodiscordant partners taking PrEP and develop a messaging campaign to improve PrEP uptake in rural Mozambique to reduce HIV transmission among serodiscordant partners.
Methods: In this qualitative study, we interviewed 20 people in serodiscordant relationships using PrEP at a rural health center in Zambézia province, Mozambique and employed inductive and deductive coding to elicit their perspectives, attitudes, and experiences related to learning their partner’s HIV status, barriers to PrEP uptake, obstacles to PrEP adherence, and decisions to disclose their PrEP use with family and friends using thematic analysis.
Results: Our analysis generated nine themes across various levels of the socioecological model. Participants reported a strong desire to stay in the discordant relationship and highlighted the importance of working together to ensure PrEP and antiretroviral therapy adherence, with the majority skeptical that adherence could be achieved without both partners’ support (individual and interpersonal). Although most participants were reticent about sharing their serodiscordant status with family and friends (individual and interpersonal), those who did found their family and friends supportive (interpersonal). Participants suggested increasing community health agent availability to help people navigate HIV prevention and treatment (organizational). We then created three oral stories, using themes from the interviews, with examples from various levels of the socioecological model that will be used to generate support for PrEP use among community members.
Conclusions: Our findings informed oral template stories that will be used to emphasize how couples can work together to improve PrEP uptake and reduce incident HIV infections in serodiscordant couples elsewhere in rural Mozambique.
Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, oncogenesis, and HER2 inhibitor sensitivity.
Hanker AB, Brown BP, Meiler J, Marín A, Jayanthan HS, Ye D, Lin CC, Akamatsu H, Lee KM, Chatterjee S, Sudhan DR, Servetto A, Brewer MR, Koch JP, Sheehan JH, He J, Lalani AS, Arteaga CL.
Cancer Cell. 2021 Jun 22:S1535-6108(21)00284-1. doi: 10.1016/j.ccell.2021.06.001. Online ahead of print.
Shape-Defined microPlates for the Sustained Intra-articular Release of Dexamethasone in the Management of Overload-Induced Osteoarthritis.
Di Francesco M, Bedingfield SK, Di Francesco V, Colazo JM, Yu F, Ceseracciu L, Bellotti E, Di Mascolo D, Ferreira M, Himmel LE, Duvall C, Decuzzi P.
ACS Appl Mater Interfaces. 2021 Jul 1. doi: 10.1021/acsami.1c02082. Online ahead of print.
MRI network progression in mesial temporal lobe epilepsy related to healthy brain architecture.
Morgan VL, Johnson GW, Cai LY, Landman BA, Schilling KG, Englot DJ, Rogers BP, Chang C.
Netw Neurosci. 2021 Apr 27;5(2):434-450. doi: 10.1162/netn_a_00184. eCollection 2021.
HDAC inhibitors induce LIFR expression and promote a dormancy phenotype in breast cancer.
Clements ME, Holtslander L, Edwards C, Todd V, Dooyema SDR, Bullock K, Bergdorf K, Zahnow CA, Connolly RM, Johnson RW.
Oncogene. 2021 Jul 10. doi: 10.1038/s41388-021-01931-1. Online ahead of print.
Immunotherapy-mediated thyroid dysfunction: genetic risk and impact on outcomes with PD-1 blockade in non-small cell lung cancer.
Luo J, Martucci VL, Quandt Z, Groha S, Murray MH, Lovly CM, Rizvi H, Egger JV, Plodkowski AJ, Abu-Akeel M, Schulze I, Merghoub T, Cardenas E, Huntsman S, Li M, Hu D, Gubens MA, Gusev A, Aldrich MC, Hellmann MD, Ziv E.
Clin Cancer Res. 2021 Jul 8:clincanres.0921.2021. doi: 10.1158/1078-0432.CCR-21-0921. Online ahead of print.
Diagnostic- and sex-based differences in depression symptoms in autistic and neurotypical early adolescents.
Schwartzman JM, Williams ZJ, Corbett BA.
Autism. 2021 Jun 26:13623613211025895. doi: 10.1177/13623613211025895. Online ahead of print.
Astrocyte Networks as Therapeutic Targets in Glaucomatous Neurodegeneration.
Boal AM, Risner ML, Cooper ML, Wareham LK, Calkins DJ.
Cells. 2021 Jun 2;10(6):1368. doi: 10.3390/cells10061368.
PMID: 34199470 Review.
Measurement of Osteoblast Cytotoxicity Induced by S. aureus Secreted Toxins.
Ford CA, Cassat JE.
Methods Mol Biol. 2021;2341:141-152. doi: 10.1007/978-1-0716-1550-8_17.
The therapeutic implications of immunosuppressive tumor aerobic glycolysis.
Reinfeld BI, Rathmell WK, Kim TK, Rathmell JC.
Cell Mol Immunol. 2021 Jul 8. doi: 10.1038/s41423-021-00727-3. Online ahead of print.
PMID: 34239083 Review.
Genetic contributions to suicidal thoughts and behaviors
DiBlasi E, Kang J, Docherty AR.
Psychol Med. 2021 May 25:1-8. doi: 10.1017/S0033291721001720. Epub ahead of print. PMID: 34030748.