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  1. Dissertation / Habilitation ; Online: Multiscale Approaches to Complex Human Diseases

    Beckmann, Noam D.

    2018  

    Abstract: Elucidating the fundamental biological mechanisms underlying complex diseases remains, to date, a challenging task. Genetic approaches have been used to implicate genes and pathways in disease, but classical (reverse) and population (forward) genetic ... ...

    Abstract Elucidating the fundamental biological mechanisms underlying complex diseases remains, to date, a challenging task. Genetic approaches have been used to implicate genes and pathways in disease, but classical (reverse) and population (forward) genetic approaches have fallen short of bringing new understanding to multi-factorial disorders. With the emergence of rapidly advancing, new technologies and the dramatic reduction of their costs, new algorithms and analytical models that maximally leverage the data these technologies generate, are being developed to uncover novel biological insights for complex traits. Furthermore, the integration of multiple strata of biological information permits the creation of better representations of disease. This thesis aims to leverage some of these models on novel multi-scale datasets to explore the mechanisms of Alzheimer’s disease and the variability of induced pluripotent stem cells.
    Schlagwörter Genetics|Systematic biology|Bioinformatics
    Sprache ENG
    Erscheinungsdatum 2018-01-01 00:00:01.0
    Verlag Icahn School of Medicine at Mount Sinai
    Erscheinungsland us
    Dokumenttyp Dissertation / Habilitation ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel: Characterizing cell type specific transcriptional differences between the living and postmortem human brain.

    Vornholt, Eric / Liharska, Lora E / Cheng, Esther / Hashemi, Alice / Park, You Jeong / Ziafat, Kimia / Wilkins, Lillian / Silk, Hannah / Linares, Lisa M / Thompson, Ryan C / Sullivan, Brendan / Moya, Emily / Nadkarni, Girish N / Sebra, Robert / Schadt, Eric E / Kopell, Brian H / Charney, Alexander W / Beckmann, Noam D

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: Single-nucleus RNA sequencing (snRNA-seq) is often used to define gene expression patterns characteristic of brain cell types as well as to identify cell type specific gene expression signatures of neurological and mental illnesses in postmortem human ... ...

    Abstract Single-nucleus RNA sequencing (snRNA-seq) is often used to define gene expression patterns characteristic of brain cell types as well as to identify cell type specific gene expression signatures of neurological and mental illnesses in postmortem human brains. As methods to obtain brain tissue from living individuals emerge, it is essential to characterize gene expression differences associated with tissue originating from either living or postmortem subjects using snRNA-seq, and to assess whether and how such differences may impact snRNA-seq studies of brain tissue. To address this, human prefrontal cortex single nuclei gene expression was generated and compared between 31 samples from living individuals and 21 postmortem samples. The same cell types were consistently identified in living and postmortem nuclei, though for each cell type, a large proportion of genes were differentially expressed between samples from postmortem and living individuals. Notably, estimation of cell type proportions by cell type deconvolution of pseudo-bulk data was found to be more accurate in samples from living individuals. To allow for future integration of living and postmortem brain gene expression, a model was developed that quantifies from gene expression data the probability a human brain tissue sample was obtained postmortem. These probabilities are established as a means to statistically account for the gene expression differences between samples from living and postmortem individuals. Together, the results presented here provide a deep characterization of both differences between snRNA-seq derived from samples from living and postmortem individuals, as well as qualify and account for their effect on common analyses performed on this type of data.
    Sprache Englisch
    Erscheinungsdatum 2024-05-01
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.05.01.24306590
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: Dual-specificity protein phosphatase 6 (DUSP6) overexpression reduces amyloid load and improves memory deficits in male 5xFAD mice.

    Pan, Allen L / Audrain, Mickael / Sakakibara, Emmy / Joshi, Rajeev / Zhu, Xiaodong / Wang, Qian / Wang, Minghui / Beckmann, Noam D / Schadt, Eric E / Gandy, Sam / Zhang, Bin / Ehrlich, Michelle E / Salton, Stephen R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Background: Dual specificity protein phosphatase 6 (DUSP6) was recently identified as a key hub gene in a causal network that regulates late-onset Alzheimer's disease. Importantly, decreased DUSP6 levels are correlated with an increased clinical ... ...

    Abstract Background: Dual specificity protein phosphatase 6 (DUSP6) was recently identified as a key hub gene in a causal network that regulates late-onset Alzheimer's disease. Importantly, decreased DUSP6 levels are correlated with an increased clinical dementia rating in human subjects, and DUSP6 levels are additionally decreased in the 5xFAD amyloidopathy mouse model.
    Methods: AAV5-DUSP6 or AAV5-GFP (control) were stereotactically injected into the dorsal hippocampus (dHc) of female and male 5xFAD or wild type mice to overexpress DUSP6 or GFP. Spatial learning memory of these mice was assessed in the Barnes maze, after which hippocampal tissues were isolated for downstream analysis.
    Results: Barnes maze testing indicated that DUSP6 overexpression in the dHc of 5xFAD mice improved memory deficits and was associated with reduced amyloid plaque load, Aß
    Conclusions: In summary, our data indicate that DUSP6 overexpression in dHc reduced amyloid deposition and memory deficits in male but not female 5xFAD mice, whereas reduced neuroinflammation and microglial activation were observed in both males and females. The sex-dependent regulation of synaptic pathways by DUSP6 overexpression, however, correlated with the improvement of spatial memory deficits in male but not female 5xFAD.
    Sprache Englisch
    Erscheinungsdatum 2023-08-25
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.08.24.554335
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Dual-Specificity Protein Phosphatase 4 (DUSP4) Overexpression Improves Learning Behavior Selectively in Female 5xFAD Mice, and Reduces β-Amyloid Load in Males and Females.

    Pan, Allen L / Audrain, Mickael / Sakakibara, Emmy / Joshi, Rajeev / Zhu, Xiaodong / Wang, Qian / Wang, Minghui / Beckmann, Noam D / Schadt, Eric E / Gandy, Sam / Zhang, Bin / Ehrlich, Michelle E / Salton, Stephen R

    Cells

    2022  Band 11, Heft 23

    Abstract: Recent multiscale network analyses of banked brains from subjects who died of late-onset sporadic Alzheimer's disease converged ... ...

    Abstract Recent multiscale network analyses of banked brains from subjects who died of late-onset sporadic Alzheimer's disease converged on
    Mesh-Begriff(e) Animals ; Female ; Male ; Mice ; Alzheimer Disease/genetics ; Alzheimer Disease/pathology ; Amyloid beta-Peptides/metabolism ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Hippocampus/metabolism ; Protein Tyrosine Phosphatases/genetics ; Learning
    Chemische Substanzen Amyloid beta-Peptides ; Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24) ; MKP2 protein, mouse (EC 3.1.3.48) ; Protein Tyrosine Phosphatases (EC 3.1.3.48)
    Sprache Englisch
    Erscheinungsdatum 2022-12-01
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11233880
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Persistent complement dysregulation with signs of thromboinflammation in active Long Covid.

    Cervia-Hasler, Carlo / Brüningk, Sarah C / Hoch, Tobias / Fan, Bowen / Muzio, Giulia / Thompson, Ryan C / Ceglarek, Laura / Meledin, Roman / Westermann, Patrick / Emmenegger, Marc / Taeschler, Patrick / Zurbuchen, Yves / Pons, Michele / Menges, Dominik / Ballouz, Tala / Cervia-Hasler, Sara / Adamo, Sarah / Merad, Miriam / Charney, Alexander W /
    Puhan, Milo / Brodin, Petter / Nilsson, Jakob / Aguzzi, Adriano / Raeber, Miro E / Messner, Christoph B / Beckmann, Noam D / Borgwardt, Karsten / Boyman, Onur

    Science (New York, N.Y.)

    2024  Band 383, Heft 6680, Seite(n) eadg7942

    Abstract: Long Covid is a debilitating condition of unknown etiology. We performed multimodal proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after confirmed severe acute respiratory syndrome coronavirus 2 infection. Analysis of > ...

    Abstract Long Covid is a debilitating condition of unknown etiology. We performed multimodal proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after confirmed severe acute respiratory syndrome coronavirus 2 infection. Analysis of >6500 proteins in 268 longitudinal samples revealed dysregulated activation of the complement system, an innate immune protection and homeostasis mechanism, in individuals experiencing Long Covid. Thus, active Long Covid was characterized by terminal complement system dysregulation and ongoing activation of the alternative and classical complement pathways, the latter associated with increased antibody titers against several herpesviruses possibly stimulating this pathway. Moreover, markers of hemolysis, tissue injury, platelet activation, and monocyte-platelet aggregates were increased in Long Covid. Machine learning confirmed complement and thromboinflammatory proteins as top biomarkers, warranting diagnostic and therapeutic interrogation of these systems.
    Mesh-Begriff(e) Humans ; Complement Activation ; Complement System Proteins/analysis ; Complement System Proteins/metabolism ; Post-Acute COVID-19 Syndrome/blood ; Post-Acute COVID-19 Syndrome/complications ; Post-Acute COVID-19 Syndrome/immunology ; Thromboinflammation/blood ; Thromboinflammation/immunology ; Biomarkers/blood ; Proteome ; Proteomics ; Male ; Female ; Young Adult ; Adult ; Middle Aged ; Aged
    Chemische Substanzen Complement System Proteins (9007-36-7) ; Biomarkers ; Proteome
    Sprache Englisch
    Erscheinungsdatum 2024-01-19
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.adg7942
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Dual-Specificity Protein Phosphatase 4 (DUSP4) Overexpression Improves Learning Behavior Selectively in Female 5xFAD Mice, and Reduces β-Amyloid Load in Males and Females

    Allen L. Pan / Mickael Audrain / Emmy Sakakibara / Rajeev Joshi / Xiaodong Zhu / Qian Wang / Minghui Wang / Noam D. Beckmann / Eric E. Schadt / Sam Gandy / Bin Zhang / Michelle E. Ehrlich / Stephen R. Salton

    Cells, Vol 11, Iss 3880, p

    2022  Band 3880

    Abstract: Recent multiscale network analyses of banked brains from subjects who died of late-onset sporadic Alzheimer’s disease converged on VGF (non-acronymic) as a key hub or driver. Within this computational VGF network, we identified the dual-specificity ... ...

    Abstract Recent multiscale network analyses of banked brains from subjects who died of late-onset sporadic Alzheimer’s disease converged on VGF (non-acronymic) as a key hub or driver. Within this computational VGF network, we identified the dual-specificity protein phosphatase 4 ( DUSP4 ) [also known as mitogen-activated protein kinase (MAPK) phosphatase 2] as an important node. Importantly, DUSP4 gene expression, like that of VGF , is downregulated in postmortem Alzheimer’s disease (AD) brains. We investigated the roles that this VGF / DUSP4 network plays in the development of learning behavior impairment and neuropathology in the 5xFAD amyloidopathy mouse model. We found reductions in DUSP4 expression in the hippocampi of male AD subjects, correlating with increased CDR scores, and in 4-month-old female and 12–18-month-old male 5xFAD hippocampi. Adeno-associated virus (AAV5)-mediated overexpression of DUSP4 in 5xFAD mouse dorsal hippocampi (dHc) rescued impaired Barnes maze performance in females but not in males, while amyloid loads were reduced in both females and males. Bulk RNA sequencing of the dHc from 5-month-old mice overexpressing DUSP4, and Ingenuity Pathway and Enrichr analyses of differentially expressed genes (DEGs), revealed that DUSP4 reduced gene expression in female 5xFAD mice in neuroinflammatory, interferon-gamma (IFNγ), programmed cell death protein-ligand 1/programmed cell death protein 1 (PD-L1/PD-1), and extracellular signal-regulated kinase (ERK)/MAPK pathways, via which DUSP4 may modulate AD phenotype with gender-specificity.
    Schlagwörter Alzheimer’s disease ; dual-specificity protein phosphatase 4 ; disease-associated microglia ; mitogen-activated protein kinase ; neuroinflammation ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2022-12-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.

    Carcamo-Orive, Ivan / Hoffman, Gabriel E / Cundiff, Paige / Beckmann, Noam D / D'Souza, Sunita L / Knowles, Joshua W / Patel, Achchhe / Hendry, Caroline / Papatsenko, Dimitri / Abbasi, Fahim / Reaven, Gerald M / Whalen, Sean / Lee, Philip / Shahbazi, Mohammad / Henrion, Marc Y R / Zhu, Kuixi / Wang, Sven / Roussos, Panos / Schadt, Eric E /
    Pandey, Gaurav / Chang, Rui / Quertermous, Thomas / Lemischka, Ihor

    Cell stem cell

    2022  Band 29, Heft 10, Seite(n) 1505

    Sprache Englisch
    Erscheinungsdatum 2022-09-20
    Erscheinungsland United States
    Dokumenttyp Published Erratum
    ZDB-ID 2375354-7
    ISSN 1875-9777 ; 1934-5909
    ISSN (online) 1875-9777
    ISSN 1934-5909
    DOI 10.1016/j.stem.2022.08.011
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C).

    Gruber, Conor N / Patel, Roosheel S / Trachtman, Rebecca / Lepow, Lauren / Amanat, Fatima / Krammer, Florian / Wilson, Karen M / Onel, Kenan / Geanon, Daniel / Tuballes, Kevin / Patel, Manishkumar / Mouskas, Konstantinos / O'Donnell, Timothy / Merritt, Elliot / Simons, Nicole W / Barcessat, Vanessa / Del Valle, Diane M / Udondem, Samantha / Kang, Gurpawan /
    Agashe, Charuta / Karekar, Neha / Grabowska, Joanna / Nie, Kai / Le Berichel, Jessica / Xie, Hui / Beckmann, Noam / Gangadharan, Sandeep / Ofori-Amanfo, George / Laserson, Uri / Rahman, Adeeb / Kim-Schulze, Seunghee / Charney, Alexander W / Gnjatic, Sacha / Gelb, Bruce D / Merad, Miriam / Bogunovic, Dusan

    Cell

    2023  Band 186, Heft 15, Seite(n) 3325

    Sprache Englisch
    Erscheinungsdatum 2023-07-19
    Erscheinungsland United States
    Dokumenttyp Published Erratum
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2023.06.012
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires.

    Ford, Easton E / Tieri, David / Rodriguez, Oscar L / Francoeur, Nancy J / Soto, Juan / Kos, Justin T / Peres, Ayelet / Gibson, William S / Silver, Catherine A / Deikus, Gintaras / Hudson, Elizabeth / Woolley, Cassandra R / Beckmann, Noam / Charney, Alexander / Mitchell, Thomas C / Yaari, Gur / Sebra, Robert P / Watson, Corey T / Smith, Melissa L

    Journal of immunology (Baltimore, Md. : 1950)

    2023  Band 210, Heft 10, Seite(n) 1607–1619

    Abstract: ... transcripts. FLAIRR-seq was benchmarked by comparing H chain V (IGHV), D (IGHD), and J (IGHJ) gene usage ...

    Abstract Current Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using short-read sequencing strategies resolve expressed Ab transcripts with limited resolution of the C region. In this article, we present the near-full-length AIRR-seq (FLAIRR-seq) method that uses targeted amplification by 5' RACE, combined with single-molecule, real-time sequencing to generate highly accurate (99.99%) human Ab H chain transcripts. FLAIRR-seq was benchmarked by comparing H chain V (IGHV), D (IGHD), and J (IGHJ) gene usage, complementarity-determining region 3 length, and somatic hypermutation to matched datasets generated with standard 5' RACE AIRR-seq using short-read sequencing and full-length isoform sequencing. Together, these data demonstrate robust FLAIRR-seq performance using RNA samples derived from PBMCs, purified B cells, and whole blood, which recapitulated results generated by commonly used methods, while additionally resolving H chain gene features not documented in IMGT at the time of submission. FLAIRR-seq data provide, for the first time, to our knowledge, simultaneous single-molecule characterization of IGHV, IGHD, IGHJ, and IGHC region genes and alleles, allele-resolved subisotype definition, and high-resolution identification of class switch recombination within a clonal lineage. In conjunction with genomic sequencing and genotyping of IGHC genes, FLAIRR-seq of the IgM and IgG repertoires from 10 individuals resulted in the identification of 32 unique IGHC alleles, 28 (87%) of which were previously uncharacterized. Together, these data demonstrate the capabilities of FLAIRR-seq to characterize IGHV, IGHD, IGHJ, and IGHC gene diversity for the most comprehensive view of bulk-expressed Ab repertoires to date.
    Mesh-Begriff(e) Humans ; Complementarity Determining Regions/genetics ; Base Sequence
    Chemische Substanzen Complementarity Determining Regions
    Sprache Englisch
    Erscheinungsdatum 2023-04-08
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3056-9
    ISSN 1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
    ISSN (online) 1550-6606
    ISSN 0022-1767 ; 1048-3233 ; 1047-7381
    DOI 10.4049/jimmunol.2200825
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel: A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses.

    Comella, Phillip H / Gonzalez-Kozlova, Edgar / Kosoy, Roman / Charney, Alexander W / Peradejordi, Irene Font / Chandrasekar, Shreya / Tyler, Scott R / Wang, Wenhui / Losic, Bojan / Zhu, Jun / Hoffman, Gabriel E / Kim-Schulze, Seunghee / Qi, Jingjing / Patel, Manishkumar / Kasarskis, Andrew / Suarez-Farinas, Mayte / Gümüş, Zeynep H / Argmann, Carmen / Merad, Miriam /
    Becker, Christian / Beckmann, Noam D / Schadt, Eric E

    medRxiv : the preprint server for health sciences

    2021  

    Sprache Englisch
    Erscheinungsdatum 2021-02-02
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2021.01.29.21250755
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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