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Rahimikollu J, Xiao H, Rosengart A, Rosen ABI, Tabib T, Zdinak PM, He K, Bing X, Bunea F, Wegkamp M, Poholek AC, Joglekar AV, Lafyatis RA, Das J. SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains. Nat Methods 2024; 21:835-845. [PMID: 38374265 DOI: 10.1038/s41592-024-02175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2024] [Indexed: 02/21/2024]
Abstract
Modern multiomic technologies can generate deep multiscale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make analyses and integration of high-dimensional omic datasets challenging. Here we present Significant Latent Factor Interaction Discovery and Exploration (SLIDE), a first-in-class interpretable machine learning technique for identifying significant interacting latent factors underlying outcomes of interest from high-dimensional omic datasets. SLIDE makes no assumptions regarding data-generating mechanisms, comes with theoretical guarantees regarding identifiability of the latent factors/corresponding inference, and has rigorous false discovery rate control. Using SLIDE on single-cell and spatial omic datasets, we uncovered significant interacting latent factors underlying a range of molecular, cellular and organismal phenotypes. SLIDE outperforms/performs at least as well as a wide range of state-of-the-art approaches, including other latent factor approaches. More importantly, it provides biological inference beyond prediction that other methods do not afford. Thus, SLIDE is a versatile engine for biological discovery from modern multiomic datasets.
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Affiliation(s)
- Javad Rahimikollu
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - AnnaElaine Rosengart
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron B I Rosen
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul M Zdinak
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kun He
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xin Bing
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Florentina Bunea
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Marten Wegkamp
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
- Department of Mathematics, Cornell University, Ithaca, NY, USA
| | - Amanda C Poholek
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Alok V Joglekar
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Robert A Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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Chau AS, Cole BL, Debley JS, Nanda K, Rosen ABI, Bamshad MJ, Nickerson DA, Torgerson TR, Allenspach EJ. Correction to: Heme oxygenase-1 deficiency presenting with interstitial lung disease and hemophagocytic flares. Pediatr Rheumatol Online J 2022; 20:19. [PMID: 35287710 PMCID: PMC8922765 DOI: 10.1186/s12969-021-00661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Alice S. Chau
- grid.34477.330000000122986657Division of Allergy & Infectious Disease, Department of Medicine, University of Washington, Seattle, Washington USA ,grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA
| | - Bonnie L. Cole
- grid.34477.330000000122986657Department of Pathology and Laboratory Medicine, University of Washington, Seattle, Washington USA ,grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA
| | - Jason S. Debley
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
| | - Kabita Nanda
- grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
| | - Aaron B. I. Rosen
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA
| | - Michael J. Bamshad
- grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA ,grid.34477.330000000122986657Genome Sciences, University of Washington, Seattle, Washington USA
| | - Deborah A. Nickerson
- grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Genome Sciences, University of Washington, Seattle, Washington USA
| | - Troy R. Torgerson
- grid.507729.eExperimental Immunology, Allen Institute, Seattle, Washington USA
| | - Eric J. Allenspach
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA ,grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
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Allenspach EJ, Soveg F, Finn LS, So L, Gorman JA, Rosen ABI, Skoda-Smith S, Wheeler MM, Barrow KA, Rich LM, Debley JS, Bamshad MJ, Nickerson DA, Savan R, Torgerson TR, Rawlings DJ. Germline SAMD9L truncation variants trigger global translational repression. J Exp Med 2021; 218:211891. [PMID: 33724365 PMCID: PMC7970252 DOI: 10.1084/jem.20201195] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 02/12/2021] [Indexed: 12/11/2022] Open
Abstract
SAMD9L is an interferon-induced tumor suppressor implicated in a spectrum of multisystem disorders, including risk for myeloid malignancies and immune deficiency. We identified a heterozygous de novo frameshift variant in SAMD9L in an infant with B cell aplasia and clinical autoinflammatory features who died from respiratory failure with chronic rhinovirus infection. Autopsy demonstrated absent bone marrow and peripheral B cells as well as selective loss of Langerhans and Purkinje cells. The frameshift variant led to expression of a truncated protein with interferon treatment. This protein exhibited a gain-of-function phenotype, resulting in interference in global protein synthesis via inhibition of translational elongation. Using a mutational scan, we identified a region within SAMD9L where stop-gain variants trigger a similar translational arrest. SAMD9L variants that globally suppress translation had no effect or increased mRNA transcription. The complex-reported phenotype likely reflects lineage-dominant sensitivities to this translation block. Taken together, our findings indicate that interferon-triggered SAMD9L gain-of-function variants globally suppress translation.
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Affiliation(s)
- Eric J Allenspach
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Frank Soveg
- Department of Immunology, University of Washington, Seattle, WA
| | - Laura S Finn
- Department of Pathology and Laboratory Medicine, University of Washington, Seattle, WA
| | - Lomon So
- Department of Immunology, University of Washington, Seattle, WA.,Division of Immunology, Benaroya Research Institute, Seattle, WA
| | - Jacquelyn A Gorman
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | - Aaron B I Rosen
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | | | | | - Kaitlyn A Barrow
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA.,Genome Sciences, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Deborah A Nickerson
- Genome Sciences, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA
| | | | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington, Seattle, WA.,Department of Immunology, University of Washington, Seattle, WA
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Chau AS, Cole BL, Debley JS, Nanda K, Rosen ABI, Bamshad MJ, Nickerson DA, Torgerson TR, Allenspach EJ. Heme oxygenase-1 deficiency presenting with interstitial lung disease and hemophagocytic flares. Pediatr Rheumatol Online J 2020; 18:80. [PMID: 33066778 PMCID: PMC7565350 DOI: 10.1186/s12969-020-00474-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/06/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Heme oxygenase-1 (HMOX1) catalyzes the metabolism of heme into carbon monoxide, ferrous iron, and biliverdin. Through biliverdin reductase, biliverdin becomes bilirubin. HMOX1-deficiency is a rare autosomal recessive disorder with hallmark features of direct antibody negative hemolytic anemia with normal bilirubin, hyperinflammation and features similar to macrophage activation syndrome. Clinical findings have included asplenia, nephritis, hepatitis, and vasculitis. Pulmonary features and evaluation of the immune response have been limited. CASE PRESENTATION We present a young boy who presented with chronic respiratory failure due to nonspecific interstitial pneumonia following a chronic history of infection-triggered recurrent hyperinflammatory flares. Episodes included hemolysis without hyperbilirubinemia, immunodeficiency, hepatomegaly with mild transaminitis, asplenia, leukocytosis, thrombocytosis, joint pain and features of macrophage activation with negative autoimmune serologies. Lung biopsy revealed cholesterol granulomas. He was found post-mortem by whole exome sequencing to have a compound heterozygous paternal frame shift a paternal frame shift HMOX1 c.264_269delCTGG (p.L89Sfs*24) and maternal splice donor HMOX1 (c.636 + 2 T > A) consistent with HMOX1 deficiency. Western blot analysis confirmed lack of HMOX1 protein upon oxidant stimulation of the patient cells. CONCLUSIONS Here, we describe a phenotype expansion for HMOX1-deficiency to include not only asplenia and hepatomegaly, but also interstitial lung disease with cholesterol granulomas and inflammatory flares with hemophagocytosis present in the bone marrow.
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Affiliation(s)
- Alice S. Chau
- grid.34477.330000000122986657Division of Allergy & Infectious Disease, Department of Medicine, University of Washington, Seattle, Washington USA ,grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA
| | - Bonnie L. Cole
- grid.34477.330000000122986657Department of Pathology and Laboratory Medicine, University of Washington, Seattle, Washington USA ,grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA
| | - Jason S. Debley
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
| | - Kabita Nanda
- grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
| | - Aaron B. I. Rosen
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA
| | - Michael J. Bamshad
- grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA ,grid.34477.330000000122986657Genome Sciences, University of Washington, Seattle, Washington USA
| | - Deborah A. Nickerson
- grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Genome Sciences, University of Washington, Seattle, Washington USA
| | - Troy R. Torgerson
- grid.507729.eExperimental Immunology, Allen Institute, Seattle, Washington USA
| | - Eric J. Allenspach
- grid.240741.40000 0000 9026 4165Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Jack MacDonald Building – 6th floor, 1900 9th Avenue, Seattle, Washington 98101 USA ,grid.507913.9Brotman Baty Institute for Precision Medicine, Seattle, Washington USA ,grid.34477.330000000122986657Department of Pediatrics, University of Washington, Seattle, Washington USA
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