Spatial Patterning Analysis of Cellular Ensembles (SPACE) discovers complex spatial organization at the cell and tissue levels.

Autor: Schrom EC; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., McCaffrey EF; Spatial Immunology Unit, T-Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., Sreejithkumar V; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., Radtke AJ; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA.; Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., Ichise H; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., Arroyo-Mejias A; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., Speranza E; Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL 34987, USA., Arakkal L; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., Thakur N; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA.; Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA., Grant S; Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892-1892, USA., Germain RN; Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA.; Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 May 30. Date of Electronic Publication: 2024 May 30.

Loss-of-function mutations in Dnmt3a and Tet2 lead to accelerated atherosclerosis and concordant macrophage phenotypes.

Autor: Rauch PJ; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. philipp_rauch@dfci.harvard.edu.; Broad Institute of Harvard and MIT, Cambridge, MA, USA. philipp_rauch@dfci.harvard.edu., Gopakumar J; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Silver AJ; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Nachun D; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Ahmad H; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., McConkey M; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Broad Institute of Harvard and MIT, Cambridge, MA, USA., Nakao T; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Bosse M; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Rentz T; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Vivanco Gonzalez N; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Greenwald NF; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., McCaffrey EF; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Khair Z; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Gopakumar M; Department of Electrical Engineering, Stanford University, Stanford, CA, USA., Rodrigues KB; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Lin AE; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Sinha E; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Fefer M; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Cohen DN; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Vromman A; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Shvartz E; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Sukhova G; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Bendall S; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Angelo M; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Libby P; Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA., Ebert BL; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Broad Institute of Harvard and MIT, Cambridge, MA, USA.; Howard Hughes Medical Institute, Boston, MA, USA., Jaiswal S; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. sjaiswal@stanford.edu.; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA. sjaiswal@stanford.edu.

Publikováno v: Nature cardiovascular research [Nat Cardiovasc Res] 2023 Sep; Vol. 2 (9), pp. 805-818. Date of Electronic Publication: 2023 Sep 04.

Spatial epitope barcoding reveals clonal tumor patch behaviors.

Autor: Rovira-Clavé X; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA., Drainas AP; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Jiang S; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Bai Y; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Baron M; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Zhu B; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA., Dallas AE; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Lee MC; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Chu TP; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Holzem A; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Ayyagari R; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Bhattacharya D; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., McCaffrey EF; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Greenwald NF; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Markovic M; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Coles GL; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Angelo M; Department of Pathology, Stanford University, Stanford, CA 94305, USA., Bassik MC; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Sage J; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address: julsage@stanford.edu., Nolan GP; Department of Pathology, Stanford University, Stanford, CA 94305, USA. Electronic address: gnolan@stanford.edu.

Publikováno v: Cancer cell [Cancer Cell] 2022 Nov 14; Vol. 40 (11), pp. 1423-1439.e11. Date of Electronic Publication: 2022 Oct 13.

Author Correction: The immunoregulatory landscape of human tuberculosis granulomas.

Autor: McCaffrey EF; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Donato M; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA.; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA., Keren L; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel., Chen Z; Calico Life Sciences LLC, South San Francisco, CA, USA., Delmastro A; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Fitzpatrick MB; Department of Pathology, University of Wisconsin, Madison, WI, USA., Gupta S; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA.; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA., Greenwald NF; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Baranski A; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Graf W; Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA., Kumar R; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Bosse M; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Fullaway CC; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Ramdial PK; Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa., Forgó E; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Jojic V; Calico Life Sciences LLC, South San Francisco, CA, USA., Van Valen D; Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA., Mehra S; Texas Biomedical Research Institute, San Antonio, TX, USA., Khader SA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA., Bendall SC; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., van de Rijn M; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA., Kalman D; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA., Kaushal D; Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA., Hunter RL; Department of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA., Banaei N; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.; Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA., Steyn AJC; Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA., Khatri P; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA.; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA., Angelo M; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. mangelo0@stanford.edu.

Publikováno v: Nature immunology [Nat Immunol] 2022 May; Vol. 23 (5), pp. 814.

Multiplexed Ion Beam Imaging: Insights into Pathobiology.

Autor: Liu CC; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., McCaffrey EF; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Greenwald NF; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Soon E; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Risom T; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu.; Current affiliation: Genentech, South San Francisco, California 94080; USA., Vijayaragavan K; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Oliveria JP; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu.; Current affiliation: Genentech, South San Francisco, California 94080; USA., Mrdjen D; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Bosse M; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Tebaykin D; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Bendall SC; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu., Angelo M; Department of Pathology, Stanford University, Stanford, California 94304 USA; email: cliu72@stanford.edu, erinmcc@stanford.edu, nfgreen@stanford.edu, erinsoon@stanford.edu, trisom@stanford.edu, kausalia@stanford.edu, oliveria@stanford.edu, mrdjend@stanford.edu, mbosse@stanford.edu, dmitry.tebaykin@stanford.edu, bendall@stanford.edu, mangelo0@stanford.edu.

Publikováno v: Annual review of pathology [Annu Rev Pathol] 2022 Jan 24; Vol. 17, pp. 403-423. Date of Electronic Publication: 2021 Nov 09.