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  1. Article ; Online: Transplant Glomerulopathy With Glomerular C3 Deposits: Why the Worse Outcome?

    Yamashita, Michifumi / Haas, Mark

    Kidney international reports

    2019  Volume 4, Issue 4, Page(s) 516–519

    Language English
    Publishing date 2019-02-25
    Publishing country United States
    Document type Editorial
    ISSN 2468-0249
    ISSN (online) 2468-0249
    DOI 10.1016/j.ekir.2019.02.011
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  2. Article ; Online: Distinct RBC alloantibody responses in type 1 interferon-dependent and -independent lupus mouse models.

    Paul, Kausik / Hernández-Armengol, Rosario / Lee, June Young / Chang, Che-Yu / Shibata, Tomohiro / Yamashita, Michifumi / Jefferies, Caroline / Gibb, David R

    Frontiers in immunology

    2024  Volume 14, Page(s) 1304086

    Abstract: During transfusion of red blood cells (RBCs), recipients are exposed to both ABO and non-ABO 'minor' antigens. RBC donor units and recipient RBCs are not routinely matched for non-ABO antigens. Thus, recipients are exposed to many RBC alloantigens that ... ...

    Abstract During transfusion of red blood cells (RBCs), recipients are exposed to both ABO and non-ABO 'minor' antigens. RBC donor units and recipient RBCs are not routinely matched for non-ABO antigens. Thus, recipients are exposed to many RBC alloantigens that can lead to RBC alloantibody production and subsequent clinically significant hemolysis. RBC alloantibodies also significantly limit the provision of compatible RBC units for recipients. Prior studies indicate that the frequency of RBC alloimmunization is increased during inflammatory responses and in patients with autoimmune diseases. Still, mechanisms contributing to alloimmune responses in patients with autoimmunity are not well understood. More than half of adult patients with systemic lupus erythematosus (SLE) produce type 1 interferons (IFNα/β) and express IFNα/β stimulated genes (ISGs). Previously, we reported that IFNα/β promote RBC alloimmune responses in the pristane mouse model, which develops a lupus-like phenotype that is dependent on IFNα/β signaling. However, it is unclear whether IFNα/β or the lupus-like phenotype induces alloimmunization in lupus models. Therefore, we tested the hypothesis that IFNα/β promotes RBC alloimmune responses in lupus by examining alloimmune responses in IFNα/β-independent (MRL-
    MeSH term(s) Humans ; Mice ; Animals ; Isoantibodies ; Mice, Inbred MRL lpr ; Erythrocytes ; Disease Models, Animal ; Interferons ; Lupus Erythematosus, Systemic ; Immunoglobulin G ; Terpenes
    Chemical Substances Isoantibodies ; pristane (26HZV48DT1) ; Interferons (9008-11-1) ; Immunoglobulin G ; Terpenes
    Language English
    Publishing date 2024-01-15
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1304086
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  3. Article ; Online: EGF-Receptor-Dependent TLR7 Signaling in Macrophages Promotes Glomerular Injury in Crescentic Glomerulonephritis.

    Tatsumoto, Narihito / Saito, Suguru / Rifkin, Ian R / Bonegio, Ramon G / Leal, Daniel N / Sen, Ganes C / Arditi, Moshe / Yamashita, Michifumi

    Laboratory investigation; a journal of technical methods and pathology

    2023  Volume 103, Issue 9, Page(s) 100190

    Abstract: Glomerulonephritis (GN) is a group of inflammatory diseases and an important cause of morbidity and mortality worldwide. The initiation of the inflammatory process is quite different for each type of GN; however, each GN is characterized commonly and ... ...

    Abstract Glomerulonephritis (GN) is a group of inflammatory diseases and an important cause of morbidity and mortality worldwide. The initiation of the inflammatory process is quite different for each type of GN; however, each GN is characterized commonly and variably by acute inflammation with neutrophils and macrophages and crescent formation, leading to glomerular death. Toll-like receptor (TLR) 7 is a sensor for self-RNA and implicated in the pathogenesis of human and murine GN. Here, we show that TLR7 exacerbates glomerular injury in nephrotoxic serum nephritis (NTN), a murine model of severe crescentic GN. TLR7
    MeSH term(s) Mice ; Humans ; Animals ; Epidermal Growth Factor ; Toll-Like Receptor 7 ; Glomerulonephritis ; ErbB Receptors ; Macrophages/metabolism
    Chemical Substances Epidermal Growth Factor (62229-50-9) ; Toll-Like Receptor 7 ; ErbB Receptors (EC 2.7.10.1) ; TLR7 protein, human
    Language English
    Publishing date 2023-06-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80178-1
    ISSN 1530-0307 ; 0023-6837
    ISSN (online) 1530-0307
    ISSN 0023-6837
    DOI 10.1016/j.labinv.2023.100190
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  4. Article ; Online: The Continuing Need for Electron Microscopy in Examination of Medical Renal Biopsies: Examples in Practice.

    Yamashita, Michifumi / Lin, Mercury Y / Hou, Jean / Ren, Kevin Y M / Haas, Mark

    Glomerular diseases

    2021  Volume 1, Issue 3, Page(s) 145–159

    Abstract: Background: For the better part of the past 6 decades, transmission electron microscopy (EM), together with routine light microscopy and immunofluorescence and/or immunohistochemistry (IHC), has been an essential component of the diagnostic workup of ... ...

    Abstract Background: For the better part of the past 6 decades, transmission electron microscopy (EM), together with routine light microscopy and immunofluorescence and/or immunohistochemistry (IHC), has been an essential component of the diagnostic workup of medical renal biopsies, particularly native renal biopsies, with increasing frequency in renal allograft biopsies as well. Studies performed prior to the year 2000 have indeed shown that a substantial fraction of renal biopsies cannot be accurately diagnosed without EM. Still, EM remains costly and labor-intensive, and with increasing pressure to reduce healthcare costs, some centers are de-emphasizing diagnostic EM. This trend has been coupled with advances in IHC and other methods in renal biopsy diagnosis over the past 2-3 decades.
    Summary: Nonetheless, it has been our experience that the diagnostic value of EM in the comprehensive evaluation of renal biopsies remains similar to what it was 20-30 years ago. In this review, we provide several key examples from our practice where EM was essential in making the correct renal biopsy diagnosis, ranging from relatively common glomerular lesions to rare diseases.
    Key messages: EM remains an important component of the diagnostic evaluation of medical renal biopsies. Failure to perform EM in certain cases will result in an incorrect diagnosis, with possible clinical consequences. We strongly recommend that tissue for EM be taken and stored in an appropriate fixative and ultrastructural studies be performed for all native renal biopsies, as well as appropriate renal allograft biopsies as recommended by the Banff consortium.
    Language English
    Publishing date 2021-06-16
    Publishing country Switzerland
    Document type Journal Article ; Review
    ISSN 2673-3633
    ISSN (online) 2673-3633
    DOI 10.1159/000516831
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  5. Article ; Online: A U-Net based framework to quantify glomerulosclerosis in digitized PAS and H&E stained human tissues.

    Gallego, Jaime / Swiderska-Chadaj, Zaneta / Markiewicz, Tomasz / Yamashita, Michifumi / Gabaldon, M Alejandra / Gertych, Arkadiusz

    Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society

    2021  Volume 89, Page(s) 101865

    Abstract: Reliable counting of glomeruli and evaluation of glomerulosclerosis in renal specimens are essential steps to assess morphological changes in kidney and identify individuals requiring treatment. Because microscopic identification of sclerosed glomeruli ... ...

    Abstract Reliable counting of glomeruli and evaluation of glomerulosclerosis in renal specimens are essential steps to assess morphological changes in kidney and identify individuals requiring treatment. Because microscopic identification of sclerosed glomeruli performed under the microscope is labor intensive, we developed a deep learning (DL) approach to identify and classify glomeruli as normal or sclerosed in digital whole slide images (WSIs). The segmentation and classification of glomeruli was performed by the U-Net model. Subsequently, glomerular classifications were refined based on glomerular histomorphometry. The U-Net model was trained using patches from Periodic Acid-Schiff (PAS) stained WSIs (n=31) from the AIDPATH - a multi-center dataset, and then tested on an independent set of WSIs (n=20) including PAS (n=6), and hematoxylin and eosin (H&E) stained WSIs (n=14) from four other institutions. The training and test WSIs were obtained from formalin fixed and paraffin embedded blocks with of human kidney specimens each presenting various proportions of normal and sclerosed glomeruli. In the PAS stained WSIs, normal and sclerosed glomeruli were respectively classified with the F1-score of 97.5% and 68.8%. In the H&E stained WSIs, the F1-scores of 90.8% and 78.1% were achieved. Regardless the tissue staining, the glomeruli in the test WSIs were classified with the F1-score of 94.5% (n=923, normal) and 76.8% for (n=261, sclerosed). These results demonstrate for the first time that a framework based on the U-Net model trained with glomerular patches from PAS stained WSIs can reliably segment and classify normal and sclerosed glomeruli in PAS and also H&E stained WSIs. Our approach yielded higher accuracy of glomerular classifications than some of the recently published methods. Additionally, our test set of images with ground truth is publicly available.
    MeSH term(s) Deep Learning ; Eosine Yellowish-(YS) ; Hematoxylin ; Humans ; Kidney/diagnostic imaging ; Staining and Labeling
    Chemical Substances Eosine Yellowish-(YS) (TDQ283MPCW) ; Hematoxylin (YKM8PY2Z55)
    Language English
    Publishing date 2021-01-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639451-6
    ISSN 1879-0771 ; 0895-6111
    ISSN (online) 1879-0771
    ISSN 0895-6111
    DOI 10.1016/j.compmedimag.2021.101865
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    Zs.A 1323: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article: Sendai Virus Propagation Using Chicken Eggs.

    Tatsumoto, Narihito / Arditi, Moshe / Yamashita, Michifumi

    Bio-protocol

    2018  Volume 8, Issue 18

    Abstract: Sendai virus is a member of the ... ...

    Abstract Sendai virus is a member of the family
    Language English
    Publishing date 2018-10-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.3009
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  7. Article: Quantification of Infectious Sendai Virus Using Plaque Assay.

    Tatsumoto, Narihito / Miyauchi, Takamasa / Arditi, Moshe / Yamashita, Michifumi

    Bio-protocol

    2018  Volume 8, Issue 21

    Abstract: Sendai virus (SeV) is an enveloped, single-stranded RNA virus of the ... ...

    Abstract Sendai virus (SeV) is an enveloped, single-stranded RNA virus of the family
    Language English
    Publishing date 2018-12-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.3068
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  8. Article ; Online: Organoid-on-a-chip model of human ARPKD reveals mechanosensing pathomechanisms for drug discovery.

    Hiratsuka, Ken / Miyoshi, Tomoya / Kroll, Katharina T / Gupta, Navin R / Valerius, M Todd / Ferrante, Thomas / Yamashita, Michifumi / Lewis, Jennifer A / Morizane, Ryuji

    Science advances

    2022  Volume 8, Issue 38, Page(s) eabq0866

    Abstract: Organoids serve as a novel tool for disease modeling in three-dimensional multicellular contexts. Static organoids, however, lack the requisite biophysical microenvironment such as fluid flow, limiting their ability to faithfully recapitulate disease ... ...

    Abstract Organoids serve as a novel tool for disease modeling in three-dimensional multicellular contexts. Static organoids, however, lack the requisite biophysical microenvironment such as fluid flow, limiting their ability to faithfully recapitulate disease pathology. Here, we unite organoids with organ-on-a-chip technology to unravel disease pathology and develop therapies for autosomal recessive polycystic kidney disease.
    MeSH term(s) Drug Discovery ; Drugs, Investigational ; Humans ; Lab-On-A-Chip Devices ; Organoids/metabolism ; Polycystic Kidney, Autosomal Recessive/genetics ; Polycystic Kidney, Autosomal Recessive/metabolism ; Polycystic Kidney, Autosomal Recessive/pathology
    Chemical Substances Drugs, Investigational
    Language English
    Publishing date 2022-09-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abq0866
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  9. Article: The histopathological spectrum of kidney biopsies in patients with thymoma and myasthenia gravis: a report of 24 biopsies from a single institution.

    Takahashi, Akira / Miyauchi, Takamasa / Tatsumoto, Narihito / Lin, Mercury Y / Hou, Jean / Doi, Toshiki / Masaki, Takao / Yamashita, Michifumi

    Clinical kidney journal

    2021  Volume 14, Issue 9, Page(s) 2090–2100

    Abstract: Background: Nephropathy in patients with thymic diseases such as thymoma and myasthenia gravis (MG) is rare and has been described mostly as isolated case reports. Here we evaluate a series of kidney biopsies from patients with thymoma and/or MG from a ... ...

    Abstract Background: Nephropathy in patients with thymic diseases such as thymoma and myasthenia gravis (MG) is rare and has been described mostly as isolated case reports. Here we evaluate a series of kidney biopsies from patients with thymoma and/or MG from a single institution in order to better define the spectrum and relative frequencies of thymic disease-associated nephropathies.
    Methods: We conducted a retrospective case series study of 32 462 native kidney biopsies from January 2005 through December 2019 at Cedars-Sinai Medical Center, Los Angeles, CA, USA.
    Results: Twenty-four biopsy specimens (0.07%) from patients with a history of thymoma and/or MG were identified. Two patients had repeat biopsies. The most common pathologic diagnosis that could be immunologically attributed to thymic disease was minimal change disease (MCD; 45%), followed by tubulointerstitial nephritis (TIN; 14%), immune complex (IC)-mediated glomerulonephritis (9%), membranous nephropathy (5%) and immunoglobulin A (IgA) nephropathy (5%). Interestingly, 50% of the MCD and 67% of TIN cases concomitantly showed mild IgG-dominant IC deposition in mesangial areas and/or in tubular basement membranes. In the two patients with repeat biopsies, mild mesangial IC deposition developed in the MCD patient but disappeared in the TIN patient with the second biopsy. Pathologic diagnoses unlikely related to the underlying thymic disease were diabetic glomerulosclerosis (9%), acute tubular necrosis (9%) and monoclonal Ig deposition disease (5%).
    Conclusions: Thymic disease is associated with a wide spectrum of kidney diseases affecting the glomerular and tubulointerstitial compartments, often with low-grade IC deposition. These findings suggest a role of immunologic dysregulation in the pathogenesis of thymic disease-associated nephropathy.
    Language English
    Publishing date 2021-01-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2655800-2
    ISSN 2048-8513 ; 2048-8505
    ISSN (online) 2048-8513
    ISSN 2048-8505
    DOI 10.1093/ckj/sfaa276
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    Zs.A 6587: Show issues Location:
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  10. Article ; Online: SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys.

    Aggarwal, Shikhar / Wang, Zhanxiang / Rincon Fernandez Pacheco, David / Rinaldi, Anna / Rajewski, Alex / Callemeyn, Jasper / Van Loon, Elisabet / Lamarthée, Baptiste / Covarrubias, Ambart Ester / Hou, Jean / Yamashita, Michifumi / Akiyama, Haruhiko / Karumanchi, S Ananth / Svendsen, Clive N / Noble, Paul W / Jordan, Stanley C / Breunig, Joshua J / Naesens, Maarten / Cippà, Pietro E /
    Kumar, Sanjeev

    Science (New York, N.Y.)

    2024  Volume 383, Issue 6685, Page(s) eadd6371

    Abstract: The steps governing healing with or without fibrosis within the same microenvironment are unclear. After acute kidney injury (AKI), injured proximal tubular epithelial cells activate SOX9 for self-restoration. Using a multimodal approach for a head-to- ... ...

    Abstract The steps governing healing with or without fibrosis within the same microenvironment are unclear. After acute kidney injury (AKI), injured proximal tubular epithelial cells activate SOX9 for self-restoration. Using a multimodal approach for a head-to-head comparison of injury-induced SOX9 lineages, we identified a dynamic SOX9 switch in repairing epithelia. Lineages that regenerated epithelia silenced SOX9 and healed without fibrosis (SOX9
    MeSH term(s) Animals ; Humans ; Acute Kidney Injury/genetics ; Acute Kidney Injury/pathology ; Epithelial Cells ; Fibrosis ; Kidney/pathology ; Renal Insufficiency, Chronic/genetics ; Renal Insufficiency, Chronic/pathology ; SOX9 Transcription Factor/genetics ; Regeneration ; Mice
    Chemical Substances SOX9 protein, human ; SOX9 Transcription Factor
    Language English
    Publishing date 2024-02-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.add6371
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