Tissue registration and exploration user interfaces in support of a human reference atlas

Seventeen international consortia are collaborating on a human reference atlas (HRA), a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, harmonizing tissue data across 25 organs and more than 15 bulk and spatial single-cell assay types poses challenges. Here, we present software tools and user interfaces developed to spatially and semantically annotate ( register ) and explore the tissue data and the evolving HRA. A key part of these tools is a common coordinate framework, providing standard terminologies and data structures for describing specimen, biological structure, and spatial data linked to existing ontologies. As of April 22, 2022, the registration user interface has been used to harmonize and publish data on 5,909 tissue blocks collected by the Human Biomolecular Atlas Program (HuBMAP), the Stimulating Peripheral Activity to Relieve Conditions program (SPARC), the Human Cell Atlas (HCA), the Kidney Precision Medicine Project (KPMP), and the Genotype Tissue Expression project (GTEx). Further, 5,856 tissue sections were derived from 506 HuBMAP tissue blocks. The second exploration user interface enables consortia to evaluate data quality, explore tissue data spatially within the context of the HRA, and guide data acquisition. A companion website is at https://cns-iu.github.io/HRA-supporting-information/

Expression of SARS-CoV-2 Entry Factors in the Pancreas of Normal Organ Donors and Individuals with COVID-19

This article is made available for unrestricted research re-use and secondary analysis in any form or be any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Diabetes is associated with increased mortality from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Given literature suggesting a potential association between SARS-CoV-2 infection and diabetes induction, we examined pancreatic expression of angiotensin-converting enzyme 2 (ACE2), the key entry factor for SARS-CoV-2 infection. Specifically, we analyzed five public scRNA-seq pancreas datasets and performed fluorescence in situ hybridization, western blotting, and immunolocalization for ACE2 with extensive reagent validation on normal human pancreatic tissues across the lifespan, as well as those from coronavirus disease 2019 (COVID-19) cases. These in silico and ex vivo analyses demonstrated prominent expression of ACE2 in pancreatic ductal epithelium and microvasculature, but we found rare endocrine cell expression at the mRNA level. Pancreata from individuals with COVID-19 demonstrated multiple thrombotic lesions with SARS-CoV-2 nucleocapsid protein expression that was primarily limited to ducts. These results suggest SARS-CoV-2 infection of pancreatic endocrine cells, via ACE2, is an unlikely central pathogenic feature of COVID-19-related diabetes.We thank the families of the organ donors and autopsy subjects for the gift of tissues. We also thank Jill K. Gregory, CMI (Icahn School of Medicine at Mount Sinai, New York, NY) for preparing the graphical abstract. These efforts were supported by NIH P01 AI042288 and UC4 DK108132 (M.A.A.); JDRF (M.A.A.); NIH R01 DK122160 (M.C.-T.); NIH R01 AI134971 and P30 DK020541 (D.H.); JDRF 3-PDF-2018-575-A-N (V.V.D.H.); R01 DK093954 , R21 DK119800-01A1 , UC4 DK104166 , and U01 DK127786 (C.E.-M.); VA Merit Award I01BX001733 (C.E.-M.); Imaging Core of NIH/ NIDDK P30 DK097512 (C.E.-M.); gifts from the Sigma Beta Sorority , the Ball Brothers Foundation , and the George and Frances Ball Foundation (C.E.-M.); the Network for Pancreatic Organ Donors with Diabetes ( nPOD ; RRID: SCR_014641 ) ( 5-SRA-2018-557-Q-R ); and The Leona M. & Harry B. Helmsley Charitable Trust ( 2018PG-T1D053 ). The authors also wish to acknowledge the Islet and Physiology Core of the Indiana Diabetes Research Center ( P30DK097512 ). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Abstract: Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions

Adenine nucleotide translocase 4 deficiency leads to early meiotic arrest of murine male germ cells

Male fertility relies on the highly specialized process of spermatogenesis to continually renew the supply of spermatozoa necessary for reproduction. Central to this unique process is meiosis that is responsible for the production of haploid spermatozoa as well as for generating genetic diversity. During meiosis I, there is a dramatic increase in the number of mitochondria present within the developing spermatocytes, suggesting an increased necessity for ATP production and utilization. Essential for the utilization of ATP is the translocation of ADP and ATP across the inner mitochondrial membrane, which is mediated by the adenine nucleotide translocases (Ant). We recently identified and characterized a novel testis specific Ant, ANT4 (also known as SLC25A31 and Aac4). The generation of Ant4-deficient animals resulted in the severe disruption of the seminiferous epithelium with an apparent spermatocytic arrest of the germ cell population. In the present study utilizing a chromosomal spread technique, we determined that Ant4-deficiency results in an accumulation of leptotene spermatocytes, a decrease in pachytene spermatocytes, and an absence of diplotene spermatocytes, indicating early meiotic arrest. Furthermore, the chromosomes of Ant4-deficient pachytene spermatocyte occasionally demonstrated sustained γH2AX association as well as synaptonemal complex protein 1 (SYCP1)/SYCP3 dissociation beyond the sex body. Large ATP supplies from mitochondria may be critical for normal progression of spermatogenesis during early stages of meiotic prophase I, including DNA double-strand break repair and chromosomal synapsis. © 2009 Society for Reproduction and Fertility

Members of the Cyr61/CTGF/NOV Protein Family: Emerging Players in Hepatic Progenitor Cell Activation and Intrahepatic Cholangiocarcinoma

Hepatic stem/progenitor cells (HPC) reside quiescently in normal biliary trees and are activated in the form of ductular reactions during severe liver damage when the replicative ability of hepatocytes is inhibited. HPC niches are full of profibrotic stimuli favoring scarring and hepatocarcinogenesis. The Cyr61/CTGF/NOV (CCN) protein family consists of six members, CCN1/CYR61, CCN2/CTGF, CCN3/NOV, CCN4/WISP1, CCN5/WISP2, and CCN6/WISP3, which function as extracellular signaling modulators to mediate cell-matrix interaction during angiogenesis, wound healing, fibrosis, and tumorigenesis. This study investigated expression patterns of CCN proteins in HPC and cholangiocarcinoma (CCA). Mouse HPC were induced by the biliary toxin 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). Differential expression patterns of CCN proteins were found in HPC from DDC damaged mice and in human CCA tumors. In addition, we utilized reporter mice that carried Ccn2/Ctgf promoter driven GFP and detected strong Ccn2/Ctgf expression in epithelial cell adhesion molecule (EpCAM)+ HPC under normal conditions and in DDC-induced liver damage. Abundant CCN2/CTGF protein was also found in cytokeratin 19 (CK19)+ human HPC that were surrounded by α-smooth muscle actin (α-SMA)+ myofibroblast cells in intrahepatic CCA tumors. These results suggest that CCN proteins, particularly CCN2/CTGF, function in HPC activation and CCA development

Hepatic oval (stem) cell expression of endothelial differentiation gene receptors for lysophosphatidic acid in mouse chronic liver injury.

Growth factor lysophosphatidic acid (LPA) regulates cell proliferation and differentiation and increases motility and survival in several cell types, mostly via G-protein-coupled receptors encoded by endothelial differentiation genes (EDG). We show herein that hepatic oval (stem) cell proliferation, induced by 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) in a mouse model of chronic liver injury, was associated with the expression of LPA1, LPA2, and LPA3 receptor subtypes; only LPA1 receptor protein was detectable in normal liver by western blot. In the injured liver, enhanced LPA1 receptor was identified predominantly in oval cells along the portal tract, proliferating ductular epithelial cells, and small cells, which were located in the nearby parenchyma and formed clusters. Interestingly, the LPA1 receptor was co-expressed in DDC-treated livers with the stem cell antigen SCA-1, suggesting that this receptor may be associated with bone marrow-derived progenitors. All three receptors for LPA were detected mostly in small cells in the vicinity of the portal tract, and co-localized with the A6 antigen, a marker of ductular oval cells. In addition, hepatic levels of endogenous LPA were significantly higher in DDC-fed mice compared to normal animals. We propose that the expression of diverse LPA receptors may be a necessary part of the mechanism responsible for activation of oval cells during liver injury. As a result, LPA and its analogs may represent critical endogenous mediators, which regulate survival, increase motility, and modulate proliferation and differentiation of hepatocyte progenitors in regenerating liver

Hepatic progenitor cell activation in liver repair

The liver possesses an extraordinary ability to regenerate after injury. Hepatocyte-driven liver regeneration is the default pathway in response to mild-to-moderate acute liver damage. When replication of mature hepatocytes is blocked, facultative hepatic progenitor cells (HPCs), also referred to as oval cells (OCs) in rodents, are activated. HPC/OCs have the ability to proliferate clonogenically and differentiate into several lineages including hepatocytes and bile ductal epithelia. This is a conserved liver injury response that has been studied in many species ranging from mammals (rat, mouse, and human) to fish. In addition, improper HPC/OC activation is closely associated with fibrotic responses, characterized by myofibroblast activation and extracellular matrix production, in many chronic liver diseases. Matrix remodeling and metalloprotease activities play an important role in the regulation of HPC/OC proliferation and fibrosis progression. Thus, understanding molecular mechanisms underlying HPC/OC activation has therapeutic implications for rational design of anti-fibrotic therapies. Keywords: Liver regeneration, Hepatic progenitor cells (HPCs), Oval cells (OCs), Liver injury, Hepatic fibrosi

Bone marrow-derived cells home to and regenerate retinal pigment epithelium after injury. Invest Ophthalmol Vis Sci

PURPOSE. To determine whether hematopoietic stem and progenitor cells (HSCs/HPCs) can home to and regenerate the retinal pigment epithelium (RPE) after induced injury. METHODS. Enriched HSCs/HPCs from green fluorescent protein (gfp) transgenic mice were transplanted into irradiated recipient mice to track bone marrow-derived cells. Physical damage was induced by breaching Bruch's membrane and inducing vascular endothelial growth factor A (VEGFa) expression to promote neovascularization. RPE damage was also induced by sodium iodate injection (40 mg/kg) into wild-type or albino C57Bl/6 mice. Cell morphology, gfp expression, the presence of the Y chromosome, and the presence of melanosomes were used to determine whether the injured RPE was being repaired by the donor bone marrow. 2 Attempts to repair the RPE include transplantation of RPE cells into the subretinal space. Animal studies, RPE transplantation in humans, and macular relocation surgery have all shown that replacing diseased RPE with healthier RPE can rescue photoreceptors, prevent further visual loss, and even promote visual improvement. RESULTS. 3,4 Also, recent work on human RPE patch graft transplantation demonstrates survival and rescue of photoreceptors for a substantial time after grafting and holds some promise. Rescue of RPE and photoreceptors beyond the area of donor cell distribution suggests that diffusible factors are also involved in the rescue process. However, some problems exist, including the ability to obtain an adequate source of autologous RPE and that homologous cells have been associated with rejection. Fetal or adult transplanted RPE cells attach to Bruch's membrane with poor efficiency and do not proliferate. 5 These transplantation procedures are complex, associated with high complication rates, and often result in only short-term success. RPE integrity is an essential component for retinal function and visual health. The RPE consists of a monolayer of cuboidal cells that separates the photoreceptors and the choroid. 8 Adult stem cells of the bone marrow include hematopoietic stem cells (HSCs), which are multipotent and have been shown to transdifferentiate into multiple tissues such as endothelium, 9,10 epithelium, 9 -11 myocardium, 12 and liver. 13,14 These cells represent a renewable source of cells within our bodies and harnessing the regenerative ability of the HSCs may aid in the cure of degenerative diseases. In our model, the bone marrow transplantation was performed using CD117 (c-kit) cells. This technique enriches for HSCs and hematopoietic progenitor cells (HPCs). 15 In addition to HSC/HPC transdifferentiation, the ability for the HSCs/HPCs to home to an area of injury is a quintessential characteristic. When injury occurs, cytokines and chemokines are released into the blood, causing an inflammatory response. HSCs/HPCs home along this chemokine gradient to repair areas of injury. Stromal cell-derived factor 1 (SDF-1) has been shown to be the primary cytokine for HSC/SPC mobilization. 16 -18 SDF-1 has also been shown to be upregulated in damaged tissues thus facilitating recruitment of stem-progenitor cells to promote repair. 21 In this article we examined two models of injury. Our first model consisted of physical damage to the RPE layer by needle rupture of Bruch's membrane and then injection of recombinant adenoassociated virus vascular endothelial growth factor A (rAAV-VEGFa) into the subretinal space. This leads to choroidal neovascularization

Vascular Endothelial Cell-Specific Connective Tissue Growth Factor (CTGF) Is Necessary for Development of Chronic Hypoxia-Induced Pulmonary Hypertension

Chronic hypoxia frequently complicates the care of patients with interstitial lung disease, contributing to the development of pulmonary hypertension (PH), and premature death. Connective tissue growth factor (CTGF), a matricellular protein of the Cyr61/CTGF/Nov (CCN) family, is known to exacerbate vascular remodeling within the lung. We have previously demonstrated that vascular endothelial-cell specific down-regulation of CTGF is associated with protection against the development of PH associated with hypoxia, though the mechanism for this effect is unknown. In this study, we generated a transgenic mouse line in which the Ctgf gene was floxed and deleted in vascular endothelial cells that expressed Cre recombinase under the control of VE-Cadherin promoter (eCTGF KO mice). Lack of vascular endothelial-derived CTGF protected against the development of PH secondary to chronic hypoxia, as well as in another model of bleomycin-induced pulmonary hypertension. Importantly, attenuation of PH was associated with a decrease in infiltrating inflammatory cells expressing CD11b or integrin αM (ITGAM), a known adhesion receptor for CTGF, in the lungs of hypoxia-exposed eCTGF KO mice. Moreover, these pathological changes were associated with activation of—Rho GTPase family member—cell division control protein 42 homolog (Cdc42) signaling, known to be associated with alteration in endothelial barrier function. These data indicate that endothelial-specific deletion of CTGF results in protection against development of chronic-hypoxia induced PH. This protection is conferred by both a decrease in inflammatory cell recruitment to the lung, and a reduction in lung Cdc42 activity. Based on our studies, CTGF inhibitor treatment should be investigated in patients with PH associated with chronic hypoxia secondary to chronic lung disease