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/

Mapping the lymphatic system across body scales and expertise domains: A report from the 2021 National Heart, Lung, and Blood Institute workshop at the Boston Lymphatic Symposium

Enhancing our understanding of lymphatic anatomy from the microscopic to the anatomical scale is essential to discern how the structure and function of the lymphatic system interacts with different tissues and organs within the body and contributes to health and disease. The knowledge of molecular aspects of the lymphatic network is fundamental to understand the mechanisms of disease progression and prevention. Recent advances in mapping components of the lymphatic system using state of the art single cell technologies, the identification of novel biomarkers, new clinical imaging efforts, and computational tools which attempt to identify connections between these diverse technologies hold the potential to catalyze new strategies to address lymphatic diseases such as lymphedema and lipedema. This manuscript summarizes current knowledge of the lymphatic system and identifies prevailing challenges and opportunities to advance the field of lymphatic research as discussed by the experts in the workshop

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

Phosphate Flow between Hybrid Histidine Kinases CheA₃ and CheS₃ Controls <i>Rhodospirillum centenum</i> Cyst Formation

<div><p>Genomic and genetic analyses have demonstrated that many species contain multiple chemotaxis-like signal transduction cascades that likely control processes other than chemotaxis. The Che₃ signal transduction cascade from <i>Rhodospirillum centenum</i> is one such example that regulates development of dormant cysts. This Che-like cascade contains two hybrid response regulator-histidine kinases, CheA₃ and CheS₃, and a single-domain response regulator CheY₃. We demonstrate that <i>cheS₃</i> is epistatic to <i>cheA₃</i> and that only CheS₃∼P can phosphorylate CheY₃. We further show that CheA₃ derepresses cyst formation by phosphorylating a CheS₃ receiver domain. These results demonstrate that the flow of phosphate as defined by the paradigm <i>E. coli</i> chemotaxis cascade does not necessarily hold true for non-chemotactic Che-like signal transduction cascades.</p></div

Model for regulation of Che₃ signal transduction pathway.

<p>(A) In the absence of unknown signals, CheA₃ is deactivated; CheS₃ autophosphorylates and transfers phosphates to its cognate response regulator CheY₃; activated CheY₃ then interacts with downstream components to repress cyst formation. (B) In the presence of an unknown signal (denoted by a red star), CheA₃ autophosphorylation is activated; His-phosphorylated CheA₃ constantly transfers the phosphates to its C-terminal REC domain, which serves as a phosphate sink. CheA₃∼P also phosphorylates the REC1 domain of CheS₃, inhibiting CheS₃ kinase activity and CheY₃ remains unphosphorylated. Cyst formation is therefore derepressed without activated CheY₃. The thickness of the arrows represents the level of phosphate flow.</p

Gene arrangement of the <i>R. centenum che₃</i> cluster and domain organizations of CheA₃, CheS₃, and CheY₃.

<p>Arrow length is proportional to gene length. Abbreviations: REC, receiver domain; PAS, <u>P</u>er, <u>A</u>rnt, <u>S</u>im domains; HWE_HK, HWE superfamily of histidine kinases; Hpt, histidine phosphotransfer domain; CA, catalytic and ATP-binding domain. Conserved histidine and aspartate residues as putative phosphorylation sites are denoted for each protein. The start and end amino acid positions of the receiver domains as well as those of the full proteins are also labeled according to the prediction by SMART <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004002#pgen.1004002-Schultz1" target="_blank">[48]</a>.</p

Identification of intramolecular phosphoryl transfer within CheA₃ and CheS₃.

<p>(A) CheA₃∼P is acid- and alkaline-labile, whereas the REC mutant CheA₃:D663A∼P is acid-labile and base-resistant. (B) Both CheS₃∼P and its REC mutant CheS₃:D54A are acid-labile and alkaline-stable. (C) CheA₃:D663A∼P phosphorylates CheA₃-REC truncation protein in Buffer 15 containing K⁺ and 18 mM Mg²⁺. (D) Phosphoryl transfer from CheS₃:D54A∼P to CheS₃-REC1 truncation protein was not observed in Buffer 15.</p

Mutations in DivL and CckA Rescue a divJ Null Mutant of Caulobacter crescentus by Reducing the Activity of CtrA

Polar development and cell division in Caulobacter crescentus are controlled and coordinated by multiple signal transduction proteins. divJ encodes a histidine kinase. A null mutation in divJ results in a reduced growth rate, cell filamentation, and mislocalized stalks. Suppressor analysis of divJ identified mutations in genes encoding the tyrosine kinase (divL) and the histidine kinase (cckA). The divL and cckA suppressor alleles all have single amino acid substitutions, some of which confer a temperature-sensitive phenotype, particularly in a wild-type background. Analysis of transcription levels from several positively regulated CtrA-dependent promoters reveals high expression in the divJ mutant, suggesting that DivJ normally serves to reduce CtrA activity. The divL and cckA suppressors reduce the amount of transcription from promoters positively regulated by CtrA, indicating that the mutations in divL and cckA are suppressing the defects of the divJ mutant by reducing the abnormally high level of CtrA activity. Immunoblotting showed no major perturbations in the CtrA protein level in any of these strains, suggesting that the high amount of CtrA activity seen in the divJ mutant and the reduced amount of activity in the suppressors are regulated at the level of activation and not transcription, translation, or degradation. In vivo phosphorylation assays confirmed that divJ mutants have elevated levels of CtrA phosphorylation and that this level is reduced in the suppressors with mutations in divL