Human pulmonary alveolar microlithiasis (PAM) scRNA-Seq with SLC34A2 (Npt2b) mutations

Yasuaki Uehara¹, Yusuke Tanaka¹, Shuyang Zhao², Nikolaos M. Nikolaidis¹, Lori B. Pitstick¹, Huixing Wu¹, Jane J. Yu¹, Erik Zhang¹, Yoshihiro Hasegawa¹, John G. Noel¹, Jason C. Gardner¹, Elizabeth J. Kopras¹, Wendy D. Haffey¹, Kenneth D. Greis¹, Jinbang Guo², Jason C. Woods², Kathryn A. Wikenheiser-Brokamp², Jennifer Kyle³, Charles Ansong³, Steven L. Teitelbaum⁴, Yoshikazu Inoue⁵, Göksel Altinişik⁶, Yan Xu², Francis X. McCormack¹

¹University of Cincinnati College of Medicine, ²Cincinnati Children's Hospital Medical Center, ³Pacific Northwest National Laboratory, ⁴Washington University School of Medicine, ⁵National Hospital Organization Kinki-Chuo Chest Medical Center, ⁶Pamukkale University, ^*Corresponding author

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Description Pulmonary alveolar microlithiasis (PAM) is an autosomal recessive lung disease caused by a deficiency in the pulmonary epithelial Npt2b sodium-phosphate co-transporter that results in accumulation of phosphate and formation of hydroxyapatite microliths in the alveolar space. The single cell transcriptomic analysis of a PAM lung explant showing a robust osteoclast gene signature in alveolar monocytes and the finding that calcium phosphate microliths contain a rich protein and lipid matrix that includes bone resorbing osteoclast enzymes suggested a role for osteoclast-like cells in the defense against microliths.

Dataset ID LMEX0000004407

Assay Type Single-cell RNA-seq

Organism Human

Stages Child | Adult

Cell Count 12084

Technology 10x Genomics Chromium Single Cell Gene Expression

Reference Uehara et al. (2023)

External databases GEO: GSE199329

File	Description	Size
PAM_library_metadata.tsv	Library metadata for the 2 libraries, one row each. Carries the donor, sex, age, age range, reported ethnicity, disease, anatomic region, cause of death and the nuclei each library contributes. The Samples tab shows only the fourteen columns the site defines for a human sample, so this file carries the rest.	0.4 KB
PAM_release_counts.h5ad	Release object for this study, HDF5 AnnData, gzip compressed. 12,084 cells x 31,782 genes over 59 CellRef2.0 v7 cell states and 2 libraries, the CD45-negative and CD45-positive sorted fractions of one donor. X holds RAW INTEGER COUNTS, not a normalized matrix. obs carries the CellRef2.0 v7 cell state, its short name, the library, the donor age, age range and reported ethnicity, and the cellHarmony alignment score of every nucleus. obsm carries the UMAP. The site viewers read a log2 counts per ten thousand matrix rebuilt from these counts.	96.1 MB

LungMAP ID	Alt ID	Species	Sex	Age	Age Group	Health Status
LMSPPAM0000001	10X_PAM1_PAMCD45_neg	Homo sapiens	Male	2 years	1-4 years	pulmonary alveolar microlithiasis, CD45-negative fraction
LMSPPAM0000002	10X_PAM2_PAMCD45_pos	Homo sapiens	Male	2 years	1-4 years	pulmonary alveolar microlithiasis, CD45-positive fraction