Citation: Li Y, Butler TC, Nardone S, Jacobs CL, Douglass AM, Madara JC, McDonough MC, Tao J, Lowenstein ED, Wang L, Pant D, Walker SJ, Wang A, Srinivasan H, Yang Z, Campbell JN, Tsai LT, Lowell BB, Resch JM. A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types. Cell Reports. 2026. 

Contact: Jon Resch (jon-resch@uiowa.edu)

GEO: GSE303256

Summary:  The paraventricular hypothalamus (PVH) controls behavioral and physiologic processes, including appetite, social behavior, autonomic outflow, and pituitary hormone secretion. However, molecular markers for centrally-projecting PVH neuron populations remain largely undefined, and a complete census of PVH cell types has not been established. Therefore, we performed extensive single-cell/nucleus RNA sequencing to catalog PVH neuron subtypes and multiplexed error-robust fluorescence in situ hybridization (MERFISH) to map them spatially. Our spatial transcriptomic atlas resolves 26 Sim1+ and 29 GABAergic neuron populations from the PVH and surrounding areas. Additionally, projection-based profiling identified neurons that project to the parabrachial region (PB) and spinal cord, helping to determine PVH populations that regulate satiety and sympathetic nervous system activity, respectively. Notably, activation of PB-projecting PVH neurons expressing Brs3 reduces food intake and silencing them causes obesity. Together, this atlas contributes high-resolution PVH spatial and circuit-based gene expression profiles, representing a valuable resource for the field of homeostasis.

Data Download: Mouse sc/snRNA-seq data from this study have been deposited into the NCBI Gene Expression Omnibus (GEO) with accession number GSE303256. Allen Brain Cell Atlas mouse sc/snRNA-seq data were downloaded from the following locations: https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/WMB-10Xv2/20230630/ (10Xv2), and   https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/WMB-10Xv3/20230630/ (10Xv3). Mouse MERFISH data from this study have been deposited in the Iowa Research Online (IRO) repository with record accession number 9984403060302771. All original code and Seurat objects have been deposited to Zenodo at: https://doi.org/10.5281/zenodo.15983704.