Penn Center for Multi-scale Molecular Mapping of the Female Reproductive System

The female reproductive system (the uterus, fallopian tubes and the ovaries), orchestrates the complex menstrual cycle, supports reproduction, and has health consequences beyond reproduction. While central to obstetrics and gynecology, it is also tied to overall health with health and reproduction intimately linked. Disorders of the female reproductive system are responsible for common, costly, and debilitating disorders. While a healthy female reproductive system is associated with vitality, longevity and general wellbeing, perturbations are linked to cardiovascular disease, non-gynecologic malignancies and all cause mortality.

Our mission is to define a molecular map of the entire female reproductive system, integrating multi-modal assays, spatial diversity, and individual variation. We will develop this comprehensive molecular characterization using multiple molecular assays, across hundreds of anatomically indexed tissue samples and include over a million individually characterized cells, creating a key resource for both basic science and women’s health. The molecular assays include single cell RNAseq, clampFISH spatial transcriptomics, simultaneous single cell open chromatin and RNA assays, and spatial open chromatin assay, among others. We will also generate a 3D anatomical model to provide spatial coordinates for our molecular characterizations. All assay data will be registered to the 3D anatomical map that will be integrated with the existing HuBMAP Common Coordinate Framework, tying in with other similarly characterized human organs. All data, including an extensive set of sample and subject metadata, will be made available as a public resource. The completion of this resource will impact reproductive medicine for women’s health and also inform basic biology of human cell communities.

Principal Investigators

Junhyong Kim, PhD, Chair and Patricia M. Williams Prof. of Biology, School of Arts and Sciences Kate O'Neill, MD MTR, Assistant Prof., Department of Obstetrics and Gynecology, Perelman School of Medicine

Co-Investigators and Collaborators

Kurt Barnhart, MD MSCE, William Shippen Jr. Prof. of Obstetrics and Gynecology, Perelman School of Medicine Ronny Drapkin, MD PhD, Franklin Payne Associate Prof. of Pathology in Obstetrics & Gynecology, Perelman School of Medicine
Jim Eberwine, PhD, Elmer Holmes Bobst Prof. of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine Michael Feldman, MD PhD, Prof. of Pathology and Laboratory Medicine, Perelman School of Medicine
James Gee, PhD, Associate Prof. of Radiologic Science and Computer and Information Science, Perelman School of Medicine Brian Gregory, PhD, Associate Prof. and Graduate Chair of Biology
Nawar Latif, MD MPH MSCE, Assistant Prof. of Obstetrics and Gynecology, Hospital of the University of Pennsylvania Alison Pouch, PhD, Assistant Prof. of Radiology and Bioengineering, Perelman School of Medicine
Arjun Raj, PhD, Prof. of Bioengineering Lauren Schwartz, MD, Assistant Prof. of Clinical Pathology and Laboratory Medicine, Perelman School of Medicine
Abraham Shaked, MD PhD, Eldridge L. Eliason Prof. of Surgery, Hospital of the University of Pennsylvania  


Eunice Kennedy Shriver National Institute of Child Health & Human Development, NIH Gift of Life Donation Program
School of Arts and Sciences, University of Pennsylvania Perelman School of Medicine, University of Pennsylvania
Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, University of Pennsylvania  

We'd like to thank the generosity of donor families and Penn patients for participating in this groundbreaking scientific research.

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