Faculty

Sydney M Shaffer, M.D., Ph.D.

Assistant Professor of Pathology and Laboratory Medicine

Department: Pathology and Laboratory Medicine

Graduate Group Affiliations

Contact information

University of Pennsylvania
Philadelphia, PA 19104

Email:
shaffers@pennmedicine.upenn.edu

Education:
B.S. (Chemical and Biomolecular Engineering)
Georgia Institute of Technology , 2010.
Ph.D. (Bioengineering)
University of Pennsylvania, 2017.
M.D. (Medicine)
Perelman School of Medicine, University of Pennsylvania, 2018.

Links
Lab website
Google scholar profile

Permanent link

> Perelman School of Medicine > Faculty > Details

Selected Publications

Bracht SA*, Rong J*, Gier RA, DeMarshall M, Golden H, Dhakal D, McDevitt JC, Mo F, Furth EE, Strauss Starling A, Muir AB, Falk GW, Katona BW, Stanger BZ, Zhang NR**, Shaffer SM** *equal contributions, **corresponding authors: Mitochondrial clone tracing within spatially intact human tissues. BioRxiv July 2025.

Gladstein AC, Poltorack CD, Solomon AMC, Venkatesh S, Adler KM, Robertson MR, Stransky S, Irizarry-Negron VM, Ruiz DA, Freeburg NF, Sidoli S, Asangani IA, Shaffer SM, Feldser DM: The H3K36M oncohistone inhibits NSD2 to activate a SETD2-dependent antiviral-like immune response in KRAS-driven lung cancer. BioRxiv May 2025.

Sasaki M, Wang JX, Zhou Y, Kennedy KV, Teranishi R, Itami T, Ishikawa S, Hara T, Winters H, McMillan EA, Mahon M, Golden H, Dhakal D, Bacarella A, Umeweni CN, Wilkins BJ, Karakasheva TA, Whelan KA, Shaffer SM, Ruffner MA, Muir AB: FOXM1 Modulation Alleviates Epithelial Remodeling and Inflammation in Eosinophilic Esophagitis. BioRxiv May 2025.

Lawson NM, Ye L, Cho CY, Zhao B, Mitchell T, Martín-Barrio I, Beernaert B, Gupta A, Banu M, Lissanu Y, Shaffer S, Tawbi H, Li J, Gule-Monroe MK, Alvarez-Breckenridge CA, Huse JT, Murphy MB, Yin F, Lang FF, Parkes EE, Weinberg JS, Akdemir KC: Recurrent ERBB2 alterations are associated with esophageal adenocarcinoma brain metastases. medRxiv February 2025.

Kinsler G, Fagan C, Li H, Kaster J, Dunne M, Vander Velde RJ, Boe RH, Shaffer S, Herlyn M, Raj A, Heyman Y: SpaceBar enables clone tracing in spatial transcriptomic data. bioRxiv February 2025.

Wahlsten M, Shaffer SM: Unveiling heterogeneity in rare cells by combining RNA-based sorting and scRNA-seq. Nature Genetics 57: 283-284, February 2025.

Han X, Burrows M, Kim LC, Xu JP, Vostrejs W, Le TNV, Poltorack C, Jiang Y, Cukierman E, Stanger BZ, Reiss KA, Shaffer SM, Mesaros C, Keith B, Simon MC: Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment. Cell Reports 43(11): 8-9, November 2024 Notes: doi: https://doi.org/10.1016/j.celrep.2024.114972.

Reyes Hueros RA, Gier RA, Shaffer SM: Non-genetic differences underlie variability in proliferation among esophageal epithelial clones. PLOS Computational Biology October 2024 Notes: doi: 10.1371/journal.pcbi.1012360.

Vargas-Castillo A, Sun Y, Smythers AL, Grauvogel L, Dumesic PA, Emont MP, Tsai LT, Rosen ED, Zammit NW, Shaffer SM, Ordonez M, Chouchani ET, Gygi SP, Wang T, Sharma AK, Balaz M, Wolfrum C, Spiegelman BM: Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle. Cell Metabolism Page: 2146-2155, July 2024 Notes: doi: 10.1016/j.cmet.2024.07.002.

Schaff DL*, Fasse AJ*, White PE, Vander Velde R, Shaffer SM: Clonal differences underlie variable responses to sequential and prolonged treatment. Cell Systems Page: 213-226, March 2024 Notes: https://doi.org/10.1016/j.cels.2024.01.011.