Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling

Allison L Hunt; Nicholas W Bateman; Waleed Barakat; Sasha C Makohon-Moore; Tamara Abulez; Jordan A Driscoll; Joshua P Schaaf; Brian L Hood; Kelly A Conrads; Ming Zhou; Valerie Calvert; Mariaelena Pierobon; Jeremy Loffredo; Katlin N Wilson; Tracy J Litzi; Pang-Ning Teng; Julie Oliver; Dave Mitchell; Glenn Gist; Christine Rojas; Brian Blanton; Kathleen M Darcy; Uma N M Rao; Emanuel F Petricoin; Neil T Phippen; G Larry Maxwell; Thomas P Conrads

doi:10.1186/s12014-024-09451-2

Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling

Clin Proteomics. 2024 Jan 22;21(1):4. doi: 10.1186/s12014-024-09451-2.

Authors

Allison L Hunt^#^{1

2}, Nicholas W Bateman^#^{2

3

4}, Waleed Barakat^{2

3}, Sasha C Makohon-Moore^{2

3}, Tamara Abulez^{2

3}, Jordan A Driscoll^{2

3}, Joshua P Schaaf^{2

3}, Brian L Hood^{2

3}, Kelly A Conrads^{2

3}, Ming Zhou^{1

2}, Valerie Calvert⁵, Mariaelena Pierobon⁵, Jeremy Loffredo^{2

3}, Katlin N Wilson^{2

3}, Tracy J Litzi^{2

3}, Pang-Ning Teng^{2

3}, Julie Oliver^{2

3}, Dave Mitchell^{2

3}, Glenn Gist^{2

3}, Christine Rojas², Brian Blanton^{2

3}, Kathleen M Darcy^{2

3

4}, Uma N M Rao^{2

3}, Emanuel F Petricoin⁵, Neil T Phippen^{2

3

4}, G Larry Maxwell^{1

2

4}, Thomas P Conrads^{6

7

8}

Affiliations

¹ Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA.
² Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
³ The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA.
⁴ Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
⁵ Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
⁶ Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA. conrads@whirc.org.
⁷ Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA. conrads@whirc.org.
⁸ Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA. conrads@whirc.org.

^# Contributed equally.

Abstract

Background: Although uterine serous carcinoma (USC) represents a small proportion of all uterine cancer cases, patients with this aggressive subtype typically have high rates of chemotherapy resistance and disease recurrence that collectively result in a disproportionately high death rate. The goal of this study was to provide a deeper view of the tumor microenvironment of this poorly characterized uterine cancer variant through multi-region microsampling and quantitative proteomics.

Methods: Tumor epithelium, tumor-involved stroma, and whole "bulk" tissue were harvested by laser microdissection (LMD) from spatially resolved levels from nine USC patient tumor specimens and underwent proteomic analysis by mass spectrometry and reverse phase protein arrays, as well as transcriptomic analysis by RNA-sequencing for one patient's tumor.

Results: LMD enriched cell subpopulations demonstrated varying degrees of relatedness, indicating substantial intratumor heterogeneity emphasizing the necessity for enrichment of cellular subpopulations prior to molecular analysis. Known prognostic biomarkers were quantified with stable levels in both LMD enriched tumor and stroma, which were shown to be highly variable in bulk tissue. These USC data were further used in a comparative analysis with a data generated from another serous gynecologic malignancy, high grade serous ovarian carcinoma, and have been added to our publicly available data analysis tool, the Heterogeneity Analysis Portal ( https://lmdomics.org/ ).

Conclusions: Here we identified extensive three-dimensional heterogeneity within the USC tumor microenvironment, with disease-relevant biomarkers present in both the tumor and the stroma. These data underscore the critical need for upfront enrichment of cellular subpopulations from tissue specimens for spatial proteogenomic analysis.

Keywords: Intratumor heterogeneity; Laser microdissection; Proteogenomics; Proteomics; Spatial proteomics; Tumor microenvironment; Uterine serous carcinoma.

Abstract

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