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1437 Proteomic profiling of tumor microenvironment in desmoplastic melanoma using the nanostring geomx digital spatial profiler
  1. David Su1,
  2. David A Schoenfeld2,
  3. Wael Ibrahim3,
  4. Raymond Baumann4,
  5. David Rimm3,5,
  6. Harriet Kluger6,
  7. Kelly Olino7,
  8. Anjela Galan3 and
  9. Jim Clune7
  1. 1Yale New Haven Hospital, Hamden, CT, USA
  2. 2Yale University, North Haven, CT, USA
  3. 3Yale New Haven Hospital, Department of Pathology, New Haven, CT, USA
  4. 4Yale New Haven Hospital, New Haven, CT, USA
  5. 5Yale New Haven Hospital, Department of Medical Oncology, New Haven, CT, USA
  6. 6Yale University, New Haven, CT, USA
  7. 7Yale New Haven Hospital, Department of Surgical Oncology, New Haven, CT, USA
  • Journal for ImmunoTherapy of Cancer (JITC) preprint. The copyright holder for this preprint are the authors/funders, who have granted JITC permission to display the preprint. All rights reserved. No reuse allowed without permission.


Background Desmoplastic melanoma (DM) is a rare melanoma subtype characterized by dense fibrous stroma and a propensity for local recurrence.1 2 Rates of occult sentinel lymph node positivity vary drastically between its two distinct histological subtypes, pure and mixed, presenting challenges in treatment and prognosis.3–5 A subset of activated cancer-associated fibroblasts (CAFs), characterized by alpha smooth muscle actin (SMA), has been associated with adverse prognosis in cancers with significant desmoplasia.6 Since DM has a high response rate to anti-PD-1 blockade,7 8 understanding the role of CAFs and lymphocytic aggregates (LA) in DM is crucial for informing therapeutic strategies and developing better prognostic biomarkers.6 9 10

Methods Tissue microarray slide was assembled, comprising 141 cores extracted from tissue sections of tumor, stroma, or LA. Samples were obtained from 45 patients with histologically confirmed DM, spanning a period from 1989 to 2018. High-plex proteomic analysis was performed using the Nanostring GeoMx platform with spatial resolution. Digital counts from a 68-plex panel of oligo-linked protein probes were quantified simultaneously in three tissue compartments defined by fluorescence colocalization [tumor (S100+/PMEL+), leukocytes (CD45+), and nonimmune stroma (S100-/PMEL-/CD45-/SYTO+)]. (figure 1a) Barcodes were normalized with internal spike-in controls to account for system variation.

Results Of 45 patients with desmoplastic melanoma, 24% were female (11/45) and the median age was 74. 82% (37/45) had pure histology, 80% (36/45) originated in the head and neck region, 41% exhibited perineural invasion, and median Breslow’s thickness was 4.9mm. 18% (8/45) received immunotherapy, 44% experienced recurrences, and 18% developed distant metastases. SMA+ CAFs were significantly enriched in the tumor compared to the stromal compartment (p=0.002), more prevalent in pure than mixed DM (p= 0.034) and associated with a worse overall survival (OS) on univariate Cox proportional hazards (p = 0.045) (figure 1b/1c). Compared to mixed DM, pure DM also expressed higher levels of intra-tumoral CD34+ (p=0.031) and fibronectin (p=0.001). When comparing LA to non-LA tumor cores, LA were more enriched with CD20+ B-cells (p=0.008), but non-LA tumor cores had higher LAG3 expression levels (p=0.014). High expressions of LAG-3 (p=0.028), CTLA-4 (p=0.033), and Ki-67 (p=0.026) within the leukocyte compartment were associated with worse OS on univariate analysis.

Conclusions Our proteomic analysis revealed an intra-tumoral population of SMA+ CAFs enriched in pure DM. Differences between pure and mixed DM might have therapeutic implications and guide treatment selection in addition to informing potential prognostic significance.


  1. Chen LL, Jaimes N, Barker CA, Busam KJ, Marghoob AA. Desmoplastic melanoma: a review. J Am Acad Dermatol. 2013;68(5):825–33. Epub 20121223. doi: 10.1016/j.jaad.2012.10.041. PubMed PMID: 23267722; PMCID: PMC4703041.

  2. Nicolson NG, Han D. Desmoplastic melanoma. J Surg Oncol. 2019;119(2):208–15. Epub 20181127. doi: 10.1002/jso.25317. PubMed PMID: 30481377.

  3. Ran NA, Veerabagu S, Miller CJ, Elenitsas R, Chu EY, Krausz AE. Local Recurrence Rates After Excision of Desmoplastic Melanoma: A Systematic Review and Meta-Analysis. Dermatol Surg. 2023;49(4):330–7. Epub 20230301. doi: 10.1097/DSS.0000000000003699. PubMed PMID: 36857167.

  4. Pavri SN, Clune J, Ariyan S, Narayan D. Malignant melanoma: beyond the basics. Plastic and reconstructive surgery. 2016;138(2):330e-40e.

  5. Laeijendecker AE, El Sharouni MA, Sigurdsson V, van Diest PJ. Desmoplastic melanoma: The role of pure and mixed subtype in sentinel lymph node biopsy and survival. Cancer Med. 2020;9(2):671–7. Epub 20191205. doi: 10.1002/cam4.2736. PubMed PMID: 31804771; PMCID: PMC6970026.

  6. Zeltz C, Primac I, Erusappan P, Alam J, Noel A, Gullberg D, editors. Cancer-associated fibroblasts in desmoplastic tumors: emerging role of integrins. Seminars in cancer biology; 2020: Elsevier.

  7. Kendra KL, Moon J, Eroglu Z, Hu-Lieskovan S, Carson WE, Wada DA, Plaza JA, In GK, Ikeguchi A, Hyngstrom JR. Neoadjuvant PD-1 blockade in patients with resectable desmoplastic melanoma (SWOG 1512). American Society of Clinical Oncology; 2022.

  8. Eroglu Z, Zaretsky JM, Hu-Lieskovan S, Kim DW, Algazi A, Johnson DB, Liniker E, Ben K, Munhoz R, Rapisuwon S, Gherardini PF, Chmielowski B, Wang X, Shintaku IP, Wei C, Sosman JA, Joseph RW, Postow MA, Carlino MS, Hwu WJ, Scolyer RA, Messina J, Cochran AJ, Long GV, Ribas A. High response rate to PD-1 blockade in desmoplastic melanomas. Nature. 2018;553(7688):347–50. Epub 20180110. doi: 10.1038/nature25187. PubMed PMID: 29320474; PMCID: PMC5773412.

  9. Stowman AM, Hickman AW, Mauldin IS, Mahmutovic A, Gru AA, Slingluff Jr CL. Lymphoid aggregates in desmoplastic melanoma have features of tertiary lymphoid structures. Melanoma research. 2018;28(3):237.

  10. Lauss M, Donia M, Svane IM, Jönsson G. B Cells and Tertiary Lymphoid Structures: Friends or Foes in Cancer Immunotherapy? B Cells in Cancer. Clinical Cancer Research. 2022:OF1-OF8.

Abstract 1437 Figure 1

Slides were stained with antibodies for S100, PMEL, and CD45 and probes were quantified in three tissue compartments defined by fluorescence colocalization [tumor (S100+/PMEL+), leukocytes (CD45+), and nonimmune stroma (S100-/PMEL-/CD45-/SYTO+)] (A). SMA was significantly more enriched in pure DM than mixed DM (p = 0.034) (B) and associated with worse OS on univariate analysis (p=0.045). (C)

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