Characterizing chromosome 3p/q genes as biomarkers of treatment response in squamous cell carcinoma of the lung and head and neck.
Authors: Schokrpur Shiruyeh , Deshmukh Sachin , Wu Sharon , Xiu Joanne , Quayle Carol , Abdulla Farah Rukshana , Kim Chul , Darabi Sourat , Demeure Michael J. , Vanderwalde Ari M. , Wise-Draper Trisha Michel 
Published: June 2023

e18048

Background: There is an urgent need to improve treatment options for lung squamous cell carcinoma (LUSC) and head and neck squamous cell carcinoma (HNSCC). Immunotherapy (IO) is used in both diseases, but response rates are ~20% to monotherapy. Chromosome alterations in 3p/3q are frequently found in both LUSC and HNSCC. Here we examined the association of expression of Chromosome 3p/3q genes with treatment outcomes and immune microenvironment. Methods: 3833 LUSC and 1386 HNSCC biopsies were analyzed by next-generation sequencing (592, NextSeq; WES, WTS NovaSeq). Selected Chr 3p ( DLEC1, FOXP1, LTF) and Chr 3q ( SOX2) genes were classified by above (-H, high) or below (-L, low) median RNA expression. HPV status inferred by staining of p16 by IHC. Real world median overall survival (mOS) was obtained from insurance claims and calculated from tissue collection or first IO treatment to last contact using Kaplan-Meier estimates. Immune cell infiltration was estimated based on RNA deconvolution method Quantiseq. Statistical significance was determined by chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q < 0.05). Results: High LTF ( LTF-H) was associated with improved OS in both LUSC (mOS: 559 vs 349 days; HR: 0.7, 95% CI (0.6-0.7)) and HNSCC (mOS: 567 vs 473 days; HR: 0.8, 95% CI (0.7-0.9)) (p < 0.01). LTF-H was also associated with improved post-IO survival in both LUSC (Pembro, mOS: 532 vs 349 days; HR: 0.8, 95% CI (0.6-0.9)) and HNSCC (Nivo, mOS: 797 vs 604 days; HR: 0.5, 95% CI (0.2-0.9)) (p < 0.05). Interestingly, this improved OS was specific to HPV+ HNSCC patients (Nivo, Pembro mOS: 1210 vs 473 days; HR: 0.39, 95% CI (0.22-0.69) (p < 0.01)) and not HPV- HNSCC patients (Nivo, Pembro mOS: 313 vs 336 days; HR 0.98, 95% CI (0.664-1.47) (p = 0.95)). LTF-H LUSC and HNSCC had increased IFNy score (-0.24 vs -0.30; -0.16 vs -0.23, p < 0.05) and immune cell infiltration of B cells (median cell fraction: 6.9% vs 5.8%; 6.9% vs 5.3%), M2 Mφ (5.7% vs 5.1%; 4.3% vs 3.8%), NK cells (3.1% vs 2.8%; 3.3% vs 2.7%), CD4 T cells (1.7% vs 1%; 1.7% vs 1%), CD8 T cells (1.5% vs 1%; 1.5% vs 1%) and Tregs (3.1% vs 2.4%; 4.1% vs 3.5%) compared to LTF-L tumors, respectively (all p < 0.05). Additionally, high DLEC1 was associated with improved OS in LUSC (mOS: 484 vs 392 days; HR: 0.8, 95% CI (0.8-0.9)) and HNSCC (mOS: 594 vs 448 days; HR: 0.7, 95% CI (0.6-0.9) (p < 0.01)). FOXP1 expression did not correlate with different survival in LUSC or HNSCC. High SOX2 expression was associated with an improved OS in LUSC (mOS: 526 vs 352 days; HR: 0.7, 95% CI (0.7-0.8)) and HNSCC (mOS: 634 vs 404 days; HR: 0.7, 95% CI (0.6-0.8)) (p < 0.01). Conclusions: Our data suggest a strong association between LTF expression and differential immune cell infiltration and improved overall survival. Future studies interrogating additional Chr 3q/3p alterations may provide further information of the prognostic implications of LTF in LUSC and HNSCC.