Wistuba, Ignacio I.

Abstract Background: Immune checkpoint inhibitors (ICIs) have improved survival in non-small-cell lung cancer (NSCLC), yet only a subset of patients benefits, and biomarkers like PD-L1 remain limited. Here, we introduce a deep learning-based pathomics framework that utilizes routine H&E-stained slides to predict therapeutic response and survival outcomes in ICI-treated metastatic NSCLC. Methods: The study included 797 ICI-treated NSCLC patients from MD Anderson, with external validation in 280 patients from Mayo Clinic, Gustave Roussy, and the Phase III ICI-naïve LUSC Lung-MAP S1400I trial receiving nivolumab with or without ipilimumab. Path-IO (Pathology-Driven Immunotherapy Optimization) comprised of four major steps: (1) pathologist-verified tissue classifier segmented WSIs into eight compartments—Background, Bronchi, Immune, Lung, Necrosis, Stroma, Tumor, and Vessel—and was validated on TCGA and CPTAC dataset; (2) a survival prediction module generating patient-level risk scores in the MD Anderson cohort and validated across external datasets; (3) integration of Path-IO risk scores with radiomics and clinical features to improve prognostic accuracy; and (4) biological interpretability analyses correlating Path-IO risk immune contexture from multiplex immunofluorescence and transcriptomic signatures from NanoString profiling. Results: Path-IO effectively stratified patients into high and low-risk groups with significant survival differences. In the MD Anderson cohort, it achieved HR = 2.11 (p < 0.001) and HR = 2.51 (p < 0.001) for OS in the discovery and validation sets, and HR = 2.34 (p < 0.001) and HR = 1.87 (p < 0.001) for PFS, respectively. In the multicenter Phase III Lung-MAP S1400I trial, Path-IO achieved HR = 1.78 (p = 0.016) for OS and HR = 2.76 (p = 0.006) for PFS. In external validation, it predicted outcomes in the Gustave Roussy (OS = 1.97, p = 0.003; PFS = 1.51, p = 0.046) and Mayo Clinic (OS = 2.46, p = 0.007; PFS = 2.45, p = 0.027) cohorts. Path-IO outperformed PD-L1 and remained an independent predictor in multivariate analysis (p < 0.001). It enabled data-driven frontline selection between anti-PD-1 monotherapy and chemo-immunotherapy, offering guidance toward more personalized treatment decisions. Integration with radiomics and clinical features further improved predictive accuracy (OS 0.63→0.75; PFS C-index 0.58→0.70), while high Path-IO risk scores correlated with immune-cold phenotypes identified by multiplex immunofluorescence and NanoString transcriptomics. Conclusions: Path-IO demonstrates that deep learning models rooted in histopathologic architecture can generate interpretable and biologically informed survival predictions in NSCLC treated with ICIs. By integrating pathology, radiology, and clinical data, Path-IO provides complementary predictive value beyond established biomarkers such as PD-L1. Citation Format: Rukhmini Bandyopadhyay, Linghzi Hong, Mihaela Aldea, Shenduo Li, Lodovica Zullo, Frank R. Rojas, Maliazurina B. Saad, Maricel C. Marin, Muhammad Waqas, Jiexin Zhang, Eman Showkatian, Claudio A. Arrechedera, Xiaoyu Han, Yuliya Kitsel, Sherif Ismail, Muhammad Aminu, Bo Zhu, Carol C. Wu, Brett W. Carter, Joe Y Chang, Zhongxing Liao, Maria R. Ghigna, Davide Soldato, Hai T. Tran, Xiuning Le, Tina Cascone, Bingnan Zhang, Haniel A. Araujo, Mehmet Altan, Simon Heeke, David Jaffray, Don L. Gibbons, Ara Vaporciyan, J Jack Lee, Neda Kalhor, Cara Haymaker, Ignacio Wistuba, John V. Heymach, Yanyan Lou, Natalie Vokes, Luisa M. Solis Soto, Jianjun Zhang, Jia Wu. Path-IO: A deep learning pathomics framework for personalized immunotherapy selection and outcome prediction in metastatic non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4003.

Multiplex immunofluorescence and immunohistochemistry (mIF/IHC) are increasingly employed antibody-based technologies that use tissue sparingly and facilitate the detection of co-localized or neighboring biomarkers. Specifically, these platforms enable spatial analyses of the tumor microenvironment as well as extended applications, for example, describing normal tissue anatomy, autoimmunity, infectious diseases, etc. mIF/IHC has greatly enhanced biomarker discovery efforts, and a growing number of studies suggest superiority to traditional IHC. Standardization of staining approaches, reporting of image analysis strategies and resultant data is critical for facilitating cross-study comparisons, validation, deployment, and generalization of findings. To address this challenge, The Society for Immunotherapy of Cancer (SITC) previously published two articles providing best practice guidelines for mIF/IHC staining, image analysis, and data sharing. Here, SITC convened stakeholders to develop the third article in the series, a consensus checklist for scientific reporting of mIF/IHC data to support and complement the best practice guidelines. The checklist includes critical components of mIF/IHC applications to be defined within publications such as detailed descriptions of analytical validation; image acquisition, selection, and registration methods; and cell clustering and spatial analysis strategies, amongst others. Such information will help with data reproducibility and comparison across studies towards future drug and assay development.

TPS4201 Background: Poorly differentiated, extrapulmonary NEC are rare cancers with median overall survival (OS) <1 year. Treatment is extrapolated from small cell lung cancer (SCLC) with use of P (cisplatin or carboplatin) + E. More effective treatment regimens and predictive biomarkers are needed to improve outcomes. In SCLC, induction therapy with combination of P/E + PD-L1 checkpoint inhibitor atezolizumab and maintenance atezolizumab improved OS (12.3 months vs 10.3 months; HR 0.70, 95% CI 0.54 – 0.91, P=0.007) vs P/E alone (1). No study to date has compared PD-1/PD-L1 inhibition during induction only vs during induction and maintenance therapy. In SCLC, distinct molecular subtypes can be identified by the presence of specific transcription factors (e.g., ASCL1, NEUROD1, POU2F3) or an inflamed gene signature (SCLC-I), with SCLC-I pts more likely to benefit clinically from the addition of immunotherapy (2). In this study we plan to test the benefit of adding atezolizumab to induction P/E as well as the role of adding maintenance atezolizumab after induction P/E plus atezolizumab. We also plan to correlate tumor- and blood-based subtype biomarkers with response to therapy. Methods: Eligible pts ≥18 years old have evaluable, histologically confirmed extrapulmonary NEC, Zubrod PS ≤2, and are allowed to have up to 1 cycle of P/E prior to enrollment. P (cisplatin 75 mg/m2 or carboplatin AUC 5, iv) on day 1, E 100 mg/m2 iv on days 1-3, and atezolizumab 1200 mg iv on day 1 of q21 day cycles. Pts are randomized to 1 of 3 arms: A) Induction P/E + atezolizumab -> maintenance atezolizumab B) Induction P/E + atezolizumab -> observation C) Induction P/E -> observation. The primary objective is to compare the overall survival (OS, from randomization) between arms in a fixed sequence: A vs C -> B vs C -> A vs B. Secondary objectives include comparing OS (from start of maintenance/observation), progression free survival, response rate, duration of response, and safety/tolerability across arms. Tumor and blood samples will be banked for future biomarker analyses, including immunohistochemistry of transcription factors on tissue and whole exome sequencing on tumor and circulating tumor DNA. With 189 pts (168 eligible), the study has 84% power to detect an improvement in 12-months OS from 35% to 57.5% (HR 0.53). This study was activated December 2021 with 3 pts enrolled over 1 year due to restricting enrollment of NEC of small cell histology only. The protocol was amended in January 2023 to broaden eligibility to all NEC subtypes (small cell, large cell, and undefined histology with Ki-67 ≥55%). As of January 2024, 35 patients have been enrolled. A protocol amendment is planned to remove the need for Ki-67 index for NEC of genitourinary origin to improve accrual. 1. Horn L, et al. N Engl J Med 2018. 2. Gay CM, et al. Cancer Cell 2021. Clinical trial information: NCT05058651 .

Abstract To investigate the cellular and molecular mechanisms associated with targeting CD30-expressing Hodgkin lymphoma (HL) and immune checkpoint modulation induced by combination therapies of CTLA4 and PD1, we leveraged Phase 1/2 multicenter open-label trial NCT01896999 that enrolled patients with refractory or relapsed HL (R/R HL). Using peripheral blood, we assessed soluble proteins, cell composition, T-cell clonality, and tumor antigen-specific antibodies in 54 patients enrolled in the phase 1 component of the trial. NCT01896999 reported high (&gt;75%) overall objective response rates with brentuximab vedotin (BV) in combination with ipilimumab (I) and/or nivolumab (N) in patients with R/R HL. We observed a durable increase in soluble PD1 and plasmacytoid dendritic cells as well as decreases in plasma CCL17, ANGPT2, MMP12, IL13, and CXCL13 in N-containing regimens (BV + N and BV + I + N) compared with BV + I (P &lt; 0.05). Nonresponders and patients with short progression-free survival showed elevated CXCL9, CXCL13, CD5, CCL17, adenosine–deaminase, and MUC16 at baseline or after one treatment cycle and a higher prevalence of NY-ESO-1-specific autoantibodies (P &lt; 0.05). The results suggest a circulating tumor-immune-derived signature of BV ± I ± N treatment resistance that may be useful for patient stratification in combination checkpoint therapy. Significance: Identification of multi-omic immune markers from peripheral blood may help elucidate resistance mechanisms to checkpoint inhibitor and antibody–drug conjugate combinations with potential implications for treatment decisions in relapsed HL.

Background: We previously reported that treatment with the anti-CD30 antibody-drug conjugate brentuximab vedotin (BV) in combination with the checkpoint inhibitors targeting CTLA-4 and/or PD-1 (ipilimumab (I) and nivolumab (N)) led to high overall response rates (ORR) and complete response (CR) rates in relapsed/refractory (R/R) Hodgkin's lymphoma patients in a Phase 1 ECOG-ACRIN sponsored clinical trial. As previously presented in the Phase 1 component of NCT01896999 (E4412), the ORR for the treatment arms were: BV+I 76%, BV+N 89%, and BV+I+N 82%, with CR rates of 57%, 61%, and 73% across the groups, respectively. This suggested that not all patients who responded derived equal benefit. Moreover, with a median follow-up of 2.24 years, the PFS of 1.1 year, NR, and 2.49 years across the groups suggest that even some patients who achieved CR progressed on or subsequent to treatment. Currently biomarkers have no ability to predict which patients will maximally benefit from these therapies. We investigated blood-based immune biomarkers mechanistically across all cohorts which may explain differential responses and guide future treatment decisions for R/R HL patients. Methods: Peripheral blood plasma for 54 of 61 (89%) patients evaluable for response was collected at up to 4 time points and tested for 92 immuno-oncology soluble analytes with Olink proximity extension assay and for antibody titers to 20 known tumor antigens by ELISA. Matching peripheral blood mononuclear cells (PBMC) were analyzed by CyTOF mass cytometry for major immune cell subsets and marker surface expression, and for T cell receptor diversity by Immunoseq®. Mixed effect linear models were used to identify significantly associated changes (P&lt;0.05) related to treatment longitudinally within groups and to ORR between groups. Results: Analysis of plasma demonstrated durable increase in soluble plasma PD-1 and decreases in CCL17, ANGPT2, MMP12, IL13, and CXCL13 in N-containing regimens, and higher GZMA and CAIX in BV+I (P&lt;0.05). Despite baseline heterogeneity in PBMC composition, we found durable increases in plasmacytoid dendritic cells (pDC) after N-containing treatments, and transient increases in plasmablasts and memory B cells, as well as early decreases in naïve CD4+ T cells and neutrophils across treatments. Treatment with BV+I+N demonstrated late increases in neutrophils, and changes in memory B cell markers. Clinical benefit analyses revealed that elevated soluble CD5, ADA, CXCL13, and CCL17 at baseline or after two treatment cycles were associated with worse ORR (P&lt;0.05), and that a module of co-regulated soluble analytes at baseline, including MUC16, was associated with worse progression free survival (PFS) (P&lt;0.05). NY-ESO-1 autoantibodies were more frequent in non-responders, and the top 10% of expanded TCR clonotypes were increased in responders after one treatment cycle (P&lt;0.05). Conclusion: This data reveals differential immune activation based on treatment modality for patients with R/R HL receiving checkpoint-based regimens in combination with an ADC. Our data highlights potential tumor- and immune-derived predictive and pharmacodynamic biomarker candidates of response and resistance. These novel findings have relevance for R/R HL patients receiving immunotherapy and other immunotherapy combinations such as immuno-chemotherapy platforms. Prospective evaluation of these biomarkers in the Phase II component of this study, a randomized comparison of BV+N vs. BV+N+I which has completed adult accrual, is planned. Figure Legend Clinical responders and non-responder patient samples were analyzed using ELISA (auto antibodies), CyTOF (Cell populations), TCRseq (T cell clonality) and Olink (proteomics). The results showed that pDCs, Neutrophils and B-Plasmablasts increased with specific drug combinations independently of clinical response. While T Cell expansion was associated with clinical response, the increase of auto antibodies against NY-ESO-1 and circulating proteins CD5, ADA, MUC16, CXCL13, CXCL9 and CCL17 were associated with worse prognosis

Abstract Patients diagnosed with germline mutations in MMR genes (Lynch Syndrome, LS) have up to 70-80% lifetime risk of colorectal cancer. Therefore, this high-risk population has the potential to benefit from effective chemopreventive strategies. Naproxen is an NSAID widely used for pain treatment with an excellent safety profile that has demonstrated to be more efficacious preventing colorectal cancer compared to aspirin in vivo using an intestinal tissue-specific mouse model of LS (VC-Msh2-LoxP). The ‘Naproxen trial' was designed to evaluate the modulation of PGE2 levels in colorectal mucosa, evaluate safety and tolerability, and discover novel molecular pathways involved in the chemopreventive activity of naproxen in LS patients. Methods: Participants were randomized to naproxen 440 mg (HD), 220 mg (LD) and placebo by mouth daily for 6 months. Modulation of prostaglandin levels, number of adverse events (AEs) observed in each treatment arm and gene expression profiles by next-generation sequencing (mRNAseq) in normal colorectal mucosa of LS patients after 6 months of intervention were examined. Results: Eighty participants diagnosed with LS were randomized, 25 participants to HD, 27 to LD, and 28 to placebo. From these patients, 54 were considered evaluable per-protocol analysis: 16 in the HD group, 15 in the LD and 23 in placebo. The level of prostaglandin E2 in the colorectal mucosa decreased significantly after treatment with both LD and HD naproxen when compared to placebo (-91.2%±14.1, -93.6%±7.9, and 23.8%±108.4, P-value&lt;0.001, respectively). Moreover, levels of PGE2 urinary metabolite (PGE-M) were significantly changed in both treatment groups when compared to placebo (-47.7%±56.9, -41.1%±40.5, 7.6%±94.3, P-Value&lt;0.018). The intervention was well tolerated, no severe AEs related to treatment were reported, and the total number of AEs was not different across treatment arms. LD and HD naproxen promoted the activity of the immune system by activating different immune cell types without any effect on lymphoid cellularity and changed the expression patterns of the intestinal crypt towards epithelial differentiation and stem cell regulation. Conclusions: Naproxen is a promising strategy for immune interception in LS that induces immune-modulation coupled with changes in the dynamics of the intestinal crypt. We have also discovered naproxen-induced gene expression profiles for their potential use as predictive biomarkers of drug activity. Citation Format: Laura Reyes Uribe, Wenhui Wu, Ozkan Gelincik, Prashant V. Bommi, Alejandro Francisco-Cruz, Luisa M. Solis, Patrick M. Lynch, Ramona Lim, Elena Stoffel, Priyanka Kanth, N. Jewel Samadder, Maureen E. Mork, Melissa W. Taggart, Ginger L. Milne, Lawrence J. Marnett, Lana Vornik, Diane D. Liu, Maria Revuelta, Kyle Chang, Y. Nancy You, Levy Kopelovich, Ignacio I. Wistuba, J. Jack Lee, Shizuko Sei, Robert H. Shoemaker, Eva Szabo, Ellen Richmond, Asad Umar, Marjorie Perloff, Powell H. Brown, Steven M. Lipkin, Eduardo Vilar. Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT111.

Objective Patients with Lynch syndrome (LS) are at markedly increased risk for colorectal cancer. It is being increasingly recognised that the immune system plays an essential role in LS tumour development, thus making an ideal target for cancer prevention. Our objective was to evaluate the safety, assess the activity and discover novel molecular pathways involved in the activity of naproxen as primary and secondary chemoprevention in patients with LS. Design We conducted a Phase Ib, placebo-controlled, randomised clinical trial of two dose levels of naproxen sodium (440 and 220 mg) administered daily for 6 months to 80 participants with LS, and a co-clinical trial using a genetically engineered mouse model of LS and patient-derived organoids (PDOs). Results Overall, the total number of adverse events was not different across treatment arms with excellent tolerance of the intervention. The level of prostaglandin E2 in the colorectal mucosa was significantly decreased after treatment with naproxen when compared with placebo. Naproxen activated different resident immune cell types without any increase in lymphoid cellularity, and changed the expression patterns of the intestinal crypt towards epithelial differentiation and stem cell regulation. Naproxen demonstrated robust chemopreventive activity in a mouse co-clinical trial and gene expression profiles induced by naproxen in humans showed perfect discrimination of mice specimens with LS and PDOs treated with naproxen and control. Conclusions Naproxen is a promising strategy for immune interception in LS. We have discovered naproxen-induced gene expression profiles for their potential use as predictive biomarkers of drug activity. Trial registration number gov Identifier: NCT02052908

6010 Background: An evolutionary action scoring algorithm (EAp53) based on phylogenetic sequence variations and speciation stratifies head and neck squamous cell carcinoma (HNSCC) patients bearing TP53 missense mutations as high-risk (high, EAp53≥75), associated with poor outcomes, or low-risk (low), with similar outcomes as TP53 wild-type (wt), and has been validated as a reliable prognostic marker. This study is designed to further validate prior findings that EAp53 is a prognostic marker for locally advanced HNSCC patients, and assess its predictive value for treatment outcomes to adjuvant bio-chemoradiotherapy. Methods: Eighty one resection specimens from patients treated surgically for stage III or IV human papillomavirus-negative (HPV(-)) HNSCC with high-risk pathologic features, who received either Arm 1) radiotherapy(RT)+cetuximab(CTX)+cisplatin or Arm 2) RT+CTX+docetaxel, as adjuvant treatment in a phase II randomized clinical trial (RTOG 0234) underwent TP53 targeted sequencing, and EAp53 scoring. The EAp53 scores were correlated with clinical outcomes. Due to limited sample sizes, patients were combined into 2 EAp53 groups: wt/low and high/other. Results: At median follow-up of 10 years, there was a significant interaction between treatment and EAp53 group for overall survival (OS) (p = 0.008), disease-free survival (DFS) (p = 0.05) and distant metastasis (DM) (p = 0.004). Within arm 2, high/other showed worse OS [HR 4.69 (1.52-14.50)], DFS [HR 2.69 (1.16-6.21)], and had higher DM [HR 11.71 (1.50-91.68)] than wt/low. Within arm 1, there was no significant difference by EAp53 in OS, DFS and DM. Within the wt/low group, arm 2 had better OS [HR 0.11 (0.03-0.36)], DFS [HR 0.24 (0.09-0.61)], and DM [HR 0.04 (0.01-0.31)] than arm 1 but this was not found in high/other. Conclusions: High/other EAp53 scores were associated with worse survival for patients in arm 2. Arm 2 is associated with better survival than arm 1 for patients with wt/low EAp53. This benefit appears to be largely driven by a reduction in DM. Further validation is required to determine whether EAp53 can be used for personalized post-operative treatment decisions in HPV(-) HNSCC.

Suppression of ZEB1 through miR-200 expression or HDAC inhibition with mocetinostat sensitizes resistant KRAS mutant lung cancers to MEK inhibition.