6075 Background: The rising incidence of oropharyngeal squamous cell carcinoma (OPSCC) is largely attributable to human papillomavirus associated (HPV+) disease, which accounts for ~70% of OPSCC cases. Circulating tumor (ct)DNA has the potential to enable more accurate treatment response assessment, guide response-adaptive management, and detect minimal residual disease to indicate persistence or recurrence. Both mutation-based tumor-informed ctDNA and ctHPV-DNA testing have demonstrated utility in HPV+ disease, but prospective intrapatient evaluations remain limited. A direct comparison of these approaches is essential to determine redundancy versus complementarity and to guide optimal integration into OPSCC patient management. Methods: In an ongoing prospective study, serial plasma samples were obtained from patients with stages I-IV OPSCC undergoing curative intent treatment. Up to 50 patient specific somatic variants were selected based on tumor whole exome sequencing to develop a personalized tumor-informed next generation sequencing (NGS) ctDNA assay (Haystack MRD) for plasma analysis. In patients with HPV+ disease (determined via ISH, IHC, and/or NGS), plasma was also analyzed using an NGS-based assay interrogating 13 high-risk HPV strains (Haystack HPV). Paired intrapatient samples were analyzed using percent agreement with 95% confidence intervals and Cohen’s kappa; concordance of dynamic changes was assessed using Spearman’s correlation. Results: As of January 2026, ctDNA results were available for 111 serial timepoints from 26 patients. The median number of timepoints per patient was 4 (range 1-9). Seventeen patients (65%) had HPV+, and 9 (35%) had HPV− disease. In HPV+ patients, across 85 longitudinal samples collected during multimodal treatment and post-treatment surveillance, mutation-based ctDNA and ctHPV demonstrated high concordance (91%; 95% CI, 82.5–95.2; κ=0.80). Of 30 ctDNA+ samples, 28 were ctHPV+ (93%; 95% CI, 78.7–98.2%), while 49 of 55 ctDNA- samples were ctHPV- (89%; 95% CI, 78.2–94.9%). Discordance was infrequent (8/85, 9.4%), predominantly ctHPV+/ctDNA- (6/85, 7.1%). All ctHPV+/ctDNA- cases occurred during neoadjuvant treatment monitoring and reflected earlier clearance of ctDNA, with ctHPV clearance lagging by several weeks to months. Two low-level (<100 parts per million) ctDNA+/ctHPV- cases were observed in the adjuvant setting. When both analytes were present, dynamic changes in ctDNA and ctHPV levels were highly concordant (Spearman’s ρ=0.94), although ctHPV was consistently detected at higher absolute levels. Conclusions: In HPV-driven OPSCC, tumor-informed ctDNA and ctHPV show high longitudinal concordance and distinct clearance kinetics, with earlier ctDNA clearance. Ongoing analyses will define how these assays can be optimally integrated into response assessment, treatment adaptation, and surveillance strategies.

ABSTRACT Emerging evidence indicates that a subset of cancer cells enriched for stemness-related gene signatures possess distinct immunomodulatory capacities, enabling these tumor-initiating stem cells (tSCs) to more effectively evade or resist anti-tumor immunity. Despite these advances, the tSC-specific molecular circuits orchestrating their specialized immune privilege program are not well defined. Here, in squamous cell carcinomas of the skin and oral cavity, we comprehensively delineate the unique immune-evasive properties of tSCs and dissect the transcriptional regulation shaping their immunomodulatory programs. By integrating transcriptome profiling, chromatin landscape mapping, genetic perturbation, and single-cell RNA sequencing, we found that the tSC-specific immune program is broadly governed by SOX2, a stemness-associated transcription factor. We demonstrate that SOX2 enables tSCs to sustain immature tumor-associated neutrophils (TANs) and subsequently trigger these myeloid cells to foster the development of tumor-associated macrophages (TAMs). This SOX2-directed tSC-TAN-TAM axis establishes a localized immunosuppressive niche for protecting tSC. SIGNIFICANCE Here, we uncover SOX2 as a master regulator that orchestrates conserved immune modulatory circuits in tSCs to sustain pro-tumor myeloid cell states. These findings place tSCs at the apex of immune landscape remodeling, asserting a central role of stemness-associated program in organizing the immunosuppressive tumor microenvironment.

6097 Background: Neoadjuvant immunotherapy is an emerging strategy in head and neck squamous cell carcinoma to enhance systemic antitumor immunity and enable response-adapted de-escalation. In HPV associated oropharyngeal squamous cell carcinoma (OPSCC), virally encoded oncoproteins represent shared, tumor-specific antigens and a rational immunologic target well suited for the neoadjuvant setting in the presence of intact tumor antigen. We conducted a phase I/II trial evaluating neoadjuvant HPV16-specific viral immunotherapy (HB200; HB201 and HB202 HPV16 therapeutic vaccines) plus chemotherapy followed by response-adapted definitive treatment in non-metastatic HPV16+ OPSCC (NCT05108870). Methods: This investigator-initiated phase I/II trial enrolled patients with previously untreated, non-metastatic HPV16+ OPSCC (N1-3 or T3-4; smokers permitted). All patients received three cycles of neoadjuvant HB200 (HB201 alone or alternating HB202/201) with carboplatin/paclitaxel, followed by radiographic response assessment. Patients with T1-2 tonsil or well-lateralized base of tongue tumors achieving ≥50% tumor shrinkage underwent transoral robotic surgery (TORS) alone. Remaining patients received response and risk adapted radiotherapy (50-70Gy based on risk/response) with or without cisplatin. The primary endpoint was deep response rate (DRR; ≥50% tumor shrinkage). Secondary endpoints included survival and toxicity. Exploratory endpoints included circulating tumor HPV-DNA (ctHPV-DNA), HPV16-specific immunity, and spatial transcriptomics. Results: Thirty-five patients were enrolled (median age 58; 89% male); Twelve patients (34%) received HB201 alone and 23 (66%) received alternating HB202/201. Nineteen patients (54%) were current or former smokers, and 49% had stage II-III (AJCC 8 th edition). The DRR was 87.9% (95% CI, 71.8-96.6). Thirty (86%) received de-escalated definitive therapy. At a median follow-up of 23 months, 2-year PFS and OS were 86% and 100% respectively. Most common AEs during neoadjuvant HB200/chemo were fatigue (97%), nausea (91%), and fever (76%). Detectable ctHPV-DNA following treatment was significantly associated with disease recurrence ( p <0.01). HPV16-specific immune responses and spatial transcriptomic analyses will be presented. Conclusions: Neoadjuvant HB200 combined with chemotherapy resulted in high deep response rates, frequent treatment de-escalation, and excellent survival outcomes in locoregionally advanced HPV16+ OPSCC. These findings support further evaluation of HPV directed immune therapy in neoadjuvant setting. Clinical trial information: NCT05108870 .

Sinonasal squamous cell carcinoma (SNSCC) is a rare malignancy arising de novo or from inverted papilloma (IP), a benign neoplasm with malignant potential. The molecular drivers of IP-associated SNSCC (IP-SNSCC) remain poorly defined, and no effective therapies are available. Progress is hindered by limited preclinical studies and prospective clinical investigations. We performed multi-omic profiling, including whole-exome, RNA, and mitochondrial DNA sequencing (mtDNA-Seq), of matched normal sinonasal epithelium, IP, and SNSCC samples from 11 patients. Analyses revealed a stepwise transcriptional continuum across histological stages, marked by progressive activation of the cell cycle, extracellular matrix remodeling, and metabolic pathways, with suppression of immune and apoptotic signaling. Shared genomic aberrations were detected in only a subset of paired IP and SNSCC specimens, whereas mtDNA-Seq revealed no overlapping mutations, indicating divergent mitochondrial evolution even in clonally related lesions. Given the need for targeted therapies, we applied PandaOmics, an AI-driven target discovery platform, to genes progressively upregulated during IP-SNSCC development. We first prioritized targets with FDA-approved inhibitors, identifying CDK6, EGFR, HDAC, and SRC/YES1 as repurposing candidates, and nominated AURKA, PLK4, TTK, and CDK1/7 as druggable preclinical targets. Together, this study defines the molecular basis of IP-SNSCC and provides a foundation for future translational investigation.

Abstract Immune evasion is a hall mark of cancer, but whether every tumor cell employs similar mechanisms to escape immune surveillance is still under debate. Recent studies pointed to a subset of cancer cells that are enriched with stemness related gene signatures can activate unique immune modulatory program, allowing these tumor initiating stem cells (tSCs) to better evade or resist anti-tumor immunity. However, the tSC specific molecular circuit that orchestrate their specialized immune privilege program remains undefined. Here, we compared the transcriptome of various tumor cell populations isolated from squamous cell carcinomas (SCCs) derived from different tissues. This comprehensive profiling defined distinct immune evasive properties of tSCs. Combining this analysis with chromatin landscape mapping, genetic perturbation, and single cell RNA-sequencing, we identified that the TIC-specific immune modulatory program is broadly regulated by SOX2, a stemness-associated transcription factor. Delving into the mechanism, we first found that SOX2 upregulates fatty acid desaturase 1 (Fads1) to produce arachidonic acid (AA). This tSC specific pathway enhances the prostaglandin E2 (PGE2) signaling in tumor-associated neutrophils (TANs), which can disrupt the interferon response and prevent the interferon induced anti tumor functions in TANs. In addition, SOX2 also promotes tSCs to produce CSF3, facilitating the immature TANs to secrete CSF1, supporting the development of CD206+ tumor-associated macrophages (TAMs). This tSCs TAN TAM crosstalk orchestrated by SOX2 then sculpts a localized immune suppressive niche that protect tSCs. This study uncovers SOX2 functions as the master regulator that governs the conserved stemness-associated immune modulatory circuits to endow the tSCs with enhanced ability to sustain the pro-tumor and immune suppressive cell states of myeloid cells. These findings placed tSCs at the apex position where they instruct the organization of the immune suppressive tumor microenvironment. Citation Format: Yuxuan Miao. Dissecting stemness associated molecular circuits that shape the immune suppressive tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(8_Suppl):Abstract nr LB311.

Macrophages are pivotal mediators of wound healing, yet the cellular programs they employ can be hijacked by cancers to drive tumorigenesis. Although similar macrophage programs support both physiological tissue regeneration and pathological cell growth, the molecular and functional difference between wound-associated macrophages (WAMs) and tumor-associated macrophages (TAMs) remain poorly defined. Here, we perform comparative single-cell RNA sequencing to delineate the dynamic cell states of macrophages during skin wound healing and the progression of cutaneous squamous cell carcinoma. Our analyses reveal that aberrantly regulated lipid metabolism is a distinct feature of TAMs. Critically, our genetic manipulations allow us to identify SOX2High tumorinitiating stem cells as key orchestrators that modulate the lipid metabolism of TAMs and shape their cell states. These findings suggest that disrupting the metabolic crosstalk between tumor-initiating stem cells and TAMs represents a promising strategy to normalize myeloid cell function and enhance cancer immunotherapy efficacy.

The abundant accumulation of neutrophils in various solid cancers has been well recognized, but the functions of tumor-associated neutrophils (TANs) remain controversial. TANs have long been believed to be immune suppressive and have thus been referred to as “myeloid-derived suppressor cells”. However, effective tumor control induced by immunotherapy was recently found to be associated with strong neutrophil signatures. These seemingly contradictory findings highlight the unexpected degree of plasticity and heterogeneity unique to TANs. How the cellular plasticity and functional heterogeneity of TANs are regulated remains unknown. Here, we show that, while anti-PDL1/CD40 agonist immunotherapy can induce interferon responses to reprogram many TANs, allowing them to regain anti-tumor activities in squamous cell carcinomas, a subset of TANs residing at the tumor-stroma interface can preserve their immune suppressive state. Importantly, we identified a group of Sox2Hi tumor-initiating stem cells (tSCs) at the tumor-stroma interface that could upregulate Fatty Acid Desaturase 1 (Fads1) to produce arachidonic acid. This tSC-specific pathway enhances the autocrine prostaglandin E2 (PGE2) signaling in TANs, which can disrupt their interferon responsive potentials, preventing the interferon-mediated reprogramming. Thus, by fine-tuning the plasticity of neutrophils, tSCs shape neutrophil heterogeneity, and sculpt a protective micro-niche to survive from immunotherapy and drive cancer relapse. Weijie Guo, Jingyun Luan, Yuxuan Miao. Tumor-initiating stem cells fine-tune the plasticity of neutrophils to sculpt a protective niche [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 924.

PURPOSE:Human papillomavirus-associated (HPV+) oropharyngeal carcinoma is associated with excellent survival, yet treatment drives substantial toxicity. Improved biomarkers are needed to select patients for de-escalated treatment. Circulating tumor HPV DNA (ctHPV-DNA) represents a promising noninvasive biomarker to gauge treatment response and surveil for disease recurrence. PATIENTS AND METHODS:A prospective biomarker clinical trial of response-stratified de-escalation was conducted. Eligible patients with non-metastatic HPV+ oropharyngeal carcinoma received neoadjuvant chemotherapy, followed by risk/response-stratified de-escalation with transoral robotic surgery, de-escalated radiation with or without chemotherapy to 50 Gy, or standard chemoradiation to 70 Gy. Deep response (≥50% tumor shrinkage per RECIST v1.1) qualified patients for de-escalation. ctHPV-DNA was measured using HPV-SEQ in plasma at baseline, during neoadjuvant chemotherapy, radiation, and following treatment. The primary endpoint was the correlation of ctHPV-DNA kinetics and radiographic response. RESULTS:Forty-six eligible patients were enrolled, and 488 ctHPV-DNA samples were analyzed (median 11 per patient). The median follow-up was 30 months, and five recurrences were observed (10.9%). Baseline ctHPV-DNA was detected in 95% of evaluable patients. Rapid early ctHPV-DNA clearance after one cycle of neoadjuvant therapy (≥95% reduction) predicted radiographic deep response (P = 0.04). Detection of ctHPV-DNA 3 months or later after treatment was associated with worse progression-free and overall survival (P < 0.001). Sensitivity, specificity, and positive and negative predictive values of longitudinal ctHPV-DNA were 100%. The longest lead time from positive ctHPV-DNA to detection of recurrent disease was 25 months. CONCLUSIONS:Rapid early clearance of ctHPV-DNA during neoadjuvant therapy demonstrates utility in predicting response to treatment. Detectable ctHPV-DNA following treatment is predictive of both disease recurrence and worse survival.

Although immunotherapy has been a key innovation in cancer treatment, tumor relapse still poses a major challenge for many patients. Recent research has shown that cancer relapse can be caused by a special group of cancer cells enriched with stemness signatures that survive treatments and repopulate tumors. These cells are referred to as tumor-initiating stem cells (tSCs). The mechanisms by which tSCs survive immunotherapy to drive cancer relapse are still unclear. Using a spontaneous squamous cell carcinoma (SCC) mouse model, we found that tSCs have elevated expression of CD80, a surface molecule that provides co-stimulation to T cells. Notably, the loss of CD80 expression on SCC cells led to diminished tumor growth by blunting the expansion of intratumoral regulatory T cells (Tregs). This interaction between epithelial stem cell and Treg cells can also be found during wound repair where CD80 expression by hair follicle stem cells promotes expansion of Tregs in the wound bed. Interestingly, we found that CD80 on epithelial stem cells facilitates Treg expansion by an unconventional mechanism in which the Foxp3 can be directly induced in preactivated tumor infiltrating CD4+ T cells. Collectively, this study reveals a unique mechanism by which tSCs may sculpt an immunosuppressive niche to evade killing and facilitate tumor relapse. Jennifer L. Good, Weijie Guo, Jingyun Luan, Benjamin T. Nicholson, Yuxuan Miao. Tumor-initiating stem cells utilize the immunomodulatory ligand CD80 to promote Treg expansion and cancer relapse [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 927.

The heterogeneous nature of tumor-associated neutrophils (TANs) has been recognized, but how different cell states of TANs emerge, evolve, distribute, and impact cancer immunotherapy efficacy remain elusive. Using single-cell RNA sequencing, spatial transcriptomics, and genetic manipulations, we show that anti-PDL1 + CD40 agonist immunotherapy can induce interferon responses in TANs, allowing them to regain anti-tumor activities in squamous cell carcinomas (SCCs). In contrast, TANs residing at the tumor-stroma interface can preserve their immune-suppressive state. Importantly, we identify a group of SOX2High tumor-initiating stem cells (tSCs) at the tumor-stroma interface that upregulate fatty acid desaturase 1 (Fads1) to produce arachidonic acid (AA). This tSC-specific pathway enhances the prostaglandin E2 (PGE2) signaling in TANs, which can disrupt the interferon response and prevent the interferon-induced anti-tumor functions in TANs. By fine-tuning the plasticity of neutrophils, tSCs shape neutrophil heterogeneity and sculpt a protective micro-niche to survive from immunotherapy and drive cancer relapse.

BACKGROUND:Adenoid cystic carcinoma (ACC) is a rare glandular malignancy, commonly originating in salivary glands of the head and neck. Given its protracted growth, ACC is usually diagnosed in advanced stage. Treatment of ACC is limited to surgery and/or adjuvant radiotherapy, which often fails to prevent disease recurrence, and no FDA-approved targeted therapies are currently available. As such, identification of new therapeutic targets specific to ACC is crucial for improved patients' outcomes. METHODS:After thoroughly evaluating the gene expression and signaling patterns characterizing ACC, we applied PandaOmics (an AI-driven software platform for novel therapeutic target discovery) on the unique transcriptomic dataset of 87 primary ACCs. Identifying protein arginine methyl transferase 5 (PRMT5) as a putative candidate with the top-scored druggability, we next determined the applicability of PRMT5 inhibitors (PRT543 and PRT811) using ACC cell lines, organoids, and patient derived xenograft (PDX) models. Molecular changes associated with response to PRMT5 inhibition and anti-proliferative effect of the combination therapy with lenvatinib was then analyzed. RESULTS:Using a comprehensive AI-powered engine for target identification, PRMT5 was predicted among potential therapeutic target candidates for ACC. Here we show that monotherapy with selective PRMT5 inhibitors induced a potent anti-tumor activity across several cellular and animal models of ACC, which was paralleled by downregulation of genes associated with ACC tumorigenesis, including MYB and MYC (the recognized drivers of ACC progression). Furthermore, as a subset of genes targeted by lenvatinib is upregulated in ACC, we demonstrate that addition of lenvatinib enhanced the growth inhibitory effect of PRMT5 blockade in vitro, suggesting a potential clinical benefit for patients expressing lenvatinib favorable molecular profile. CONCLUSION:Taken together, our study underscores the role of PRMT5 in ACC oncogenesis and provides a strong rationale for the clinical development of PRMT5 inhibitors as a targeted monotherapy or combination therapy for treatment of patients with this rare disease, based on the analysis of their underlying molecular profile.

Supplemental Table 2. Correlation coefficients (p-values) for ctHPV-DNA kinetics and radiographic response following neoadjuvant chemotherapy.

Squamous cell carcinoma (SCC) is the most common malignancy of the head and neck. Stagnating survival rates in recent decades, despite advances in the treatment paradigms, surveillance technologies, and multidisciplinary care, leave clinicians with a need for better options for screening, risk-stratifying, and monitoring patients. A growing proportion of patients with HPV-associated SCC have improved outcomes but continue to have a heterogenous response to treatment. Advances in the platforms and assays measuring circulating tumor DNA offer an opportunity to monitor disease status at the molecular level for both virally mediated and traditional risk-factor-driven SCC of the head and neck. This overview will discuss experimental, clinically used, and commercially available liquid biopsy platforms and their recent applications in patients with head and neck SCC malignancies.

Immunotherapy has become a key new pillar of cancer treatment, and this has sparked interest in understanding mechanisms of cancer immune evasion. It has long been appreciated that cancers are constituted by heterogeneous populations of tumour cells. This feature is often fuelled by specialized cells that have molecular programs resembling tissue stem cells. Although these cancer stem cells (CSCs) have capacity for unlimited self-renewal and differentiation, it is increasingly evident that some CSCs are capable of achieving remarkable immune resistance. Given that most immunotherapy regiments have overlooked CSC-specific immune-evasive mechanisms, many current treatment strategies often lead to cancer relapse. This Review focuses on advancements in understanding how CSCs in solid tumours achieve their unique immune-evasive properties, enabling them to drive tumour regrowth. Moreover, as cancers often arise from tissue stem cells that acquired oncogenic mutations, we discuss how tissue stem cells undergoing malignant transformation activate intrinsic immune-evasive mechanisms and establish close interactions with suppressive immune cells to escape immune surveillance. In addition, we summarize how in advanced disease stages, CSCs often hijack features of normal stem cells to resist antitumour immunity. Finally, we provide insights in how to design a new generation of cancer immunotherapies to ensure elimination of CSCs. Immunotherapy shows promise in treating cancers by engineering T cells or using antibodies to activate them. However, cancer stem cells (CSCs) resist immunotherapies and drive cancer relapse. In this Review, Agudo and Miao highlight the mechanisms through which normal stem cells and CSCs in solid tumours achieve immune resistance, offering insights for the development of more effective cancer treatments.

Following tissue damage, epithelial stem cells (SCs) are mobilized to enter the wound, where they confront harsh inflammatory environments that can impede their ability to repair the injury. Here, we investigated the mechanisms that protect skin SCs within this inflammatory environment. Characterization of gene expression profiles of hair follicle SCs (HFSCs) that migrated into the wound site revealed activation of an immune-modulatory program, including expression of CD80, major histocompatibility complex class II (MHCII), and CXC motif chemokine ligand 5 (CXCL5). Deletion of CD80 in HFSCs impaired re-epithelialization, reduced accumulation of peripherally generated Treg (pTreg) cells, and increased infiltration of neutrophils in wounded skin. Importantly, similar wound healing defects were also observed in mice lacking pTreg cells. Our findings suggest that upon skin injury, HFSCs establish a temporary protective network by promoting local expansion of Treg cells, thereby enabling re-epithelialization while still kindling inflammation outside this niche until the barrier is restored.

Abstract Head and neck squamous cell carcinoma (HNSCC) is a leader in cancer incidence worldwide. Recently, immunotherapies such as immune checkpoint blockade (ICB) have offered great promise in treating many solid tumors, including HNSCCs, that are refractory to chemotherapy and radiation. Challengingly, HNSCC patients often relapse following ICB treatment due to the lack of a thorough understanding of the mechanisms underlying cancer immune evasion. These disparities in patient outcomes strongly suggest the existence of genetic variations that underlie their distinct responses to ICB. Although the specific oncogenic mutations responsible for driving relapse in SCC patients remain unclear, it is imperative to grasp the mechanisms of cancer immune evasion in individuals with specific genetic profiles to enhance the precision of immunotherapy. Cancer immune evasion has emerged as a hallmark of cancer and is facilitated by a highly complex tumor microenvironment (TME). We aim to understand the genetic basis shaping the immune suppressive TME and hypothesize that oncogenic driver mutations play a dominant role in preventing the immune clearance of transformed cells by reprogramming the immune landscape in the tumors. To determine the critical genetic signatures enriched in SCC patients that can impact anti-tumor immunity, we analyzed TCGA data which revealed a strong negative correlation between PIK3CA level and CD8 T cell signatures. We have identified that activating mutations in the PIK3CA gene, found in 20% of HNSCCs, promote rapid tumor relapse after initial response to anti-PD-L1 and anti-CTLA-4 ICB treatments. Utilizing single-cell analysis, quantitative immune profiling, and multiplexed imaging, our lab showed that tumor-initiating cells (TICs) in SCCs can have an intricate dialogue with myeloid-derived suppressor cells (MDSCs) where TICs secrete factors to enhance MDSC recruitment and suppressive function on cytotoxic T cells. Additionally, our data supports that the tumor interstitial fluid (TIF) of PIK3CA mutant SCC tumors can enhance the suppressive activity of MDSCs on cytotoxic T cells. These results suggest that the acquisition of PIK3CA mutation may trigger TICs to release additional factors to further modify MDSC activities. A critical method by which MDSCs suppress T cells is through the production and respiratory burst of reactive oxygen species (ROS). RNA sequencing revealed that PIK3CA mutant SCCs have multiple mechanisms of increasing ROS in the TME and specifically in MDSCs, while simultaneously upregulating lipid metabolism genes, such as SCD1, to protect itself from MDSC-derived ROS. This study reveals a potential strategy for targeting PIK3CA mutant SCCs as a promising precision immunotherapy to enhance the efficacy of ICB treatments. Citation Format: Benjamin T. Nicholson, Weijie Guo, Yuxuan Miao. PIK3CA activating mutation promotes an immune suppressive microenvironment in squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6861.

The proto-oncogene MYC encodes a nuclear transcription factor that has an important role in a variety of cellular processes, such as cell cycle progression, proliferation, metabolism, adhesion, apoptosis, and therapeutic resistance. MYC amplification is consistently observed in aggressive forms of several solid malignancies and correlates with poor prognosis and distant metastases. While the tumorigenic effects of MYC in patients with head and neck squamous cell carcinoma (HNSCC) are well known, the molecular mechanisms by which the amplification of this gene may confer treatment resistance, especially to immune checkpoint inhibitors, remains under-investigated. Here we present a unique case of a patient with recurrent/metastatic (R/M) HNSCC who, despite initial response to nivolumab-based treatment, developed rapidly progressive metastatic disease after the acquisition of MYC amplification. We conducted comparative transcriptomic analysis of this patient’s tumor at baseline and upon progression to interrogate potential molecular processes through which MYC may confer resistance to immunotherapy and/or chemoradiation and used TCGA-HNSC dataset and an institutional cohort to further explore clinicopathologic features and key molecular networks associated with MYC amplification in HNSCC. This study highlights MYC amplification as a potential mechanism of immune checkpoint inhibitor resistance and suggest its use as a predictive biomarker and potential therapeutic target in R/M HNSCC.

Fusion genes are well-known cancer drivers. However, most known oncogenic fusions are proteincoding, and very few involve non-coding sequences due to lack of suitable detection tools. We develop SFyNCS to detect fusions of both protein-coding genes and non-coding sequences from transcriptomic sequencing data. The main advantage of this study is that we use somatic structural variations detected from genomic data to validate fusions detected from transcriptomic data. This allows us to comprehensively evaluate various fusion detection and filtering strategies and parameters. We show that SFyNCS has superior sensitivity and specificity over existing algorithms through extensive benchmarking in cancer cell lines and patient samples. We then apply SFyNCS to 9565 tumor samples across 33 tumor types in The Cancer Genome Atlas cohort and detect a total of 165,139 fusions. Among them, 72% of the fusions involve non-coding sequences. We find a long non-coding RNA to recurrently fuse with various oncogenes in 3% of prostate cancers. In addition, we discover fusions involving two non-coding RNAs in 32% of dedifferentiated liposarcomas and experimentally validated the oncogenic functions in mouse model.