Faculty Bibliography

Thymomas are rare thymic epithelial tumors classified by the World Health Organization into type A/AB thymomas, which commonly harbor GTF2I mutations and behave indolently, and type B thymomas and thymic carcinomas, in which these mutations are less common. Type A and AB thymomas are uniquely enriched for a recurrent somatic hotspot mutation in GTF2I (p.L424H); yet this gene is rarely included in clinical sequencing panels, limiting its diagnostic utility. YAP1, the principal effector of the Hippo signaling pathway, and β-catenin, the central transcriptional effector of the Wnt pathway, have emerging roles in thymoma biology; however, their relationship to GTF2I mutation status and histologic subtype has not been systematically characterized. We analyzed the TCGA thymoma dataset and an institutional cohort of 38 thymic epithelial tumors to evaluate YAP1 and β-catenin immunohistochemistry (IHC) as surrogate markers for GTF2I mutation status and histologic classification. In the TCGA dataset, YAP1 and CTNNB1 mRNA expression were markedly elevated in type A/AB thymomas relative to type B and carcinoma subtypes, and GTF2I-mutant tumors exhibited significantly higher YAP1 mRNA expression than GTF2I-wildtype tumors. Targeted next-generation sequencing of our institutional cohort confirmed enrichment of the canonical GTF2I p.L424H hotspot in indolent subtypes. By IHC, nuclear YAP1 positivity and cytoplasmic β-catenin localization were both significantly more frequent in indolent thymomas. Cytoplasmic β-catenin demonstrated high specificity (94%) for indolent histology, supporting its use in diagnostically challenging cases such as the type A versus B3 distinction on small biopsies. YAP1 IHC showed a high negative predictive value for GTF2I mutations, such that a YAP1-negative result reliably excludes a GTF2I-mutant tumor. These findings implicate crosstalk between Hippo and Wnt signaling in GTF2I-mutant thymomas and position YAP1 and β-catenin IHC as accessible, cost-effective surrogates for molecular subtyping in a tumor where standard sequencing panels have limited coverage.

Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related mortality. While for Stage IA LUAD surgery is often curative, recurrence rates remain significant. Liquid biopsy enables monitoring residual disease and predicts recurrence, however utility in Stage IA LUAD is not well-established. Tumor-informed whole genome sequencing (WGS) represents a highly sensitive liquid biopsy method for the analysis of circulating-tumor cell-free DNA (ctDNA) without designing and maintaining patient-specific probes. We aimed to determine the prognostic value of genome-wide tumor-informed minimal residual disease (MRD) monitoring in Stage IA NSCLC using WGS of ctDNA. WGS was performed on 42 patients with Stage IA NSCLC. Tumor was sequenced at 40x and germline DNA and plasma derived ctDNA at 20x and patient specific mutational signatures were developed from the tumor-normal comparison and applied to ctDNA WGS at each time point using AI-supported pattern recognition algorithm. ctDNA results were compared with clinical recurrence. WGS ctDNA was able to predict recurrence with 0.75 sensitivity and 0.83 specificity, with median 16.7 months lead time compared to clinical or imaging recurrence. ctDNA WGS was able to distinguish between a second primary and recurrence in histologically or clinically challenging cases. Whole genome sequencing of ctDNA can predict recurrence in the earliest clinical stage of NSCLC, identifying patients who will recur, and providing information to help guide radiological follow-up and adjuvant therapy.

INTRODUCTION/UNASSIGNED:The International Association for the Study of Lung Cancer grading system for resected invasive lung adenocarcinoma provides robust prognostic stratification for recurrence risk and overall survival. However, most patients present at advanced stages, where only small biopsy samples are available, leaving no established prognostic tool for such cases. We propose a practical biopsy-based grading method for pulmonary adenocarcinoma. METHODS/UNASSIGNED:We analyzed 267 paired biopsies and resections. The following two biopsy grading (bxG) models were tested:•Model 1: Based on the predominant pattern-grade 1 (lepidic), grade 2 (acinar/papillary), grade 3 (solid/micropapillary/complex glandular).•Model 2: Any percentage of high-grade patterns classified as grade 3, regardless of predominance. BxG 1 and 2 are defined as predominant patterns as described.For analysis, grades 1 and 2 were combined (G1-2), and grade 3 was considered a separate category. Diagnostic performance was assessed using resections as the reference standard. Interobserver reliability was evaluated, and discrepant cases were reviewed. RESULTS/UNASSIGNED:= 21) were primarily due to sampling limitations and artifacts, such as tangential sectioning. Adjusting for these factors improved interobserver agreement from moderate to almost perfect. CONCLUSION/UNASSIGNED:Biopsy grading using the presence of any high-grade pattern correlates well with International Association for the Study of Lung Cancer-based resection grading. Although bxG1 to 2 biopsies may underestimate tumor grade, bxG3 biopsies demonstrate more than 90% specificity and PPV for predicting G3 resections, supporting their potential utility as a clinical prognostic marker.

Acute myeloid leukemia (AML) is a blood cancer with poor survival outcomes. Acute respiratory failure frequently occurs due to leukemia infiltration of the lungs. Underlying mechanisms remain unexplored and therapeutic interventions remain empiric. Here we map the AML lung microenvironment at spatial and single-cell resolution. We show that extensive remodeling is coupled with inflammation and impaired tissue integrity and function. Steroid treatment significantly reduces AML burden and lung infiltration, improving oxygenation and pulmonary function. As a mechanistic correlate, the S-type lectin Lgals9 is triggered by inflammation and mediates cell-cell interactions within infiltrated lungs. Also, the alarmin IL-33 and its receptor (IL-1RL1) are involved in cell-cell interactions within the leukemic lung microenvironment. Targeting either the Lgals9 or IL-33 axis significantly decreases overall AML burden and lung infiltration through effects on both the immune microenvironment and AML cells. Our studies delineate pulmonary infiltration phenotypes in acute leukemia, enabling new treatment strategies.

UNLABELLED:LKB1 mutations in lung cancer promote an immunosuppressive tumor microenvironment, but the underlying mechanisms remain unknown. Using genetically engineered mouse models and human tumor samples, we demonstrate that LKB1 loss leads to high expression of the cytokine leukemia-inhibitory factor (LIF), which through a cancer cell-autonomous autocrine loop, orchestrates the infiltration of immunosuppressive SiglecFHi neutrophils and Arg1+ interstitial macrophages. Genetic deletion of Lifr, the receptor for LIF, on Lkb1-mutant lung tumors revealed that autocrine LIF signaling induces tumor plasticity and the emergence of a Sox17+ dedifferentiated inflammatory cell state. Antibody-mediated LIF neutralization selectively eliminates the Sox17+ tumor cell state, reduces immunosuppressive myeloid cells, and enhances antitumor T-cell responses. Our study uncovers a novel LKB1-LIF axis driving immune evasion and identifies LIF as a potential therapeutic target in LKB1-mutant lung cancer. This work highlights the interplay between tumor genetics, cellular plasticity, and immune regulation in lung cancer progression. SIGNIFICANCE/UNASSIGNED:LKB1-mutant lung cancers express LIF, which induces an immunosuppressive Sox17+ tumor state. Anti-LIF therapy eliminates this state and restores antitumor immunity, revealing a novel vulnerability in this aggressive cancer subtype lacking effective targeted therapies.

Cancer cells activate the integrated stress response (ISR) to adapt to stress and resist therapy¹. ISR signals converge on activating transcription factor 4 (ATF4), which controls cell-intrinsic transcriptional programs that are involved in metabolic adaptation, survival and growth^2,3. However, whether the ISR-ATF4 axis influences anti-tumour immune responses remains mostly unknown. Here we show that loss of ATF4 decreases tumour progression considerably in immunocompetent mice, but not in immunocompromised ones, by enhancing T cell-dependent anti-cancer immune responses. An unbiased genetic screen of ATF4-regulated genes identifies lipocalin 2 (LCN2) as the principal ATF4-dependent effector that impairs anti-tumour immunity by favouring infiltration with immunosuppressive interstitial macrophages. Furthermore, we find that LCN2 promotes T cell exclusion and immune evasion in preclinical mouse models, and correlates with decreased T cell infiltration in patients with lung and pancreatic adenocarcinomas. Anti-LCN2 antibodies promote robust anti-tumour T cell responses in mouse models of aggressive solid tumours. Our study shows that the ATF4-LCN2 axis has a cell-extrinsic role in suppressing anti-cancer immunity, and could pave the way for an immunotherapy approach that targets LCN2.

Dendritic cells (DCs) facilitate the maintenance of immunological tolerance in the steady state. We report that transcription factor Etv3 is preferentially expressed in mature DCs, including tissue-derived migratory DCs (migDCs), and facilitates their homeostatic maturation and CCR7-dependent migration. Mice with global or DC-specific deletion of Etv3 manifested the expansion of CD25^low regulatory T (T_reg) cells, spontaneous activation of conventional T cells, and multiorgan T cell infiltration. Etv3 deficiency exacerbated TLR7-driven systemic lupus erythematosus (SLE)-like disease, supporting the reported genetic association of human ETV3 with SLE. Etv3-deficient migDCs up-regulated multiple costimulatory molecules, including OX40 ligand (OX40L/TNFSF4), whose blockade partially rescued the T_reg cell abnormalities. These results identify Etv3 as an essential regulator of the tolerogenic function of DCs and implicate it in the regulation of human autoimmunity.

OBJECTIVES/OBJECTIVE:With the development of genomic technologies, the isolation of genomic DNA (gDNA) from clinical samples has become more important for both clinical diagnostics and research studies. Blood samples collected in PAXgene Blood RNA Tubes, which are typically used for RNA extraction, can be used for gDNA extraction, particularly in clinical studies when only such blood samples are available. METHODS:We optimized the pre-treatment of blood samples collected in PAXgene Blood RNA Tubes. For the first time, three magnetic bead-based automated platforms (QIAsymphony SP, Maxwell RSC and KingFisher Apex) were compared for gDNA extraction from these blood samples. Additionally, the effects of storage at 4 °C or freeze-thaw cycles of the blood samples on gDNA yield were investigated. High-throughput extraction in 96-well format was evaluated. RESULTS:Systematic optimization of blood sample pre-treatment shows that prolonged incubation at room temperature and/or increased centrifugation speed and time improved gDNA yield from blood samples collected in PAXgene Blood RNA Tubes. QIAsymphony SP (4.27 ± 2.19 µg) and Maxwell RSC (4.82 ± 2.96 µg) produced significantly higher gDNA yields than KingFisher Apex (1.09 ± 0.61 µg). Higher gDNA yields were obtained with shorter storage time at 4 °C or fewer freeze-thaw cycles of the blood samples. In the 96-well format extraction, gDNA yields ranged from 0.24 to 13.46 µg. CONCLUSIONS:Not all magnetic bead-based automated platforms are suitable for gDNA extraction from blood samples collected in PAXgene Blood RNA Tubes. Systematic pre-treatments optimization provides guidance for routine and high-throughput workflows, and storage conditions and freeze-thaw cycles offer practical reference for biobanking.

Thoracic SMARCA4-deficient undifferentiated tumor (SMARCA4d-UT) is an uncommon, aggressive lung neoplasm associated with smoking and characterized by loss of SMARCA4 (BRG-1) expression. Although originally considered to be a primary sarcoma, there is growing evidence that these lesions may represent transformation of conventional non-small cell carcinoma. In this study, we probe this relationship based on the clinical, histologic and molecular findings of 18 SMARCA4-deficient malignancies of the lung. Cases diagnosed as SMARCA4d-UT and SMARCA4-deficient carcinoma were retrospectively reviewed, including histologic and immunophenotypic features, and next generation sequencing studies. Of the 18 tumors, 5 were considered to represent undifferentiated SMARCA4d-UT, and 13 SMARCA4-deficient carcinomas, including 11 adenocarcinomas, 1 squamous cell carcinoma, and 1 poorly differentiated non-small cell carcinoma. All 13 carcinomas had a morphologically identifiable undifferentiated component. Survival outcomes were similar in both SMARCA4d-UT and carcinomas. Genetic alterations often seen in lung cancer were identified in 8 cases, including mutations in EGFR (in 2 SMARCA4-deficient adenocarcinomas), KRAS (1 SMARCA4d-UT and 1 SMARCA4-deficient adenocarcinoma), MAP2K1 (1 SMARCA4-deficient adenocarcinoma), and a gene fusion involving EML4::ALK (1 SMARCA4d-UT). The patient with EML4::ALK fusion was treated with alectinib with partial response. Fusions involving BRAF::CHCHD3 and FGFR1::FILIP1 were identified in 2 SMARCA4-deficient adenocarcinomas. High expression of PD-L1 (TPS >50 %) was seen in 12 cases (67 %). These finding further suggest that SMARCA4d-UT and carcinomas with SMARCA4 loss may be on the same spectrum of disease, and accurate histologic distinction between these lesions may be challenging. A unified terminology may be beneficial for appropriate diagnosis and treatment.

BACKGROUND AND OBJECTIVE/UNASSIGNED:Accurate diagnosis of mediastinal tumors is of critical importance to establish appropriate therapy. However, these lesions are relatively uncommon and may be challenging to evaluate, particularly in small biopsy specimens. Thymomas and thymic carcinomas are the most common primary malignant tumors of the mediastinum, but the site can be affected by many other neoplasms that can pose significant difficulty in diagnosis. The objective of this article is to bring awareness to these rarer tumors and offer a diagnostic approach using ancillary techniques guided by clinical and morphological features. METHODS/UNASSIGNED:We discuss and review six challenging cases of mediastinal tumors with overlapping morphologic features. We discuss their unique morphologic, immunophenotypic, and relevant molecular characteristics to support their definitive diagnosis, based on current literature. Sources were obtained via PubMed search and include original studies and review articles published in the English language between 1990 and 2025. Search terms include the diagnostic entities discussed in the article. KEY CONTENT AND FINDINGS/UNASSIGNED:Judicious use of immunohistochemistry and molecular studies is necessary to accurately diagnose mediastinal neoplasms with overlapping histologic features, such as those seen in the cases discussed. CONCLUSIONS/UNASSIGNED:Diagnosis of uncommon mediastinal lesions may be challenging, particularly in small biopsies, as morphological features may be shared among different entities. Awareness of these rare entities, their clinical characteristics and presentation, and differential diagnosis can guide in the selection of appropriate immunohistochemical panels, molecular markers, and molecular diagnostics when appropriate to support the diagnoses.