Mutational Landscape Research Articles

Application value of multi-gene mutation detection in the clinical management of pediatric papillary thyroid carcinoma: a preliminary exploration.

Thyroid cancer rarely occurs in children and adolescents. Molecular markers such as BRAF, RAS, and RET/PTC have been widely used in adult PTC. It is currently unclear whether these molecular markers have equivalent potential for application in pediatric patients. This study aims to explore the potential utility of a multi-gene conjoint analysis based on next-generation targeted sequencing for pediatric papillary thyroid carcinoma (PTC). The patients diagnosed with PTC (aged 18 years or younger) in the pediatrics department of Lishui District Hospital of Traditional Chinese Medicine were retrospectively screened. A targeted enrichment and sequencing analysis of 116 genes associated with thyroid cancer was performed on paraffin-embedded tumor tissues and paired paracancerous tissue of fifteen children (average age 14.60) and nine adults (average age 49.33) PTC patients. Demographic information, clinical indicators, ultrasonic imaging information and pathological data were collected. The Kendall correlation test was used to establish a correlation between molecular variations and clinical characteristics in pediatric patients. A sample of 15 pediatric PTCs revealed a detection rate of 73.33% (11/15) for driver gene mutations BRAF V600E and RET fusion. Compared to adult PTCs, the genetic mutation landscape of pediatric PTCs was more complex. Six mutant genes overlap between the two groups, and an additional seventeen unique mutant genes were identified only in pediatric PTCs. There was only one unique mutant gene in adult PTCs. The tumor diameter of pediatric PTCs tended to be less than 4cm (p<0.001), and the number of lymph node metastases was more than five (p<0.001). Mutations in specific genes unique to pediatric PTCs may contribute to the onset and progression of the disease by adversely affecting hormone synthesis, secretion, and action mechanisms, as well as the functioning of thyroid hormone signaling pathways. But, additional experiments are required to validate this hypothesis. BRAF V600E mutation and RET fusion are involved in the occurrence and development of adolescent PTC. For pediatric thyroid nodules that cannot be determined as benign or malignant by fine needle aspiration biopsy, multiple gene combination testing can provide a reference for personalized diagnosis and treatment by clinical physicians.

Deciphering the role of zinc homeostasis in the tumor microenvironment and prognosis of prostate cancer

BackgroundDysregulation of zinc homeostasis is widely recognized as a hallmark feature of prostate cancer (PCa) based on the compelling clinical and experimental evidence. Nevertheless, the implications of zinc dyshomeostasis in PCa remains largely unexplored.MethodsIn this research, the zinc homeostasis pattern subtype (ZHPS) was constructed according to the profile of zinc homeostasis genes. The identified subtypes were assessed for their immune functions, mutational landscapes, biological peculiarities and drug susceptibility. Subsequently, we developed the optimal signature, known as the zinc homeostasis-related risk score (ZHRRS), using the approach won out in multifariously machine learning algorithms. Eventually, clinical specimens, Bayesian network inference and single-cell sequencing were used to excavate the underlying mechanisms of MT1A in PCa.ResultsThe zinc dyshomeostasis subgroup, ZHPS2, possessed a markedly worse prognosis than ZHPS1. Moreover, ZHPS2 demonstrated a more conspicuous genomic instability and better therapeutic responses to docetaxel and olaparib than ZHPS1. Compared with traditional clinicopathological characteristics and 35 published signatures, ZHRRS displayed a significantly improved accuracy in prognosis prediction. The diagnostic value of MT1A in PCa was substantiated through analysis of clinical samples. Additionally, we inferred and established the regulatory network of MT1A to elucidate its biological mechanisms.ConclusionsThe ZHPS classifier and ZHRRS model hold great potential as clinical applications for improving outcomes of PCa patients.

Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor.

Profiling circulating cell-free DNA (cfDNA) has become a fundamental practice in cancer medicine, but the effectiveness of cfDNA at elucidating tumor-derived molecular features has not been systematically compared to standard single-lesion tumor biopsies in prospective cohorts of patients. The use of plasma instead of tissue to guide therapy is particularly attractive for patients with small cell lung cancer (SCLC), a cancer whose aggressive clinical course making it exceedingly challenging to obtain tumor biopsies. Here, a prospective cohort of 49 plasma samples obtained before, during, and after treatment from 20 patients with recurrent SCLC, we study cfDNA low pass whole genome (0.1X coverage) and exome (130X) sequencing in comparison with time-point matched tumor, characterized using exome and transcriptome sequencing. Direct comparison of cfDNA versus tumor biopsy reveals that cfDNA not only mirrors the mutation and copy number landscape of the corresponding tumor but also identifies clinically relevant resistance mechanisms and cancer driver alterations not found in matched tumor biopsies. Longitudinal cfDNA analysis reliably tracks tumor response, progression, and clonal evolution. Genomic sequencing coverage of plasma DNA fragments around transcription start sites shows distinct treatment-related changes and captures the expression of key transcription factors such as NEUROD1 and REST in the corresponding SCLC tumors, allowing prediction of SCLC neuroendocrine phenotypes and treatment responses. These findings have important implications for non-invasive stratification and subtype-specific therapies for patients with SCLC, now treated as a single disease.

Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.

Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.

Mutational landscape and evolutionary pattern of peritoneal metastases in colorectal cancer.

Mutational landscape and evolutionary pattern of peritoneal metastases in colorectal cancer.

Study of single live circulating tumor cells capture and their genomic profile and enriched mutations of PIK3CA and HRR pathway in patients with breast cancer.

e13161 Background: Capturing live single circulating tumor cells (sCTC) for intra-cellular compressive genomic profiling and concordance with ctDNA is highly challenging. Utilization of single sCTC genomics holds promise for detecting clinically relevant, actionable insights to tailor personalized therapy, especially when No Mutations Detected (NMDs) using CfDNA. Despite numerous studies providing valuable insights on mutational landscapes from breast tumors, predicting cancer progression, metastasis, and relapse continue to pose major challenges. ctDNA is suboptimal for 30-40% population with disease relapse/progression after a primary therapy. We show comprehensive genetic profile (CGP) of live sCTCs and paired ctDNA from a diverse breast cancer population. Methods: 26 live sCTCs (2 CTC clusters) were isolated from 12 patients. Live sCTCs were isolated from 12 Breast Cancer patients using OncoRadar live sCTC capture method. Whole genomes were amplified using multiple displacement amplification, target enriched with hybridization capture using OncoIndx (CGP 1080 gene panel) to obtain sequencing libraries, and sequenced on Illumina platform in paired end mode (depth 500x). The raw sequence alignment and variant calling was performed using iCare software. Paired ctDNA samples were processed the same way, except for sequencing depth (5500x). Results: Compared to paired ctNDA, genomic profiling of sCTCs revealed complex mutational patterns. Whereas sCTCs showed least two pathogenic (P) or likely pathogenic (LP) variants, paired ctDNA was negative for 25% cases (3/12). 92% sCTCs showed mutations in the PIK3CA-MTOR pathway with PIK3CA being the most prevalent (73 %). A significant association was observed between co-occurrence of HER2 amplification and PIK3CA mutations (P =0.04, OR=10). Similarly, sCTCs showed a strong correlation between HRR pathway and PIK3CA pathway mutations (r=0.76, P =0.003, OR=3.43). Genomic profile of sCTCs and paired ctDNA showed concordance with at least one gene mutation when compared at individual patient level. Additionally, at individual mutation level, PIK3CA exon 10 mutations were most frequent (61.5%) along with BRCA2 pathway variants, followed by IDH1/2(54%), ARID1A (50%), NRAS (46%), FGFR2 (42%) and TP53 (42%). Interestingly, 70% sCTCs showed the presence of therapy resistance conferring variants (NF1, ARID1A, ESR1, RB1 and PTEN), compared to only 25 % observed in paired ctDNA. Conclusions: The genomic profile of sCTCs represents true tumor heterogeneity and can be combined with ctDNA for better clinical outcome. sCTCs exhibited high mutational heterogeneity compared to paired ctDNA. Therapy resistance signatures were more prevalent in sCTCs and may offer valuable clinical insights for patients unable to provide tissue biopsy or show negative ctDNA.

Genomic profiling of non-small cell lung cancer with rare aberrations in EGFR codon L858 and the survival outcome under real-world first-line EGFR tyrosine kinase inhibitor treatment compared to classic EGFRL858R.

8596 Background: Rare genomic aberrations in EGFR codon L858 causing L858R (rare EGFRL858R) or non-L858R mutations have been reported, besides the predominant c.2573T&gt;G genomic mutation leading to classic EGFRL858R. However, molecular features, survival benefit under EGFR tyrosine kinase inhibitors (TKIs), and resistance mechanisms of these rare mutations lack comprehensive investigation in non-small cell lung cancer (NSCLC). Methods: We retrospectively included 489 NSCLCs with treatment-naive tumor tissues/plasma biopsies harboring rare EGFRL858R (N=124), EGFRL858Q/M (N=17), or classic EGFRL858R mutations (N=348). Mutational landscapes, tumor mutation burden (TMB), and chromosome instability (CIN) scores, were investigated using tissue samples subject to a targeted next-generation sequencing panel covering 437 cancer-related genes. Advanced NSCLCs receiving EGFR TKIs as first-line therapy were sub-grouped to study survival benefit and resistance mechanisms. Results: NSCLCs with rare EGFRL858R had less-frequently mutated TP53 (59% vs. 72%, P=0.04) and lower CIN scores (0.29 vs. 0.23, P=0.02) than those with classic EGFRL858R, while age, sex, stage at diagnosis, histology subtype, and TMB were comparable. We also detected the cooccurrence of EGFRL858Q/M with EGFRL861Q ( P&lt;0.01), particularly in patients carrying EGFRL858M (100%). Compared to 233 advanced NSCLCs harboring classic EGFRL858R, 58 patients with rare EGFRL858R exhibited superior first-line progression-free survival (PFS) [median: 13.0 vs. 10.0 months, hazard ratio (HR): 0. 57, 95% confidence interval (CI): 0.41–0.80], with a similar association observed in approximately 80% of included patients who received first-generation EGFR TKIs (median: 12.0 vs. 10.0 months, HR: 0.64, 95% CI: 0.45–0.92). After controlling for age, sex, histological subtype, EGFR TKI category, and anti-vascular therapy, rare EGFRL858R remained associated with improved PFS (adjusted HR: 0.55, 95% CI: 0.39–0.77). Patients with EGFRL858Q/M also had better PFS than those with classic EGFRL858R (adjusted HR: 0.26, 95% CI: 0.10–0.67). Of note, NSCLCs with combined EGFRL858M and EGFRL861Q appeared to have lower progression risks when receiving afatinib than using gefitinib/icotinib as first-line therapy. Furthermore, matched samples at baseline and progression revealed similar resistance mechanisms between NSCLCs with rare and classic EGFRL858R. Conclusions: NSCLCs carrying rare genomic aberrations in EGFR codon L858 were likely to get more survival benefits from first-line EGFR TKI treatment than those with classic EGFRL858R, giving scientific evidence supporting the clinical application of EGFR TKIs in these patients.

Characterization of T-cell receptor repertoire and correlation with tumor mutational landscape in lung cancer.

2577 Background: T-cell receptor (TCR) repertoire represents an overall immune condition which is closely related to pathogens- or tumor-associated T cell responses. Increasing evidence suggests that TCR repertoire is expected to undergo cancer-specific changes during tumorigenesis, supporting that TCR characteristics can serve as novel markers to indicate early cancer progression. Here, we performed a systematic T cell repertoire analysis in lung cancer. We identified cancer-enriched TCR signatures and constructed a comprehensive lung cancer database integrating TCR diversity, tumor mutational profiles, immune markers expression and HLA genotypes. Methods: A total of 988 tissue samples and 3,360 blood samples were obtained from patients with lung cancer, in addition to 2,699 blood samples from healthy individuals. Multiplex-PCR-based sequencing of the CDR3 regions of TCR-β chains was applied to the tissue and blood samples. TCR repertoires were analyzed using MiXCR and VDJtools. Whole exome sequencing was performed on partial tumor tissues to profile the mutational landscape and HLA genotypes. An in-house pipeline, considering the frequency and distribution of CDR3, was utilized to identify cancer-enriched CDR3 sequences. The PD-L1 expression was evaluated and quantified using CPS. Furthermore, an enrich score was developed to measure the content of cancer-related TCRs by aligning against the built cancer-enriched CDR3 dataset. Spearman's rank correlation was used to assess relationships between variables. Results: Lung cancer exhibited significantly lower Shannon index, Simpson index and evenness index in TCR repertoire (p&lt;0.001), both in tissue and blood samples, when compared with healthy blood samples. Approximate 3% T-cell clonotypes within lung tissues were detected in blood TCR repertoires. A correlation was observed between the decreased TCR diversity and a higher tumor mutational burden (TMB)(r = -0.15, p &lt; 0.01), as well as a higher variant allele frequency (VAF) (r = -0.19, p &lt; 0.01). In this study, 3,652 and 3,840 CDR3 sequences were identified to be enriched in lung cancer tissue and blood respectively. A significant difference in cancer-enriched score was observed between cancer and healthy TCR repertoires (p &lt; 0.001). The cancer-enriched score showed a significant positive correlation with TMB, particularly in TP53- mutant tumors (r = 0.27, p &lt; 0.001). A higher CPS (PD-L1) was associated with a higher cancer-enriched score (r = 0.18 ,p &lt; 0.01). Conclusions: Cancer-related T-cell clonotypes in the tumor microenvironment and peripheral blood informs the changes in anti-tumor responses, supporting the potential application of TCR signatures in early cancer detection. This study identified the lung cancer-related TCR signatures and provided a comprehensive lung cancer TCR database, revealing the relationship between TCR characteristics and mutational profiles. Clinical trial information: ChiCTR2200055761.

Application of ctDNA sequencing in patients with metastasized lung cancer.

e20033 Background: Circulating tumor DNA (ctDNA) is a form of cell-free DNA (cfDNA) found in blood that originates from tumor cells, which has emerged as a promising non-invasive biomarker in monitoring cancer prognosis and precision medicine with the advancement of deep sequencing. Here we compared the mutational landscape between solid tumor and cfDNA in metastasis-free and metastasized lung cancer patients using targeted NGS to investigate the feasibility of ctDNA sequencing in monitoring cancer prognosis. Methods: Blood-derived cfDNA samples and formalin-fixed paraffin embedded tissue were collected from 217 Chinese patients with metastatic lung cancer (n = 39) or metastasis-free lung cancer (n = 178). Blood samples were collected after surgery. Panel sequencing targeting 680 cancer-related genes was performed on both samples. Somatic single nucleotide variations and indels were analyzed. Results: Among the 178 metastasis-free patients, 89.3% of the patients have at least one mutation both detected in tumor and blood samples. On average, 50.4% of tumor mutations were detected in blood for each patients. EGFR, TP53, CSMD3, LRP1B and SYNE1 were the top five most frequently mutated genes, with the proportion of tumor mutation found in blood of 89.1%, 80.2%, 70.0%, 61.3% and 64.3% respectively. In the metastasized cohort, all 39 individuals have at least one tumor mutations found in blood, achieving a concordance of 100%. On average, 59.9% of tumor mutations were detected in blood for each patients. Notably, the proportion of tumor mutations detected in blood for each patients is significantly higher than the metastasis-free cohort (unpaired T-test, p = 0.0167). EGFR, TP53, RBM10, PIK3CA and CSMD3 were the top five most frequently mutated genes, with the proportion of tumor mutation found in blood of 93.5%, 80.8%, 57.1%, 83.3% and 42.9% respectively. Moreover, the proportion of patients having EGFR p.L858R mutation in metastasized cohort was higher than the metastasis-free cohort (54.3% vs 32.8%). While within the metastasized cohort, blood samples detected a higher proportion of EGFR p.T790M (12.9% vs 7.69%) but a lower proportion of EGFR exon19 deletion (p.E746_A750del, 19.4% vs 27.7%) comparing to tumor sample, which can indicate drug resistance. Conclusions: We demonstrated a high mutation detection concordance between tumor and blood using targeted NGS, with an exceptional performance especially in driver oncogenes like EGFR and TP53. Our findings showed that metastasized lung cancer patients exhibit a higher positive concordance rate compared to metastasis-free cohort using ctDNA. We also showed a varied mutational landscape between ctDNA and tumor sequencing in metastasized lung cancer patients. Overall, this study not only reaffirms the viability of using blood as an alternative of tissue biopsy, but also provides new insights on application of ctDNA monitoring lung cancer metastasis and its clinically targetable mutations.

Exploring the significance of MET overexpression by gene expression profiling versus immunohistochemistry in an EGFR-mutant lung cancer cohort.

e20600 Background: Amivantamab, an innovative EGFR-MET bispecific antibody, approved for use in EGFR exon 20 mutated lung cancers, recently demonstrated substantial clinical benefits in advanced/metastatic lung cancers with EGFR exon 19 deletion and/or L858R mutation according to data from the MARIPOSA clinical trial. Recent findings from the CHRYSALIS 2 trial indicate a potential role for MET overexpression as a predictive biomarker for response to Amivantamab combination therapy, particularly in cases resistant to Osimertinib. Methods: We retrospectively analyzed genomic profiling data in a large lung cancer cohort to characterize EGFR mutations. Additionally, we assessed MET expression via gene expression profiling (GEP) in a smaller EGFR-mutation positive sub-cohort to explore its prevalence. Results: Genomic profiling data from 799 tissue samples was included in our analysis. EGFR mutations were detected in 36%; higher prevalence of EGFR mutations was noted in our cohort (36%) vs the TCGA cohort (26%). Consistent with other studies, exon 19 deletion was the most frequent category of EGFR mutations (46%,), with EGFR p.E746_750del being the most frequent variant among them (60%). Exon 21 L858R mutation was the next most frequently detected variant (28%). Uncommon EGFR mutations were identified in 26% samples, with G719X being the most frequent among these. EGFR Exon 20 insertions contributed 6% of the EGFR variants. EGFR amplification was detected in 4.6% of samples. Of particular significance was the analysis of 21 EGFR-mutated tissue samples for targeted transcriptome analysis as a part Exacta Encyclopedic Tumor Analysis. The MET gene overexpression was detected in 52% of these samples. MET overexpression based on differential GEP identified a higher positivity rate than previously reported using MET immunohistochemistry (IHC) expression (52% vs. 36%), suggesting that GEP may be useful in identifying more patients with MET overexpression. This finding underscores the potential value of MET GEP as a biomarker, especially considering emerging data suggesting MET overexpression as a predictor for enhanced clinical benefit from the combination of Amivantamab and Lazertinib in EGFR-mutated, Osimertinib resistant patients. Furthermore, ongoing clinical trials are exploring MET overexpression as a biomarker for Amivantamab monotherapy. Conclusions: In conclusion, our study not only characterizes the landscape of EGFR mutations in a large lung cancer cohort but also highlights the prevalence of MET overexpression in EGFR-mutated samples, suggesting that MET GEP may serve as a promising predictive biomarker for enhanced clinical outcomes from Amivantamab therapy. In view of small sample size, further exploration and validation of MET overexpression by GEP is warranted in the context of EGFR-mutated advanced lung cancer.

A risk score based on polyamine metabolism and chemotherapy-related genes predicts prognosis and immune cells infiltration of lung adenocarcinoma.

We aimed to explore whether the genes associated with both platinum-based therapy and polyamine metabolism could predict the prognosis of LUAD. We searched for the differential expression genes (DEGs) associated with platinum-based therapy, then we interacted them with polyamine metabolism-related genes to obtain hub genes. Subsequently, we analysed the main immune cell populations in LUAD using the scRNA-seq data, and evaluated the activity of polyamine metabolism of different cell subpopulations. The DEGs between high and low activity groups were screened to identify key DEGs to establish prognostic risk score model. We further elucidated the landscape of immune cells, mutation and drug sensitivity analysis in different risk groups. Finally, we got 10 hub genes associated with both platinum-based chemotherapy and polyamine metabolism, and found that these hub genes mainly affected signalling transduction pathways. B cells and mast cells with highest polyamine metabolism activity, while NK cells were found with lowest polyamine metabolism activity based on scRNA-seq data. DEGs between high and low polyamine metabolism activity groups were identified, then 6 key genes were screened out to build risk score, which showed a good predictive power. The risk score showed a universal negative correlation with immunotherapy checkpoint genes and the cytotoxic T cells infiltration. The mutation rates of EGFR in low-risk group was significantly higher than that of high-risk group. In conclusion, we developed a risk score based on key genes associated with platinum-based therapy and polyamine metabolism, which provide a new perspective for prognosis prediction of LUAD.

Characterizing TP53 mutations in bone and soft tissue sarcoma.

e23521 Background: Tumor protein P53 (TP53) is the most frequently mutated gene in cancer and most mutations inactivate wild type TP53 activity through heterogenous mechanisms. Whether different variants of mutant TP53 have different biologic potencies or clinical outcomes remain unclear. This ongoing study aims to characterize the spectrum of TP53 mutations in patients with bone and soft tissue sarcoma. Methods: We retrospectively identified and analyzed patients with bone and soft tissue sarcoma who underwent MSK-IMPACT (Memorial Sloan Kettering Cancer Center - Integrated Mutation Profiling of Actionable Cancer Targets) next-generation sequencing panel and had at least one mutation in the TP53 gene at Memorial Sloan Kettering Cancer Center. Mutations in the TP53 gene were categorized into the following sub-types: fusion, missense, splice site, or protein-truncating. Hotspots were defined as variants with frequency of 10 or greater. We queried the missense variants for the 800 most frequent variants recorded in the International Agency for Research on Cancer R20 (IARC), which were structurally characterized based on their impact on TP53 protein and rescue potencies with arsenic trioxide (ATO) in vitro (Song et al. Sci Transl Med. 2023). Results: We identified a total of 1257 patients with bone and soft tissue sarcoma who had at least one mutation in TP53. 92.5% of patients had only 1 mutation in TP53. In total, 1363 mutations were detected with 541 variants identified across all sarcoma subtypes. Most TP53 mutations were identified in soft tissue leiomyosarcoma (18.05%), uterine leiomyosarcoma (12.84%), sarcoma not otherwise specified (15.62%), undifferentiated pleomorphic sarcoma (12.11%), and osteosarcoma (7.78%). Of the 541 variants identified, the most frequent alterations were intragenic fusion (6.23%), R175H missense (2.93%), R248Q missense (2.27%), R273H missense (2.13%), and R213* protein-truncating (2.05%) mutations. Of the 800 most frequent missense variants in IARC R20 database, 233 missense variants were detected representing 52% of all mutations detected. Structural or likely structural mutations represented most of the identified missense mutations (77.46%). These mutations were clustered in the following hotspots: R175H, Y220C, R282W, H179Y, and C135Y. DNA-contact mutations were clustered in the following hotspots: R248Q, R273H, R273C, and R248W. Conclusions: This analysis highlights the heterogenous landscape of TP53 mutations in bone and soft tissue sarcomas. Structural variants are prevalent in sarcoma and occur at hotspots that may represent novel drug targets in the future.

A pan-cancer analysis of SMARCA4 alterations and the unique clinicogenomic characteristics associated with SMARCA4 mutation types.

3073 Background: SWI/SNF complexes are regulators of cell lineage and alterations in these proteins occur in &gt;20% of solid tumors with SMARCA4being the most common. SMARCA4 mutations are associated with worse clinical outcomes in various cancer types but are also vulnerable to novel SMARCA2 inhibitors currently being evaluated in clinical trials. We examined SMARCA4 alterations across cancer types to understand their interplay with other genomic abnormalities and clinical consequences. Methods: We analyzed the Memorial Sloan Kettering (MSK) institutional cohort profiled by MSK-IMPACT tumor-normal sequencing. SMARCA4 mutations were annotated based on OncoKB and literature. FACETS resolved zygosity and genomic metrics of complexity including tumor mutational burden (TMB) and fraction genome altered (FGA). The pan-cancer landscape of somatic SMARCA4 mutations was mapped by both category (Class I vs II) and zygosity (mono- vs biallelic). DISCOVER was employed to evaluate mutational signatures and frequency-adjusted co-occurring and mutually exclusive mutations. We then extracted progression-free (PFS) and overall survival (OS) to systemic therapy using natural language processing. Results: We identified 3,385 tumors from 3,049 patients across cancer types with a total 3,965 oncogenic somatic SMARCA4 alterations. Copy number estimation was successful for 2,343 (69%). Non-small cell lung cancer (NSCLC) was the most abundant SMARCA4-altered histology ( n=493, 7.1% of all NSCLC), and the majority (87%) were biallelic. Other common histologies were colorectal ( n=163, 2.9%), bladder ( n=122, 5.5%), uterine ( n=88, 4.3%), pancreatic ( n=81, 3.2%) and esophagogastric ( n=92, 4%). SMARCA4biallelic mutated tumors had higher chromosomal instability compared to WT (FGA = 0.53 vs 0.47; p&lt;0.001), while monoallelic had lower (FGA = 0.3; p&lt;0.001). Monoallelic SMARCA4 altered tumors had a higher TMB (10.5) than both WT (4.4) and biallelic cancers (6.1; p&lt;0.001). Monoallelic and biallelic SMARCA4 cancers exhibited distinct mutational signatures in most tumor types. Patients with biallelic SMARCA4 mutations had worse outcomes with both immune checkpoint blockade (ICB) and platinum chemotherapy across in certain tumor types, whereas monoallelic uterine cancers were associated with improved outcomes with ICB. Conclusions: This pan-cancer clinicogenomic analysis demonstrates that monoallelic and biallelic SMARCA4-mutated tumors have distinguishable genomic features. In addition, biallelic SMARCA4 alterations correlated with poor outcomes across different cancer-types and classes of therapy, while improved outcomes to ICB in monoallelic SMARCA4alterations were potentially due to higher representation of MSI-H tumors in this subset. Our findings suggest SMARCA4 zygosity may be important biomarkers for ongoing clinical trials in SMARCA4-deficient tumors.

Clinical features, molecular findings, and clinical outcomes of follicular dendritic cell sarcoma.

e23554 Background: Follicular dendritic cell sarcoma (FDCS) is a low-grade neoplasm arising from follicular dendritic cells. Its diagnosis is challenging due to its extreme rarity, and the optimal management remains unknown. Methods: We conducted a retrospective study of FDCS patients (pts) seen at Mayo Clinic, MN since 2018. Time to event analyses were done from the time of diagnosis. Results: Ten pts with FDCS were identified (Table). The median age was 60 years (range, 38-76) and 5 were males. Abdominal pain was the most common presenting symptom (30%) followed by constitutional symptoms, shortness of breath, and vision change. In 3 pts, the diagnosis was incidental. The 2 most common primary locations were abdomen/pelvis (50%) and mediastinum (30%). Six pts (60%) presented with advanced disease and 3 (30%) had Castleman’s disease. Most (60%) had advanced disease. Six pts had Epstein-Barr virus in situ hybridization and all tested negative. Seven pts had next generation sequencing and 5 (83%) had genetic alterations detected with CDKN2A/B alterations being most frequent (3 pts, all with advanced disease). The median follow up was 4.3 years (range, 0.2-13.3). In the 4 patients with localized disease, 3 underwent complete surgical excision resulting in complete remissions (CRs). The one who received radiation had a partial remission (PR). The median time to progression after 1st line treatment was 4 months (all with advanced disease). All 3 pts who died had advanced disease and 2 had CDKN2A/B alterations. Conclusions: In FDCS, localized diseases managed by surgical excision with or without radiation can achieve long term remissions. Advanced diseases generally do not respond to multimodality therapy including immunotherapy but can have disease stabilization with variable survival. CDKN2A/B mutations were common and potentially associated with a worse outcome. Better understanding of the impact of the FDCS mutational landscape on prognosis may provide novel approaches to therapy. [Table: see text]

Evaluation of a novel Pan-RAS/β-Catenin inhibitor, ADT-030, for treatment of pancreatic cancer.

e15084 Background: Pancreatic ductal adenocarcinoma (PDAC) remains a formidable challenge due to its late diagnosis and limited treatment options. KRAS mutations and activation of Wnt/β-catenin pathway components that drive aberrant signaling cascades resulting in uncontrolled cellular proliferation and metastasis occur in a majority of PDAC patients. The development of mutant specific KRAS inhibitors has emerged as a promising approach to counter the oncogenic impact of KRAS mutations, although have limited use for PDAC given the complex mutational landscape, while inhibitors of Wnt/β-catenin signaling remain elusive. Novel target-directed drugs that effectively tackle the complex mutational status in KRAS mutant PDAC are urgently needed. A novel pan-RAS/β-catenin inhibitor, ADT-030, was evaluated in mouse tumor models of PDAC harboring KRASG12C or KRASG12D mutations. Methods: PDAC cell lines 2838c3 (KRASG12D), MIA PaCa-2 (KRASG12C), and BxPC-3 (RASWT) were utilized to evaluate in vitro growth inhibitory potency and selectivity of ADT-030. Assays for colony formation, apoptosis, and cell cycle, along with western blotting for RAS signaling were also conducted. A murine model involving 2838c3-Luc KRASG12D PDAC cells injected into the pancreas of C57BL/6J mice was used to evaluate in vivo antitumor activity of ADT-030. ADT-030 was administered orally once daily at dosages of 50, 100, and 150mg/kg body weight, 5x/week for 4 weeks. Tumor growth was monitored by bioluminescence imaging using an IVIS Xenogen system. Body weights were measured twice weekly. Pancreatic tumors were collected and weighed at the end of treatment. Results: ADT-030 produced potent inhibition of proliferation of human and murine PDAC cells harboring KRASG12D and KRASG12C mutations. Annexin V assay revealed the capacity of ADT-030 to trigger apoptosis, specifically in KRAS mutant cells with minimal impact on BxPC3 RASWT cells. Cell cycle analysis using Propidium Iodide staining revealed the ability of ADT-030 to arrest cells in the G2/M phase of the cell cycle. Western blot for detecting the key RAS signaling molecule P-ERK1/2 showed decreased levels following ADT-030 treatment. Other experiments revealed that ADT-030 and related analogs simultaneously suppress both MAPK/AKT signaling and β-catenin transcriptional activity (doi: 10.1186/s13048-022-01050-9). In an orthotopic xenograft model in which 2838c3-Luc cells were implanted in the pancreas, oral administration of 50, 100, and 150mg/kg of ADT-030 was well tolerated and inhibited tumor growth by 64.2%, 72.8%, and 80%, respectively, after 4 weeks of treatment. Conclusions: These compelling results position ADT-030 as a novel dual pan-RAS/β-catenin inhibitor for combating the challenges posed by complex mutations in PDAC and other RAS driven cancers and support its clinical evaluation as a valuable therapeutic alternative to mutant-specific KRAS inhibitors.

Clinical application of individualized tumor-informed circulating tumor DNA for therapeutic response and relapse prediction in patients with neuroblastoma.

10053 Background: Patients with high-risk neuroblastoma (NB) generally present with widely metastatic disease and often relapse despite intensive therapy. At present, circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) has been studied in various tumors and proven to be valuable in guiding treatment and predicting recurrence, but its application in NB has rarely been reported. This study aimed to assess the effectiveness of tumor-informed ctDNA monitoring for evaluating the response to induction therapy in NB patients, as well as its role in predicting the risk of relapse. Methods: We conducted a prospective cohort study of NB patients. Primary tumor samples were collected at baseline and blood samples were collected sequentially from baseline until disease progression or the last follow-up. Tumor tissue samples were subjected to whole exome sequencing (WES), and clonal mutations were selected for the individualized MRD panel. Sequencing was conducted at OrigiMed, a College of American Pathologists accredited and Clinical Laboratory Improvement Amendments certified laboratory. Results: Our cohort included 43 individuals diagnosed with NB, with a median age of 3.5 years (0.42-40 years). WES revealed that 75% (2054/2753) of the mutated genes were unique to each patient, and 98.9% (704/712) of the selected tumor-informed single nucleotide variants were variants of unknown significance, suggesting that individualized tumor-informed MRD (n = 23) is superior to fixed tumor-agnostic panel (n = 20) MRD in NB. A successful individualized MRD panel was constructed for 53.5% (23/43) of patients, with a remarkable 92.3% success rate for those older than 5 years (p &lt; 0.01). The initial positivity rate for ctDNA detection was 68%, with the initial positivity rate being associated with the stage (p &lt; 0.01). During treatment and follow-up, 0/6 of the patients whose ctDNA levels remained negative experienced a relapse, whereas 2/5 patients who had a negative conversion or an increase in positivity experienced a relapse. In addition, ctDNA changes matched radiological evaluations in 94% of patients. Notably, ctDNA was detected prior to radiological relapse, with a lead time of 6 months in one patient. Patients can be divided into four groups according to the mutation landscape: ALK mutation, MYCN amplification, chromosome amplification, and other groups. Among them, the rate of ctDNA clearance was the highest in the chromosome amplification group, indicating that patients in this group were the most sensitive to chemotherapy. Conclusions: Individualized tumor-informed ctDNA monitoring shows promise for evaluating therapeutic response and forecasting relapse in NB patients. This approach proves more effective than fixed tumor-agnostic panel-based MRD due to high genetic mutation uniqueness. Clinical trial information: NCT05076071 .

Predictive biomarkers of response to the IRAK4/FLT3 inhibitor emavusertib in hematological malignancies.

6550 Background: Myelodysplastic neoplasms (MDS) and acute myeloid leukemia (AML) display a dynamic and diverse mutational landscape. Various mutations can induce the overexpression of a highly active long isoform of interleukin-1 receptor-associated kinase 4 (IRAK4), leading to downstream activation of transcription factors such as NFκB. This activation triggers inflammation, oncogenesis, and the survival of cancer cells. Emavusertib, a potent oral inhibitor of IRAK4 and FLT3, has demonstrated efficacy in pre-clinical leukemia models and in patients. In this abstract, we present data suggesting potential biomarkers of response to emavusertib based on clinical samples from the ongoing TakeAim Leukemia trial. Methods: In Phase I/IIa of the TakeAim Leukemia trial (NCT04278768), patients with relapsed/refractory (R/R) AML or high-risk MDS (hrMDS) received treatment with emavusertib monotherapy. Baseline and on treatment patient samples underwent RNA sequencing and proteomic analyses. RNA-seq was conducted on mononuclear cells from bone marrow or peripheral blood (n=42). Plasma proteins were quantified by the Luminex platform (n=51). Results: hrMDS patients responding to emavusertib monotherapy exhibited decreased gene expression levels of the NFκB target gene IL1β (P≤0.05) compared to non-responders. Protein analyses revealed that hrMDS responders had lower baseline levels of proliferation and migration-related factors, like Vascular Endothelial Growth Factor (VEGF-A) and CXCL12, in plasma compared to non-responders (P≤0.05). In AML samples, baseline VEGF-A levels were significantly higher in responders. The concentration of soluble PD1 (sPD1) increased in on-treatment samples in hrMDS patients (P≤0.05), but not in AML patient samples. Additionally, hrMDS samples presented lower IL2 and higher sCD47 levels compared to AML (P≤0.05). Conclusions: In this work, several baseline biomarkers indicative of a response to emavusertib were identified in patients with hematological malignancies. Responders in hrMDS showed lower baseline expression of the NFκB-associated pro-inflammatory gene, IL1β, and lower protein levels in plasma of the angiogenic factor VEGF-A and the chemokine CXCL12. In AML samples, responders have higher baseline levels of VEGF-A, indicating distinct predictive biomarkers for both pathologies. Other molecules of clinical interest, such as sPD1, showed increased concentrations in on-treatment plasma samples of hrMDS patients regardless of their response to emavusertib. Our findings highlight distinct baseline biomarkers for AML and hrMDS related to the pathophysiology of hematological malignancies. These results suggest that inflammatory and migration mediators, along with angiogenesis factors, hold potential as predictive biomarkers for assessing responses to emavusertib monotherapy treatment in hematological malignancies. Clinical trial information: NCT04278768 .

Multi-omics profiling the genomic origin and adeno-squamous transdifferentiation mechanism in adenosquamous carcinoma.

e20032 Background: Adenosquamous carcinoma (ASC) represents a rare subtype (0.4-4%) of non-small-cell lung cancer (NSCLC), with its multi-omic landscape yet to be fully elucidated. This study aims to explore the genomic origins and molecular mechanisms of adeno-squamous transdifferentiation in lung ASC through comprehensive multi-omics. Methods: We analyzed 69 samples from 31 lung ASC patients, including 16 FFPE samples with microdissected paired adenocarcinoma (AC) and squamous cell carcinoma (SCC) components, and additionally, incorporated pure Lung Adenocarcinoma (LUAD, n = 51) and pure Squamous Cell Carcinoma (LUSC, n = 28) for comparative analysis. Techniques included whole-exome sequencing, whole-genome methylation profiling, transcriptomics, single-cell RNA sequencing, and spatial transcriptomics. Results: AC and SCC exhibited similar genomic mutation landscapes, indicating a common genomic origin for AD and SCC. The SCC component in ASC displayed higher homologous recombination repair deficiency (HRD) and a notable 16p13.3 deletion in 31% of ASC transformations. Differential methylation analysis highlighted TP63's lower methylation in SCC, correlating negatively with RNA expression (P &lt; 0.001), indicative of methylation-driven regulation. DMR binding motif analysis revealed hypo-methylation in p63, p53, and AP-1 motifs, and hyper-methylation in MKX2-1, FOXA1/2 motifs (P &lt; 0.05). The transition from AC to SCC in ASC was marked by upregulated MYC signaling, proliferation, and DNA repair, with EMT changes not methylation-driven. Metabolic pathways were upregulated, and EMT/KRAS pathways downregulated in SCC compared to LUSC. Immune infiltration in LUAD-AC-ASC transformation showed an initial increase and subsequent decrease, transitioning from immune-infiltrated and immune-excluded to immune-desert phenotypes. IL36G of the IL1 family was highly expressed in the SCC component and strongly correlated with the squamous marker P63 (Pearson r = 0.72, P &lt; 0.001). Single-cell RNA-seq data demonstrated a significant increase in IL36G in squamous cells of lung ASC. In vivo models showed adeno-squamous differentiation in adenocarcinoma cells expressing IL36G. Conclusions: This study provides a comprehensive multi-omic insight into the complex genomic and epigenomic landscape of ASC, highlighting a shared genomic origin and distinct molecular mechanisms in the adeno-squamous transdifferentiation process. The findings, particularly the role of TP63 methylation and IL36G expression in the SCC component, offer novel insights into the molecular heterogeneity of ASC. These results not only deepen our understanding of ASC but also pave the way for future investigations into targeted therapies that could potentially exploit these molecular distinctions for more effective treatment strategies in ASC.

Preliminary safety, efficacy and molecular characterization of emavusertib (CA-4948) in patients with relapsed/refractory (R/R) acute myeloid leukemia (AML) with FLT3 mutation (FLT3m).

6539 Background: AML is a heterogenous disease and exhibits a dynamic mutational landscape as the disease progresses. Internal tandem duplication (ITD) of FLT3 is considered an acquired late-event mutation and is associated with a poor prognosis in AML. Emavusertib is a potent oral inhibitor of both IRAK4 and FLT3, conferring potential dual efficacy advantages compared to other IRAK4 or FLT3 inhibitors as single agents. IRAK4 is upregulated during anti-FLT3- or other cytotoxic therapies, which drives a resistance pathway of early relapse and progression. Methods: The safety, clinical activity, and potential biomarkers of emavusertib in R/R AML and higher-risk myelodysplastic syndrome are being investigated in the ongoing open-label, Phase 1/2a TakeAim Leukemia trial (NCT04278768). Next generation sequencing (NGS) of 68 genes was performed on genomic DNA from bone marrow or peripheral blood mononuclear cells at baseline and on treatment. Here, we present preliminary safety, efficacy data and molecular characterization in a subset of enrolled AML patients who carried FLT3m at baseline and were treated with emavusertib monotherapy. Results: In this study, we treated 11 R/R AML patients with FLT3m at dose levels of 200-400 mg BID. The median number of prior anti-cancer therapies was 2 (range 1-6). 8 of 11 patients had prior exposure to FLT3 inhibitors. Treatment-related adverse events (TRAEs) Grade ≥ 3 were reported in 2 of 11 (18%) patients. All responders were dosed at the Recommended Phase 2 Dose (RP2D) of 300 mg BID and with &lt; 3 lines of prior therapy. In addition, responders demonstrated more than 90% bone marrow blast reduction compared to baseline. The most common co-mutations in this subset of patients included RUNX1, NRAS, and TET2. Emavusertib treatment significantly decreased the variant allele frequency of these mutations. FLT3-ITD levels were decreased or became undetectable in responders. Additional corelative analysis between bone marrow blast counts and mutation status indicates that AML patients with FLT3m demonstrated increased bone marrow blast reductions (P≤0.05) on emavusertib treatment, when compared to FLT3 WT AML patients. Conclusions: Emavusertib has a favorable safety and tolerability profile in pretreated AML patients with FLT3m and demonstrated monotherapy anti-cancer activity in patients with FLT3m, including patients who have progressed on prior FLT3 inhibitors. Mutational profiles are suggestive of disease-modifying activity of emavusertib. We will present updated safety and efficacy data, including data for patients who proceeded to stem cell transplant. Enrollment in this ongoing trial is continuing at RP2D in patients with &lt; 3 lines of prior anti-cancer therapies. Clinical trial information: NCT04278768 .

Molecular characterization and biomarker identification in pediatric B-cell acute lymphoblastic leukemia.

6524 Background: B-cell acute lymphoblastic leukemia (B-ALL) is the most prevalent hematologic malignancy in children and a leading cause of mortality. Despite high cure rates, the management of B-ALL remains challenging due to its high heterogeneity and propensity for relapse. This study aimed to delineate molecular features of pediatric B-ALL and explore the clinical utility of circulating tumor DNA (ctDNA) as a biomarker in B-ALL. Methods: The study analyzed 146 primary pediatric B-ALL patients who were diagnosed from August 2020 to April 2023 and received systemic chemotherapy in Wuhan Children's Hospital. Baseline bone marrow (BM) and plasma samples were collected for next-generation sequencing (NGS) to profile the mutational landscape. BM samples collected on day 19 of the treatment were utilized for minimal residual disease (MRD) testing to assess treatment efficacy. Transcriptomic profiling of baseline BM samples was performed via bulk RNA sequencing. Fisher's exact test and the Wilcoxon rank sum test were utilized to compare categorical and continuous variables between groups, respectively. A two‐tailed P-value&lt;0.05 was considered statistically significant unless indicated otherwise. Results: Transcriptomic analysis revealed that 86.3% of patients (126 out of 146) could be categorized into 13 distinct molecular subtypes, with hyperdiploidy emerging as the predominant subtype. Baseline BM NGS identified gene fusions in 61% of patients, including 37 novel fusions previously unreported in B-ALL. Specifically, the KMT2A-TRIM29 novel fusion was detected and validated in a male child diagnosed with the KMT2A-rearranged subtype. Despite initially responding well to therapy, the patient experienced disease progression after a year, indicating a poor prognosis. We also found that elevated mutant counts and maximum-variant-allele-frequency (maxVAF) in baseline BM were associated with significantly poorer response to chemotherapy ( P=0.0012 and 0.028, respectively). Additionally, MRD-negative patients exhibited upregulated expression of immune-related pathways ( P&lt;0.01) and increased CD8+ T cell infiltration ( P=0.047), indicating a more active immune microenvironment in better responding tumors. Baseline plasma ctDNA, which exhibited high mutational concordance with paired baseline BM samples, also demonstrated significant associations with chemotherapy efficacy, highlighting its potential as a non-invasive tool for disease monitoring and treatment outcome prediction. Conclusions: This study elucidated novel gene fusions and potential biomarkers for treatment response in pediatric B-ALL. Importantly, both baseline plasma ctDNA and BM samples offer promising prognostic insights into chemotherapy responses, paving the way for non-invasive monitoring strategies in the management of pediatric B-ALL.