Targetable Driver Mutations Research Articles

Therapeutic strategies targeting aberrant RNA splicing in myeloid malignancies.

In recent years, large-scale sequencing efforts have identified targetable driver mutations in haematopoietic stem cells. These efforts have led to the development and approval of nine novel agents for relapsed or refractory acute myelogenous leukaemia (R/R AML). However, despite an expansion in targeted therapies, achieving a durable remission in AML and high-risk myelodysplastic syndrome (HR-MDS) remains a significant challenge, and there is an urgent need for new effective treatments. Modulation of aberrant RNA splicing has emerged as a novel therapeutic approach in myeloid diseases. Aberrant splicing drives dysregulated gene expression that promotes tumourigenesis through increased proliferation and metastatic potential, immune evasion, decreased apoptosis, and chemotherapy resistance. Mutations in spliceosomal components have been identified in numerous cancer subtypes, with mutations in RNA binding proteins SF3B1, SRSF2, U2AF1, and ZRSR2 occurring frequently in AML and in up to 60% of patients with MDS, as well as in chronic myelomonocytic leukaemia and in 10% of patients with chronic lymphocytic leukaemia. In this review, we explore therapeutic strategies targeting aberrant splicing and the potential of these approaches to drive clinical responses.

The antitumor activity of osimertinib plus palbociclib in non-small cell lung cancer patient-derived xenograft (PDX)/2D/3D culture models harboring EGFR amplification and CDKN2A/2B homozygous deletions

Non-small cell lung cancer (NSCLC) patients without targetable driver mutation have limited treatment options. In this study, we aimed to explore a new therapeutic strategy by using established nine patient-derived xenograft (PDX) and two-dimensional (2D) /3D culture models with specific genetic alternations. The gene mutations and copy number aberrations were detected by next-generation sequencing and confirmed using polymerase chain reaction (PCR) followed by DNA sequencing, and genomic DNA quantitative PCR. Protein expression was evaluated by immunohistochemistry. Drug sensitivities of PDX/2D/3D models were evaluated by in vivo and in vitro antitumor assays. RNA interference was performed to silence gene expression. Our study found that 44.4 % (4/9) of cases had CDKN2A homozygous deletion (homdel), while 33.3 % (3/9) had CDKN2B homdel. Additionally, 22.2 % (2/9) had amplification (amp) in wildtype CDK4, 44.4 % (4/9) in CDK6, and 44.4 % (4/9) in EGFR. Among the cases, 77.8 % (7/9) lacked CDKN2A, and 33.3 % (3/9) had high CDK4, CDK6, and EGFR had high protein expression. Moreover, 33.3 % (3/9) had KRAS mutations, and 66.7 % (6/9) had TP53 mutations. Antitumor activity of osimertinib plus palbociclib was assessed in four PDX/2D/3D models, two of which had simultaneous EGFR amp and CDKN2A/2B homdel. The data showed that NSCLC with EGFR amp and CDKN2A/2B homdel were sensitive to combined drugs. Additional oncogenic KRAS mutation reduced the drug's antitumor effect. EGFR amp is responsible for osimertinib sensitivity. Osimertinib plus palbociclib effectively treat NSCLC with wildtype EGFR and CDK6 amp and CDKN2A/2B homdel in the absence of oncogenic KRAS mutation.

Assessing the Sensitivity of Nested PCR Followed by Direct Sequencing on Exosomal DNA for EGFR Mutation Detection in NSCL

Early and minimally invasive detection of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) patients is a promising tool to select patients for targeted therapy in order to improve their prognosis. This study aimed to identify a sensitive, cost-effective, and easily accessible noninvasive method for detecting the EGFR-targetable mutations in the plasma exosomal DNA (exoDNA)+ of patients with NSCLC. This retrospective observational study was conducted over 10 months, from December 2022 to October 2023, at Masih Daneshvari Hospital in Tehran, Iran. A total of 30 patients with stage II-IV NSCLC and targetable mutation in the EGFR gene were included in the study. Nested PCR and Sanger sequencing were used to evaluate EGFR mutations in the DNA extracted from circulating exosomes. The study found a sensitivity of 76.6% for EGFR mutation detection on exoDNA compared to tissue results. No significant impact was observed based on tumor staging, histology, mutation type, smoking status, gender, or age. Therapeutically targetable driver mutations in the EGFR gene can be accurately detected using nested PCR followed by direct sequencing of plasma exoDNA from patients with NSCLC. This approach facilitates timely and more personalized treatment for NSCLC patients, ultimately improving patient prognosis. Additionally, this method reduces the reliance on invasive tissue biopsies and their associated complications.

An open-label, phase 1, multicenter study to evaluate the safety and preliminary anti-tumor activity of NT-112 in human leukocyte antigen-C*08:02–positive adult patients with unresectable, advanced, and/or metastatic solid tumors that are positive for the KRAS G12D mutation.

TPS2677 Background: The landscape of cancer treatment is evolving with the emergence of innovative immunotherapies. Among these, T cell receptor-engineered T cell (TCR-T) therapy has shown promise for patients with solid tumor malignancies. Targeting driver mutations, such as KRAS, may offer novel therapeutic options for patients with limited treatment options. Oncogenic driver mutations in KRAS typically involve single-base mutations at genomic hotspot locations. The KRAS isoform is mutated in 84% of RAS-driven cancers and in nearly 100% of pancreatic ductal adenocarcinoma (PDAC). The KRAS G12D mutation is the most frequent mutation in PDAC (28%), followed by colorectal cancers (12%). Despite its well-established target role in tumorigenesis, there is no FDA-approved therapy targeting the G12D variant. NT-112 is an autologous TCR-T cell therapy targeting the KRAS G12D mutation presented by HLA-C*08:02, armored by disruption of the gene encoding the transforming growth factor beta receptor type 2 (TGFBR2) in order to reduce the immunosuppressive effect of TGF-β in the tumor microenvironment. Methods: This first-in-human, open label, multicenter, Phase 1, dose escalation study aims to assess the safety, identify the MTD and evaluate potential anti-tumor activities of NT-112 in subjects with solid tumors. The study will enroll up to 24 adult subjects harboring the KRAS G12D mutation that are HLA-C*08:02 positive, who exhibit progressive or recurrent disease after at least one line of standard of care treatment. Enrolled patients will undergo leukapheresis, from which, CD4 and CD8 T cells will be enriched and activated ex vivo. The genes encoding the TGFBR2 and the endogenous TCR α and β chains are knocked out from the activated T cells utilizing clustered regularly interspaced short palindromic repeats (CRISPR-Cas9). The HLA-C*08:02-restricted TCR specific to the KRAS G12D mutation is knocked-in in the TCR α locus. Subjects will undergo standard lymphodepletion followed by a single infusion of NT-112 and concurrent, daily, subcutaneous, recombinant IL-2 for up to 8 days. Dose escalation will occur across 3 ascending dose levels following the BOIN design. Subjects will be monitored for dose-limiting toxicities for 28 days following NT-112 infusion. Disease response will be assessed according to the RECIST v1.1 criteria. Comprehensive translational analysis will be conducted to gain insights into the mechanism of action, biomarkers associated with treatment response, and potential mechanisms of resistance. All subjects will be followed for up to 15 years. Clinical trial information: NCT06218914 .

Nature and distribution of methyl thioadenosine phosphorylase (MTAP) genomic loss in human tumors.

3067 Background: MTAP genomic loss, often but not exclusively a bi-allelic homozygous deletion, has recently emerged as important biomarker guiding a novel synthetic lethality mechanism for drugs in the class of PRMT5 and MAT2A inhibitors. In the current study, we assessed the nature and distribution of MTAP complete and partial loss in a variety of tumor samples. Methods: A total of 291,391 tissue samples underwent comprehensive genomic profiling (CGP) using a hybrid-capture method to evaluate all classes of genomic alterations (GA), and determine the microsatellite instability (MSI) status, tumor mutational burden (TMB), homologous recombination deficiency (HRD) score and genomic ancestry. The distribution of both complete and partial loss of MTAP was also determined. Results: MTAP GA were found in 8.6% of total with 9.3% genomic loss and 0.1% each short variant mutations and rearrangements. Important (not rare) tumor types with the most frequent MTAP loss included: 42.6% of glioblastoma (GBM), 13.4% of non-small cell lung cancer (NSCLC), 22.3% of pancreatic ductal and 24.9% of bladder urothelial carcinomas. The most frequently co-altered GA included CDKN2A (99.7%), CDKN2B (95.1%), TP53 (55.4%), KRAS (30.1%), TERT(20.5%) and PIK3CA (12%). In tumor types with frequent known targetable driver GA including short variant mutations in EGFR, ERBB2, BRAF, FGFR2-3and MET and fusions involving ALK, RET, ROS1 and NTRK1-3, MTAP loss was not associated with decreased frequencies of GA in these genes. The frequencies of MSI-high status was 0.3% and of TMB≥10 mut/Mb was 17%. In total, 63.7% of the MTAP loss cases involved deletion of all 8 MTAP exons (complete loss) with partial loss accounting for 36.3% of cases. All partial loss cases involved loss of multiple exons (35.8%) except for loss of only exon 8 (0.5%). There was no impact of MTAP loss status on genomic ancestry, cosmic trinucleotide signature and HRD score. The multiple exon loss frequencies included exons 2-8 loss in 24.7%, exons 5-8 loss in 4.1%, exons 6-8 loss in 3.3%, exons 3-8 loss in 1.6%, exons 7-8 in 1.1%, exon 4-8, 1-5, 2-7,2-5, 1-4, 2-6, 3-7 and 5-7 all at less than 1% frequencies. Conclusions: MTAPloss is a frequent GA of emerging clinical importance as the trials using PRMT5 and MTA-2 inhibitors progress. MTAPloss is frequent in common cancers of the brain, lung, pancreas and bladder and not associated with diminishment of other targetable driver mutations. Although one-third of MTAP loss is a partial loss, the partial loss cases involve near total (exons 2-8) loss and may well also be indicative of PRMT5/MAT2A inhibitor benefit. This study strengthens the opportunity to consider a tumor-agnostic approach to targeted therapies. [Table: see text]

5-hydroxymethylcytosine in cell-free DNA as liquid biomarker for immune checkpoint inhibitor therapy in non–small cell lung cancer.

e20563 Background: Immune checkpoint inhibitors (ICIs) targeting programmed cell death 1 (PD-1), and its ligand (PD-L1) are the mainstay of treatment for metastatic non-small cell lung cancer (NSCLC) in patients lacking targetable driver mutations. However, optimal predictive biomarkers are lacking. We used a plasma cell-free DNA (cfDNA) 5-hydroxymethylcytosine (5hmC) signature-based predictive model to assess treatment response and potentially select patients eligible for ICI monotherapy. Methods: 40 plasma samples were collected from adult patients with stage III or IV lung cancer at Houston Methodist Hospital between 2019 and 2022. These were divided into a training (n = 24) and validation (n = 16) set. By identifying genes associated with progression free survival (PFS), a 16-gene signature was used to develop a 5hmC predictive model. A weighted predictive score (wp-score) based on the model was calculated for each patient and grouped into low and high wp-scores. Results: Low wp-scores were associated with higher objective response rate(ORR) in both training and validation set and better correlated with response rates compared to PD-L1. In the training set, PFS was longer in low wp-scores compared to high wp-scores (median 12.3 versus 3.0 months; p = 3.5x10-6; hazard ratio (HR) 4.6x10-10). This was also seen in the validation set (median 7.6 versus 1.8 months p = .0012; HR 0.12). Contrarily, high ( > 1%) or low ( < 1%) PD-L1 was not associated with PFS (median 6.8 versus 6.0 months; p = .40; HR 0.70; 95% CI, 0.30–1.60) or overall survival (OS) (median 10.1 versus 12.0 months; p = .38; HR 0.56; 95% CI, 0.15–2.10). 15 out of the 40 total patients received ICI monotherapy. Among these, low wp-scores (n = 8) were significantly associated with longer PFS compared to high wp-scores (n = 7), (median 19.6 versus 2.8 months; p = .00073; HR: 0.059). OS although longer, was not significant among the two groups (median 38.1 versus 10.5 months; p = .12). Conclusions: Our study provides a proof of concept that cfDNA 5hmC signature can be used to predict response to ICI therapy and select patients appropriate for monotherapy. It is a more sensitive and specific biomarker to PD-L1. Larger studies are underway to further validate cfDNA 5hmC based-signature predictive model. [Table: see text]

Abstract PO4-16-05: Identification of functional HLA-A*11:01-restricted driver gene PIK3CA mutation specific T-cell receptors

Abstract The adoptive transfer of genetically engineered T-cell receptors (TCR-T) has emerged as a promising therapeutic strategy for the treatment of solid tumors. Recent clinical trials have demonstrated the safety and efficacy of TCR-T cell therapies against certain types of metastatic solid cancers. In our study, we aimed to investigate the potential of TCR-T cell therapies targeting neoantigens, which are exclusively expressed in cancer cells, with a focus on metastatic breast cancer (MBC). Specifically, we identified four driver missense mutations (PIK3CA E542K, E545K, H1047L, and H1047R) frequently observed in MBC patients and utilized computational tools to predict the generation of neoantigens. Utilizing NetMHCpan V.4.1, we performed screening of peptides spanning the mutation region and predicted a neoantigen epitope, PIK3CA_H1047L, to bind with HLA-A*11:01. To validate the presentation and stability of the neoantigen epitope, we employed TAP1-deficient K562 cells and observed stable expression of the mutant peptide-major histocompatibility complex (MHC) complex on the cell membrane. Subsequently, we isolated T cells from healthy donors possessing the HLA-A11:01 genotype, and subjected them to successive stimulations with neopeptide-pulsed dendritic cells. T cells stimulated with neopeptide were examined for neoantigen specificity using an IFN-γ ELISpot assay. Employing pMHC tetramer staining and single-cell sorting via flow cytometry, we successfully isolated five HLA-A11:01-restricted PIK3CA_H1047L-specific TCRs. Through lentivirus transduction of these TCRs into T cells, we achieved the generation of TCR-T cells that exhibited potent and specific activity exclusively against the PIK3CA_H1047L neoantigen. The functionality of the TCR-T cells was confirmed through assessments of CD137 expression, IFN-γ secretion, and cytotoxicity assays. In conclusion, our study demonstrates T cell responses towards neoantigens derived from PIK3CA, a commonly observed driver mutation in MBC. Furthermore, we successfully isolated five distinct neoantigen-specific TCRs that specifically recognized the PIK3CA_H1047L mutation and were restricted to the prevalent HLA-A*11:01 allele. The transfer of these TCRs into T cells resulted in the generation of TCR-T products exhibiting remarkable activity against the PIK3CA_H1047L neoantigen. These findings strongly encourage further investigation into TCRs targeting driver mutations in MBC, with the aim of advancing neoantigen-targeted TCR-T therapies into clinical trials. Additionally, the PIK3CA_H1047L neoantigen holds great promise as a potential candidate for the development of effective cancer vaccines. Citation Format: Meiying Shen, Xiaojian Han, Siyin Chen, Aishun Jin, Shengchun Liu. Identification of functional HLA-A*11:01-restricted driver gene PIK3CA mutation specific T-cell receptors [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-16-05.

Mutational Profiling by Next-Generation Sequencing in Patients with Metastatic Non-Small Cell Lung Carcinoma: Our Experience

Introduction According to GLOBOCAN 2020, overall lung cancer is the second most common cancer in both sexes (11.4%) accounting for highest cancer-related mortality (18%).1 Adenocarcinoma subtype of non-small cell lung cancer (NSCLC) is the most common subtype and is divided into further molecular subtypes based on oncogenic driver mutations. Overall survival in these patients is poor with the use of conventional platinum-based double chemotherapy and various recent studies on targeted therapy studies have showed improved survival. Therefore, broad panel-based testing like next-generation sequencing (NGS) is strongly recommended to identify these targetable driver mutations. Aims and Objectives The aim of this study was to evaluate the mutational profile in patients with metastatic NSCLC (mNSCLC) by NGS method. Materials and Methods A hospital-based prospective observational study done on 88 patients under the Department of Medical Oncology, State Cancer Institute during a period of 1 year. All patients above 18 years of age diagnosed as mNSCLC having Eastern Cooperative Oncology Group performance status 0 to 2 and evaluated for mutational profiling by NGS method were included. Five gene panel tests including endothelial growth factor receptor (EGFR), echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (EML4-ALK), BRAF, mesenchymal epithelial transition (MET), and ROS proto-oncogene 1 (ROS1) were used. Results and Observations Majority of mNSCLC cases were in the age group of 41 to 50 years (n = 30, 34.1%) with average age at presentation being 53.74 years. Male: female ratio was 1.14:1 and most patients were nonsmokers. Adenocarcinoma subtype of mNSCLC cases had the highest mutational burden (n = 55, 62.5%). EGFR (n = 32, 56.14%) was the most common mutation followed by EML4-ALK (n = 19, 33.33%). Most common EGFR mutation was in Exon 19. Other rare mutations were ROS1 (n = 4), BRAF V600E (n = 1), and MET (n = 1). Skeleton was the most common site of metastasis across all driver mutations. Conclusion EGFR and EML4-ALK were the commonest targetable mutations detected in the study. As there is very limited data from North Eastern region of India regarding mutational status in mNSCLC, this study opens up possibilities for further studies targeting multiple mutations to give us more comprehensive understanding of the mutational landscape of mNSCLC in this era of precision medicine.

Abstract CT021: Preliminary clinical results of a therapeutic cancer vaccine PDC*lung01 in combination with anti-PD-1 in patients (pts) with stage IV NSCLC

Abstract Background PDC*lung01 (IMP) is a therapeutic cancer vaccine based on an irradiated plasmacytoid dendritic cell line loaded with HLA-A*02:01-restricted peptides (NY-ESO-1, MAGE-A3, MAGE-A4, Multi-MAGE-A, MUC1, Survivin and Melan-A), able to prime and expand peptide-specific CD8+ T cells in vitro and in vivo, and is synergistic with anti-PD-1. Methods In this phase I/II study, HLA-A*02 positive NSCLC pts were enrolled in 4 cohorts: resected stage II/IIIA in adjuvant setting treated with low dose (A1) or high dose (A2) of IMP following SOC; or untreated stage IV NSCLC with measurable disease, PD-L1≥50% and no targetable driver mutation, treated with low dose (B1) or high dose (B2) of IMP in combination to pembrolizumab 200mg q3w, continuously. IMP was simultaneously administered by SC and IV route weekly for 6 consecutive doses. Objective response rate (ORR) and progression-free survival (PFS) were assessed in cohort B2. We report herein preliminary efficacy results of the first 21 pts analysed when the 19th evaluable patient reached the 9-months PFS and the safety of 38 pts. Results Out of 21, 19 pts receiving at least 5 doses of IMP and having 1 post-baseline radiological evaluation were evaluated. The median follow-up was 12.5 months. The best objective response (BOR) included 12 PR (63.2%) and 7 SD (36.8%) with ORR of 63.2% (80% CI 45.9% - 78.2%) and a disease control rate (DCR) of 94.7%. The 9mPFS according to the Kaplan-Meier estimate was 52.1% (80% CI 36.5% - 65.56%). The mPFS was 10.9 months. The median duration of response was 9.49 months. An antigen-specific CD8+ T-cell response was induced against the lung antigens of the IMP in 68.4% of pts. Immune responses with remarkable expanded anti-tumor CD8+ T-cells were observed both in PR and SD. More immune response results will be available in the final analysis of the 45 pts of cohort B2. Treatment-related AEs (TRAEs) were mostly Grade 1-2. Only 1 severe TRAE occurred, a Grade 4 allergic infusion-related reaction, leading to IMP discontinuation. Thirteen pts experienced a serious AE, of which 3 were considered causally related to the IMP. Conclusions The BOR, ORR, DCR, PFS, duration of response and safety of PDC*lung01 in combination with anti-PD-1 showed encouraging signals suggesting that this combination may provide a clinical meaningful tumour response in stage IV NSCLC population with a mild safety profile. Interestingly, the immune response observed confirms the mechanism of action of the IMP in relation to clinical activity. Citation Format: Willemijn Theelen, Maurice Perol, Kristof Cuppens, Ingel Demedts, Frank Borm, Bonne Biesma, Els Wauters, Benoit Colinet, Eva-Lotte Buchmeier, Friederike Althoff, Elvire Pons-Tostivint, Charlotte Van de Kerkhove, Denis Moro-Sibilot, Anne Sibille, Sofie Derijcke, Marcin Skrzypski, Joel Plumas, Beatrice De Vos, Channa Debruyne, Frederique Cantero, Stefanie Adriaenssens, Florence Renard, Johan Vansteenkiste. Preliminary clinical results of a therapeutic cancer vaccine PDC*lung01 in combination with anti-PD-1 in patients (pts) with stage IV NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT021.

CT Imaging Patterns in Major Histological Types of Lung Cancer.

Lung cancer ranks as the second most prevalent cancer globally and is the primary contributor to neoplastic-related deaths. The approach to its treatment relies on both tumour staging and histological type determination. Data indicate that the prognosis of lung cancer is strongly linked to its clinical stage, underscoring the importance of early diagnosis in enhancing patient outcomes. Consequently, the choice of an appropriate diagnostic method holds significant importance in elevating both the early detection rate and prognosis of lung cancer. This paper aims to assess computer tomography features specific to the most common lung cancer types (adenocarcinoma, squamous cell carcinomas and small cell lung cancer). Data were collected retrospectively from CT scans of 58 patients pathologically diagnosed with lung cancer. The following CT features were evaluated and recorded for each case: location, margins, structure, lymph node involvement, cavitation, vascular bundle-thickening, bronchial obstruction, and pleural involvement. Squamous cell carcinoma (SQCC) and small cell lung cancer (SCLC) showed a higher incidence of central location, while adenocarcinoma (ADC) showed a significant predilection for a peripheral location. Internal cavitation was mostly observed in SQCC, and a solid structure was observed in almost all cases of ADC. These features can provide information about the prognosis of the patient, considering that NSCLCs are more frequent but tend to demonstrate positive results for targetable driver mutations, such as EGFR, thereby increasing the overall survival. In addition, SCLC presents with early distant spreads, which limits the opportunity to investigate the evolution of tumorigenesis and gene alterations at early stages but can have a rapidly positively response to chemotherapy. The location of the lung cancer exhibits distinct forecasts, with several studies suggesting that peripheral lung tumours offer a more favourable prognosis. Cavity formation appears correlate with a poorer prognosis. Histopathological analysis is the gold standard for diagnosing the type of lung cancer; however, using CT scanning for the purpose of a rough, but fast, preliminary diagnosis has the potential to shorten the waiting time for treatment by helping clinicians and patients to know more about the diagnosis and prognosis.

Characterization of BRAFThr599dup Mutation as a Targetable Driver Mutation Identified in Lung Adenocarcinoma by Comprehensive Genomic Profiling.

Understanding the function of BRAF mutants is crucial for determining the best treatment strategy. This study aimed to characterize a rare BRAF variant, BRAFThr599dup, which was identified in a patient with lung adenocarcinoma (LUAD) by comprehensive genomic profiling. We report a case of LUAD with BRAFThr599dup treated with dabrafenib and trametinib. We conditionally expressed wild-type BRAF, BRAFV600E, or BRAFThr599dup in Ba/F3 cells and BEAS-2B cells. Ba/F3 cells carrying double-mutant BRAF (BRAFThr599dup/R509H, BRAFV600E/R509H, or BRAFK601E/R509H) that lacked the dimerizing ability were also established. Knockout of endogenous BRAF or CRAF in Ba/F3-BRAFThr599dup cells and Ba/F3-BRAFV600E cells was performed using the CRISPR/Cas9 system. Cell viability, mitogen-activated protein kinase (MAPK) signaling activity, and sensitivity to dabrafenib and trametinib were evaluated. The patient was revealed to have BRAFThr599dup-positive tumor cells as a predominant clone, and dabrafenib and trametinib treatment showed modest efficacy. In Ba/F3 cells, both BRAFThr599dup and BRAFV600E similarly caused interleukin-3-independent proliferation and activated the MAPK pathway. Moreover, BRAFThr599dup and BRAFV600E similarly caused a significant increase in the anchorage-independent growth ability of BEAS-2B cells. Along with Ba/F3-BRAFV600E cells, Ba/F3-BRAFThr599dup cells were highly sensitive to a monomer-specific BRAF inhibitor, dabrafenib, with a half-maximal inhibitory concentration value of 29.7 nM. In the absence of wild-type BRAF, wild-type CRAF, or an intact dimer interface, the ability to induce oncogenic addiction and MAPK pathway activation in Ba/F3-BRAFThr599dup cells was not affected, which was in contrast to the findings in the BRAFK601E/R509H double-mutant model. BRAFThr599dup is a potent driver oncogene that activates the MAPK pathway without the requirement for dimerization in vitro. Because BRAFThr599dup has been recurrently reported across various cancer types, our findings should be further investigated both mechanistically and clinically.

Abstract 6401: Predictive models for first-line immunotherapy based on spatial tumor immune microenvironment in patients with advanced non-small cell lung cancer (NSCLC)

Abstract Background: Anti-programmed cell death protein 1/programmed cell death ligand 1 (anti-PD1/PDL1) based immunotherapy is the standard first-line treatment for advanced NSCLC patients without targetable driver mutations, but PDL1 immunohistochemistry (IHC) shows limited predictive value as companion diagnostics. Recent studies have elucidated a strong relationship between immunotherapy efficacy and tumor immune microenvironment (TIME) using single-cell multi-omics technology. In this study, we aim to develop predictive models for both objective response rate (ORR) and progression-free survival (PFS) using TIME features with machine learning in advanced NSCLC patients treated with first-line immunotherapy. Methods: A total of 210 patients with advanced NSCLC who received anti-PD-1/PDL-1 therapy at Shanghai Chest Hospital from Jan. 2020 to Jan. 2023 were included in this study. Among them, 110 cases who received pembrolizumab were randomly split into training set and validation set with a 2:1 ratio. The remaining patients were designated as independent validation cohort. Five multiplex immunohistochemistry (mIHC) panels were developed based on literature review and in-house dataset mining. mIHC tests were performed using baseline tumor samples. Immunotherapy efficacy was evaluated by ORR and PFS (RECIST v1.1). ORR and PFS models were developed using machine learning methods in training set with 5-fold cross-validation and further validated in validation set and independent validation cohort. Results: After data cleaning, 68 cases in training set and 34 cases in validation set were further analyzed. In terms of single immune- or spatial- based biomarker, positive rate of PD1+ cells in stroma and spatial relationship of PD1+/PDL1+ cell pairs exhibited the highest correlation with ORR. In addition, positive rate of PDL1+ tumor cells and nearest distance between FOXP3+ cells and tumor cells were highly correlated with PFS. Our ORR model achieved an AUC of 0.82 in the training set and 0.82 in the validation set. When applying optimal cutoff in our PFS model to stratify patients into low- and high- risk groups, low-risk group showed prolonged PFS in both training set (p < 0.0001; HR: 0.25, 95% CI [0.13 - 0.51]) and validation set (p = 0.00046; HR: 0.22, 95% CI [0.09 - 0.55]). Moreover, our ORR model outperformed PDL1 IHC (AUC: 0.81 vs 0.60; DeLong’s test p = 0.005) in these 102 patients. Independent validation of the models is still awaited. Conclusion: Using machine learning methods, we developed and validated ORR and PFS predictive models for first-line immunotherapy in advanced NSCLC patients based on mIHC technology. Our models displayed superior diagnostic performance compared to PDL1 IHC results. Citation Format: Chan Xiang, Jianjian Zheng, Sidong Chen, Zhanxian Shang, Shi Yang, Lianying Guo, Lei Jiao, Yang Wang, Yuchen Han. Predictive models for first-line immunotherapy based on spatial tumor immune microenvironment in patients with advanced non-small cell lung cancer (NSCLC) [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 6401.

Abstract 7236: Selective deletion of the KRAS mutant gene with ADGN-123 and ADGN-121 peptide-RNA nanoparticles: A new strategy to overcome acquired resistance to KRASG12C and KRASG12D small molecule inhibitors

Abstract KRAS codon12 mutations are among the most commonly observed mutations in cancers. Recently, KRASG12C inhibitors (sotorasib and adagrasib) have been approved and KRASG12D inhibitor MTRX-1133 has shown preclinical efficacy in KRASG12D mutated cancers. However, these inhibitors are limited by adaptive resistance, mainly associated with the emergence of secondary KRAS mutations, activation of feedback pathway and amplification of KRASG12C allele. We have developed a new potent strategy combining gene editing with tumor selective peptide nanoparticles, to overcome acquired resistance to KRASG12C and KRASG12D inhibitors. ADGN-123 and ADGN-121 are gene-editing complexes containing proprietary sgRNA targeting KRASG12C and KRASG12D respectively, complexed with proprietary peptides. ADGN-123 and ADGN-121 were evaluated on pancreas, colorectal, and lung cancer cells harboring KRASG12C or G12D mutations. ADGN-123 was evaluated on NCI-H358 and Mia-PACA generated clones resistant to sotorasib/adagrasib and harboring KRASG12C,R68M and KRASG12C,Y96D secondary mutations. ADGN-121 was evaluated on ASPC-1 and PANC-1 generated clones resistance to MRTX-1133. In-vivo efficacy of IV-administered ADGN-121 (0.25-1.0 mg/kg, day 1 and 7) was evaluated in PANC-1 (KRASG12D) mouse xenografts. ADGN-123 and ADGN-121 selectively silenced KRASG12C and KRASG12D, respectively, in cancer cells resulting in inhibition of cell proliferation (IC50: 10-30 nM) and of the phosphorylation of ERK and AKT. we showed that ADGN-123 containing gRNAG12C/mRNACas9 blocks the proliferation (IC50 : 10-20 nM) of cells with secondary KRASG12C/R68M and KRASG12C/Y96D mutations or with KRAS in a permanent active state and effectively inhibits ERK phosphorylation. We showed that ADGN-121 containing gRNAG12D/mRNACas9 can effectively inhibit the proliferation (IC50 : 10-15 nM) of ASPC-1 MRTX-1133R and PANC-1 MRTX-1133R cells with high level of KRASG12D-GTP active state. No resistance was detected after ADGN-123 or ADGN-121 treatments. We demonstrated that only two IV-administrations of ADGN-121 containing gRNAG12D/mRNACas9 abolished PANC-1 tumor growth in a dose dependent manner, resulting in significant tumor regression at 1.0 mg/kg. In contrast, no effect on tumor growth was observed with nonspecific gRNA. ADGN treatments were well tolerated, with no signs of clinical toxicity detected after single or repeat administration. Our study provides a proof-of-concept that ADGN complexes can be applied to target driver mutations of cancers in vivo and permanently disrupt the oncogenic alleles, leading to major tumor regression. ADGN-123 and ADGN-121 constitute a potent alternative strategy to overcome resistance associated to small molecule inhibitors of KRASG12C and KRASG12D Citation Format: Gilles Divita, Audrey Grunenberger, Veronica Guzman-gonzalez, Elodie Czuba, Khadidja Boularache, Melanie Guidetti, Veronique Josserand, Neil Desai. Selective deletion of the KRAS mutant gene with ADGN-123 and ADGN-121 peptide-RNA nanoparticles: A new strategy to overcome acquired resistance to KRASG12C and KRASG12D small molecule inhibitors [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 7236.

Translational Insights in the Landscape of Salivary Gland Cancers: Ready for a New Era?

Salivary gland carcinomas (SGCs) are rare neoplasms, representing less than 10% of all head and neck tumors, but they are extremely heterogeneous from the histological point of view, their clinical behavior, and their genetics. The guidelines regarding their treatment include surgery in most cases, which can also play an important role in oligometastatic disease. Where surgery cannot be used, systemic therapy comes into play. Systemic therapy for many years has been represented by polychemotherapy, but recently, with the affirmation of translational research, it can also count on targeted therapy, at least in some subtypes of SGCs. Interestingly, in some SGC histotypes, predominant mutations have been identified, which in some cases behave as "driver mutations", namely mutations capable of governing the carcinogenesis process. Targeting these driver mutations may be an effective therapeutic strategy. Nonetheless, it is not always possible to have drugs suitable for targeting driver mutations-and targeting driver mutations is not always accompanied by a clinical benefit. In this review, we will analyze the main mutations predominant in the various histotypes of SGCs.

Emerging therapeutic strategies for metastatic uveal melanoma: Targeting driver mutations.

Uveal melanoma (UM) is the most common primary malignant intraocular tumor in adults. Although primary UM can be effectively controlled, a significant proportion of cases (40% or more) eventually develop distant metastases, commonly in the liver. Metastatic UM remains a lethal disease with limited treatment options. The initiation of UM is typically attributed to activating mutations in GNAQ or GNA11. The elucidation of the downstream pathways such as PKC/MAPK, PI3K/AKT/mTOR, and Hippo-YAP have provided potential therapeutic targets. Concurrent mutations in BRCA1 associated protein 1 (BAP1) or splicing factor 3b subunit 1 (SF3B1) are considered crucial for the acquisition of malignant potential. Furthermore, in preclinical studies, actionable targets associated with BAP1 loss or oncogenic mutant SF3B1 have been identified, offering promising avenues for UM treatment. This review aims to summarize the emerging targeted and epigenetic therapeutic strategies for metastatic UM carrying specific driver mutations and the potential of combining these approaches with immunotherapy, with particular focus on those in upcoming or ongoing clinical trials.

Advances in the targeted treatment of non-small cell lung cancer

Non-small cell lung cancer (NSCLC) paradigmatically shows the potential of personalized and therefore precise cancer treatment. For around one third of the patients, predominantly suffering from adenocarcinoma, targetable driver mutations could be characterized in the meantime. Targeted therapies, mostly with kinase inhibitors, achieve impressive advances in the prolongation of overall survival often over many years and excellent quality of life in patients with advanced NSCLC. Targeted treatment is also increasingly evaluated as adjuvant or neoadjuvant treatment in early inoperable stages of NSCLC. An absolute prerequisite for the use of personalized treatment is upfront broad molecular diagnostics before the decision on first line treatment. The limitations of personalized treatment are the so far unavoidable development of resistance mutations and increasing clonal heterogeneity during the course of the treatment. Approaches to further improve treatment results comprise the development of next-generation inhibitors, the combination of targeted substances, also with chemotherapy and the use of new immunoconjugates.

Immunotherapy outcomes in non-small cell lung cancer according to a gender perspective.

In the last few years, immune checkpoint inhibitors (ICIs) improved treatment strategies for advanced non-small cell lung cancer (NSCLC) with no targetable driver mutations. Empirical evidence strongly suggests that males and females differ in outcomes following the use of ICIs for treatments of solid cancers. Women in fact exhibit greater humoral and cell-mediated immune responses and an even more advanced immune editing which plays an important role in controlling cancer rising and evolution. However, at present, no conclusive studies have addressed differences in response to ICIs regarding sex and, to note, reproductive status in women or autoimmune diseases in both sexes are often not recorded in clinical trials. Consequently, it can be argued that to assess cancer responses and study cancer spread, results of published studies in men may not unconditionally be applied on female patients treated with ICIs, and vice versa. In this chapter have been discussed recent data about gender differences in the immune system and in NSCLC patients treated with ICIs, highlighting sex as a key factor in evaluating different responses in the two sexes.

Comparison study of clinic radiological profile of primary lung cancer using EDAS method

When bodily cells transform and proliferate out of control, it is called cancer. Cells are the minuscule building blocks that make up your body. Normal cells develop as required by the organism and degenerate when no longer required. The aberrant cells that make up cancer develop even if your body doesn't require them to. The aberrant cells in the majority of malignancies develop into a bump or mass known as a tumor. Long enough for cancer cells to exist in the body, they can spread (invade) into surrounding regions. They may even spread to various body regions (metastasis). Two key turning points for the practical application of targeted therapy in lung cancer patients were the sequencing of the malignant tumors genome and the development of medicines that target driver mutations. Understanding euplastic cells and mutational mechanisms, along with how they change as tumors form and how different cancer cells differ genetically, are all necessary for this. It is hoped that ongoing global initiatives to systematically identify the most pertinent genetic alterations for each subgroup of pulmonary cancer will raise the proportion of tumors that always respond better to novel medications targeting different genetic profiles. Oral medicines with significantly higher responder rates and lower toxicity than chemotherapy can be used to target many genetic changes. Methology: Alternative: Brain, Bone, Liver, Contra lateral lung, Adrenal gland. Evaluation Preference: Squamous cell carcinoma, denocarcinoma, Small cell lung carcinoma, undifferentiated carcinoma Result: As a result, Adrenal gland and top ranking, whereas the Brain rating received a low ranking received Conclusion: The value of the dataset for Lung cancer in EDAS method shows that it results in Adrenal gland and top ranking.

Hepatoid adenocarcinoma of the lung with PD-L1 expression and the response to anti-PD-1 therapy: a case report

Hepatoid adenocarcinoma of the lung (HAL) is extremely rare; a standardized treatment strategy for HAL has not been established. The prognosis of patients with unresectable HAL is extremely poor. Here, we reported a 64-year-old male patient with unresectable alpha-fetoprotein-producing HAL who showed moderate harboring programmed death ligand 1 (PD-L1) expression and no targetable driver mutations. The patient was treated with brain radiotherapy, multiple lines of chemotherapies, and PD-1 inhibitor and achieved a survival rate of 9 months. The patient finally died because of the progression of brain metastasis. The case report provides valuable information for the treatment strategy development of advanced HAL patients and reminds us of the therapeutic particularity of brain metastasis.

Optimizing the Integration of Genetic Testing in AML Care in Community Practice: Insights from a Quality Improvement Initiative

Background The treatment landscape for acute myeloid leukemia (AML) is rapidly evolving, and with many of the more recently FDA approved treatments being targeted therapies, timely and actionable molecular and cytogenetic testing is critical to the management of AML patients. However, many challenges and barriers to optimal testing workflows impede clinicians' ability to integrate genetic testing in treatment decision-making. To improve quality care related to genetic testing in AML, we conducted a quality improvement (QI) study focused on evidence-based integration of genetic testing into routine practice for AML patients in community oncology clinics. Methods This QI initiative is comprised of baseline (N = 72) and follow-up provider surveys, and pre- and post-surveys of providers participating in small-group, team-based audit-feedback (AF) sessions across 5 community clinics. Survey questions were designed to assess knowledge, confidence, and experiences with genetic testing in AML. Care teams from each clinic, along with an expert AML oncologist and a hematopathologist, participated in AF sessions to (a) assess system-specific practice gaps identified via the provider surveys, (b) prioritize areas for improvement, and (c) develop action plans for addressing root causes. Results Provider Surveys: Providers top reported challenges encountered with integrating genetic testing into routine practice include determining whether to begin treatment prior to receipt of genetic testing result (56%)and applying genetic testing results to treatment decision-making (29%). For patients with AML, 70% of providers stated they were likely to start treatment prior to receiving testing results. When asked to report routine molecular testing practice patterns, 72% of providers reported testing for FLT3 mutations, 62% for IDH1/2 mutations, 65% for TP53 mutations, and 63% for NPM1 mutations; with further suboptimal reported practices in the use of NGS panels (58%; average turnaround time 15 days) and PCR (52%; average turnaround time 8 days). Overall, providers reported a 56% satisfaction rate with the processes implemented in the clinic related to sample preparation, timely review, and turnaround time of molecular diagnostics testing reports. AF Sessions: Providers participating in the AF sessions also reported determining whether to begin treatment prior to receipt of molecular testing results, long turnaround times and deciding on the appropriate molecular tests as top barriers to integrating testing in routine AML care. Clinicians reported improvements in high/very high confidence in their ability to select appropriate genetic tests to order for patients with AML (35% to 50%) and select targeted therapies based on genetic test results for AML patients (34% to 59%). Care teams set goals to improve turnaround times and testing workflows with pathology partners, as well as to maximize opportunities for patients to receive AML therapies for their specific mutation profile. Action plans to achieve these goals include improve team skills in choosing guideline-based genetic testing methods and targeted therapies and collaborate among clinical teams to improve ordering workflow and diagnostic sample preparation for genetic testing. Follow-Up Surveys: In 90-day follow up surveys, 100% of clinic champions reported upshifts in patients with targetable driver mutations receiving guideline-recommended treatment based on genetic testing results, and 4/5 clinics reported improved selection of guideline-recommended genetic testing prior to treatment initiation for AML patients. Conclusions Through this QI initiative, clinical teams identified barriers to integrating genetic testing into routine AML care, creating and implementing action plans to optimize genetic testing workflows and guideline-recommended targeted therapy selection. While meaningful confidence and action plan gains were demonstrated, these data underscore clinical practice gaps to address in future initiatives to support the integration of evidence-based genetic testing into AML care, including integrated education sessions with clinicians and pathologists. Study Sponsor Statement The study reported in this abstract was funded by independent educational grants from AbbVie, Inc. and Astellas Pharma Global Development, Inc., who had no role in the study design, execution, analysis, or reporting.