Secondary Mutations Research Articles

Discovery of a highly potent pan-RAF inhibitor IHMT-RAF-128 for cancer treatment

Although rat sarcoma viral oncogene homolog (RAS) mutations occur in about 30% of solid tumors, targeting RAS mutations other than KRAS-G12C is still challenging. As an alternative approach, developing inhibitors targeting RAF, the downstream effector of RAS signaling, is currently one of the main strategies for cancer therapy. Selective v-raf murine sarcoma viral oncogene homolog B1 (BRAF)-V600E inhibitors Vemurafenib, Encorafenib, and Dabrafenib have been approved by FDA and received remarkable clinical responses, but these drugs are ineffective against RAS mutant tumors due to limited inhibition on dimerized RAF. In this study, we developed a highly potent pan-RAF inhibitor, IHMT-RAF-128, which exhibited similarly high efficacies in inhibiting both partners of the RAF dimer, and showed potent anti-tumor efficacy against a variety of cancer cells harboring either RAF or RAS mutations, especially Adagrasib and Sotorasib (AMG510) resistant-KRAS-G12C secondary mutations, such as KRAS-G12C–Y96C and KRAS-G12C–H95Q. In addition, IHMT-RAF-128 showed excellent pharmacokinetic profile (PK), and the bioavailability in mice and rats were 63.9%, and 144.1%, respectively. Furthermore, IHMT-RAF-128 exhibited potent anti-tumor efficacy on xenograft mouse tumor models in a dose-dependent manner without any obvious toxicities. Together, these results support further investigation of IHMT-RAF-128 as a potential clinical drug candidate for the treatment of cancer patients with RAF or RAS mutations.

Circulating tumor DNA reveals mechanisms of lorlatinib resistance in patients with relapsed/refractory ALK-driven neuroblastoma

Activating point mutations in Anaplastic Lymphoma Kinase (ALK) have positioned ALK as the only mutated oncogene tractable for targeted therapy in neuroblastoma. Cells with these mutations respond to lorlatinib in pre-clinical studies, providing the rationale for a first-in-child Phase 1 trial (NCT03107988) in patients with ALK-driven neuroblastoma. To track evolutionary dynamics and heterogeneity of tumors, and to detect early emergence of lorlatinib resistance, we collected serial circulating tumor DNA samples from patients enrolled on this trial. Here we report the discovery of off-target resistance mutations in 11 patients (27%), predominantly in the RAS-MAPK pathway. We also identify newly acquired secondary compound ALK mutations in 6 (15%) patients, all acquired at disease progression. Functional cellular and biochemical assays and computational studies elucidate lorlatinib resistance mechanisms. Our results establish the clinical utility of serial circulating tumor DNA sampling to track response and progression and to discover acquired resistance mechanisms that can be leveraged to develop therapeutic strategies to overcome lorlatinib resistance.

Curious cases of GATA2 deficiency: clonal evolution or dual diagnoses?

GATA2 deficiency can often predispose individuals to hematologic malignancies. While many pathogenic/likely pathogenic germline variants have been characterized in GATA2 deficiency, less is known about other variants that arise during clonal evolution of hematologic malignancies or as potential dual diagnoses in these patients. Here, we present two cases enrolled in the NIAID Centralized Sequencing Program with GATA2 variants and additional pathogenic/likely pathogenic variants in WT1 and KRAS detected via genome sequencing.The first case is a 9-year-old female with myelodysplastic syndrome with monosomy 7, pulmonary alveolar proteinosis, and sepsis. Genome sequencing in the proband detected 3 rare variants in GATA2: one pathogenic heterozygous NM_032638.5:c.202del (p.Ala68ArgfsTer12) frameshift variant, one heterozygous c.1031_1087dup (p. Arg344_Arg362dup) duplication variant of uncertain significance (VUS), and one apparently somatic mosaic c.1306_1307insTCCA p. (His436LeufsTer101) frameshift VUS. Two variants were also detected in WT1: a likely pathogenic, apparently somatic mosaic, NM_024426.6: c.1159_1163del (p.Ala387Ter) nonsense variant and a heterozygous c.887G>A (p.Ser296Asn) missense VUS. The WT1 p.Ser296Asn variant was previously published in a female affected with Wilms tumor who inherited the variant from her unaffected father, however our participant does not have a personal history of Wilms tumor.The second case is a 6-year-old male diagnosed with acute myeloid leukemia (AML). Genome sequencing detected a heterozygous GATA2 NM_032638.5(GATA2):c.575C>T (p.Ser192Phe) missense VUS that has not been previously published in individuals with GATA2 deficiency. Additionally, a pathogenic, apparently somatic mosaic, NM_004985.5: c.173C>T (p.Thr58Ile) missense variant in KRAS was detected, which has been reported in the literature as a germline variant in individuals with Noonan syndrome and cardiofaciocutaneous syndrome. The variant allele fraction of the KRAS p.Thr58Ile variant was 27%, however it is unknown if this variant could be somatic mosaic in association with the subject's AML clone, or if the subject has a genetic diagnosis of RAS-associated autoimmune lymphoproliferative syndrome (RALD). Future studies include segregation analysis in family members.These cases highlight the importance of additional variants found in patients with GATA2 variants that may be contributing to dual diagnoses or acting as secondary mutations via clonal evolution of myeloid malignancies.

Abstract A38: Pediatric Germline CSF3R T618I mutation gives insight into disease progression and long-term therapy options of Chronic Neutrophilic Leukemia

Abstract Chronic Neutrophilic Leukemia (CNL) is a rare BCR-ABL negative myeloproliferative neoplasm that affects approximately 1 in a million individuals. The typical age of onset and disease presentation is in elderly patients with a median age of 63 and a range of 9-84. The oncogenic driver of CSF3R, the G-CSF receptor protein, in CNL has been classified over the last decade and has improved therapies for patients with targeted Tyrosine Kinase Inhibitors, such as Ruxolitinib (a potent JAK1/2 inhibitor). Currently, the only curative option is an allogeneic hemopoietic stem cell transplant with typical median overall survival of 2 years. Because of the low occurrence rate of CNL, there have only been 3 germline cases of CSF3R classified in literature. With these patients, they exhibit a lifelong skewing of the myeloid lineage causing gross neutrophilia. Our patient presented at 13 months with leukocytosis and neutrophilia, resulting in genetic testing revealing the diagnosis of the youngest documented case of CNL. A germline CSF3R T618I constitutive activating mutation was documented in our patient and in her father. Her father had documented lifelong leukocytosis of indeterminate origin and it was not until 33 that genetic testing was done, and he was diagnosed with CNL. He underwent an allogeneic stem cell transplant after being admitted with gross hepatosplenomegaly with a WBC of 322, the highest recorded in a germline CNL patient in literature. Our patient presented to clinic with leukocytosis ranging from 45-98 and hepatosplenomegaly. After a bone marrow aspirate and biopsy was taken to determine disease stage and severity, we immediately began Ruxolitinib therapy. We began 20 mg BID dosing based on platelets and monitored response to therapy while conducting targeted RNA-seq for myelodysplastic and myeloid leukemia genes on the bone marrow, which did not detect any secondary mutations. Ruxolitinib dosing was tapered down in a stepwise fashion, until the patient arrived at the current dose of 7.5 mg BID Ruxolitinib, resulting in stable leukocyte counts around 25. As part of monitoring, we are currently conducting 6-month BM procedures and NGS for AML/MDS genes and Ruxolitinib resistance mutations alongside monthly CBCs. Our patient has been on Ruxolitinib for 9 months and has not developed any secondary contributing mutations and remains sensitive to therapy. We continue to monitor our patient’s response to Ruxolitinib to determine if germline predisposition alters the transformative nature of the disease. Within T618I germline CNL cases, we are investigating the difference in phenotype and disease burden that we observe in our patient’s family compared to literature. Based on current cases, it seems that germline CNL does not transform during childhood and adolescence into AML without the influence of a secondary mutation. Retrospective studies into previous cases of CNL to determine if there is a higher frequency of germline origin could pave the way for potential early-stage therapies and detection of CNL prior to transformation. Citation Format: Kevin Zhang, Matthew Rees, Mahsa Khanlari, Laura Rooms, Raul Ribeiro, Marcin Wlodarski. Pediatric Germline CSF3R T618I mutation gives insight into disease progression and long-term therapy options of Chronic Neutrophilic Leukemia [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A38.

Precision Oncology in Gastrointestinal Stromal Tumors

GIST (gastrointestinal stromal tumors) represent 20% of sarcomatous tumors and 1-2% of primary gastrointestinal cancers. They have an excellent prognosis when localized and resectable, though their prognosis is poor in the metastatic setting, with limited options after the second line until recently. Four lines are now standard in KIT-mutated GIST and one in PDGFRA-mutated GIST. An exponential growth of new treatments is expected in this era of molecular diagnostic techniques and systematic sequencing. Currently, the main challenge remains the emergence of resistance linked to secondary mutations caused by selective pressure induced by TKIs. Repeating biopsies to tailor treatments might be a step in the right direction, and liquid biopsies at progression may offer a non-invasive alternative. New molecules with wider KIT inhibition are under investigation and could change the catalog and the sequence of existing treatments. Combination therapies may also be an approach to overcome current resistance mechanisms. Here, we review the current epidemiology and biology of GIST and discuss future management options, with an emphasis on genome-oriented therapies.

Circulating tumor DNA analysis of the phase III VOYAGER trial: KIT mutational landscape and outcomes in patients with advanced gastrointestinal stromal tumor treated with avapritinib or regorafenib

The current treatment paradigm of imatinib-resistant metastatic gastrointestinal stromal tumor (GIST) does not incorporate KIT/PDGFRA genotypes in therapeutic drug sequencing, except for PDGFRA exon 18-mutant GIST that is indicated for avapritinib treatment. Here, circulating tumor DNA (ctDNA) sequencing was used to analyze plasma samples prospectively collected in the phase III VOYAGER trial to understand how the KIT/PDGFRA mutational landscape contributes to tyrosine kinase inhibitor (TKI) resistance and to determine its clinical validity and utility. VOYAGER (N = 476) compared avapritinib with regorafenib in patients with KIT/PDGFRA-mutant GIST previously treated with imatinib and one or two additional TKIs (NCT03465722). KIT/PDGFRA ctDNA mutation profiling of plasma samples at baseline and end of treatment was assessed with 74-gene Guardant360® CDx. Molecular subgroups were determined and correlated with outcomes. A total of 386/476 patients with KIT/PDGFRA-mutant tumors underwent baseline (pre-trial treatment) ctDNA analysis; 196 received avapritinib and 190 received regorafenib. KIT and PDGFRA mutations were detected in 75.1% and 5.4%, respectively. KIT resistance mutations were found in the activation loop (A-loop; 80.4%) and ATP-binding pocket (ATP-BP; 40.8%); 23.4% had both. An average of 2.6 KIT mutations were detected per patient; 17.2% showed 4-14 different KIT resistance mutations. Of all pathogenic KIT variants, 28.0% were novel, including alterations in exons/codons previously unreported. PDGFRA mutations showed similar patterns. ctDNA-detected KIT ATP-BP mutations negatively prognosticated avapritinib activity, with a median progression-free survival (mPFS) of 1.9 versus 5.6 months for regorafenib. mPFS for regorafenib did not vary regardless of the presence or absence of ATP-BP/A-loop mutants and was greater than mPFS with avapritinib in this population. Secondary KIT ATP-BP pocket mutation variants, particularly V654A, were enriched upon disease progression with avapritinib. ctDNA sequencing efficiently detects KIT/PDGFRA mutations and prognosticates outcomes in patients with TKI-resistant GIST treated with avapritinib. ctDNA analysis can be used to monitor disease progression and provide more personalized treatment.

Molecular markers impacting survival in patients receiving concurrent chemoradiation and Tumor-Treating Fields (TTF) in patients with newly diagnosed glioblastoma: secondary analysis of SPARE trial (P13-13.003)

<h3>Objective:</h3> The objective of this study was to evaluate the impact of molecular markers (PTEN, TP53, EGFR, and TERT) on overall survival (OS) and progression-free survival (PFS) of SPARE trial patients. <h3>Background:</h3> SPARE trial (Scalp-sparing radiation with concurrent temozolomide (TMZ) and tumor treating fields; NCT03477110) is a single-arm pilot study that demonstrated the safety and feasibility of concurrent TTF with chemoradiation for newly diagnosed glioblastomas (GBM). <h3>Design/Methods:</h3> This is a secondary analysis of the SPARE trial. Molecular markers of histologically-confirmed, IDH-wildtype GBM patients age ≥ 18 years old with a Karnofsky performance status (KPS) ≥ 60 who received concurrent chemoradiation and TTF followed by maintenance TMZ + TTF were evaluated. Molecular profile was evaluated with next-generation sequencing. Interaction of mutations in PTEN, TP53, EGFR, and TERT with TTF on OS and PFS was evaluated using a multivariable model. <h3>Results:</h3> A total of 30 patients were enrolled in the SPARE trial. 1 patient with IDH-mutant histology was excluded. The median age was 58 (range; 19–77). The median KPS was 90 (range; 70–100). 9 patients (31.0% ) had a methylated MGMT promotor. 14 patients (48.3%) were found to have PTEN mutation, 9 patients (31.0%) with EGFR alteration, 7 (24.1%) with TP53 mutation, and 23 patients (79.3%) with TERT mutated. MGMT methylation remained statistically significant for an increased OS (p=0.032; HR 7.18). TERT had a statistically significant OS benefit (p=0.012; HR 7.60). TERT also showed significant improvement in PFS. However, neither EGFR, TP53, nor PTEN showed any association of PFS or OS for patients who received concurrent TTF and chemoradiation treatment. <h3>Conclusions:</h3> In this secondary analysis, neither EGFR, TP53, nor PTEN mutation showed any association of PFS or OS. However, patients with TERT mutations showed improved OS. Due to the small sample size, further validation studies should be conducted. <b>Disclosure:</b> Ms. Kayne has nothing to disclose. Dr. Poiset has nothing to disclose. Dr. Ali has nothing to disclose. Dr. Miller has nothing to disclose. Dr. Niazi has nothing to disclose. Dr. Cappelli has nothing to disclose. The institution of Dr. Alnahhas has received research support from Novocure. Dr. Shi has received personal compensation in the range of $5,000-$9,999 for serving as a Consultant for Novocure. Dr. Shi has received personal compensation in the range of $5,000-$9,999 for serving as a Consultant for zai lab. Dr. Shi has received personal compensation in the range of $500-$4,999 for serving as a Consultant for varian. Dr. Shi has received personal compensation in the range of $5,000-$9,999 for serving on a Scientific Advisory or Data Safety Monitoring board for novocure.

LIX1 Controls MAPK Signaling Reactivation and Contributes to GIST-T1 Cell Resistance to Imatinib.

Gastrointestinal stromal tumor (GIST), the most common sarcoma, is mainly caused by an oncogenic mutation in the KIT receptor tyrosine kinase. Targeting KIT using tyrosine kinase inhibitors, such as imatinib and sunitinib, provides substantial benefit; however, in most patients, the disease will eventually progress due to KIT secondary mutations leading to treatment failure. Understanding how GIST cells initially adapt to KIT inhibition should guide the selection of appropriate therapies to overcome the emergence of resistance. Several mechanisms have been broadly implicated in the resistance to imatinib anti-tumoral effects, including the reactivation of MAPK signaling upon KIT/PDGFRA targeted inhibition. This study provides evidence that LImb eXpression 1 (LIX1), a protein we identified as a regulator of the Hippo transducers YAP1 and TAZ, is upregulated upon imatinib or sunitinib treatment. LIX1 silencing in GIST-T1 cells impaired imatinib-induced MAPK signaling reactivation and enhanced imatinib anti-tumor effect. Our findings identified LIX1 as a key regulator of the early adaptative response of GIST cells to targeted therapies.

Experimental and Numerical Study of Cross-Domain Hydrodynamics in an Integrated Pneumatic-Spouted Bed

As an essential resource, the drying, upgrading, and efficient utilization of lignite are of great significance to the development of the low-carbon economy. In this work, a novel drying system, combining a pneumatic and spouted bed, is designed to achieve lignite deeply dewatering. The system is investigated experimentally and numerical simulated to characterize the hydrodynamics of particles moving across the domain, such as pressure drop, fountain height, and pressure fluctuation. The results show that there is a critical gas velocity that changes the flow pattern of the bed when the static bed is higher than 50 mm. When the gas velocity increases to the critical value, the spouting state becomes unstable and the corresponding pressure drop will undergo a secondary mutation. This work provides a deeper understanding of the flow structure and particle motion in the novel drying system under various industrial operating conditions.

Abstract 3885: A secondary Gαq mutation confers resistance to Gαq inhibitors in uveal melanoma

Abstract Uveal melanoma (UM) is a rare subtype of melanoma that originates from melanocytes of the choroidal plexus, ciliary body and iris. Despite successful treatment of the primary by radiation or surgery, 50% of UM patients develop metastases, mostly in the liver, as an invariably lethal complication. Over 90% of UM harbor activating mutations in the closely related GNAQ or GNA11 genes, mainly at codons Q209, compromising the GTPase activity. Mutant GNAQ and GNA11 can be successfully targeted by the cyclic depsipeptide YM-254890. To anticipate mechanisms of resistance that might arise under treatment with this novel class of Gαq inhibitors, we generated UM cell lines resistant to YM-254890 using an in-vitro cell culture system. Upon chronic growth suppression of a GNA11Q209L mutant UM cell line, we established 12 YM-254890 resistance clones. We identified a secondary GNA11F75Y mutation in one clone and GNA11Y192H mutations in the other 11 clones. The secondary mutations were present in cis with the original GNA11 Q209L mutations. To validate the functional role of these secondary mutations in conveying resistance, we engineered two double mutants, GNA11Q209L/F75Y and GNA11Q209L/Y192H, and introduced them into 293FT cells respectively and confirmed that both F75Y and Y192H convey resistance to YM-254890 treatment. The proliferation of YM-254890-resistant cell lines was still dependent on GNA11 and downstream PKC/MAPK signaling. Combined inhibition of PKC and MEK synergistically reduced cell viability in YM-254890 resistant UM cells. Analysis of the crystal structure of YM-2548890 in complex with GNAQ predicts both F75Y and Y192H mutations directly affect the binding of YM-254890 to Gαq. Our data suggest that direct targeting mutant GNAQ/11 is promising but will select for secondary mutations within GNAQ/11 that will result in resistance. Combinatorial targeting of other components in the Gαq signaling pathway will increase clinical efficacy. Citation Format: Jiafang Ma, Meng Wang, Aashish Manglik, Boris C. Bastian, Xu Chen. A secondary Gαq mutation confers resistance to Gαq inhibitors in uveal melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3885.

Abstract 4033: Pan-exon mutant KIT inhibitor DCC-3009 demonstrates tumor regressions in preclinical gastrointestinal stromal tumor models

Abstract Introduction: Gastrointestinal stromal tumors (GISTs) are typically driven by primary mutations in KIT exons 9 or 11. Heterogeneous drug-resistant secondary mutations arise in patients treated with FDA approved KIT inhibitors, including imatinib and sunitinib. Drug resistant secondary mutations are found at multiple regions in the ATP pocket (encoded by exons 13 and 14) or activation switch (encoded by exons 17 and 18) of KIT kinase. In addition, multiple drug-resistant clones can arise within a tumor or in metastatic tumor sites. An inhibitor that can broadly and potently inhibit the spectrum of KIT mutations is highly sought. Ripretinib has been FDA approved as a 4th line treatment for GIST and has broad activity against KIT mutations, including clinical potency in patients with mutations in KIT exons 11, 17, or 18. DCC-3009 was designed as a next generation KIT inhibitor that broadly and potently inhibits primary KIT mutations in exons 9 and 11 and secondary drug-resistant mutations across exons 13, 14, 17, and 18. DCC-3009 is a potent and selective inhibitor in enzyme and cell-based assays, and has demonstrated efficacy in xenograft models driven by drug resistant KIT mutations. Methods: DCC-3009 was tested for inhibition of KIT mutants using standard enzyme and cell-based assays. Levels of phosphorylated KIT were determined by Western blot or ELISA. Proliferation was measured using the fluorescent dye resazurin. KIT mutant xenograft or patient-derived xenograft models were performed at Crown Biosciences or Labcorp, AAALAC accredited facilities, with the approval of Animal Care and Use Committees. Results: In BaF3 cells transfected with KIT mutants, DCC-3009 was shown to potently inhibit the spectrum of known primary and secondary drug-resistant mutations in GIST. The pan-mutant KIT profile of DCC-3009 was shown in vitro to be superior to 2nd and 3rd line standard of care therapies sunitinib and regorafenib. DCC-3009 was selective for KIT when screened against a large panel of kinases. DCC-3009 has optimized pharmaceutical properties for oral administration. In pharmacokinetic/pharmacodynamic studies DCC-3009 achieved sufficient free drug levels to significantly inhibit drug-resistant KIT mutants for 12 hr post dose. In xenograft studies, treatment with DCC-3009 twice daily led to tumor regression in drug-resistant models with KIT exon 9/13, 11/13 or 11/17 mutations. Conclusions: DCC-3009 is a pan-exon mutant KIT inhibitor exhibiting high potency in KIT mutants in pre-clinical models spanning exons 9, 11, 13, 14, 17 and 18. In vivo, DCC-3009 exhibited efficacy in drug-resistant models with KIT exon 9/13, 11/13 or 11/17 mutations. Based on this profile, DCC-3009 has entered formal preclinical development. Citation Format: Bryan D. Smith, Subha Vogeti, Timothy M. Caldwell, Hanumaiah Telikepalli, Yu Mi Ahn, Gada Al-Ani, Stacie L. Bulfer, Andrew Greenwood, Cale L. Heiniger, Joshua W. Large, Cynthia B. Leary, Wei-Ping Lu, Kylie Luther, William C. Patt, Max D. Petty, Yeni K. Romero, Forrest A. Stanley, Kristen L. Stoltz, Daniel C. Tanner, Sihyung Yang, Yu Zhan, Bertrand Le Bourdonnec, Daniel L. Flynn. Pan-exon mutant KIT inhibitor DCC-3009 demonstrates tumor regressions in preclinical gastrointestinal stromal tumor models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4033.

Abstract 3887: ATP-binding pocket substitutions as secondary or tertiary in-cis mutations are major on-target ripretinib resistance mechanisms in gastrointestinal stromal tumor

Abstract Introduction: Ripretinib (Rip) is a kinase inhibitor with broad preclinical activity against mutant KIT. Based on the INVICTUS trial, Rip was approved for patients with Gastrointestinal Stromal Tumors (GIST) after treatment with 3 or more kinase inhibitors. Most patients in this ≥4th-line setting progress on Rip within one year. Here, we characterized Rip-progressing GIST samples to identify resistance mechanisms. Methods: Progressing lesions in 25 patients were analyzed by NGS after Rip failure. KIT mutations (muts) were recapitulated by gene editing. Activities of Rip, sunitinib (SU), and novel TKIs were characterized by cell viability assays and immunoblot. Mutagenesis experiments were performed using ENU. SU- and Rip-resistant cell lines were pooled and treated with various regimens, with clonal composition deconvoluted by cDNA-based amplicon sequencing. Results: 19/25 Rip-progressing GISTs displayed muts in the ATP-binding pocket (ATP-BP; e13/14). Four of these had pre-existing muts in the activation loop (AL; e17/18), which were confirmed to be in-cis with the primary and ATP-BP muts (triple in cis; TIC). Mutagenesis screens using a double KIT-mutant GIST line (e11 + AL) as a starting point confirmed that TIC-muts are a predominant escape mechanism when treated with Rip. A GIST subline (T1-triple) with TIC-muts in e11, e18 (A829P), and e13 (V654A) was highly resistant to Rip (GR50 &amp;gt; 2µM). Structural analyses of ATP-BP muts suggest steric interference and loss of van der Waals interactions that impede Rip binding and thereby confer Rip resistance. Another 3/25 Rip-progressing GISTs harbored pathogenic KIT muts in e9 only. A novel GIST cell line with primary KIT e9 mut (T1-e9) was 14-fold less sensitive to Rip than isogenic e11-driven cells (GR50 = 115 vs 8nM). Notably, adding a typical AL mut to T1-e9 (T1-e9-N822K) sensitized the cells to Rip (GR50 = 20nM). Immunoblots showed &amp;gt;95% inhibition of phospho-KIT in AL-mutant cell lines at Rip 100nM, whereas inhibition was weaker in T1-e9 (77%) and T1-V654A (46%), and absent in T1-triple. A compound screen of FDA-approved kinase inhibitors identified Nintedanib (NIN) as the most active compound against T1-triple. Clonal outgrowth assays of mixed cultures revealed SU (93% inhibition), and a weekly switch between Rip and either SU (96%) or NIN (79%) as the most effective inhibitors of pooled cell growth. Conclusions: KIT e9 primary muts and e13/14 (ATP-BP) secondary muts are enriched in post-progression biopsies following Rip treatment. KIT TIC-muts are novel frequent events driving GIST clinical progression and confer a high degree of resistance. Strategies to overcome resistance may include combinations or sequences of approved drugs, and novel drugs that more efficiently inhibit TIC-mutant KIT. Citation Format: Thomas Mühlenberg, Johanna Falkenhorst, Tom Schulz, Benjamin S. Fletcher, Alina Teuber, Dawid Krzeciesa, Isabella Klooster, Jonas Lategahn, Wen-Bin Ou, Meijun Lundberg, Margaret von Mehren, Susanne Grunewald, Alicia I. Tüns, Mehdi Brahmi, Michael C. Heinrich, Cesar Serrano, Hans-Ulrich Schildhaus, Sonja Sievers, Jürgen Treckmann, Lydia Wilson, Chandrajit P. Raut, Adrian Marino-Enriquez, Suzanne George, Daniel Rauh, Jonathan A. Fletcher, Sebastian Bauer. ATP-binding pocket substitutions as secondary or tertiary in-cis mutations are major on-target ripretinib resistance mechanisms in gastrointestinal stromal tumor. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3887.

Abstract 3419: TY-1091, a highly selective and potent second-generation RET inhibitor, demonstrates superior antitumor activity in multiple RET-mutant models

Abstract Proto-oncoprotein RET (rearranged during transfection) is a receptor tyrosine kinase and belongs to the cadherin superfamily. RET fusion proteins and gatekeeper mutations represent strong cancer drivers involved in the development of a variety of cancers. Although selective RET inhibitors selpercatinib (LOXO-292) and pralsetinib (BLU667) were recently marketed for patients with RET-dependent NSCLC and thyroid cancers, RET solvent front mutations G810R/S/C/V and other secondary mutations such as Y806C/N and V728A have been identified as mechanisms counting for acquired resistance to the two drugs and limits the applications of the kinase inhibitors. To provide novel RET inhibitors effective to a broader spectrum of RET fusions and mutations, we identified TY-1091 as a novel next-generation RET inhibitor through the in-house RET program and systemic screening of RET compound candidates. TY-1091 was characterized for its anti-tumor activity through in vitro and in vivo testing of a variety of RET-dependent tumor models including a panel of 17 engineered RET mutant Ba/F3 cell lines and 2 cancer cell models. The results show that TY-1091 inhibits wild type and major RET mutants (IC50, nM): RET G810S (9.5 nM), RET V804M/L/E (2.8-12.6 nM), and double mutants RET V804M/G810S (23.5 nM) and M918T/G810S (47.0 nM) through a biochemical screening against a panel of 17 engineered RET mutant Ba/F3 cell lines. Importantly, the inhibitory activity of TY-1091 is much higher than that of first-generation RET inhibitor Cabozantinib, and comparable to other second-generation compounds LOXO-292 and BLU-667. Consistent with its mode of action, TY-1091 grants extraordinary inhibition effects to tumor cell proliferation compared to its peer compounds LOXO-292 and BLU-667 (including TT (thyroid cancer, RET C634W) and LC2/ad (NSCLC, CCDC6-RET)), and the inhibition of the RET pathway activation, i.e., inhibition of RET phosphorylation (IC50 &amp;lt; 1 nM), SHC phosphorylation (IC50 = 4.6 nM) and ERK phosphorylation (IC50 = 9.8 nM) in Ba/F3-KIF5B-RET cells further validated the above in vitro phenotype. The therapeutic potential of TY-1091 was then further validated through mouse pharmacology in that TY-1091 demonstrated remarkable anti-tumor efficacy in a variety of xenograft models including Ba/F3 KIF5B-RET (wt), Ba/F3 KIF5B-RET (V804L), TT (thyroid cancer, RET C634W), and LC2/ad (NSCLC, CCDC6-RET). Detailed data will be presented. In summary, TY-1091 is a highly potent, orally available, and safe small molecule inhibitor to pan-RET mutations in cancer, and may attenuate SFMs-mediated resistance to existing RET therapy. The IND clearance from the US FDA was received and Phase I clinical investigations of TY-1091 shall be launched in the US soon. *To Whom Correspondence should be addressed to: Jun Li, Chengshan Niu and Yusheng Wu Citation Format: Chengshan Niu, Maolin Zheng, Huan Wang, Kaige Ji, Meihua Li, Guohui Wang, Rongzhen Ni, Apeng Liang, Aishen Gong, Yazhen Zhang, Hui Su, Mingyu Jiang, Shaoqing Chen, Xiugui Chen, Jun Li, Yusheng Wu. TY-1091, a highly selective and potent second-generation RET inhibitor, demonstrates superior antitumor activity in multiple RET-mutant models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3419.

Abstract 2623: Identification of KRAS suppressor genes: an ORFeome library screening

Abstract The RAS family genes encode small GTP-binding cytoplasmic proteins that are important signaling molecules. They regulate cell growth, survival and differentiation by coupling receptor activation to downstream effector pathways. Activating mutations of oncogenic RAS pathway genes are frequently detected in human cancers. KRAS is the most frequently mutated oncogene in human cancers. Most of these tumors are addicted to KRAS signaling. However, tumors can become resistant to RAS signaling pathway inhibitors through the activation of suppressor mechanisms. A possible explanation is that these tumors carry a second genomic perturbation that can compensate for the detrimental effects of the RAS signaling inhibitors, a phenomenon referred to as suppression. In model organisms, suppression interactions are generally divided into two classes: genomic suppressors which are secondary mutations in the genome that bypass a mutant phenotype, and dosage suppression interactions in which overexpression of a suppressor gene rescues a mutant phenotype. We decided to use the latter strategy in human cancer cells to identify KRAS suppressor genes. KRAS suppressor genes can be involved in resistance mechanisms of RAS pathway inhibitors and this approach could identify new targets for drug research programs and/or novel drug combinations. In this study we performed a screen on a human Open Reading Frame library (hORFeome collection) to identify potential KRAS suppressor genes. First, we engineered a SW620 cell line with a conditional expression of KRAS G12V by replacing the KRAS endogenous promoter by the doxycycline regulated TREG3 promoter. Second, we transduced this conditional cell line with a human ORFeome collection, and we looked for suppressors among the transduced cells that lead to cell proliferation in absence of KRAS G12V protein. Then candidate suppressors have been identified by NGS and validated after individual cloning and expression in SW620 KRAS conditional cells. Finally, two transcription factors and two orphan G protein-coupled receptors have been validated as KRAS suppressor genes when they are highly expressed. Citation Format: Christophe Marcireau, Philippine Furge, Fanny Sennechael, Alice Willart, Anne-Marie Blanchet, Veeranagouda Yaligara, Michel Didier, Frederic Lacroix, Melina Meunier, Laurent Debussches. Identification of KRAS suppressor genes: an ORFeome library screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2623.

Abstract 3935: CRISPR/Cas9 screens to identify proliferation and resistance mechanisms in uveal melanoma

Abstract Purpose: Uveal (ocular) melanoma (UM) is a highly aggressive and frequently fatal cancer of the eye. While only 2-4% of patients have metastases at diagnosis, up to 50% of develop metastatic disease, overwhelmingly to the liver. Almost all UM harbor an initiating mutation in the Gαq signaling pathway, most commonly in GNAQ. Most UM also contain secondary mutations that drive tumor progression, the most common being BAP1 loss. Targeted therapies such as MEK inhibitors have been utilized in UM, but tumors rapidly become refractory. The aims of this study were to identify novel mechanisms specifically activated in UM cells that drive proliferation and escape from MEK inhibitor therapy. Procedures: We performed CRISPR-Cas9 mediated gene disruption screening of UM cell lines 92.1, Mel202 and Mel270 using the Brunello sgRNA library targeting the whole genome. Cells were transduced at 0.3 MOI and 500X coverage then split into two groups to compare treatment with the MEK inhibitor (MEKi) trametinib (6nM) vs. untreated control cells. Cell pellets were collected at day 2 (baseline) and after every 3 cell divisions for 21 cell divisions (treated and control). In addition, we generated 92.1 and Mel270 cell lines stably expressing Cas9 and transduced cells at 1000x coverage with a sgRNA library targeting either 192 epigenetic regulators or 482 kinases. At least two replicates for each screen were performed. sgRNA representation between samples was compared using MAGeCK. Genes specifically essential in UM cell lines were distinguished from commonly essential genes using the Broad institute dependency map (DepMap). These hits were validated by individual sgRNAs and pharmacological inhibition. Results: Whole genome screens revealed a set of 84 genetic dependencies unique for UM cells that were required for proliferation. Among these genes were those required for the lipoic acid biosynthesis pathway: MCAT, MECR, LIPT2, LIAS as well as genes encoding the MITF-SOX10-TFAP2 transcription factors, the H3K9 methyltransferase SETDB1, and members of the MLL3/4 complex. Screening of UM cell lines with a focused guide RNA library targeting epigenetic regulators revealed that BRD2, TRIM28, KMT2D, SETD1B and HDAC1 were specifically required for UM survival. Screens with a sgRNA library targeting the kinome revealed CDK2, CDK4 and TRRAP were required for UM survival. After 1 week of treatment with MEKi trametinib, we identified 112 genes whose disruption increased the anti-proliferative effects of trametinib in Mel202 and Mel270 cells and 10 of these genes were essential only in UM. These genes included metabolic enzymes critical for fatty and lipoic acid synthesis such as MECR, MCAT and TAZ. By contrast disruption of TP53, NF1, or PTEN led to MEKi resistance. Conclusions: These results identify novel mechanisms of proliferation and therapy resistance specifically required in GNAQ mutant UM cells that may represent new therapeutic targets. Citation Format: Richard L. Bennett, Darby Monagle, Katelyn R. Raburn Smith, Amin Sobh, Keiran S. Smalley, J William Harbour, Jonathan D. Licht. CRISPR/Cas9 screens to identify proliferation and resistance mechanisms in uveal melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3935.

Abstract 3864: Targeting IL-6/STAT3 signaling in EGFR-mutant drug tolerant persister cells

Abstract While the majority of epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC) patients initially respond to treatment with an EGFR tyrosine kinase inhibitor (TKI), most will eventually develop acquired resistance to these agents. The evolution of tumor cells with acquired resistance to targeted agents initially involves the persistence of a drug-tolerant subpopulation of tumor cells which display a transient and flexible resistant state. These persister cells can remain quiescent for prolonged periods of time, but eventually give rise to fully drug resistant tumor cells that resume growth and metastatic spread. The signaling pathways that allow persister cells to remain viable or to re-activate expansive growth are poorly understood. We and others have reported that EGFR TKI resistance that occurs independent of secondary EGFR mutations or MET amplification is associated with an epithelial to mesenchymal transition (EMT). Our analysis of tumor cells that had undergone EMT-mediated resistance to the EGFR TKI osimertinib revealed that interleukin-6 (IL-6) was highly upregulated in resistant cells as compared to parental cells. We find that in the setting of EGFR mutant NSCLC, IL-6 suppresses the anti-tumor cell activity of T cells and NK cells. To assess the role of IL-6 in the early events of EGFR TKI resistance, we generated drug-tolerant persister cells by treating EGFR mutant HCC4006 and HCC827 NSCLC cells with the EGFR TKI osimertinib for 10 days and then assessed IL-6 expression. We observed that IL-6 was upregulated at both the RNA and protein levels in EGFR-TKI persister cells as compared to parental cells. While the cell surface expression of IL6R was not significantly increased in EGFR-TKI persister cells as compared to parental cells, we observed increased secretion of soluble IL6R in persister cells by ELISA assay. We next assessed changes in protein expression and activation in drug tolerant persister cells by reverse phase protein array (RPPA) and observed that p-STAT3, a key component of the IL-6 signaling pathway, was significantly elevated in persister cells as compared parental cells or cells treated with osimertinib for 24 hours. Using genetically engineered mouse models (GEMM) of EGFRL858R mutant lung cancer, we also observed a similar upregulation of both IL-6 and p-STAT3 expression at the RNA and protein levels in EGFR-mutant tumors treated with osimertinib for 2 or 4 weeks. Additionally, circulating levels of IL-6 also are elevated in EGFRL858R GEMMs treated with osimertinib for 2 or 4 weeks. Collectively, our data indicates that upregulation of IL-6 is an early event in the evolution of drug resistance. Given the role of IL-6 in promoting EGFR TKI resistance, further studies investigating whether targeting of IL-6 signaling may impair the survival or outgrowth of persister populations are warranted. Citation Format: Sonia A. Patel, Monique Nilsson, Yan Yang, Li Shen, Jing Wang, Alissa Poteete, Xiaoxing Yu, Xiaoyang Ren, Xiuning Le, John Heymach. Targeting IL-6/STAT3 signaling in EGFR-mutant drug tolerant persister cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3864.

Abstract 5501: Vertical inhibition of the MAPK pathway with D3S-002, a potent and selective ERK1/2 inhibitor, to improve anti-tumor activity of and overcome resistance to KRAS G12C inhibitors

Abstract While covalent KRAS G12C inhibitors have demonstrated encouraging clinical efficacy in patients with KRAS G12C mutation, the overall response rate and progression-free survival appear to be suboptimal. Achieving deeper and more durable responses in these patients remain as major challenges. Preclinical and clinical translation research highlights adaptive feedback reactivation of the RAS-RAF-MEK-ERK signaling cascade as key molecular mechanisms driving primary and acquired resistance to KRAS G12C inhibitors. Concurrent inhibition of KRAS G12C and downstream MAPK pathway is thus an attractive combination strategy to improve clinical outcomes for KRAS G12C-mutant population. D3S-002 is a potent and selective kinase inhibitor targeting ERK1/2, the final node of the RAS-MAPK pathway and the central mediator of the feedback activation loop. To investigate the combination effect of D3S-002 with KRAS G12C inhibitor D3S-001, this study utilized multiple preclinical in vivo models including cancer cell line-derived xenograft (CDX) tumors that are sensitive to, or primarily resistant to KRAS G12C inhibitors, and patient-derived xenograft (PDX) tumors that have progressed on KRAS G12C inhibitor treatment in the clinic. In NCI-H358 NSCLC and SW837 CRC models that are sensitive to KRAS G12C inhibitor monotherapy, adding D3S-002 to D3S-001 or to D3S-001 and cetuximab doublet regimen led to faster, deeper, and more durable anti-tumor responses at dose levels that are well tolerated in mice with no body weight loss observed. In NCI-H2122 NSCLC model that is primarily resistant to KRAS G12C inhibitor alone, the addition of D3S-002 resulted in near complete tumor growth inhibition. Furthermore, CR9537 PDX model was established from tumor biopsy of a CRC patient who had progressed on combination treatment of KRAS G12C inhibitor MRTX849 and a SHP2 inhibitor in a clinical trial. Next generation sequencing (NGS) analysis identified secondary KRAS Q61H mutation as an acquired resistance mechanism. In this PDX model, KRAS G12C inhibitor, D3S-001 or MRTX849, monotherapy only achieved approximately 50% tumor growth inhibition, highlighting the acquired resistant phenotype. Adding D3S-002 to D3S-001 or MRTX849 resulted in over 80% tumor growth inhibition and significantly prolonged survival, suggesting the combination treatment can be beneficial for KRAS G12C inhibitor pre-treated patient population. Collectively, vertical inhibition by concurrently targeting KRAS G12C and ERK1/2 with respective inhibitor D3S-001 and D3S-002 demonstrated enhanced anti-tumor activity in NSCLC and CRC models with different sensitivity to KRAS G12C inhibitor monotherapy. These results provide a strong rationale for further investigation of the combination strategy of D3S-001 and D3S-002 in KRAS G12C-mutant solid tumors in the clinic. Citation Format: Jing Zhang, Jingtao Lu, Zhiqiang Zheng, Jiang Lu, Allison Wang, Jia Wang, Janet Chen, Haopeng Rui, Cheng Chen, Zhi Jian Chen. Vertical inhibition of the MAPK pathway with D3S-002, a potent and selective ERK1/2 inhibitor, to improve anti-tumor activity of and overcome resistance to KRAS G12C inhibitors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5501.

Abstract 2859: High-resolution lineage tracing for the study of cancer drug persistence at the single-cell level

Abstract Cancer drug persistence allows small fractions of otherwise drug-sensitive populations of cancer cells to survive treatment with anti-cancer drugs. Unlike drug resistance, persistence mechanisms are not driven by genetic mutations, and are thus considered reversible after a ‘drug holiday’ period. While most persistent cells remain in cell cycle arrest under drug treatment, recent work with EGFR-mutant Non-Small Cell Lung Cancer (NSCLC) cell lines has demonstrated that a small fraction of persister cells continue to undergo cell divisions under treatment with EGFR inhibitors. Thus, persister cells have a two-fold potential clinical significance: (i) they can serve as an intermediate state, allowing a non-resistant cancer cell to survive long enough and continue to divide under drug treatment to acquire a resistance mutation; and (ii) cycling persister cells might directly contribute to relapse, without a secondary resistance-driving mutation. Despite this, little is known about the underlying mechanisms by which affect the potential of a given cell to persist, or about the epigenetic traits that govern the distribution of persistence potential in a cell population. In this work, we use high-resolution lineage tracing to study lineages of drug persistent cells within a cancer cell population. Using the PC9 NSCLC cell line as a model, we demonstrate that while most lineages within the PC9 cell population can generate persisters, certain branches within the lineage tree have significantly higher persistence potentials than other branches, suggesting that inherited events determine the probability of a cell to persist under treatment. Moreover, we analyze the rate of change of the potential to persist within a single-cell-derived lineage of NSCLC cells and assess which branches within the lineage tree generate cycling persisters. Furthermore, we couple single-cell RNAseq data with lineage tracing information to identify gene expression patterns that correlate with the probability of drug-naïve cells to persist under drug treatment, allowing for insight into the cellular and molecular mechanisms underlying the continuum of the probability to persist. Finally, we demonstrate that while persistent-derived PC9 cells are indeed resensitized after a drug holiday, they give rise to a significantly higher proportion of cycling persister cells upon resumption of drug treatment, allowing for a rapid repopulation of the cell culture by cycling persisters. These results suggest that lineage tracing is a powerful tool to study drug-induced persistence and resistance and we will apply it to multiple other cell lines and tumor types. Citation Format: Benny Zhitomirsky, Jideofor Ezike, Elizabeth Hopkins, Brian P. Danysh, Laxmi Parida, Yaara Oren, Gad Getz. High-resolution lineage tracing for the study of cancer drug persistence at the single-cell level [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2859.

Abstract 3851: Targeting RET solvent-front mutants with an alkynyl nicotinamide-based inhibitor

Abstract Selpercatinib (LOXO-292, LY3527723) and pralsetinib (BLU-667) are first-in-class RET-targeted cancer therapy drugs. However, secondary RET mutations that confer selpercatinib/pralsetinib resistance have been identified, necessitating development of next-generation RET Tyrosine kinase inhibitors (TKIs). While the G810C/R/S/V mutations located at the RET kinase solvent-front site were detected in selpercatinib-treated patients, it was unclear whether all of these and other potential G810 mutants are resistant to selpercatinib and pralsetinib. We profiled selpercatinib and pralsetinib on all six possible G810 mutants derived from single nucleotide substitution. Surprisingly, the G810V mutant found in a clinical study was not resistant to selpercatinib or pralsetinib. Besides G810C/R/S, G810D also conferred selpercatinib/pralsetinib resistance. We found that alkynyl nicotinamide compounds such as HSN608 have better drug-like properties than alkynyl benzamides. HSN608 inhibited RET and RET V804M gatekeeper mutant, and all six G810 mutants with low nanomolar IC50s in the BaF3/KIF5B-RET mutant cell model. In cell derived xenograft (CDX) tumors driven by KIF5B-RET(G810C), HSN608 caused regression of the selpercatinib-resistant tumors. This study clarifies the sensitivities of different RET solvent-front mutants to selpercatinib and pralsetinib, and identifies an alkylnyl nicotinamide-based RET TKI for inhibiting selpercatinib/pralsetinib-resistant G810 mutants. Citation Format: Ujjwol Khatri, Neetu Dayal, Xueqing Hu, Elizabeth Larocque, Nimishetti Naganna, Tao Shen, Xuan Liu, Frederick W. Holtsberg, M. Javad Aman, Herman O. Sintim, Jie Wu. Targeting RET solvent-front mutants with an alkynyl nicotinamide-based inhibitor. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3851.

Abstract 926: Genomics-based personalized oncology of advanced thymic epithelial tumors

Abstract Introduction: Thymic epithelial tumors (TETs) are very rare. Thymoma A and AB have a better prognosis than more aggressive thymoma B, thymic carcinoma (TC) and neuroendocrine tumors of the thymus (NET). While previous efforts such as TCGA have mainly characterized thymomas (Radovich et al., Cancer Cell 2018), the molecular landscape of TCs and NETs is still elusive. Patients and Methods: Between 03/2014 and 07/2020, we enrolled 44 TET patients (27 TCs, 11 thymomas, 6 NETs) in a prospective observational study (MASTER) conducted by the National Center for Tumor Diseases (NCT) Heidelberg, NCT Dresden and the German Cancer Consortium (DKTK). MASTER applied whole genome/exome sequencing (WGS, n=22; WES, n=22), transcriptome (n=40) and germline analysis to inform therapy recommendations by a dedicated molecular tumor board (MTB). We systematically gathered follow-up data to evaluate outcome and compared progression-free survival (PFS) of the first treatment according to an MTB recommendation (PFS2) to the last prior systemic treatment (PFS1) in each patient (PFS ratio). Results: Tumor mutational burden (TMB) was low (median=0.99 mutations/Mb, range 0.08-3.48) but higher than in TCGA (p&amp;lt;0.05). TMB was higher in TCs than in thymoma (p&amp;lt;0.05). Most frequently mutated genes were TP53 (30%), CYLD (16%), SETD2 (14%) and KIT (14%). Germline analysis revealed (likely) pathogenic germline alterations in 25% of patients (MUTYH, n=3; BRCA1, n=2; BRCA2, BAP1, CHEK2, FANCA, TP53, MEN1, n=1). A comprehensive analysis of candidate biomarkers of homologous recombination repair (HRR) defects revealed a subgroup of TET patients with a rationale for PARP inhibitor therapy. Unsupervised clustering of RNA sequencing data mainly revealed clustering that correlated with WHO classification. Additionally, TCs clustered in two subgroups that we identified as immunologically hot and cold tumors using immunohistochemistry validation. Overall survival of patients with hot tumors was significantly longer (p&amp;lt;0.05). The MTB recommended therapies for 42 patients (95%), which were implemented in 24 cases (57%). Five patients had a PFS2 &amp;gt; 6 months and a PFS ratio &amp;gt; 1.3. The best outcome was achieved using imatinib in a patient with a KIT mutation (p.W557R). After progression, the MTB recommended ponatinib based on a secondary KIT mutation (p.V654A). The patient was still on ponatinib when the observation period ended. Conclusion: We demonstrate that comprehensive molecular analysis provides clinically relevant information in a subgroup of TET patients. Thymoma, TCs, and NETs present with different molecular characteristics. Distinction between immunologically hot and cold TCs may have value for risk stratification and therapeutic strategies. PARP inhibition could be a potential new treatment option in a small subgroup of TETs. Molecular testing of KIT, germline analysis and genetic counseling should be recommended for all patients with advanced TETs. Citation Format: Lino Möhrmann, Lysann Rostock, Małgorzata Oleś, Arne Jahn, Marie Arlt, Nagarajan Paramasivam, Korinna Jöhrens, Luise Rupp, Marc Schmitz, Daniela Richter, Sebastian Uhrig, Martina Fröhlich, Barbara Hutter, Jennifer Hüllein, Elena E. Wolf, Dorothea Hanf, Laura Gieldon, Simon Kreutzfeldt, Christoph E. Heilig, Veronica Teleanu, Daniel B. Lipka, Andreas Mock, Ivan Jelas, Damian T. Rieke, Marcel Wiesweg, Melanie Boerries, Anna L. Illert, Alexander Desuki, Thomas Kindler, Angela M. Krackhardt, C. Benedikt Westphalen, Heidrun Grosch, Leonidas Apostolidis, Albrecht Stenzinger, Irina A. Kerle, Christoph Heining, Daniel Hübschmann, Evelin Schröck, Stefan Fröhling, Hanno Glimm. Genomics-based personalized oncology of advanced thymic epithelial tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 926.