Wild-type Tumors Research Articles

Molecular and Immune Landscape of Fumarate Hydratase-mutated Renal Cell Carcinoma

Fumarate hydratase-deficient renal cell carcinomas are an aggressive form of kidney cancer that often results in poor prognosis and high fatality rates. The implications of somatic mutations are not well described, and standard treatment has not been established for this renal cell carcinoma subtype. Further molecular characterization of fumarate hydratase-deficient renal cell carcinomas could potentially help to identify biomarkers that can be exploited with future targeted therapies. 2199 renal cell carcinomas were analyzed by DNA sequencing (592-gene panel) and whole- transcriptome sequencing and 40 tumors were identified with pathogenic FH mutations. Co-occurrence of mutation with other cancer-related genes were assessed along with immune profiles and immunotherapy biomarkers. Fumarate hydratase-deficient renal cell carcinomas had a lower prevalence of co-mutation with common renal cell carcinoma driver mutations such as VHL and chromatin remodeling genes when compared to wild type renal cell carcinoma. Conversely, prevalence of several cancer-related genes (MAX, BRCA1, PMS2, BRAF, NF2, and AKT1) was higher in fumarate hydratase-deficient renal cell carcinomas. Immunotherapy biomarkers (mismatch repair deficiency and tumor mutational burden) were detected at low frequency in mutant and wild type renal cell carcinomas, while PDL1 expression occurred at higher frequency in fumarate hydratase-deficient renal cell carcinomas. Fumarate hydratase-mutated kidney tumors may have a different mutational and immune landscape than wild type tumors. The absence of VHL mutations in a significant number of fumarate hydratase deficient renal cell carcinomas suggest that FH mutations may drive tumorigenesis using distinct angiogenic pathways. Our study highlights potential therapeutic implications that will require further study.

Precision medicine for KRAS wild-type pancreatic adenocarcinomas

BackgroundKRAS mutation is the most common molecular alteration in pancreatic adenocarcinoma (PDAC), and around 10% of patients harbor KRAS wild-type tumors (KRASWT). MethodsA retrospective chart review of clinical/molecular data was performed including all PDAC patients with a determined KRAS status (tumor molecular profiling on tissue or liquid biopsy). Results342 patients were included with 54 KRASWT PDAC (16%) compared to 288 patients with KRASm PDAC. Median age was 61 years [IQR:54.0;67.0] and 164 pts (48%) were female. At diagnosis, KRASWT patients (63%) were more frequently diagnosed at a non-metastatic stage compared to KRASm patients (41%) (p = 0.003). Regarding metastatic sites, liver was less frequent in KRASWT (39%, p < 0.0001).Median overall survival (mOS) from initial diagnosis was significantly higher in the KRASWT group compared to KRASm (50.8 months, CI95% [32.0-NR] vs 21.1 months, CI95% [18.9–23.4] (p < 0.004 after adjustment on age, ECOG and stage at diagnosis). In first-line systemic treatment, (mostly FOLFIRINOX) progression-free survival (PFS) was also higher in KRASWT.Based on ESCAT classification, a putative actionable alteration (ESCAT I-III) was identified in 19 (36%) KRASWT pts and 46 (16%) KRASm patients (p < 0.0001) with more alterations in FGFR2, BRAF(V600E), NRTK and more MSI tumors. KRASWT harbored also fewer alterations in TP53, CDKN2A, and SMAD4. 12 KRASWT patients received a molecularly-matched treatment with clinical benefit and improved outcomes compared to KRASm patients. ConclusionsKRASWT patients display distinct disease characteristics and outcomes with prolonged overall survival. KRASWT patients also harbor more actionable molecular alterations, leading to higher survival rates after receiving molecularly matched treatments.

Survival Analysis and Correlates with Molecular Epidemiology: 10-Year Retrospective Series of High-Grade Glioma in Pakistan.

High-grade gliomas are malignant, recurring primary central nervous system (CNS) tumors requiring extensive postoperative chemotherapy and radiation treatment. Isocitrate dehydrogenase (IDH), 1p19q, and ATRX mutations significantly influence survival and response to chemotherapy, as seen in many extensive studies from the Global North. This study aims to report data from the local region regarding progression-free survival and overall survival in light of molecular characteristics. A 10-year retrospective series was conducted at the Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan, with 285 patients presenting from 2008 to 2018. Prospective follow-up data was collected, and complete molecular profiles were available for patients presenting from 2010 onwards. Survival analysis was conducted through the Kaplan-Meier method, with log-rank reported. 70.53% (201) of patients were male, with a mean age at diagnosis of 43.33 ± 15.1 years. 265 patients within the cohort completed postoperative radiotherapy, while 141 patients underwent chemotherapy (procarbazine, lomustine, and vincristine, or temozolomide). Mean survival, in months, within the cohort was as follows: glioblastoma (14.1), anaplastic astrocytoma (27.5), and anaplastic oligodendroglioma (39.8). Survival curves showed a lower survival for IDH wild-type (P < 0.0001), ATRX mutated (P = 0.029), and 1p19q non-deleted (P = 0.008) tumors from Pakistan. Our findings quantified long-term survival outcomes for high-grade glioma from Pakistan, analyzing the various treatment patterns. Of particular importance, molecular sub-classification significantly predicted survival outcomes for IDH, ATRX, and 1p19 co-deletion mutations. Expanding brain tumor epidemiology will benefit assessing the efficacy of regional oncological centers and establishing standards of care.

RAD50 Deficient in a Breast Cancer Model Predicts Sensitivity to PARP Inhibitors.

Breast and ovarian tumors with pathogenic variants in BRCA1 or BRCA2 genes are more sensitive to poly (ADP-ribose) polymerase inhibitors (PARPi) treatment than wild-type tumors. Pathogenic variants in non-BRCA1/2 homologous recombination repair genes (HRR) also concede sensitivity to PARPi treatment. RAD50 participates in the Mre11-Rad50-Nbn (MRN) complex of the HRR pathway and plays an important role in DNA repair. The objective of this study is to evaluate whether RAD50 protein deficiency modulates the PARPi response in breast cancer cell lines. T47D breast cancer cell line was modified using small interfering RNA and CRISPR/Cas9 technology, to knockout the RAD50 gene. PARPi response (niraparib, olaparib and rucaparib alone or in combination with carboplatin), in T47D and T47D-edited clones, was evaluated by cell viability, cell cycle, apoptosis and protein expression analyses. Treatment with niraparib and carboplatin exerted a synergistic effect on T47D-RAD50 deficient cells and an antagonistic effect on T47D cells parental. Cell cycle analysis demonstrated an increase in the G2/M population in cells treated with niraparib or rucaparib alone or in combination with carboplatin. T47D-RAD50 deficient cells treated with rucaparib and carboplatin exhibited twofold levels in late apoptosis, also showing differences in PARP activation. All T47D RAD50 deficient clones treated with niraparib or rucaparib combined with carboplatin, or rucaparib alone showed increased levels of H2AX phosphorylation. T47D RAD50 deficient cells treated with PARP inhibitors alone or in combination with carboplatin showed cell cycle arrest in the G2/M phase, leading to death by apoptosis. Thus, RAD50 deficiency may be a good biomarker for predicting PARPi response.

Abstract C097: Understanding rare cancers in Hispanic/Latinx populations: Insights from the MyPART natural history study of rare solid tumors

Abstract PURPOSE: Rare cancers (&amp;lt;15 cases per 100,000 people/year) are poorly understood, particularly in Hispanic/Latinx populations. The My Pediatric and Adult Rare Tumor (MyPART) network conducts a Natural History Study of Rare Solid Tumors (NHSRT) to better understand rare tumor biology and develop effective therapeutic strategies. We analyzed NHSRT Hispanic/Latinx participants. METHODS: Patients of any age with rare solid tumors are eligible. All participants complete medical and family history forms, patient-reported outcomes (PRO) and provide saliva for DNA. Tumors undergo comprehensive molecular analysis and are discussed in a molecular tumor board. A subset of participants is invited to NIH Clinical Center (NIHCC) to undergo a clinical evaluation, genetic counseling, blood collection, and imaging studies, as indicated. Spanish-speaking participants are offered a medical interpreter. Forms are only available in English. RESULTS: Between January 2019 and December 2020, 16 of 200 participants identified as Hispanic/Latinx. Additionally, two international patients, a 15-year-old from Panama with Medullary Thyroid Carcinoma (MTC) who underwent total thyroidectomy with lymphadenectomy, and a 19-year-old from Mexico with Fibrolamellar Carcinoma (FLC) who underwent left hepatectomy and lymphadenectomy were enrolled later and received surgical treatment at NIHCC, which was not accessible in their home countries. Tumor types were neuroendocrine tumors (NET) (n=7), wild-type gastrointestinal stromal tumors (wt-GIST) (n=4), adrenocortical carcinoma (ACC) (n=1), MTC (n=3), and FLC (n=1). Two participants were relatives of patients with an SDHA mutation. Females accounted for 66% of the cohort; the median age was 35 years (range 15-69), enrolled from five US states and five countries. Nine patients used interpreter services. The median time from diagnosis to enrollment was 5.3 years. Half had metastatic disease at diagnosis. At enrollment, 57% of cases with local disease at diagnosis had progressed to metastasis, and 20% showed no evidence of disease. Twelve patients had successful tumor sequencing, and eight were found to have Pathogenic/Likely Pathogenic (Path/LP) variants. MEN1, SMAD4, and LZTR/RPS6KB2 in NET; SDHC in GIST; CDKN2B loss in ACC; DNAJB1-PRACA fusion in FLC; and RET mutations in MTC. Of 12 participants with germline mutation testing, Path/LP variants were found in 10, including SDHA, SDHC, and MUTYH in GIST patients and their relatives; PMS2 and RET in MTC; MEN1 and PALB2 in NET; SLC26A2, OTOF, XPC, and DNAH8 in ACC. CONCLUSION: Enrollment and comprehensive data collection were feasible, granting access to specialty care unavailable to several participants. Hispanic/Latinx representation was low, indicating recruitment challenges and the need for targeted strategies. Remote enrollment facilitated international participation. Making all forms available in Spanish is a priority. Ongoing analysis with over 500 NHRST participants will yield further insights. Citation Format: Juan C. Fierro Pineda, Shadin Ahmed, Karlyne Reilly, Robin Lockridge, Margarita Raygada, Barbara Thomas, John Glod, Abby Sandler, Brigitte Widemann, Mary Frances Wedekind Malone. Understanding rare cancers in Hispanic/Latinx populations: Insights from the MyPART natural history study of rare solid tumors [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C097.

Abstract A050: Enhancing immune checkpoint inhibitor efficacy by targeting neurotrophic receptor tyrosine kinase 1 signaling in immune resistant non-small cell lung cancer patients

Abstract Introduction: The FDA’s approval of immune checkpoint inhibitors (ICI) in 2015 drastically changed the survival of late-stage non-small cell lung cancer (NSCLC) patients. However, only about 30% of NSCLC patients respond to treatment, while the other 70% are immune resistant. Through an analysis of 424 NSCLC patients at Atrium Wake Forest, we have identified a loss-of-function mutation in Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1) as a biomarker for response to ICI. We hypothesize that by treating wild-type immune-resistant tumors with Entrectinib, we can mimic the effect of the mutation in NTRK1 and induce immune responses. Methods: To identify biomarkers, we collected genomic sequencing data and comprehensive clinical characteristics on 424 NSCLC patients who received ICI or chemo-ICI treatment at Atrium Health Wake Forest Baptist. To determine the role of NTRK1 in vivo, we implanted LL/2-scramble (wild-type NTRK1) or LL/2-shNTRK1, which diminished NTRK1, into C57/B6 mice. The animals were injected with either IgG or Anti-PD1. To determine if we could mimic the effect of a mutation in NTRK1, C57/B6 mice were inoculated with LL2-wildtype NTRK1 and treated with either a) IgG, b) Entrectinib, c) Anti-PD-1, or d) Anti-PD-1 + Entrectinib. All in vivo experiments had tumor growth monitored, and a flow cytometry panel was performed at the endpoint to understand the immune responses. Bulk RNA-Sequencing was performed on cell cultures and tumors. Results: Mice given the LL/2-shNTRK1 responded to Anti-PD-1 treatment and had a significant increase in CD4+ stem-like effector T cells in the spleen and tumor-draining lymph nodes. Animals that were inoculated with the LL/2 cell lines and treated with Anti-PD-1 + Entrectinib also responded. Mice treated with Anti-PD-1 + Entrectinib were found to have a significant increase in CD4+ stem-like effector T cells as well. RNA-Sequencing revealed that in the mutant cell line LL/2-shNTRK1 and LL/2 tumors treated with Anti-PD-1 + Entrectinib, there was a significant upregulation of C3 production. Conclusion: Our studies demonstrate that the loss of NTRK1 function, through either genetic ablation or enzymatic inhibition combined with Anti-PD-1, provides a potent treatment for immune-resistant NSCLC tumors. Citation Format: Margaret R Smith, Yuezhu Wang, Caroline B. Dixon, Ralph D'Agostino, Yin Liu, George C. Oliver, Lance D Miller, Umit Topaloglu, Michael D Chan, Micahel Farris, Jing Su, Kathryn F Mileham, Wencheng Li, Jason M. Grayson, Thomas Lycan, Fei Xing. Enhancing immune checkpoint inhibitor efficacy by targeting neurotrophic receptor tyrosine kinase 1 signaling in immune resistant non-small cell lung cancer patients [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A050.

Abstract B034: A phase 2 basket study of the oral MDM2 inhibitor milademetan for MDM2-amplified advanced solid tumors (MANTRA-2)

Abstract Milademetan is an oral, selective, small molecular inhibitor of the MDM2-p53 complex that reactivates p53 to induce cancer cell apoptosis and tumor regressions in nonclinical models. Clinically, MDM2 gene amplification (amp) occurs in 1–2% of advanced solid tumors and is associated with a poor prognosis. Preliminary antitumor activity was seen in patients with MDM2 amp and TP53 wild-type (WT) tumors in a phase 1 clinical trial [Tirunagaru et al. AACR-NCI-EORTC 2021]. We conducted a phase 2 basket study to evaluate the efficacy of milademetan in patients with advanced or metastatic solid tumors (except liposarcoma, intimal sarcoma, and primary CNS tumors) with MDM2 copy number (CN) ≥8 and WT TP53 status based on local next-generation sequencing (NGS) (NCT05012397). Milademetan was administered at 260 mg on days 1–3 and 15–17 of a 28-day cycle. Tumor assessments were performed every 8 weeks (RECIST v1.1). MDM2 CN was retrospectively analyzed centrally using a commercial NGS assay, which also allowed correlation with other co-occurring alterations. As of June 23, 2023, 39 patients were enrolled with 13 distinct tumor types. The most common histologies were biliary tract cancers (8, 20.5%), sarcomas (7, 17.9%), and breast cancer (6, 15.3%). Median number of prior systemic therapies was 3 (range 0–12). Thirty-eight patients were evaluable for safety. The most common hematologic grade 3/4 adverse events (AEs) related to milademetan were thrombocytopenia (26.3%), neutropenia (15.8%), and anemia (10.5%). All grade treatment-related AEs (&amp;gt;15% incidence) included thrombocytopenia (44.7%), nausea (42.1%), fatigue (36.8%), vomiting (31.6%), anemia (23.7%), diarrhea (23.7%) and neutropenia (18.4%). No bleeding or neutropenic sepsis events were reported, and no grade 5 events were observed. The dose reduction rate was 13.2%, and 7.9% of patients discontinued milademetan due to AEs. Central tumor testing was available on 30 (76.9%) patients and only 2 (6.7%) patients demonstrated MDM2 CN below the threshold of 8. Thirty-two patients were efficacy evaluable and had confirmed CN ≥8 or pending central analysis. Five partial responses (15.6%) were observed (4 unconfirmed, 1 confirmed) with one each in lung adenocarcinoma (co-alteration of EGFR + KRAS), pancreatic (KRAS), bladder (pending), gastric cancer (DNAB1-PRKACA) and endometrial sarcoma (CCND2). No clear correlation between MDM2 CN and tumor regression was observed. The median progression-free survival was 3.3 months (95% CI, 2.5–6.1). The longest patient on milademetan therapy was 41 weeks (biliary, best RECIST 1.1 response SD with –29% tumor reduction). Ten patients are currently ongoing. Milademetan monotherapy demonstrated clinically meaningful antitumor responses with a manageable toxicity profile in a variety of MDM2 amp, TP53 WT solid tumors, including those with other oncogenic drivers such as KRAS. Rational combination strategies with milademetan should be considered in tumors with WT TP53 to further enhance durable anti-tumor activity. Citation Format: Ecaterina E. Dumbrava, Christopher T. Chen, Gregory M. Cote, Glenn J. Hanna, Thomas E. Stinchcombe, Bradley Sumrall, Trisha Wise-Draper, Mohammed Kanaan, Steven Duffy, Christopher Sumey, Patrick Cobb, Naisargee Shah, Bo Zhang, Nora Ku, Robert C. Doebele, Mrinal Gounder. A phase 2 basket study of the oral MDM2 inhibitor milademetan for MDM2-amplified advanced solid tumors (MANTRA-2) [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B034.

Variant Analysis of miRNA Regulatory Genes in 35 Sporadic Lung Carcinoma Tumors.

In this study, sequence analyses of AGO2, DICER, and DROSHA genes involved in miRNA biogenesis and EGFR, KRAS, and BRAF genes were performed in 35 patients with sporadic lung cancer. We found variations in genes involved in miRNA biogenesis that have not been previously reported in the literature. In addition, we found 4 different variants in the EGFR gene that have been described in the literature. In addition, a statistically significant association was found between the presence of mutations in at least one of the genes involved in miRNA biogenesis and metastasis (p:0.02). In conclusion, genomic dysregulation of key miRNA biogenesis genes may be one of the possible reasons for the differential response of patients to therapeutic agents and the development of metastasis in EGFR wild type tumours.

Abstract C134: The MDM2 degrader KTX-049 is highly potent in TP53 wild-type (p53 WT) Merkel cell carcinoma (MCC)

Abstract Background and aims: MCC is a highly aggressive neuroendocrine carcinoma of the skin with a high fatality rate. Clonal integration of Merkel cell polyomavirus (MCPyV) occurs in about 80% of all MCCs. These virus positive MCC (MCCP) tumors have a low tumor mutational burden and usually express wild type (WT) p53 (TP53). In contrast, virus negative MCC (MCCN) tumors present a predominantly UV mutational signature, a high mutational burden and often have alterations in p53. MCCP tumors express MCyV small T antigen (ST) and a truncated form of large T antigen (LT). The MCyV ST in MCCP tumors, recruits MYCL and EP400 to form the SLaP complex that specifically trans-activates several genes. A direct target of the SLaP complex is MDM2, an E3 ubiquitin ligase of p53 that inhibits p53-mediated tumor suppression. The use of MDM2 inhibitors can stabilize p53 in p53 WT tumors. However, currently, no MDM2 inhibitors are approved for treatment of MCC. Furthermore, MDM2 degraders have not been studied in the context of MCC. Here, we aim to analyze the efficacy of KTX-049, a potent MDM2 degrader, in MCC and compare its efficacy to the previously reported and highly potent MDM2 inhibitor, DS-3032. Experimental procedures: Established MCCP cell lines with functional p53, non-functional p53 and two p53 WT MCCP patient derived cell lines (PDCLs) were treated with KTX-049 or DS-3032 and the effect on cell viability was analyzed using a luminescence-based assay. Apoptosis induction was studied using the caspase 3-7 Glo assay. The p53 response in MCC cells post KTX-049 or DS-3032 treatment was assessed by western blot (WB) analysis of p53 and its downstream effectors. Results: KTX-049 and DS-3032 reduced cell viability of p53 WT MCCP cell lines but not cell lines with non-functional p53. Notably, all sensitive cell lines had ≥100-fold lower absolute IC50 values for KTX-049 as compared to DS-3032. Additionally, KTX-049 effectively reduced cell viability of the sensitive cell lines even after brief exposures. KTX-049 also triggered a rapid and sustained p53 response and apoptosis induction in p53 WT MCC cells. Conclusions: KTX-049 is a promising MDM2 degrader effective against p53 WT MCC cell lines. These results provide evidence for in vivo exploration of KTX-049 in models of MCC. Citation Format: Varsha Ananthapadmanabhan, Yogesh Chutake, Jessica Filiatrault, Stefanie Schalm, Alice McDonald, James A DeCaprio. The MDM2 degrader KTX-049 is highly potent in TP53 wild-type (p53 WT) Merkel cell carcinoma (MCC) [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C134.

Opposing roles by KRAS and BRAF mutation on immune cell infiltration in colorectal cancer – possible implications for immunotherapy

BackgroundThe immune response has important clinical value in colorectal cancer (CRC) in both prognosis and response to immunotherapy. This study aims to explore tumour immune cell infiltration in relation to clinically well-established molecular markers of CRC.MethodsMultiplex immunohistochemistry and multispectral imaging was used to evaluate tumour infiltration of cytotoxic T cells (CD8+), Th1 cells (T-bet+), T regulatory cells (FoxP3+), B cells (CD20+), and macrophages (CD68+) in a cohort of 257 CRC patients.ResultsWe found the expected association between higher immune-cell infiltration and microsatellite instability. Also, whereas BRAF-mutated tumours displayed increased immune-cell infiltration compared to BRAF wild-type tumours, the opposite was seen for KRAS-mutated tumours, differences that were most prominent for cytotoxic T cells and Th1 cells. The opposing relationships of BRAF and KRAS mutations with tumour infiltration of cytotoxic T cells was validated in an independent cohort of 608 CRC patients. A positive prognostic importance of cytotoxic T cells was found in wild-type as well as KRAS and BRAF-mutated CRCs in both cohorts.ConclusionA combined evaluation of MSI status, KRAS and BRAF mutational status, and immune infiltration (cytotoxic T cells) may provide important insights to prognosis and response to immunotherapy in CRC.

Abstract A116: TSC1 mutant bladder cancer is characterized by a TSC-associated gene expression signature due to TFE3 transcriptional activity

Abstract Background: Mutations and inactivation of the tumor suppressor gene TSC1 are recurrent (6-10%) events in invasive bladder cancer, but the mechanism by which TSC1 loss promotes bladder cancer development beyond mTORC1 activation is uncertain. The purpose of this study was to assess the functional effects of TSC1 loss in bladder cancer and uncover new therapeutic targets for patients with TSC1 mutations. Materials and methods: We performed differential gene expression and pathway analyses using The Cancer Genome Atlas (TCGA) expression data for TSC1-mutated bladder cancer (TSC1mt-BLCA, n=26) and TSC1 wild-type tumors (TSC1wt-BLCA, n=382) and compared them to an internal cohort of TSC1/TSC2-mutant tumors (n=48). Transcriptomic, epigenetic, and functional analyses, including RNA-seq, H3K27ac ChIP-seq, TFE3 CUT&amp;RUN, ATAC-seq and TFE3 knock-out using CRISPR/Cas9 were conducted on TSC1-mt/wt BLCA cell lines. Results: Comparison of TSC1mt-BLCA and TSC1wt-BLCA TCGA tumors identified 26 genes upregulated in TSC1mt-BLCA out of 60 genes commonly upregulated in Tuberous Sclerosis Complex (TSC) syndromic tumors. Among them, GPNMB showed the greatest increase in expression (median fold change 9.8). GSEA and DESeq2 analyses implicated both mTORC1 hyperactivation and increased lysosomal gene expression in TSC1mt-BLCA. Expression differences in several genes, including GPNMB, and in pS6 were confirmed by immunohistochemistry (IHC) of 5 independent BWH TSC1mt-BLCA and TSC1wt-BLCA specimens each. TFE3, a key regulator of lysosomal gene expression, was elevated in expression and localized to the nucleus in TSC1mt-BLCA by IHC. Molecular studies of TSC1-mt/wt BLCA isogenic cell lines (HCV29, RT4) recapitulated the phenotype found in human tumors. TFE3 was both post-translationally modified (assessed by immunoblot) and predominantly nuclear in TSC1-null cell lines compared to TSC1wt cells, and the localization was partially reversed by rapamycin treatment leading to reduced expression of lysosomal genes. TSC1mt HCV29 cells showed higher expression of multiple genes increased in TSC1mt-BLCA tumors (GPNMB, SQSTM1, GNPDA1). TFE3 knock-out HCV29 clones showed markedly reduced growth, which was not seen with TFE3 KO in TSC1-addback HCV29 cells. GSEA of RNA-seq data indicated that TFE3 KO led to significant reduction in expression of lysosome genes, as well as those involved in ribosome synthesis, DNA replication and DNA excision repair processes. TFE3 CUT&amp;RUN confirmed that TFE3 binds to promoter regions of those genes, thereby directly regulating these pathways. In contrast, TFE3 KO led to an increase in inflammatory and cellular stress genes that could impede TSC1mt cell growth. Conclusions: Our findings show that TSC1mt-BLCA tumors and cell lines have a transcriptional signature similar to that of TSC syndromic tumors and show nuclear localization and transcriptional activation of TFE3. Aberrant TFE3 activation likely contributes to TSC1mt-BLCA development and may therefore be amenable to targeted therapy. Citation Format: Magdalena Losko, Clemens K Probst, Elio Adib, Heng Du, Michelle Hirsch, Krinio Giannikou, David J Kwiatkowski. TSC1 mutant bladder cancer is characterized by a TSC-associated gene expression signature due to TFE3 transcriptional activity [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A116.

Abstract LB_A25: Updated Phase 1 results from the PYNNACLE Phase 1/2 study of PC14586, a selective p53 reactivator, in patients with advanced solid tumors harboring a TP53 Y220C mutation

Abstract Background: Mutations in the TP53 gene leading to p53 inactivation are the most common mutational event across human cancers. PC14586 is a first-in-class p53 reactivator that selectively binds to the mutated p53 Y220C protein and restores p53 wild-type activity. Preclinical data support potential for activity of PC14586 across TP53 Y220C-bearing tumors, with enhanced activity in KRAS wild-type (WT) models, consistent with the important parallel roles for p53 inactivation and oncogenic KRAS in tumorigenesis. Preliminary analysis of Phase 1 data from the Phase 1/2 PYNNACLE trial (NCT04585750) evaluating PC14586 in patients with advanced TP53 Y220C solid tumors showed that PC14586 was well tolerated with preliminary clinical activity across multiple tumor types in the efficacious dose range (1150 mg QD to 1500 mg BID). This updated Phase 1 analysis assesses PC14586 in patients treated across the efficacious dose range. Methods: Eligible patients (≥12 years) with locally advanced or metastatic solid tumors with a TP53 Y220C mutation received increasing oral doses of PC14586 to evaluate safety, PK, and preliminary efficacy via RECIST v1.1, and to determine the Recommended Phase 2 Dose (RP2D). Tumor molecular profiling was assessed for the impact of KRAS status on response. Results: As of 1 May 2023, 61 patients were treated in the efficacious dose range (safety population): median age 63 (range 32-84) years, 62% female, and median of 3 (range 1–9) prior lines of systemic therapy. The most frequent treatment-related adverse events (TRAEs) (≥10%) were nausea (42.3%), vomiting (35.2%), diarrhea (19.7%), increased creatinine (18.3%), fatigue (14.1%), and increased AST and ALT (12.7% each); 3% of patients discontinued PC14586 due to TRAEs. Most TRAEs were grade 1 or 2; the most common grade 3 TRAEs were anemia (4.2%) and increased ALT (2.8%). PC14586 administered with food led to improvement in nausea and vomiting. Dose proportional and linear PK was observed with a median half-life of 19 hours. Among patients with measurable disease, 36 patients had KRAS WT and 15 patients had KRAS mutated tumors. A total of 12 PRs (ORR 33.3%) were observed (9 confirmed and 3 unconfirmed - pending confirmation) in patients with KRAS WT disease across multiple tumor types including ovarian, breast, prostate, small-cell lung, and endometrial cancer. The median duration of confirmed response was 7 months. In patients with a KRAS mutation, there were no confirmed responses, although clinical activity was observed. At 2000 mg QD, the ORR was 46.2% in patients with TP53 Y220C and KRAS WT tumors (n=13). A RP2D of 2000 mg QD was selected based on overall safety, PK and preliminary efficacy. Conclusions: PC14586 was well-tolerated with a favorable safety profile. Efficacy was achieved in heavily pre-treated patients across multiple tumor types. The PYNNACLE registrational Phase 2 trial will assess PC14586 as monotherapy at the RP2D of 2000 mg QD in patients with TP53 Y220C and KRAS WT advanced solid tumors. Additional/updated data will be presented at the conference. Citation Format: Alison M Schram, Geoffrey I Shapiro, Melissa L Johnson, Anthony W. Tolcher, John A Thompson, Anthony B El-Khoueiry, Andrae L Vandross, Shivaani Kummar, Aparna R Parikh, Dale R Shepard, Ursula Garczarek, Kim LeDuke, Lisa Sheehan, Marc Fellous, Leila Alland, Ecaterina E Dumbrava. Updated Phase 1 results from the PYNNACLE Phase 1/2 study of PC14586, a selective p53 reactivator, in patients with advanced solid tumors harboring a TP53 Y220C mutation [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_A25.

Navtemadlin, a Novel MDM2 Inhibitor, Potentiated Venetoclax-Induced Antitumor Efficacy in TP53 Wild-Type Acute Myeloid Leukemia (AML)

Introduction: The tumor suppressor p53 ( TP53) maintains genomic integrity, and nearly 50% of cancers are characterized by a loss or mutation in the TP53 gene. Murine double minute 2 (MDM2) negatively regulates p53 expression and promotes oncogenesis in TP53 wild-type ( TP53 WT) tumors. Navtemadlin (nvtm) is a potent, selective, orally available MDM2 inhibitor that overcomes MDM2 dysregulation by restoring p53 activity and inducing apoptosis in TP53 WT tumors. AML is a heterogeneous hematological malignancy resulting from the transformation of stem cells and is characterized by poor therapy response. Thus, combination therapies are required to avoid tumor escape mechanisms, such as alterations in apoptotic machinery and metabolism. Venetoclax (ven), a BCL-2 inhibitor, is a promising therapy in AML. Overexpression of anti-apoptotic members of the BCL-2 family, including myeloid cell leukemia-1 (MCL-1) limits ven response, thus requiring MCL-1 inhibitors to further improve sensitivity. A proof-of-concept study with idasanutlin (idasa), a first-generation MDM2 inhibitor and ven demonstrated manageable safety and encouraging efficacy in relapsed/refractory AML patients (Daver et al. Blood 2023). Here, we present a preclinical evaluation of nvtm alone and in combination with ven in the setting of TP53 WT AML, with a focus on metabolic pathways, pro-survival signaling, and bone marrow (BM) niche. Methods: AML-derived cell line, MOLM-13 ( TP53 WT, FLT3-ITD) was cultured alone, with HS5 AML stromal cells or with cytokines. Cultures were treated with DMSO, nvtm (0.1-1.5 μM), or ven (0.5 μM) for short-term (4-8 hrs) or long-term (48-72 hrs) and analyzed for changes in cell cycle progression, viability, clonogenicity potential, and metabolism (glycolysis and mitochondrial oxidative phosphorylation by analyzing extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) respectively). Primary AML BM mononuclear cells (MNCs) were cultured in cytokine support media. Results: In MOLM-13 cells, short-termnvtm (0.5 µM) treatment rapidly restored p53 expression and phosphorylation, with greater efficacy than idasa. Long-term treatment significantly induced apoptosis in a dose-dependent manner from 0.25 μM (p&amp;lt;0.01) with 80% cytotoxicity at 0.75 μM (p&amp;lt;0.001). Cell cycle analysis at 48 hr showed that nvtm significantly arrested cells in the sub-G0-G1 phase. Clonogenicity potential was significantly lowered in nvtm-treated cells. Metabolic alterations in the Mito Stress and Glycostress tests showed nvtm significantly lowered EACR, OCR, and mitochondrial membrane potential, as compared to idasa. We next evaluated the effects of nvtm in ven-treated MOLM-13 cells. Combination treatment significantly lowered the metabolism, cell viability, and clonogenicity potential of MOLM-13 cells, compared to nvtm or ven treatment. Immunoblotting analysis revealed a reduction in key anti-apoptosis proteins (BCL-2, MCL-1, PARP). Strikingly, nvtm downregulated ven-induced MCL-1 expression in a dose-dependent manner. Culturing MOLM-13 cells in HS5-conditioned media, transwells overlying HS5 cells, or with HS5 cells increased MOLM-13 cell resistance to nvtm. However, in HS5 co-cultures, a combination of nvtm and ven strongly re-sensitized MOLM-13 cells for apoptosis. Nvtm also significantly blocked the cytoprotective effects of AML-relevant cytokines (IL-6, SCF, FLT3 ligand, TPO, and GM-SCF). In cultures of primary AML BM-MNCs (n=11), nvtm alone at clinically relevant concentrations reduced viability (14-40%), and a combination nvtm and ven significantly enhanced AML cytotoxicity (30-52%). Conclusions: Nvtm, a potent second-generation MDM2 inhibitor, rapidly restored p53 function, induced apoptosis in p53 WT AML MOLM-13 by impeding cell cycle, viability, clonogenicity potential, and reducing both glycolysis and oxidative phosphorylation. Nvtm combined with ven significantly enhanced these effects. Importantly, this combination blocked stromal cell-mediated (contact and soluble factors) cytoprotection. These encouraging results provide a mechanistic basis for the evaluation of this combination in vivo and as a therapeutic strategy to overcome documented ven resistance mechanisms in TP53 WT AML patients.

Immune Checkpoint Blockade Promotes Thrombosis Via T-Cell and Neutrophil Activation, and Tumor-Cell Associated Tissue Factor (TF) in a Murine Model of Colorectal Cancer

Background: Immune checkpoint blockade (ICB) is a paradigm shift in cancer therapy. Despite clinical benefit, various adverse events are associated with ICB using immune checkpoint inhibitors (ICI). Venous thrombosis is an emerging clinical problem in cancer patients receiving ICI. Little is known about how ICI promotes thrombosis in cancer. To define the underlying mechanisms of ICI-associated thrombosis (IAT), we assessed the ICI impact on blood hypercoagulability and tumor TF expression using a mouse thrombosis model of colorectal cancer. Methods: We developed a CT26 mouse thrombosis model with ICI (aPD-1+aCTLA4) administration. Systemic hypercoagulability was assessed by measurement of circulating nucleosomes (Nu.Q H3.1 Immunoassay), neutrophil extracellular traps (NETs) (CitH3 immunofluorescence), circulating neutrophil-platelet aggregates (immunophenotyping), and levels of thrombin-antithrombin (TAT) complexes in ICI-treated mice. Tumor-associated TF and TF activity in circulating extracellular vesicles (EV) were assessed by western blotting and Factor Xa generation assays. To gain mechanistic insights into TF induction by ICI, tumor cytokines were also profiled (proteome profiler array). The role of cancer cell-derived TF in IAT was determined using mice implanted with CRISPR/Cas9-mediated TF knockout (TFKO) CT26 tumor cells. Results: ICI treated tumor-bearing mice developed larger thrombi than control mice and demonstrated elevated levels of circulating nucleosomes (114 vs 82 ng/ml), NET (15.8 vs 6.8%), platelet-neutrophil aggregates (44.8 vs 22.3%), and TAT complexes (12.6 vs 7.9 ng/ml) compared to IgG-treated mice. Tumor TF expression was increased in tumor extracts. Cytokine profiling suggested enhanced production of IFNɣ (2-fold) and TNFα (5-fold), as well as CXCL11 (6.8-fold), an effector T cell-recruiting chemokine. IFNɣ-increased TF expression in cultured CT26 cells, suggesting that T-cell derived IFNɣ may play a role in enhancing tumor TF expression in vivo. Circulating EV TF antigen and procoagulant activity were increased by ICI. CRISPR/Cas9-mediated TF KO in CT26 cells resulted in complete loss of TF expression, and mice bearing these cells showed reduced tumor and EV-associated TF (Fig. A), associated with a significant decrease in thrombus formation after ICI treatment (24.2 vs 20.5 mg, Fig. B). There was no significant difference in growth of wild-type and TF KO CT26 tumors. Conclusions: Our findings provide insights into cellular and molecular mechanisms associated with ICI-induced thrombosis, and suggest a role for neutrophil and granulocyte activation, and tumor-associated TF. Additional studies are ongoing to further define these pathways in the murine model and in patients.

Cebpβ/IL1/TNFα Positive Feedback Loop Drives Drug Resistance of BCL2 and MDM2 Inhibitors in Monocytic Leukemia Cells

Introduction:Ventoclax-based combinations have emerged as a new standard of care for patients with acute myeloid leukemia (AML) who are not suitable for intense chemotherapy. Not all patients respond to these treatments, and those who do may relapse. MDM2 inhibitors are promising therapeutics for treating TP53 wild-type tumors, including most de novo AML cases, with numerous compounds currently in pre-clinical and clinical evaluation. However, clinical trials of MDM2 inhibitors have shown modest and variable clinical activity. Functional genomic data showed that monocytic leukemia (FAB M4/M5) is resistant to venetoclax-based therapies and MDM2 inhibitors. Notably, venetoclax and an MDM2 inhibitor, idasanutlin, demonstrated a strong positive correlation in the Beat AML cohort. We hypothesize that upregulation of certain myeloid transcription factors in monocytic leukemia may confer intrinsic resistance to BCL2 and MDM2 inhibitors, while certain environmental cues upregulated in these cells may confer extrinsic drug resistance. Additionally, there may be crosstalk between these intrinsic and extrinsic mechanisms. Methods: We performed differential expression gene (DEG) analysis of transcription factors (TFs) between M4/M5 and M0/M1 samples in the Beat AML and TCGA AML cohort. We overexpressed seven myeloid TFs (SPI1, CEBPB, CEBPD, JUNB, IRF8, KLF4, and MAFB) that are upregulated in M4/M5 and performed competitive drug assays. We treated M4/M5 and M0/M1 samples with venetoclax and idasanutlin, in the presence of a panel of myeloid cytokines and measured cell viabilities. A Luminex assay on monocyte supernatants from M4/M5 and M0/M1 AML samples were conducted to identify dysregulated cytokines. Furthermore, RNAseq DEG and immunoblot analysis were performed on CEBPB-overexpressing cell lines and IL-1-treated AML samples to elucidate the underlying mechanisms. Results: CEBPB overexpression conferred drug resistance to a broad range of BH3 mimetics, venetoclax combinations, and MDM2 inhibitors. RNA-seq and immunoblot analyses demonstrated that CEBPB overexpression downregulated CASP3, CASP6, BCL2, and TP53 pathway targets (CDKN1A, PMAIP1, BBC3, BMF, TP53), while upregulated MCL1, BCL2A1, and the NF-κB/IL-1/TNF pathway at transcription and/or translation levels. Phenotyping analysis showed that CEBPB overexpression drives myelo/monocytic differentiation. In accordance, CEBPB expression in primary AML correlates with drug responses of idasanutlin, venetoclax, and many venetoclax combinations. Additionally, primary monocytic leukemia expresses significantly higher levels of IL-1/TNF family genes, BCL2A1, and reduced CASP3, CASP6, and BCL2. Abnormal monocytes, but not granulocytes, T cells, or blasts from M4/M5 leukemia, extrinsically protect leukemia blasts from venetoclax and MDM2 inhibition by secreting elevated IL-1 and TNFα. IL-1β/TNFα treatment drove myelo/monocytic differentiation and up-regulated inflammatory cytokines, including an autoregulatory loop, as well as a number of cytokine receptors, such as IL1R1, TNFRSF1R, TNFRSF2R, and CSF2RB. Remarkably, IL-1α/IL-1β and TNFα uniquely upregulated CEBPB expression in M4/M5 cells and protected them from apoptosis induced by venetoclax and MDM2 inhibitors. Conversely, TNFα treatment induced augmented extrinsic apoptosis in M0/M1 leukemia cells. Interestingly, treatment with venetoclax and idasanutlin led to a feedback upregulation of CEBPB, IL-1β, and/or TNFα, along with their respective receptors, and promoted myelomonocytic differentiation. IL-1/TNFα antagonists or an IRAK inhibitor alone did not kill leukemia cells, but they showed synergistic cytotoxicity when combined with venetoclax and idasanutlin. Conclusions: In summary, we have described a positive feedback loop between CEBPB, IL-1/TNFα, and monocytic differentiation in monocytic leukemia that contributes to intrinsic and extrinsic drug resistance against BCL2 and MDM2 inhibitors. This crosstalk and the consequent drug resistance are further reinforced by venetoclax/MDM2 inhibition treatment. Combining venetoclax or idasanutlin with IL-1/TNFα antagonists or an IRAK inhibitor can abrogate the feedback loop and induce synergistic cytotoxic effects, offering promising therapeutic strategies to enhance the treatment efficacy of venetoclax and MDM2 inhibitors for monocytic leukemia.

The role of BATF2 deficiency in immune microenvironment rearrangement in cervical cancer – New biomarker benefiting from combination of radiotherapy and immunotherapy

Despite the significant progress in immunotherapy for certain cancers, including cervical cancer, most patients remain unresponsive or derive limited benefits from combined radiotherapy and chemotherapy. The factors underlying treatment resistance are unknown and there are few reliable predictive biomarkers. BATF2 is a member of the basic leucine zipper transcription factor family and is involved in immune response and immune cell development. However, the role of BATF2 in the immune microenvironment of patients with cervical cancer after radiotherapy remains unclear. In this study, immunohistochemistry and multicolour immunofluorescence analyses of patient tumor samples were used to assess BATF2 expression. We found that cervical cancer patients with high BATF2 expression had higher infiltration levels of CD4+ T cells, CD8+ T cells, and macrophages within the tumor than those with low expression levels. Furthermore, BATF2 expression was positively correlated with the prognosis of patients after concurrent chemoradiotherapy. A wild-type mouse model with BATF2-knockdown U14 cell-derived subcutaneous tumors and a Batf2−/− mouse model with wild-type U14 cell-derived subcutaneous tumors were used to assess CD8+ T cell infiltration and function. As expected, the knockdown of BATF2 in the U14 cell line substantially promoted tumor growth, which was mediated by a reduction in CD8+ T cell infiltration and antitumor function in vivo. Additionally, the Batf2−/− mouse model demonstrated that host BATF2 is also involved in controlling tumor growth. Furthermore, the combination of radiotherapy and anti-PD-1 therapy showed synergistic antitumour effects. These findings collectively suggest that BATF2 may serve as a potent positive regulator of the tumor immune microenvironment of cervical cancer after radiotherapy, and has the potential to be a prognostic biomarker to guide the application of a combination of radiotherapy and immunotherapy.

Radiosynthesis and biological evaluation of [18F]AG-120 for PET imaging of the mutant isocitrate dehydrogenase 1 in glioma

Glioma are clinically challenging tumors due to their location and invasiveness nature, which often hinder complete surgical resection. The evaluation of the isocitrate dehydrogenase mutation status has become crucial for effective patient stratification. Through a transdisciplinary approach, we have developed an 18F-labeled ligand for non-invasive assessment of the IDH1R132H variant by using positron emission tomography (PET) imaging. In this study, we have successfully prepared diastereomerically pure [18F]AG-120 by copper-mediated radiofluorination of the stannyl precursor 6 on a TRACERlab FX2 N radiosynthesis module. In vitro internalization studies demonstrated significantly higher uptake of [18F]AG-120 in U251 human high-grade glioma cells with stable overexpression of mutant IDH1 (IDH1R132H) compared to their wild-type IDH1 counterpart (0.4 vs. 0.013% applied dose/µg protein at 120 min). In vivo studies conducted in mice, exhibited the excellent metabolic stability of [18F]AG-120, with parent fractions of 85% and 91% in plasma and brain at 30 min p.i., respectively. Dynamic PET studies with [18F]AG-120 in naïve mice and orthotopic glioma rat model reveal limited blood-brain barrier permeation along with a low uptake in the brain tumor. Interestingly, there was no significant difference in uptake between mutant IDH1R132H and wild-type IDH1 tumors (tumor-to-blood ratio[40−60 min]: ~1.7 vs. ~1.3). In conclusion, our preclinical evaluation demonstrated a target-specific internalization of [18F]AG-120 in vitro, a high metabolic stability in vivo in mice, and a slightly higher accumulation of activity in IDH1R132H-glioma compared to IDH1-glioma. Overall, our findings contribute to advancing the field of molecular imaging and encourage the evaluation of [18F]AG-120 to improve diagnosis and management of glioma and other IDH1R132H-related tumors.

Prognostic and predictive biomarkers for anti-EGFR monoclonal antibody therapy in RAS wild-type metastatic colorectal cancer: a systematic review and meta-analysis

BackgroundRAS mutations affect prognosis in patients with metastatic colorectal cancer (mCRC) and have been identified as strong negative predictive markers for anti-epidermal growth factor receptor monoclonal antibody (anti-EGFR mAb) therapy, but many tumors containing wild-type RAS genes still do not respond to these therapies. Some additional biomarkers may have prognostic or predictive roles, but conclusions remain controversial.MethodsWe performed a meta-analysis and systematic review of randomized controlled trials comparing anti-EGFR mAb therapy with alternative therapy that investigated the prognostic and predictive impact of additional biomarkers in RAS wild-type (wt) mCRC patients. Hazard ratios (HRs) and 95% confidence intervals (CIs) for progression-free survival (PFS) and overall survival (OS) and odds ratios (ORs) for objective response rate (ORR) were calculated. The prognostic value of biomarkers was investigated by separately pooling HR and OR for different treatment groups in an individual study. The predictive value was assessed by pooling study interactions between treatment effects and biomarker subgroups.ResultsThirty publications reporting on eighteen trials were selected, including a total of 13,507 patients. In prognostic analysis, BRAF mutations were associated with poorer PFS [HRs = 3.76 (2.47–5.73) and 2.69 (1.82–3.98)] and OS [HRs = 2.66 (1.95–3.65) and 2.45 (1.55–3.88)] in both the experimental and control arms; low miR-31-3p expression appeared to have longer PFS and OS. In terms of predictive effect, a lack of response to anti-EGFR therapy was observed in patients with BRAF mutant tumors (Pinteraction < 0.01 for PFS). Patients with tumors with any mutation in the KRAS/NRAS/BRAF/PIK3CA gene also showed similar results compared with all wild-type tumors (Pinteraction for PFS, OS, and ORR were < 0.01, < 0.01 and 0.01, respectively). While low miR-31-3p expression could predict PFS (Pinteraction = 0.01) and OS (Pinteraction = 0.04) benefit. The prognostic and predictive value regarding PIK3CA mutations, PTEN mutations or deletions, EGFR, EREG/AREG, HER2, HER3, and HER4 expression remains uncertain.ConclusionsIn RAS wt mCRC patients receiving EGFR-targeted therapy, BRAF mutation is a powerful prognostic and therapy-predictive biomarker, with no effect found for PIK3CA mutation, PTEN mutation or deletion, but the combined biomarker KRAS/NRAS/BRAF/PIK3CA mutations predict resistance to anti-EGFR therapy. Low miR-31-3p expression may have positive prognostic and therapy predictive effects. Evidence on the prognostic and predictive roles of EGFR and its ligands, and HER2/3/4 is insufficient.

Copy number loss of KDM5D may be a predictive biomarker for ATR inhibitor treatment in male patients with pulmonary squamous cell carcinoma.

A limited number of patients with lung squamous cell carcinoma (SCC) benefit clinically from molecular targeted drugs because of a lack of targetable driver alterations. We aimed to understand the prevalence and clinical significance of lysine-specific demethylase 5D (KDM5D) copy number loss in SCC and explore its potential as a predictive biomarker for ataxia-telangiectasia and Rad3-related (ATR) inhibitor treatment. We evaluated KDM5D copy number loss in 173 surgically resected SCCs from male patients using fluorescence in situ hybridization. KDM5D copy number loss was detected in 75 of the 173 patients (43%). Genome-wide expression profiles of the transcription start sites (TSSs) were obtained from 17 SCCs, for which the cap analysis of gene expression assay was performed, revealing that upregulated genes in tumors with the KDM5D copy number loss are associated with 'cell cycle', whereas downregulated genes in tumors with KDM5D copy number loss were associated with 'immune response'. Clinicopathologically, SCCs with KDM5D copy number loss were associated with late pathological stage (p = 0.0085) and high stromal content (p = 0.0254). Multiplexed fluorescent immunohistochemistry showed that the number of tumor-infiltrating CD8+ /T-bet+ T cells was lower in SCCs with KDM5D copy number loss than in wild-type tumors. In conclusion, approximately 40% of the male patients with SCC exhibited KDM5D copy number loss. Tumors in patients who show this distinct phenotype can be 'cold tumors', which are characterized by the paucity of tumor T-cell infiltration and usually do not respond to immunotherapy. Thus, they may be candidates for trials with ATR inhibitors.

Effect and Interactions of BRAF on Lymph Node Metastasis in Papillary Thyroid Carcinoma With Hashimoto Thyroiditis.

The role of B-Raf proto-oncogene (BRAF) in papillary thyroid carcinoma (PTC) with Hashimoto thyroiditis (HT) is unknown. We aimed to explore risk factors affecting lymph node (LN) metastasis and interaction effect of BRAF in PTC patients with HT. We retrospectively collected the data of 994 PTC patients with HT who underwent surgery at the West China Hospital. We analyzed the correlations between preoperative characteristics and LN metastasis in overall, and different BRAFV600E-mutation patients. Logistic regression was applied to analyze the risk factors for LN metastasis. Finally, we performed an interaction effect analysis to identify the interaction effect of BRAF. The overall LN metastasis rate was 52.71% (524/994); the overall BRAF mutation rate was 26.9% (268/994). BRAF mutation rates were significantly different in LN metastasis and nonmetastasis patients (31.7% vs 21.5%; P < .001). In all 994 patients, age, body mass index (BMI), hypertension, tumor maximum diameter, BRAF mutation, tumor location, aspect ratio, calcification, and extrathyroidal invasion were risk factors for LN metastasis (P < .05). In BRAF-mutant patients, smoking, hypertension, maximum diameter, calcification, and multifocality were risk factors for LN metastasis (P < .05). In BRAF wild-type patients, age, BMI, maximum diameter, tumor location, aspect ratio, tumor shape, calcification, and extrathyroidal invasion were risk factors (P < .05). Additionally, we found statistically significant interactions between BRAF and BMI, hypertension, maximum diameter, and calcification (P < .05), suggesting the potential interaction effect of BRAF. BRAF is a risk factor for LN metastasis in PTC with HT. Meanwhile, BRAF can interact with age, BMI, hypertension, and calcification, which together influence LN metastasis.