Germline TP53 Mutations Research Articles

PATH-19. CLINICAL AND MOLECULAR FEATURES OF GLIOBLASTOMA, IDH-WILDTYPE ARISING IN THE SETTING OF LI FRAUMENI SYNDROME

Abstract INTRODUCTION Li Fraumeni Syndrome (LFS) is a rare autosomal dominant tumor predisposition syndrome caused by germline alterations of the TP53. Brain tumors are included in LFS core cancers. Choroid plexus carcinomas and medulloblastomas tend to occur in pediatric LFS patients, while gliomas tend to occur in adult LFS patients. There are few previous reports about gliomas arising in the setting of LFS. Here, we report clinical and molecular features of three cases of glioblastoma, IDH-wildtype arising in the setting of LFS. RESULTS Mean age at diagnosis was 40 years (range: 32-45). Two patients were male. Two patients had medical history of multiple tumors and family history of brain tumors. Magnetic resonance imaging of each patients revealed a left cerebellar peduncle lesion with faint contrast-enhancement, a right parietal lobe lesion with nodular contrast-enhancement and two lesions in the pons (no enhancement) and right parietal lobe (ring enhancement), respectively. All patients underwent chemotherapy including temozolomide and/or bevacizumab combined with radiation therapy (60Gy) after surgery. Mean progression free survival was 10.4 months (range: 5.1-17.0). All patients were admitted to palliative care mean 17.3 months (range: 14.4-21.4) after diagnosis. All patients harbored heterozygous germline mutations of TP53. Whole exome sequencing and copy number analysis of tumor tissues revealed TP53 mutation and PDGFRA amplification in all patients. However, EGFR amplification, the combination of gain of chromosome 7 and loss of chromosome 10 (7+/10-) and mutations of IDH, H3F3A, BRAF and TERT promoter were not detected in all tissues. CONCLUSION We experienced three cases of glioblastoma, IDH-wildtype arising in the setting of LFS. Although tumor locations and radiographic features were varied, all clinical courses were poor. Notably, all tumor tissues harbored TP53 mutation and PDGFRA amplification, while no tumor tissues harbored TERT promoter mutation, EGFR amplification and 7+/10-.

43. Association between Clonal Hematopoiesis and Inherited Cancer Susceptibility Genes

<h3>Background</h3> Understanding how germline mutations affect Clonal Hematopoiesis (CH) will provide insights into germline predisposition to MN. <h3>Methods</h3> We leveraged blood whole-exome sequencing data from 200,643 individuals in the UK Biobank (UKBB). The association between CH and germline mutations in 211 cancer susceptibility genes were tested among participants without hematologic malignancies at baseline using logistic regression adjusted for known confounders. Genes suggestive of association with CH were validated in 17,037 solid tumor patients with blood sequenced using Memorial Sloan Kettering (MSK) IMPACT panel. <h3>Results</h3> Germline pathogenic/likely pathogenic mutations were detected in 8,967 UKBB participants (4.5%). Germline mutations in TP53, ATR, ATM, and MPL were associated with increased risk of CH with odds ratios (ORs) and confidence intervals (CIs) of 4.33(1.31-14.32), 2.53(1.11-5.76), 2.21(1.23-3.97) and 1.44(1.00-2.08), correspondingly. Among 37 subjects with Li Fraumeni in the MSK-IMPACT cohort, TP53 was also associated with CH (OR: 3.75, 95% CI: 1.40-8.94) and this association was independent of cancer therapy (ORuntreated: 13.52, 95% CI: 2.94-57.48). The significant positive associations between germline TP53 mutations and CH were driven by somatic mutations in TP53 (OR:18.5, 95% CI: 2.8-72.8) and DNMT3A (OR: 5.1, 95% CI: 1.8-12.4). The rate of MN in TP53 mutation carriers was significantly increased (incidence rate ratio: 23.3; 95% CI: 6.0-65.4). The transition to MN was demarcated by a second TP53 loss of function mutation or deletion and by complex karyotype. <h3>Conclusions</h3> Germline mutations in cancer susceptibility genes, particularly those in the DNA damage response pathway are independent risk factors for CH and MN development.

A novel germline mutation of TP53 with breast cancer diagnosed as Li–Fraumeni syndrome

TP53 is a tumor suppressor gene and, when dysfunctional, it is known to be involved in the development of cancers. Li–Fraumeni syndrome (LFS) is a hereditary tumor with autosomal dominant inheritance that develops in people with germline pathogenic variants of TP53. LFS frequently develops in parallel to tumors, including breast cancer. We describe a novel germline mutation in TP53 identified by performing a multi-gene panel assay in a breast cancer patient with bilateral breast cancer.

Disruption of tp53 leads to cutaneous nevus and melanoma formation in Xenopus tropicalis.

In humans, germline TP53 mutations predispose carriers to a wide spectrum of cancers, which is known as Li–Fraumeni syndrome (LFS). To date, the association of melanomas with LFS remains unestablished. No melanomas have been reported in any P53‐modified mouse models either. In this study, we show that targeted disruption of P53 at the DNA‐binding domain in Xenopus tropicalis recapitulates LFS, with the formation of soft‐tissue sarcomas and pancreatic ductal adenocarcinoma. Interestingly, 19% of the 14‐month‐old tp53 Δ7/Δ7 homozygotes and 18% of tp53 +/Δ7 heterozygotes spontaneously developed small nevi and non‐invasive melanomas. Large invasive melanomas were also observed in other older homozygous mutants, with about 7.9% penetrance. Our data suggest that more dermatologic investigation of LFS patients should be able to settle the association of melanoma with LFS in epidemiology. Our model is also valuable for further investigation of the molecular mechanism underlying melanoma progression upon germline alteration of the tp53 locus.

Myxiod pleomorphic liposarcoma: a clinicopathological and molecular genetic analysis of six cases

Objective: To investigate the clinicopathologic and molecular genetic characteristics of myxoid pleomorphic liposarcoma (MPLPS). Methods: Six cases of MPLPS diagnosed and consulted in Fujian Provincial Hospital from 2015 to 2021 were collected for histomorphological observation, immunohistochemistry, and fluorescence in situ hybridization (FISH) detection of DDIT3 (CHOP) gene translocation and MDM2/CDK4 gene amplification. Results: There were four males and two females, aged 26-74 years (mean 53.8 years). The tumor size was 3.8-16.0 cm (mean 11.8 cm). All six cases had similar histopathologic features, showing overlapping histologic morphology of myxoid liposarcoma and pleomorphic liposarcoma. Four cases (4/6) were positive for S-100 protein, and the Ki-67 index was 50%-95%. All cases (6/6) were negative for DDIT3 (CHOP) translocation and MDM2/CDK4 amplification by FISH. TP53 (p.R248w) germline mutation was found in one case. Conclusions: MPLPS is a rare subtype of liposarcoma, characterized by overlapping morphology of myxoid liposarcoma and pleomorphic liposarcoma. Genetically, a few of them have TP53 gene germline mutations, but they lack of DDIT3 (CHOP) translocation or MDM2/CDK4 amplification.

DNA methylation is a comprehensive marker for pediatric adrenocortical tumors.

Children diagnosed with pediatric adrenocortical tumors (pACT) have variable outcomes, and, to date, the disease lacks robust prognostic biomarkers. The prognostic potential of tumor methylation has been demonstrated in several cancers. We aimed to evaluate the pACT methylation profile and its association with disease presentation and survival. In this cross-sectional study, we accessed the DNA methylation (MethylationEPIC Array, Illumina) of 57 primary pACT from Southeastern Brazil and the respective patients' clinicopathological features. We also applied our analysis in an independent 48 pACT methylation dataset. Unsupervised learning whole-methylome analysis showed two groups with distinct methylation signatures: pACT-1 and pACT-2. Compared to pACT-2, pACT-1 tumors were enriched with higher methylation in CpG islands, mainly in gene promoter regions. The topmost hypermethylated gene in these samples was shown to be underexpressed. Patients in the pACT-1 group were older at diagnosis and were more likely to have carcinomas and nonlocalized/advanced and recurrent/metastatic disease. Univariate and bivariate regressions showed that pACT-1 methylation signature confers superior hazard ratio of disease progression and death than known prognostic features. The methylation groups had similar frequencies of germline mutations in the TP53 gene, including the regionally frequent p.R337H. Our analysis replication validated our findings and reproduced those recently described in pACT. We demonstrated the existence of different tumor methylation signatures associated with pACT presentation and clinical evolution, even in the context of germline TP53 mutations. Our data support tumor methylation profiling as a robust and independent prognostic biomarker for pACT and suggest a list of candidate genes for further validation.

Targeted Mutational Analysis of Circulating Tumor DNA to Decipher Temporal Heterogeneity of High-Grade Serous Ovarian Cancer.

Simple SummaryThe issue of spatial and temporal heterogeneity of high-grade serous ovarian cancer (HGS-EOC) has hampered the possibility to shape the molecular portrait of relapsed disease, which ultimately impacts our ability to develop a more rational second-line treatment. Liquid biopsy offers the unique opportunity to track tumor evolution over time and infer the dynamic changes of tumor clonal architecture. Differently from other tumors, no actionable driving lesions characterize HGS-EOC, thus genome-scale analysis like whole-exome sequencing is not compatible with the clinical turnaround time. In the present work, we provided a novel framework based on the analysis of both qualitative and quantitative features of circulating tumor DNA (ctDNA) in order to identify, at the time of molecular relapse, the early genetic vulnerabilities that will characterize the clinical recurrence and thus be amenable of a more rational second-line treatment.We have previously demonstrated that longitudinal untargeted analysis of plasma samples withdrawn from patients with high-grade serous ovarian cancer (HGS-EOC) can intercept the presence of molecular recurrence (TRm) earlier than the diagnosis of clinical recurrence (TRc). This finding opens a clinical important temporal window to acquire through plasma sample analysis a real-time picture of those emerging molecular lesions that will drive and sustain the growth of relapsed disease and ultimately will confer resistance. In this proof of principle study, the same genomic libraries obtained at the diagnosis (T0), TRm and TRc were further analyzed by targeted resequencing approach to sequence the coding region of a panel of 65 genes to provide longitudinal analysis of clonal evolution as a novel strategy to support clinical decisions for the second-line treatment. Experiments were performed on plasma and tumor tissues withdrawn on a selection of previously analyzed cohorts of cases (i.e., 33 matched primary and synchronous lesions and 43 plasma samples from 18 patients). At T0, the median concordance of mutations shared by each tumor tissue biopsy and its matched plasma sample was 2.27%. This finding confirms the limit of a single tumor biopsy to be representative of the entire disease, while plasma analysis can recapitulate most of the main molecular lesions of the disease. A comparable scenario was observed during longitudinal analysis, where, with the exception of the TP53 gene and germline mutations in BRCA1/2 genes, no other gene shared the same locus specific gene mutation across T0, TRm and TRc time points. This high level of temporal heterogeneity has important implications for planning second-line treatment. For example, in three out of 13 cases, plasma ctDNA analysis at TRm or TRc reported acquired novel variants in the TP53BP1 gene not present at T0. In particular, patient 21564, potentially eligible for PARP-inhibitor (PARPi) treatment at the time of diagnosis (BRCA1 c.5182delA mutation), would unlikely respond to these drugs in second-line therapy due to the presence of eight distinct TP53BP1 variants in plasma samples collected TRc. This study demonstrates that liquid biopsy provides a real-time molecular picture to intercept those actionable genetic vulnerabilities or drug resistance mechanisms that could be used to plan a more rational second-line treatment.

Abstract 5840: The characteristics of TP53 germline mutations analyzed in a large-scale cohort of Chinese glioma patients

Abstract Backgrounds:TP53 germline mutation is well known to be the cause of Li-Fraumeni syndrome (LFS), a rare autosomal dominant cancer syndrome, characterized by predisposition of breast cancer, soft tissue carcinoma, osteosarcoma, brain cancer and etc. LFS has been reported in cases or small-scale cohorts for decades, while the characteristics of TP53 germline mutations carried by glioma patients were still less studied due to rarity. We performed large-scale retrospective research to identify TP53 germline mutations in Chinese glioma patients, which would extend the genetic knowledge of LFS related glioma. Methods:We enrolled 3325 glioma patients in this study (female=1423, male=1902). Next-generation sequencing panel targeting 825 genes was performed to identify TP53 germline mutations. Mutations were annotated pathogenic or likely pathogenic according to ACMG guidelines or referring to the literatures. Results:After annotation, 20 pathogenic or likely pathogenic germline mutations (PGMs) in TP53 were found in 3325 glioma patients. There was no statistical significance of gender ratio between all glioma patients and mutation carriers (female=6, male=14, p=0.25). The highest incidence rate of PGMs occurred in glioblastoma (n=16, 80.0%), followed by anaplastic astrocytoma (n=2, 10.0%), oligodendroglioma (n=1, 0.5%) and diffuse midline glioma (n=1, 0.5%). Significant difference of onset age between TP53 mutation carriers and non-carriers was pronounced (22.90YO vs 43.35YO avg, p&amp;lt;0.0001). Furthermore, the carrier rate of PGMs was prone to decrease with increasing onset age (table 1). Conclusions:This research indicated that TP53 PGMs were prone to occur in younger glioma patients, suggesting the importance of TP53 germline mutations being screened. It might be able to assist with early detection and treatment of glioma. The carrier rate of TP53 PGMs in each onset age intervals onset age glioma patient number PGM carrier number carrier rate 0-18 444 10 2.25% 19-30 263 4 1.52% 31-45 826 4 0.48% 46-55 717 1 0.14% 56-65 687 1 0.15% 66-75 337 0 0.00% 76+ 51 0 0.00% Citation Format: Xinyu Hong, Ximeng Zhao, Zeshang Guo, Xiaochen Yang, Bella Guo, Xiang Zhang, Tonghui Ma. The characteristics of TP53 germline mutations analyzed in a large-scale cohort of Chinese glioma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5840.

Abstract 3364: Diagnosing Li-Fraumeni syndrome from the somatic genome

Abstract Background: Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome caused by germline mutations in the tumor suppressor gene TP53. LFS is estimated to occur in 1:1000 - 1:5000 people and is associated with a 80% lifetime cancer risk. This syndrome is diagnosed using familial cancer history and germline TP53 sequencing; however, clinical heterogeneity and variants of unknown significance limit diagnostic precision. Accurate diagnosis is imperative to implement surveillance for secondary malignancies and familial genetic testing. Methods: We hypothesized that LFS cancers evolve uniquely from sporadic cancers, implying that the somatic genomes of LFS patients exhibit distinct characteristics that can infer the predisposition syndrome. To investigate this, we interrogated mutational signatures, TP53 copy number, TP53 loss of heterozygosity, ploidy, and the incidence of chromothripsis in tumor compared to normal samples (blood or fibroblast) of individuals with germline TP53 mutations (n=27), somatic TP53 mutations (n=17) and WT for TP53 (n=158). We created a random forest model with 10-fold cross validation to determine if somatic features could diagnose LFS. Results: No signatures were significantly associated with LFS (Wilcoxon rank-sum test, Benjamin-Hochberg FDR correction). As previously reported in the literature, LFS compared to non-LFS cancers in our cohort were more likely to: be hyperdiploid (odds ratio (OR) = 11.83, FDR &amp;lt; 0.0001, Fisher exact test), have undergone TP53 loss of heterozygosity (OR = 23.15, FDR &amp;lt; 0.0001, Fisher exact test) and experience chromothripsis (OR = 7.76, FDR &amp;lt; 0.001, Fisher exact test). The area under the receiver operating curve (AUROC) for our random forest model with 10-fold cross validation was 0.90, the area under the precision recall curve (AUPRC) was 0.59, the positive predictive value (PPV) was 0.70, the negative predictive value (NPV) was 0.93 and the F1-score was 0.52. This implies that the somatic genomic features are reliable indicators of this germline syndrome. We have obtained access to a future 50 LFS samples from the Pediatric Cancer Genome Project dataset, which we hope will improve our model’s performance. Conclusion: We have developed a machine learning tool that uses somatic features to identify LFS, a germline cancer predisposition syndrome. As the importance of precision oncology becomes apparent, a tool to identify LFS patients from the somatic genome will facilitate early diagnosis. This will allow individuals to enter a surveillance program for early detection of secondary tumors, leading to improved outcomes. Citation Format: Brianne Laverty, Vallijah Subasri, Nicholas Light, David Malkin. Diagnosing Li-Fraumeni syndrome from the somatic genome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3364.

Abstract 5875: Germline gene alterations in high grade and low grade gliomas: A multi-center, large scale study in China

Abstract Backgrounds: Germline gene alterations in gliomas play a significant role during malignant transformation of progenitor glial cells. Previous pan-caner studies suggested 6-10% of gliomas patients harboring germline gene mutations. However, these studies are limited to only known cancer predisposition genes and a small scale of gliomas patients. In this study, we performed a multi-canter, large scale study to investigate the contribution of germline gene alterations to LGG and HGG. Methods: Genomic DNA was extracted from white blood cells from 1006 LGG patients and 1578 HGG patients and was subjected to Next-generation sequencing with Onco PanScan. Pathogenic or likely pathogenic germline variants (PGVs) were identified in 150 putative cancer-predisposition genes according to ACGM guideline. Fisher’s exact test was used for the statistics analysis (two-sided). Results: We identified 54 PGVs in LGG patients and 112 PGVs in HGG patients which were located in 31 and 40 unique genes, respectively (Table 1). There was a significant difference between HGG and LGG in younger patients with germline gene mutations (A group, p &amp;lt; 0.001), while not in B and C group. The results indicated that the incidence rate of TP53 or MSH2 germline mutations in HGG patients was much higher than in LGG patient (p &amp;lt; 0.01), while a lower incidence rate of ERCC5 germline mutations was observed in HGG patients in comparison with LGG patients (p &amp;lt; 0.05). Conclusions: This study indicated a higher PGVs frequency in HGG than in LGG, especially in younger group. In addition, there is different contribution of germline gene alterations to risk the formation of LGG or HGG. It might aid in the early diagnosis of these patients and genetic counseling of their families. Informations of PGVs in LGG and HGG LGG HGG Numbers of mutation carriers Numbers of LGG Mutation rate Numbers of mutation carriers Numbers of HGG Mutation rate Age A: 0-30 years 14 a*** 292 4.1% 29 b*** 189 15.3% B: 31-55 years 30 554 5.4% 41 639 6.4% C: &amp;gt;55 years 10 160 6.3% 42 c*** 750 5.6% Total 54 1006 5.4% 112 1578 7.1% Gender Male 35 567 6.2% 65 935 7.0% Female 19 439 4.3% 50 643 7.8% Total 54 1006 5.4% 112 1578 7.1% Top ten of high mutation rate ERCC5*, MUTYH, BRCA2, CHEK2, WRN, PRSS1, MSH6, FANCD2, ERCC2, FANCA TP53**, MSH2**, BRCA2, NF1, RAD51D, MSH6, PRSS1, BUB1B, PDE11A, BLM Note: LGG 1, Low Grade Glioma; HGG 2, High Grade Glioma; aNumbers of mutation carriers in A group were statistical different in LGG and HGG patients; bNumbers of mutation carriers in A group and B group were statistical different in HGG patients; cNumbers of mutation carriers in A group and C group were statistical different in HGG patients; * p &amp;lt; 0.05; ** p &amp;lt; 0.01; *** p &amp;lt; 0.001 Citation Format: Jie Wang, Bella Guo, Xiang Zhang, Ximeng Zhao, Dongsheng Wang, Fei Sun, Tonghui Ma. Germline gene alterations in high grade and low grade gliomas: A multi-center, large scale study in China [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5875.

NFB-06. Laser Interstitial Thermal Therapy as a Radiation-Sparing Approach for Children with Cancer Predisposition

BACKGROUND: Li-Fraumeni (LFS) syndrome confers a predisposition for the formation of a broad range of tumors. Estimates of post-radiation secondary malignancy in the context of LFS cohorts range from 20-50%. Therefore, alternative therapeutic strategies are prioritized. Laser interstitial thermal therapy (LITT) is a minimally invasive technique utilizing thermal ablation for tumor control that is not associated with any ionizing radiation or known mutagenic effect. We describe the case of a child with LFS previously treated for CPC who developed a secondary low-grade glial neoplasm of the brain treated safely with MR-guided LITT as part of a radiation-sparing therapeutic approach. METHODS: Retrospective chart review identified a patient with recurrent CPC associated with LFS who was treated with LITT for a secondary low-grade glial tumor. A descriptive report is provided, including a review of clinical and radiologic outcomes of the procedure. RESULTS: A 4-year-old male with left parietal WHO Grade III CPC associated with a TP53 germline mutation met inclusion criteria. The patient underwent neoadjuvant platinum-based chemotherapy before near-total resection, followed by immunotherapy with 131I-8H9 and 30 fractions of 54Gy total proton therapy. He remained without evidence of disease for two years prior to developing a slow-growing mass adjacent to the left frontal horn. This lesion demonstrated radiographic progression on neuroimaging and was deemed to be a poor candidate for surgical removal. Stereotactic biopsy revealed a low-grade glial neoplasm staining positive for GFAP and Olig2. MR-guided LITT was concurrently performed for ablative therapy of the lesion without complication. Greater than 8-month follow-up has revealed no subsequent disease. CONCLUSIONS: Alternatives to ionizing radiation for brain tumors should be explored for patients with cancer predisposition, such as LFS. Long-term follow up will be needed to ensure local disease control and avoidance of treatment-related neoplasms.

The correlation between tumor mutation burden and TP53 or CHEK2 germline mutations in malignant tumors.

e22527 Background: Li-Fraumeni syndrome (LFS) is a rare autosomal dominant cancer predisposition syndrome, mainly caused by the lack of tumor suppressor gene TP53. The LFS related tumors include breast cancer, brain tumors, malignant sarcoma, bone cancer and central nervous system tumors. In addition to TP53 germline mutations, studies have shown that CHEK2 is also a susceptibility gene for LFS, and CHEK2 germline mutations is related to a series of cancer types. However, the correlation between tumor mutation burden (TMB), age, gender, PD-L1 expression and TP53 or CHEK2 germline mutations in malignant tumors remains unknown. Methods: In this study, we retrospectively analyzed the mutation characteristics of TP53 or CHEK2 germline mutations in patients with solid tumors without selecting age or family history. We identified 631 patients harboring TP53 or CHEK2 mutations from 9337 patients with malignant solid tumors. According to the ACMG (American College of Medical Genetics and Genomics) guidelines in pathogenicity, the 631 patients in the retrospective cohort were divided into three groups, including P/LP group (with pathogenic or likely-pathogenic mutations), VUS group (with uncertain significance mutations) and B/LB group (with benign or likely-benign mutations). We also analyzed the differences in TMB, age, gender and PD-L1 expression among the three groups. Statistical significance was defined as P-value less than 0.05. Results: The 631 (631/9337) patients carried TP53 or CHEK2 germline mutations were identified, in which 33 patients with pathogenic mutations and 15 patients with likely-pathogenic mutations. These pathogenic or likely-pathogenic mutations mainly occurred in lung cancer, brain tumors, colorectal cancer and liver cancer, accounting for about 35.4%, 20.8%, 16.7% and 12.5%, respectively. Among the three groups, TMB was significantly different between P/LP group and B/LB group (P = 0.037), and the B/LB group was higher. In addition, we found that the three groups had no significant differences in age, gender and PD-L1 expression. Conclusions: Our data showed that 0.823% (48/8535) malignant solid tumor patients carried TP53 (28/48) or CHEK2 (20/48) germline pathogenic or likely_ pathogenic mutations. In addition, the TMB value in B/LB group was significantly higher than that in P/LP group. The other characteristics of LFS will be studied in the future.

Determining concordance of LFSPRO TP53 germline carrier risk predictions to standard genetic counseling practice.

10593 Background: Li-Fraumeni Syndrome (LFS) is a hereditary cancer syndrome associated with a germline mutation in the TP53 tumor suppressor gene and an increased risk of developing a spectrum of cancers throughout a carrier’s lifetime. Early cancer detection in patients with TP53 mutations can dramatically improve cancer survival rates. However, it can be difficult to identify patients at risk of LFS due to the overlap of the multiple cancer types with other inherited cancer syndromes. Risk prediction modeling has been widely accepted by the clinical community, however, currently there is not an available tool to assist in risk prediction of LFS during genetic counseling sessions. LFSPRO is a statistical model that has previously been validated on large research cohorts in predicting the likelihood of a proband having LFS based off detailed patient and family history information. To improve the clinical utility of LFSPRO, a user-friendly interface is still needed. Additionally, we aim to evaluate concordance between LFSPRO’s abilities in predicting the likelihood of a proband having LFS and currently established clinical testing criteria. Methods: We developed a Shiny App to create a user-friendly interface for genetic counselors (GCs) to run LFSPRO. Determining concordance of LFSPRO to standard germline testing criteria and the clinical utility of the LFSPRO Shiny App is underway by GCs within the Department of Clinical Cancer Genetics at MD Anderson Cancer Center through prospective data collection and completion of user surveys. Following a standard genetic counseling session, individuals identified as concerning for a potential germline TP53 mutation are evaluated with LFSPRO to compare performance of the model to established TP53 testing guidelines. Concordance is then evaluated in prediction of TP53 mutation carrier status from LFSPRO, current clinical criteria and clinical judgment. Data collection began 12/21/2021 and is currently ongoing. Results: Close collaboration with GCs and clinicians on the development of the LFSPRO Shiny App has achieved automated de-identified input data, clear pedigree drawing, important demographic data, interpretable risk results and risk visualizations to be used at the GC's discretion. To date, 29 individual’s family data have been run through LFSPRO. Of these, 11 have not currently completed TP53 testing and concordance cannot be determined. Of the 18 remaining, 14 individuals’ LFSPRO results were concordant with current clinical criteria. Further data collection is needed to appropriately analyze concordance. Conclusions: The LFSPRO Shiny App aims to provide an additional tool for GCs and clinical providers to assess patient risk for LFS. This ongoing study will help establish the clinical utility of LFSPRO in a single institution’s genetic counseling practice with the potential to be applied to other patient care settings in the future.

Actionable genomic landscapes from a real-world cohort of localized urothelial carcinoma patients.

525 Background: Recent targeted therapies for advanced and metastatic urothelial cancer have generated enthusiasm, but the actionable genomic landscape of early-stage disease remains largely unknown. Here, we used real-world evidence to investigate differences between somatic and germline mutations in localized, early-stage urothelial cancers and advanced urothelial cancers. Methods: We retrospectively analyzed de-identified NGS data from 1,146 bladder cancer patients (stages I-IV) with formalin-fixed, paraffin-embedded tumor biopsies sequenced using the Tempus|xT solid tumor assay (DNA-seq of 595-648 genes at 500x coverage; whole-exome capture RNA-seq). For the subset of patients with tumor-normal match sequencing (n=758), additional incidental germline alterations in 46 different genes were assessed. Results: A total of 1,146 bladder cancer tumors were investigated: stage I-II (n=124), stage III (n=159), and stage IV (n=863)—summarized in Table. Tumor mutational burden (TMB) was calculated for 1,126 tumors, and TMB-high (TMB-H; ≥10 mutations per megabase) was similar across tumor stages. PD-L1 immunohistochemical staining was performed on 698 tumors, and no significant differences were observed. Microsatellite instability high (MSI-H) status was detected in only 2 (1.6%) stage I-II tumors and 8 (0.9%) stage IV tumors. Alterations—single nucleotide variants, insertions/deletions, and copy number variants—in FGFR2/3, homologous recombination repair genes (18 genes including BRCA1/2 and ATM), additional DNA repair gene mutations ( ERCC2, RB1, FANCC) and NTRK fusions were detected at similar frequencies across disease stages. In 758 patients with tumor/normal matched sequencing, we identified a low rate of incidental germline mutations in MUTYH (stage III, 1%; stage IV, 1.9%), BRCA2 (stages I-II, 1.2%; stage III, 1%; stage IV, 0.5%), BRIP1 (stages I-II, 1.2%), ATM (stage III, 1%; stage IV, 0.7%), MSH6 (stage III, 1%; stage IV, 0.2%), and TP53 (stage III, 1%; stage IV, 0.2%). Conclusions: Patients with bladder cancer have similar rates of potentially actionable mutations and genomic landscapes regardless of clinical disease stage. These findings provide a rationale for further investigating targeted therapies among early-stage bladder cancer patients.[Table: see text]

Longitudinal ctDNA alterations in germline positive CRPC patients.

275 Background: Circulating tumor-derived DNA (ctDNA) is an accessible method for characterizing somatic alterations. We report longitudinal ctDNA screenings of mCRPC patients (pts) who have had germline testing. Methods: Patients with both germline testing and ctDNA assessment were included. Germline testing was performed with a multi-gene cancer panel from Invitae (50-83 genes) and somatic alterations in ctDNA were identified by testing with Guardant 360 (70-83 genes). ctDNA alterations were characterized as deletions, frameshift, missense, nonsense, and other mutations. A total of 177 patients in various stages of therapy had both ctDNA and germline DNA tested. Results: From 2015-2021, 177 mCRPC patients were included and had an average of 3 ctDNA tests. 11.3% (20/177) had pathogenic or likely-pathogenic germline mutations. The common pathogenic germline mutations were in BRCA2 (25%; 5/20), ATM (10%; 2/20), and MSH2 (10%; 2/20). In ctDNA, missense mutations were the most prevalent type of gene alteration in germline negative (n = 539/790, 68%) and germline positive (n = 124/218, 57%) followed by frameshift mutations at 22% (n = 48/218) in germline positive and 10% (n = 80/790) in germline negative patients. Germline positive patients were more likely to have somatic frameshift mutations (OR = 2.09, 95% C.I. (1.3792, 3.1618), p = 0.001) and less likely to have missense mutations (OR = 0.61, 95% C.I. (0.4519, 0.8351), p = 0.002). Other alterations including deletions, nonsense, and other mutations were not significantly different. Of the germline positive pts, BRCA2 mutation was associated with the highest number of somatic alterations. Conclusions: Germline positive CRPC patients were more likely to have frameshift mutations and less likely to missense mutations compared to germline negative CRPC patients. Patients with germline mutations in BRCA2 and TP53 had the highest number of somatic alterations detected in ctDNA over the course of ctDNA evaluation.

Molecular Features and Clinical Management of Hereditary Pancreatic Cancer Syndromes and Familial Pancreatic Cancer.

Hereditary pancreatic cancers are caused by several inherited genes. Familial pancreatic cancer is defined as pancreatic cancer arising in a patient with at least two first-degree relatives with pancreatic cancer in the absence of an identified genetic cause. Hereditary pancreatic cancer syndromes and familial pancreatic cancers account for about 10% of pancreatic cancer cases. Germline mutations in BRCA1, BRCA2, ATM, PALB2, CDKN2A, STK11, and TP53 and mismatch repair genes (MLH1, MSH2, MSH6, PMS2, and EPCAM) are among the well-known inherited susceptibility genes. Currently available targeted medications include poly (ADP-ribose) polymerase inhibitors (PARP) for cases with mutant BRCA and immune checkpoint inhibitors for cases with mismatch repair deficiency. Loss of heterozygosity of hereditary pancreatic cancer susceptibility genes such as BRCA1/2 plays a key role in carcinogenesis and sensitivity to PARP inhibitors. Signature 3 identified by whole genome sequencing is also associated with homologous recombination deficiency and sensitivity to targeted therapies. In this review, we summarize molecular features and treatments of hereditary pancreatic cancer syndromes and surveillance procedures for unaffected high-risk cases. We also review transgenic murine models to gain a better understanding of carcinogenesis in hereditary pancreatic cancer.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

Primary EWS/PNET of the lung with TP53 germline and SKT11 somatic mutation: A case report and review of the literature

Primary pulmonary EWS/PNET is extremely rare. This report describes a 20 year‐old man with primary pulmonary EWS/PNET with TP53 germline and SKT11 somatic mutation. After four neoadjuvant chemotherapy cycles (VAC with alternating IE) combined with anlotinib, a left pneumonectomy was performed. Maintenance anlotinib monotherapy was then continued with no sign of recurrence to date. It is suggested that before the treatment and prognosis of children or young adults with primary EWS/PNET of the lung that consideration should be given to genetic testing.

A Functional Precision Medicine Pipeline Combines Comparative Transcriptomics and Tumor Organoid Modeling to Identify Bespoke Treatment Strategies for Glioblastoma.

Li Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome caused by germline mutations in TP53. TP53 is the most common mutated gene in human cancer, occurring in 30–50% of glioblastomas (GBM). Here, we highlight a precision medicine platform to identify potential targets for a GBM patient with LFS. We used a comparative transcriptomics approach to identify genes that are uniquely overexpressed in the LFS GBM patient relative to a cancer compendium of 12,747 tumor RNA sequencing data sets, including 200 GBMs. STAT1 and STAT2 were identified as being significantly overexpressed in the LFS patient, indicating ruxolitinib, a Janus kinase 1 and 2 inhibitors, as a potential therapy. The LFS patient had the highest level of STAT1 and STAT2 expression in an institutional high-grade glioma cohort of 45 patients, further supporting the cancer compendium results. To empirically validate the comparative transcriptomics pipeline, we used a combination of adherent and organoid cell culture techniques, including ex vivo patient-derived organoids (PDOs) from four patient-derived cell lines, including the LFS patient. STAT1 and STAT2 expression levels in the four patient-derived cells correlated with levels identified in the respective parent tumors. In both adherent and organoid cultures, cells from the LFS patient were among the most sensitive to ruxolitinib compared to patient-derived cells with lower STAT1 and STAT2 expression levels. A spheroid-based drug screening assay (3D-PREDICT) was performed and used to identify further therapeutic targets. Two targeted therapies were selected for the patient of interest and resulted in radiographic disease stability. This manuscript supports the use of comparative transcriptomics to identify personalized therapeutic targets in a functional precision medicine platform for malignant brain tumors.

Prevalence of germline TP53 mutation among early onset middle eastern breast cancer patients

BackgroundThe data on prevalence and clinical relevance of TP53 germline mutations in early onset Middle-Eastern breast cancer (BC) is limited.MethodsWe determined TP53 germline mutations in a cohort of 464 early onset BC patients from Saudi Arabia using capture sequencing based next generation sequencing.ResultsGermline TP53 pathogenic mutations were found in 1.5% (7/464) of early onset Saudi BC patients. A total of six pathogenic missense mutations, one stop gain mutation and two variants of uncertain significance (VUS) were detected in our cohort. No TP53 pathogenic mutations were detected among 463 healthy controls. TP53 mutations carriers were significantly more likely to have bilateral breast cancer (p = 0.0008). At median follow-up of 41 months, TP53 mutations were an unfavorable factor for overall survival in univariate analysis. All the patients carrying TP53 mutations were negative for BRCA1 and BRCA2 mutations. Majority of patients (85.7%; 6/7) carrying TP53 mutation had no family history suggestive of Li-Fraumeni Syndrome (LFS) or personal history of multiple LFS related tumors. Only one patient had a positive family history suggestive of LFS.ConclusionsTP53 germline mutation screening detects a clinically meaningful risk of early onset BC from this ethnicity and should be considered in all early onset BC regardless of the family history of cancer, especially in young patients that are negative for BRCA mutations.