Li-Fraumeni Syndrome Families Research Articles

Molecular insights into TP53 mutation (p. Arg267Trp) and its connection to Choroid Plexus Carcinomas and Li-Fraumeni Syndrome.

Choroid plexus carcinomas (CPCs) are rare malignant tumors primarily affecting pediatric patients and often co-occur with Li-Fraumeni Syndrome (LFS), an inherited predisposition to early-onset malignancies in multiple organ systems. LFS is closely linked to TP53 mutations, with germline TP53 gene mutations present in approximately 75% of Li-Fraumeni syndrome families and 25% of Li-Fraumeni-like syndrome families. Individuals with TP53 mutations also have an elevated probability of carrying mutations in BRCA1 and BRCA2 genes. To investigate the structural and functional implications of the TP53: 799C > T, p. (Arg267Trp) missense mutation, initially identified in a Saudi family, and understand its impact on TP53 functionality and related intermolecular interactions. Computational analyses were conducted to examine the structural modifications resulting from the TP53: 799C > T, p. (Arg267Trp) mutation. These analyses focused on the mutation's impact on hydrogen bonding, ionic interactions, and the specific interaction with Cell Cycle and Apoptosis Regulator 2 (CCAR2), as annotated in UniProt. The study revealed that the native Arg267 residue is critical for a salt bridge interaction with glutamic acid at position 258. The mutation-induced charge alteration has the potential to disrupt this ionic bonding. Additionally, the mutation is located within an amino acid region crucial for interaction with CCAR2. The altered properties of the amino acid within this domain may affect its functionality and disrupt this interaction, thereby impacting the regulation of catalytic enzyme activity. Our findings highlight the intricate intermolecular interactions governing TP53 functionality. The TP53: 799C > T, p. (Arg267Trp) mutation causes structural modifications that potentially disrupt critical ionic bonds and protein interactions, offering valuable insights for the development of targeted mutants with distinct functional attributes. These insights could inform therapeutic strategies for conditions associated with TP53 mutations.

Increased risk for thyroid carcinoma in patients with Li-Fraumeni syndrome.

10612 Background: Patients with Li-Fraumeni syndrome (LFS) are predisposed to a 90% lifetime risk of cancer, thus undergoing extensive cancer surveillance. While thyroid cancer is not a core LFS-associated malignancy, increased incidence of thyroid carcinoma has been reported within the LFS tumor spectrum. In the general population, thyroid cancer incidence has soared mainly via incidental detection. We investigated the rate of thyroid carcinoma in relation to p53 mutational process and increased screening. Methods: A retrospective chart review was conducted for clinico-pathological features for adult carriers of confirmed germline TP53 variants at three tertiary cancer centers. Standardized incidence ratio (SIR) was calculated using age, sex, and year-specific expected incidence rates of thyroid cancer from Surveillance, Epidemiology, and End Results (SEER) 1975 – 2020 data. Results: Among 600 patients from 400 families with LFS, 39 (6.5%) patients from 36 (9%) families developed thyroid carcinoma at an average age of 42 years (median = 40, ranged from 23 to 70 years of age). The majority of LFS patients with thyroid carcinoma were female (N=30, 77%). Thyroid carcinoma was the presenting cancer diagnosis in 17 (44%) patients. Over 70% of thyroid carcinoma diagnoses (N=31) were detected incidentally either via LFS cancer screening (N=12, 39%) or via an imaging study unrelated to LFS screening (N=10, 32%). All 39 thyroid carcinomas were of follicular cell origin (non-medullary), most were multifocal (67% of N=32), and 30% had nodal metastasis (N=10 of 33). Of 35 tumors with histologic data, papillary carcinoma (papillary, follicular, and tall cell subtypes) was most common (N=29, 83%), followed by follicular carcinoma (N=4, 11%) and oncocytic carcinoma (N=2, 6%). LFS patients most often underwent a total thyroidectomy (N=27, 69%) compared to a hemithyroidectomy (N=10, 26%) or hemithyroidectomy with completion surgery within three months (N=2, 5%). Intermediate to high risk of recurrence based on tumor characteristics was noted in 17 patients (44%), warranting consideration of radioactive iodine (RAI) therapy, including tall cell subtype (N=3), oncocytic or follicular histology, incomplete resection (N=2), extrathyroidal extension (N = 6), and greater than five positive lymph nodes (N=6). Five (29%) of these 17 patients received RAI. The SIR for thyroid carcinoma in LFS compared to SEER was 13 (95% CI 9.2-17.8, p<0.0001). The SIR was elevated for LFS patients diagnosed with thyroid carcinoma both prior to and after genetic testing (SIR 9.0, CI 5.3-14.2, p<0.0001 and SIR 20, CI 12.2- 30.9, p<0.0001, respectively). Conclusions: In this multi-institutional cohort, a 6-9% prevalence rate of thyroid carcinoma was observed in LFS patients and families, with >70% of the tumors identified incidentally. The rate of thyroid carcinoma in LFS is significantly elevated over the general population.

Lessons learnt from the clinico-genomic profiling of families with Li Fraumeni syndrome at a tertiary care centre in North India.

Li Fraumeni syndrome (LFS) is an inherited cancer predisposition syndrome due to TP53 gene mutation. There is sparse literature on LFS in the Indian population. We conducted a retrospective study of patients diagnosed with LFS and their family members, registered at our Medical Oncology Department between September 2015 and 2022. 9 LFS families consisted of 29 patients diagnosed currently or historically with malignancies including 9 index cases and 20 first or second-degree relatives. Of these 29 patients, 7 (24.1%) patients developed their first malignancy before the age of 18 years, 15 (51.7%) were diagnosed between 18and and 60 years, and 7 (24.1%) were diagnosed at age more than 60 years. A total of 31 cancers occurred among the families, including 2 index cases who had metachronous malignancies. Each family had a median of three cancers (range 2-5); sarcoma (n = 12, 38.7% of total cancers) and breast cancer (n = 6, 19.3% of total cancers) being the commonest malignancies. Germline TP53 mutations were documented among 11 patients with cancers and 6 asymptomatic carriers. Of these nine mutations, the most common types were missense (n = 6, 66.6%) and nonsense (n = 2, 22.2%), and the commonest aberration was replacement of arginine with histidine (n = 4, 44.4%). Eight (88.8%) families met either classical or Chompret's diagnostic criteria and two (22.2%) satisfied both. Two (22.2%) families fit the diagnostic criteria prior to onset of malignancy in the index cases but were untested till the index cases presented to us. Four mutation carriers from three families are undergoing screening as per the Toronto protocol. No new malignancies have been detected so far during the mean surveillance duration of 14 months. The diagnosis of LFS has socio-economic implications for patients and their families. Delay in genetic testing misses out a crucial window wherein asymptomatic carriers could initiate surveillance in a timely fashion. Greater awareness on LFS and genetic testing in Indian patients is warranted for better management of this hereditary condition.

Abstract 5240: Validation of research cohort based penetrance estimates for multiple cancer types and multiple primary cancers on clinically ascertained families

Abstract Age-at-onset penetrance is the probability of developing disease by a certain age given a patient’s characteristics. Accurate penetrance estimates are important for cancer screening and diagnosis, and for policy making in public health. We developed two Bayesian semi-parametric models: a model that estimates cancer-specific penetrances to the first primary (CS), and a model that estimates penetrances to the second primary without distinguishing between the cancer types (MPC). Model training requires a dataset that is enriched with enough MPC cases, as well as with competing risks from a variety of cancer types. Thus, we trained our models using data from families affected by the Li-Fraumeni Syndrome (LFS), a genetic disorder characterized by germline mutation in the gene TP53. This dataset consists of 189 families, all of which were ascertained via probands who were diagnosed with pediatric sarcoma at MD Anderson Cancer Center (MDACC) between 1944 and 1983. We have validated our penetrance estimates on independent LFS datasets with different ascertainment criteria, namely a patient cohort prospectively collected from high-risk clinics at MDACC, and another cohort from the National Cancer Institute (NCI). These datasets were meticulously collected for research purposes. However, clinical datasets, which resemble the data that genetic counselors encounter in counseling sessions, are severely impacted by missing data, most commonly missing ages at diagnosis and ages at last contact, and only represent a snapshot of family history without extended follow-up. To investigate the utility of our research-based risk prediction models in real-world clinics, we evaluated our penetrance estimates on clinically ascertained LFS families that were collected through the Clinical Cancer Genetics (CCG) program at MDACC in the past 10 years. The CCG dataset consists of 3,275 individuals across 124 families, of which 645 were diagnosed with at least one primary and 127 tested positive for TP53 mutation. Our CS model showed good performance when making cancer-specific predictions of the first primary, with Areas Under the Curve (AUCs) of 0.76, 0.81, and 0.68 for breast cancer, sarcoma, and all other cancer types combined. Our MPC model showed an AUC of 0.7 when predicting patients with MPC versus those with a single primary. Both the CS and MPC models perform better than the Chompret criteria when predicting TP53 mutation, with AUCs of 0.75 and 0.77 respectively. These results suggest that our models can be utilized for personalized risk predictions in clinical settings, despite being trained on a research-based dataset. Given that the Chompret criteria tends to predict TP53 mutation more conservatively, the ability of our models to cast a wider net is especially meaningful in the identification of potential carriers, which assists efficient genetic testing and screening. Citation Format: Nam H. Nguyen, Elissa B. Dodd-Eaton, Jessica L. Corredor, Jacynda Woodman-Ross, Nathaniel D. Hernandez, Angelica M. Gutierrez Barrera, Banu K. Arun, Wenyi Wang. Validation of research cohort based penetrance estimates for multiple cancer types and multiple primary cancers on clinically ascertained families. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5240.

Abstract OT2-13-01: Willingness to Participate in a Trial Comparing Standard Genetic Counseling versus Genetic Counseling with Personalized Cancer Risks Estimates in Patients with Li-Fraumeni Syndrome

Abstract Background: Individuals with Li-Fraumeni Syndrome (LFS) have increased risk of developing breast cancer, sarcomas, brain tumors, leukemia, and other cancers throughout their lifetime. LFS is primarily caused by autosomal dominant germline mutations in the TP53 tumor suppressor gene. Due to the large number of cancers caused by LFS, and their variable age of presentation, each LFS family often presents very differently. Currently, standard genetic counseling for patients with LFS often involves general lifetime risk predictions for developing several primary cancers. At present, there are no standard tools available to help genetics providers obtain a personalized risk assessment for a patient with LFS based on their unique personal and family history data. To address this, the LFSPRO risk model was developed to estimate the likelihood of a proband having LFS, to provide cancer-specific risks of a first primary cancer, and to estimate risk of time to second primary cancer diagnosis by utilizing detailed personal and family history information. Specific Aims: This study aims to understand patients’ willingness to participate in a randomized trial comparing standard genetic counseling practice to personalized genetic counseling via LFSPRO risk estimates. Trial Design: Eligible patients or parents/guardians are invited via email to complete a survey assessing interest in a hypothetical clinical trial scenario where patients are randomized to receive one of two types of post-disclosure genetic counseling approaches: standard genetic counseling for TP53 results, involving generic risk predictions for developing cancers, or personalized risk information provided from LFSPRO. Following the hypothetical scenario, participants are asked about their perceived benefits and barriers to this research scenario and interest in receiving personalized risk results. Demographic information is also collected. Eligibility Criteria: Individuals who receive genetic counseling through MD Anderson Cancer Center genetics clinics specifically for TP53 genetic testing and who consent to undergo TP53 genetic testing or individuals who genetic testing already indicates a TP53 germline mutation are offered this survey. Patients must be 13 years or older to complete the survey, otherwise a parent/guardian may complete the survey on their behalf. Patients must have English fluency. Statistical methods: Descriptive statistics will be used to analyze the data and summarize the opinion of the participants. Accrual: Enrollment is set to open in July 2022. Currently, 157 patients have been identified to be invited to participate in the study. Funding: This research is supported by the Cancer Research and Prevention Institute of Texas. Contact: Jacynda Woodman-Ross, MS, CGC, The University of Texas MD Anderson Cancer Center, jawoodman@mdanderson.org Citation Format: Jacynda Woodman-Ross, Sierra O. Green, Jessica Corredor, Elissa Dodd-Eaton, Nathaniel Hernandez, Susan K. Peterson, Wenyi Wang, Banu K. Arun. Willingness to Participate in a Trial Comparing Standard Genetic Counseling versus Genetic Counseling with Personalized Cancer Risks Estimates in Patients with Li-Fraumeni Syndrome [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT2-13-01.

Family communication challenges of adolescents and young adults with Li-Fraumeni syndrome: Implications for psychosocial care

ObjectivesThis qualitative-descriptive study explored adolescent and young adult (AYA) perspectives, experiences, and challenges with openness and closedness in family communication about Li-Fraumeni syndrome (LFS). MethodsWe conducted interviews with AYAs (aged 15–39 years) with LFS enrolled in the National Cancer Institute’s LFS study (NCT01443468). An interprofessional clinician-researcher team analyzed transcribed data using the constant comparative method and interpretive description. ResultsAYAs (N = 38; 26 females, 12 males, mean age=29 years) reported navigating openness and closedness about LFS in their families, which varied by LFS topic, relationship, disease trajectory, and developmental phase. AYAs described communication challenges, including broaching difficult topics (e.g., reproductive decision-making, end-of-life), balancing information-sharing with emotionally protecting family and self, and struggling with interactions that cause relational tensions. ConclusionsAYAs reported experiencing LFS family communication challenges that disrupted their psychosocial well-being. LFS-related stressors and life transitions complicated and were complicated by these challenging family interactions. Practice implicationsClinicians may support AYAs with LFS by inquiring about family communication, responding empathically to communication concerns, providing resources to support difficult conversations, and engaging mental health providers as needed. Researchers could partner with AYAs to develop tailored communication skills training and social support tools.

Pancreatic Cancer with Mutation in BRCA1/2, MLH1, and APC Genes: Phenotype Correlation and Detection of a Novel Germline BRCA2 Mutation.

Pancreatic ductal adenocarcinoma (PDAC) is the seventh leading cause of cancer death worldwide; most of cases are sporadic, however about 5% to 10% report a hereditary predisposition. Several hereditary syndromes have been associated with familial pancreatic cancer (FPC) onset, including hereditary breast and ovarian cancer syndrome (HBOC), Lynch syndrome (LS), Familial atypical multiple mole melanoma (FAMMM), Familial adenomatous polyposis (FAP), Li–Fraumeni syndrome (LFS), Peutz–Jeghers syndrome (PJS), and Hereditary pancreatitis (HP).The aim of this study was to determine the mutational status of a cohort of 56 HBOC families, 7 LS families, 3 FAP and FAMMM families, and 1 LFS family with at least one case of PDAC. Mutation analysis of BRCA1/2, ATM, CHEK2, PALB2, RAD51C, RAD51D, NBN, CDH1, TP53, MLH1, MSH2, MSH6, and PMS2 genes, showedmutation in BRCA1/2, MLH1, and APC genes. We founda high mutation rate in patients belong HBOC and LS families, with a percentage of 28.6% in both syndromes and prevalence in HBOC of BRCA2 mutations with one case of double mutation in BRCA2 gene. In FAP family, we found a pathogenic mutation in APC gene in 1/3 families. We observed an early onset of PDAC and a lower survival in PDAC patients belonging to mutated families, while no evidence of possible pancreatic cancer cluster regions was found. Moreover, we identified a novel BRCA2 germline mutation, c.5511delT (p.Phe1837LeufsX3), not reported in any database, that segregated with disease in HBOC patients. Mutational analysis was extended to family membersof mutated patients, both healthy and cancer affected, which revealed 23 unaffected family members that inherited the proband’s mutation. Although correlative by its nature, the presence of a BRCA mutation in PDAC patients may have benefits in terms of optimized treatment and longer outcome.

Identification and characterization of de novo TP53 mutation carriers in Li-Fraumeni syndrome families: A single institution experience.

10538 Background: Li-Fraumeni syndrome (LFS) is an inherited cancer syndrome mainly caused by a deleterious mutation in TP53. An estimated 48% of LFS patients present due to a deleterious de novo mutation (DNM) in TP53. The knowledge of DNM status, DNM or familial mutation (FM), of an LFS patient requires genetic testing of both parents which is often inaccessible, making de novo LFS patients an understudied population. Famdenovo.TP53 is a Mendelian Risk prediction model used to predict DNM status of TP53 mutation carriers based on the cancer-family history and several input genetic parameters, including disease-gene penetrance. The good predictive performance of Famdenovo.TP53 was demonstrated using data collected from four historical US cohorts. We hypothesize that by incorporating penetrance estimates that are specific for different types of cancers diagnosed in family members, we can develop a model with further improved calibration, accuracy and prediction. Methods: We present Famdenovo.CS, which uses cancer-specific penetrance estimates that were derived previously using a Bayesian semi-parametric competing risk model, to calculate the DNM probability. We use our model to analyze 101 families recently collected from the Clinical Cancer Genetic program at MD Anderson Cancer Center (CCG-TP53) that includes 20 families with known DNM status and 81 families with unknown DNM status. We used the concordance index (AUC), observed:expected ratios (OE) and Brier score (BS) to measure our model’s discrimination, calibration and accuracy, respectively. We estimate the proportion of probands that present a DNM and compare DNM to FM carriers in several areas including: cancer types diagnosed, age at diagnosis, number of primary cancers diagnosed, sex, amino acid change caused by mutation in TP53. Results: Famdenovo.CS showed equally good discrimination and calibration performance to Famdenovo.TP53, while improving the overall accuracy, demonstrated by a decrease in the Brier score of -0.09 (95% CI: [-0.02, -0.19]). Of the 101 probands in the CCG-TP53 cohort, we predict 39 to be DNMs and 62 to be FMs. The cancer types and ages of diagnosis observed in FMs and DNMs are similarly distributed. Conclusions: Famdenovo.CS shows improved model accuracy in the CCG cohort. DNMs in TP53 are a prevalent cause of LFS and we did not find differences in the clinical characteristics of DNM and FM carriers. Our model allows for a systematic identification and characterization of TP53 DNM carriers.

Abstract 2036: The Bull's Eye: A research tool to characterize family, friends and social networks within a Li-Fraumeni Syndrome family

Abstract Background:Li-Fraumeni Syndrome (LFS) is a rare autosomal dominant cancer predisposition syndrome associated with early age of onset and high lifetime risk of multiple malignancies. Pathogenic germline variants (PV) in TP53 cause ~70% of LFS. Our prior work using the Colored Eco-Genetic Relationship Map found that non-bloodline relationships (i.e., spouses or friends) provide significant support to individuals with LFS. The Bull's Eye (BE) is a simplified tool to capture the types and degree of support obtained from family members (FMs) and social networks. We report on pilot BE data from a large family with LFS. Methods: Guided by investigators, patients in NCI's longitudinal LFS cohort (ClinicalTrials.gov Identifier: NCT01443468) independently completed a BE during annual screening visits. This tool is comprised of four concentric circles, with the innermost signifying the patient and outer circles indicating increasingly limited support. Individuals identified on the BE were coded 0-8 to indicate proximity to the patient. Independent sample T-tests and a linear regression were used in analyses. Results: Fifteen FMs from 1 family participated, including 10 TP53 PV carriers, 4 spouses of carriers, and 1 untested FM. The 7 males and 8 females ranged from 14-56 years of age (Median = 29). No significant association was detected between gender and number of FMs reported. Women cited significantly more non-family members (NFMs) than did men (Mean [M] = 7.6 ± 4.1 and M = 3.1 ± 2.4, respectively; p = 0.02.). There was no significant association between participant PV status and number of FMs reported. Spouses cited significantly more NFMs than did TP53 PV carriers (M = 8.8 ± 2.5 and M = 4.0 ± 3.9, respectively; p = 0.04). We assessed the relationship between gender, PV status and number of NFMs identified. The overall model explained a significant amount of variance in number of NFMs reported (r2 = 0.46; p = 0.02), driven by female gender and spouses of PV carriers. Gender independently contributed significantly to the model (B = 3.88, p = 0.04) while PV status did not (B = 0.03, p = 0.13). Conclusion: The BE is a practical and efficient tool to evaluate support in this LFS kindred. Women in this family had larger social networks than men, particularly through NFM relationships. In contrast, men primarily received support from close kin (i.e., siblings). Notably, spouses reported larger NFM networks than did TP53 PV carriers, seeking emotional support from friends, coworkers, and church groups. It is possible that PV carriers may be more comfortable sharing their LFS-related life experiences with FMs. Additional research with larger samples will clarify relative impacts of gender and PV status. Future analyses will evaluate other NCI LFS families to determine if: 1) patterns hold, 2) differences exist based on cancer history, 3) generational differences exist, and 4) bi-directional responses differ between FMs. Citation Format: Radhika Srivastava, Renee Bremer, Jessica Bayer, Allison Werner-Lin, Megan Frone, Sharon Savage, Payal P. Khincha, Jennifer Loud. The Bull's Eye: A research tool to characterize family, friends and social networks within a Li-Fraumeni Syndrome family [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2036.

A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome.

De novo mutations (DNMs) are increasingly recognized as rare disease causal factors. Identifying DNM carriers will allow researchers to study the likely distinct molecular mechanisms of DNMs. We developed Famdenovo to predict DNM status (DNM or familial mutation [FM]) of deleterious autosomal dominant germline mutations for any syndrome. We introduce Famdenovo.TP53 for Li-Fraumeni syndrome (LFS) and analyze 324 LFS family pedigrees from four US cohorts: a validation set of 186 pedigrees and a discovery set of 138 pedigrees. The concordance index for Famdenovo.TP53 prediction was 0.95 (95% CI: [0.92, 0.98]). Forty individuals (95% CI: [30, 50]) were predicted as DNM carriers, increasing the total number from 42 to 82. We compared clinical and biological features of FM versus DNM carriers: (1) cancer and mutation spectra along with parental ages were similarly distributed; (2) ascertainment criteria like early-onset breast cancer (age 20–35 yr) provides a condition for an unbiased estimate of the DNM rate: 48% (23 DNMs vs. 25 FMs); and (3) hotspot mutation R248W was not observed in DNMs, although it was as prevalent as hotspot mutation R248Q in FMs. Furthermore, we introduce Famdenovo.BRCA for hereditary breast and ovarian cancer syndrome and apply it to a small set of family data from the Cancer Genetics Network. In summary, we introduce a novel statistical approach to systematically evaluate deleterious DNMs in inherited cancer syndromes. Our approach may serve as a foundation for future studies evaluating how new deleterious mutations can be established in the germline, such as those in TP53.

Abstract 2406: A general probabilistic algorithm to predict de novo mutations in familial diseases as demonstrated in Li-Fraumeni Syndrome

Abstract Purpose: Germline variants (mutations) occurring in the carrier but not in the carrier's parents are defined as de novo mutations (DNMs). DNMs have been increasingly recognized as causal factors for rare diseases. Given this important role, the ability to identify DNM carriers, scarcely distributed among all mutation carriers, will allow researchers to study the likely distinct molecular mechanisms of DNMs in these diseases. However, testing the mutation status of the parents is often impractical in retrospective studies due to lack of blood samples. Methods: To fill this need, using Li-Fraumeni syndrome (LFS) as a representative of a rare inherited syndrome, we developed a method called Famdenovo to predict the de novo status (de novo or familial) of germline mutations, such as in TP53. We have collected a total 324 LFS family pedigrees with confirmed TP53 germline mutations from four medical centers in the US, with 186 pedigrees having TP53 genetic testing results available in at least one full trio in the pedigree, serving as a validation set. We further apply Famdenovo to the remaining 138 families (discovery set) to identify individuals who may carry a de novo mutation in TP53. Results: In the validation set, the area under the ROC curve (AUC) of Famdenovo is 0.95 (95% CI: [0.92, 0.98]), suggesting excellent ability for discrimination, and the ratio of the observed to expected (OE) is 1.32 suggesting good concordance. In the discovery set, we predict that an additional 40 individuals (95% CI: [30, 50]) are DNM carriers, which increases the total number of DNM carriers to 82. The corresponding predicted DNM rate is 28.9%, also consistent with what is observed in the validation set. Across the validation and discovery sets, we observed similar distributions of ages-of-onset for DNM carriers at specific cancer sites: breast, brain, leukemia, osteosarcoma, soft tissue sarcoma, lung, and adrenal cortical carcinoma. Interestingly, Lung cancer only occurred in female DNM carriers. Among TP53 hotspot mutations, R248Q is most enriched in DNMs. Conclusions: Our new statistical method Famdenovo provides the probability of a person carrying a de novo germline mutation in rare inherited syndromes when the mutation status of both parents is not available. Famdenovo is freely available as an R package from http://bioinformatics.mdanderson.org/main/Famdenovo. The LFS family cohorts not only served as a validation set for the accuracy of Famdenovo in predicting DNMs, but also benefited from using Famdenovo to discover additional individuals carrying DNMs in TP53. The computer-based identification of DNM carriers in TP53, who are otherwise hidden in a wide population, enabled epidemiological interpretation of the cancer outcomes for DNM carriers. Famdenovo is a general tool and can be applied to other cancer genes where there is a good understanding of the penetrance of the associated disease phenotype. Citation Format: Xuedong Pan, Fan Gao, Elissa B. Dodd, Jasmina Bojadzieva, Phuong L. Mai, Valen E. Johnson, Kristin Zelley, Kim E. Nichols, Judy E. Garber, Sharon A. Savage, Louise C. Strong, Wenyi Wang. A general probabilistic algorithm to predict de novo mutations in familial diseases as demonstrated in Li-Fraumeni Syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2406.

Couples coping with screening burden and diagnostic uncertainty in Li-Fraumeni syndrome: Connection versus independence

Purpose: Li-Fraumeni Syndrome (LFS) is an inherited tumor predisposition syndrome with lifetime cancer risks approaching 100% and evolving risk-management strategies. This study evaluated couples’ coping with LFS-related burdens.Research approach: Constructivist grounded theory and anticipatory loss frameworks guided design and analysis.Sample and methods: Twenty-six individuals enrolled in the NCI LFS Family Study completed semi-structured interviews with their partner during annual screening visits. An interdisciplinary team completed open and focused coding to identify patterns of coping and adaptation.Findings: Couples described living with ambiguous danger, a state of chronic apprehension resulting from LFS-associated uncertainties. Most couples communicated openly and alternated shouldering the burden, while others engaged in protective buffering to shield each other from distress and sustain the appearance of normalcy.Interpretation: Optimally, coping reduces shared psychosocial distress, yet some strategies may inadvertently increase disconnection.Implications: Mental health support is critical for both partners coping with LFS, together and separately.

1732P - Descriptive analysis of families with TP53 mutations: Is there a genotype/phenotype correlation?

Background: Li-Fraumeni syndrome (LFS) is a rare and serious hereditary cancer syndrome caused by germline mutations in the TP53 gene. Our objective is to review the molecular and clinical characteristics of our LFS families. Methods: Retrospective descriptive analysis. Molecular germinal diagnosis was done either by Sanger or NG Sequencing (Trusight Cancer, Illumina); Large Genomic rearrangements were tested by MLPA (MRC Holland). Results: Among 4952 non-related families registered in our multidisciplinary program, 395 are BRCA1/2 families and 36 haver other molecular diagnoses with 7/36 confirmed TP53 families. Twenty-nine pts were reviewed, including 2 male carriers, (36, 40 years) that haven’t developed cancers yet. Forty-one tumours were registered (median of 1,41 tumours/carrier, 0–4). Female/male was 2:1. Median age for the first tumour was 24 years (1-45) in the index cases and 35 (1,5-61) in relatives (p > 0,05). Breast cancer (BC) (34% of cancers/48% pts) and sarcomas (31% of cancers/44% pts) were the most common malignancies. For BC cases hormone receptor status was confirmed in 8/14 (positive in 6/8, simultaneous HER2 positivity in 2 cases). Median age of death was 40 (34-58). Most mutations were missense (5 - 2 dominant-negative affecting the DNA binding domain: c.743G>A, p.R248Q and c.725G>A, p.C242Y), none was recurrent and the only frequent mutation observed was c.743G>A, p.R248Q. One of the missense and the 2 frameshift mutations have never been described as germinal: c.481G>A, p.A161T; c.86del, p.N29Tfs*15 and c.990del, p.Q331Rfs*14 Chompret criteria were met in 6/7 (85%) of cases and didn't identitfy a breast cancer only family, with 3 consecutive generations affected. Conclusions: Our data confirms the heterogeneity and complexity of malignancies and mutations in LSF. Breast cancer and sarcomas were the most frequent cancers and missense, non-recurrent mutations were mostly observed. In this study c.481G>A, p.A161T; c.86del, p.N29Tfs*15 and c.990del, p.Q331Rfs*14 are, for the first time, identified as germinal mutations. At this time no genotype-to-phenotype correlation could be confirmed. Chompret’s criteria had only 85% sensitivity for the identification of TP53 families. Legal entity responsible for the study: Instituto Português de Oncologia de Lisboa Francisco Gentil Funding: None Disclosure: J.P. Silva: Travel grants for oncology Congresses: Bristol Meyers-Squibb. All other authors have declared no conflicts of interest.

Abstract NG05: TP53-mediated human cancer susceptibility is defined by epigenetic dysregulation of microRNA-34A

Abstract NG05: TP53-mediated human cancer susceptibility is defined by epigenetic dysregulation of microRNA-34A

Abstract 973: Methylation accurately predicts age of cancer onset in patients with Li Fraumeni Syndrome

Abstract Introduction: Li Fraumeni Syndrome (LFS) is a rare hereditary genetic cancer predisposition syndrome. Germline mutations of the TP53 tumor suppressor gene are the underlying cause in >80% of patients with LFS, and are associated with an increased risk of second tumors and a spectrum of early onset cancers, even in the absence of a family history of cancer. We have previously developed and implemented a comprehensive life-long clinical surveillance protocol for individuals with a germline TP53 mutation. We set out to make this screening process more targeted by building a predictive model of age of onset. We accomplished this goal by implementing machine learning methods on germline methylation data. Methods: We made use of the Toronto Hospital for Sick Children (SickKids) LFS family cohort in our predictive model of age of onset. In all, we have 74 patients with germline methylation data, consisting of ~450,000 probe sites. We subset this data by identifying probes that fall into differentially methylated regions between LFS and cancer patients with wild-type TP53. The probes identified in these regions were used in our predictive model of age of onset. Because age of sample collection was highly correlated with age of onset (r2 ~ .90), we corrected for confounding using a strategy that is two-fold: (1) we extracted the variation of each probe that is independent of the age of sample collection (the residual after regressing on the age of sample collection) and use these as predictors in our model, and (2) we test our models on the task of predicting the age of sample collection for LFS patients that do not have cancer. The former provided us with more robust predictions while the latter verified that we are in fact predicting age of onset, rather than simply predicting age at which the sample was collected. Results: Our machine learning model was able to achieve 86% correlation between true and predicted values of the age of onset. Additionally, we have tested the ability of our models to predict whether an individual will be diagnosed before or after the age of 4. Our classification machine learning model achieved 91% accuracy on average. We verified that our model does not simply predict age of sample collection by using our cohort of LFS patients that do not have cancer (n = 37). The distribution of the age of sample collection matched those of the patients used in our model. The model has no predictive power on the age of sample collection, thus confirming that our model is highly predictive of the age of cancer onset in LFS TP53 Mutation patients. Conclusions: We identified two predictive models for age of cancer onset in LFS patients that achieve high accuracy, both when predicting the age of onset as a continuous variable (86% correlation) and whether cancer onset will occur before or after the age of 4 (91% accuracy). Our model will assist clinicians in targeting high risk patients for screening, lower the cost of treatment, and raise the likelihood of survival among LFS patients. Citation Format: Benjamin M. Brew, David Malkin, Lauren Erdman, Andrea Doria, Jason Berman, Adam Shlien, Tanya Guha, Ana Novokmet, Anna Goldenberg. Methylation accurately predicts age of cancer onset in patients with Li Fraumeni Syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 973. doi:10.1158/1538-7445.AM2017-973

Inherited TP53 Mutations and the Li-Fraumeni Syndrome.

Li-Fraumeni syndrome (LFS) is a complex hereditary cancer predisposition disorder associated with early-onset cancers in diverse tissues of origin. Germline TP53 mutations are identified in 75% of patients with classic LFS. The lifetime likelihood of a TP53 mutation carrier developing cancer approaches 75% in males and almost 100% in females. Several genetic modifiers have been implicated to account for the phenotypic variability within and across LFS families; however, efforts to develop predictive algorithms of age of onset and type of cancers in individual patients have not yet found clinical use. Although it is not possible to prevent cancers from forming in LFS patients, novel protocols have been developed for surveillance for early tumor detection, leading to improvements in survival. Comprehensive studies of the genome and epigenome in LFS families in the context of germline TP53 mutations is anticipated to shed light on this intriguing, yet devastating, disease and to transform the clinical management of patients.

The effect of epigenetic silencing and TP53 mutation on the expression of DLL4 in human cancer stem disorder.

The Li-Fraumeni Syndrome (LFS), a genetically rare heterogeneous cancer syndrome, is characterized primarily by a germline p53 (TP53) gene mutation. We recently discovered a balanced reciprocal chromosomal translocation t(11;15)(q23;q15) in the non-cancerous skin fibroblasts of a bilateral breast cancer patient in LFS family. This prompted us to investigate the breakpoint region of the translocation, which uncovered a gene that encodes a Notch ligand, DLL4, (locus at 15q15.1), a key target in tumor vasculature. We analyzed DLL4 gene expression and protein level in LFS non-cancerous skin fibroblast cell lines and non-LFS cancer cell lines. DLL4 is abrogated in all the LFS cells and drastically down-regulated in breast (MCF7) and brain (IMR32) cancer cells and tumor tissue samples. However, DNA methylation studies revealed that DLL4 promoter is silenced only in MCF7 but not in LFS cells. We further investigated the regulation of DLL4 gene expression by ChIP assays, which demonstrated that p53 binds to DLL4 promoter through its association with CTCF, a chromosomal networking protein CCCTC binding factor. This implies a possible karyotype-phenotype correlation with respect to DLL4 in LFS and breast cancer initiation and progression. The drastic reduction or absence in the expression of DLL4 in LFS as well as breast and brain cancer cells is significant and supports the concept that this ligand may also play a role in cancer immune-surveillance; and its resuscitation in the tumor microenvironment may stimulate T-cell immunity and suppress tumor growth. Therefore, DLL4 may provide a strong platform as an immuno-therapeutic target in LFS and cancer patients.

Abstract 3473: Psychosocial functioning in research participants at enrollment in a Li-Fraumeni syndrome study

Abstract Background: Li Fraumeni Syndrome (LFS) is an autosomal dominant cancer predisposition syndrome in which about 90% of individuals develop cancer by age 60. Approximately 70% of individuals with LFS have germline TP53 mutation. We hypothesized that this high level of cancer risk may be associated with increased emotional distress, cancer risk perceptions and cancer worry in individuals from LFS families. Methods: Data from 276 adult (≥18 years old) TP53 mutation carriers (TP53+), mutation negative (TP53-) and untested (UT) participants enrolled in an IRB-approved study at the Clinical Genetics Branch, NCI were obtained between January 2011 and June 2014.. Using questionnaires at baseline, we assessed emotional distress (global distress, somatization, anxiety and depression) as measured by the BSI-18, cancer risk perceptions (comparative: scores 1-5; 1 = much less than other people your age to 5 = much more than other people your age and absolute: 10-point scale; 1 = no chance; 5 = may or may not; 10 = almost certainly) and cancer worry scales (frequency of cancer thoughts, interference with mood and daily activity, scores 1-4; = not at all or rarely to 4 = several times a day). Results: TP53+ estimated their comparative lifetime risk of cancer as higher than TP53- and UT; [4.9 (SD = 0.5) vs. 3.8 (SD = 1) and 3.2 (SD = 1.3) p<0.01], respectively]. TP53+ also estimated their absolute cancer risk as significantly higher than TP53- and UT on a [8.6(SD = 1.5) vs. 6.3 (SD = 1.6) and 5.7 (SD = 2.1), p<0.01].Cancer worry was higher in TP53+ than TP53-or UT. TP53+ also indicated they thought about their cancer risk more frequently thanTP53- and UT [2.3 (SD = 0.9) vs. 1.3 (0.6) and 1.3 (SD = 0.6), p<0.01]. There was a small but statistically significant difference between TP53+, TP53- and UT in their appraisal of whether cancer worry affected their mood over the past month [1.6 (SD = 0.6) vs. 1.2 (SD = 0.6) and 1.1 (SD = 0.2), p = <0.01] and whether thoughts of cancer affected their ability to perform daily activities [1.2 (SD = 0) vs. 1.1 (SD = 0.4) and 1 (SD = 0.2), p = <0.01]. No statistically significant differences were observed on measures of emotional distress between TP53+, TP53- or UT somatization [46.7 (SD = 8.1) vs. 45.9 (SD = 9.3) and 45.9 (SD = 7.6); depression [50.1 (SD 9.7) vs. 49.6 (SD - 9.3) and 45.9 (SD = 7.6); anxiety [48.2 (SD = 9.1) vs. 45.4 (SD = 9.7) and 45.8 (SD = 7.9) or global distress [47.9(SD = 9.9); vs. 45.1(12.1) and 44.9 (SD = 9.5)]. Conclusions: Participants in the LFSS do not demonstrate high levels of emotional distress. TP53+ appropriately identify their comparative and absolute cancer risk as high, but have levels of cancer worry that appears to be only slightly affecting their mood or ability to perform daily activities. Future research will focus on longitudinal changes in risk perception, cancer worry and emotional well-being while enrolled in a cancer screening study. Citation Format: Jennifer T. Loud, Renee C. Bremer, Rosamma Decastro, June A. Peters, Phuong L. Mai, Sharon A. Savage. Psychosocial functioning in research participants at enrollment in a Li-Fraumeni syndrome study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3473.

Abstract 3698: The effect of epigenetic silencing and p53 mutation on DLL4 expression in human cancer stem cell disorder: The Li-Fraumeni syndrome

Abstract Tumorigenesis results from an accumulation of mutational and epigenetic changes that alter normal cell growth and survival pathways. Li-Fraumeni syndrome (LFS) is a clinically and genetically heterogeneous inherited cancer syndrome that can provide powerful insights into our understanding of the somatic mutations present in sporadic cancers. LFS is currently linked to heterozygous mutation in the tumor suppressor gene p53 (TP53), which encodes a transcription factor that responds to diverse cellular stresses through the regulation of target genes that induce apoptosis, cell cycle arrest, DNA repair, and senescence. We previously showed a balanced reciprocal chromosomal translocation t(11;15)(q23;q15) in the non-cancerous skin fibroblasts of a bilateral breast cancer patient in LFS family. This prompted us to investigate the breakpoint region of the translocation, which uncovered a gene that encodes DLL4, (Delta-like ligand 4; locus at 15q15.1), a Notch ligand that is a key target in tumor vasculature. DLL4 regulates T-cell lineage thymopoiesis and further affects cancer immunosurveillance. In the breakpoint region of chromosome 15q15, we examined THBS1, DNAJC17, Rad51, DLL4, CHAC1 and INO80 gene expression levels. We found that specifically DLL4 is abrogated in all the LFS cell lines as well as MDA231 breast cancer cell line, and drastically down-regulated in MCF7 breast and IMR32 brain cancer cell lines and several human organ-specific tumor samples. Furthermore, DNA methylation studies revealed that DLL4 promoter is silenced only in MCF7 and MDA231 but not in LFS cell lines. ChIP and siRNA knockdown assays demonstrated that p53 binds to DLL4 promoter through its association with CTCF, a chromosomal networking protein CCCTC binding factor. These results imply a possible karyotype-phenotype correlation with respect to DLL4 in LFS and breast cancer initiation and progression. The drastic reduction or absence in the expression of DLL4 in normal skin fibroblasts of LFS patients as well as breast and brain cancer cells is significant and supports the concept that this ligand may also play a role in cancer immune-surveillance; and its resuscitation in the tumor microenvironment may stimulate T-cell immunity and suppress tumor growth. Citation Format: Zhixing Yao, Zaki A. Sherif. The effect of epigenetic silencing and p53 mutation on DLL4 expression in human cancer stem cell disorder: The Li-Fraumeni syndrome. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3698.

Genetic and functional analysis of a Li Fraumeni syndrome family in China.

Li Fraumeni syndrome (LFS) is a rare familial cancer predisposition syndrome with autosomal-dominant inheritance, occurring as frequently as one in 5,000–20,000 individuals. However, no LFS case has been reported from mainland China although it constitutes one quarter of population on earth. In this study, we identified, to our best knowledge, the first Li Fraumeni syndrome family in China. Six family members were affected with various tumors. A TP53 mutation (c.730G > A; p.G244S) co-segregated with the tumor phenotype within this family. Functional analysis indicated that G244S mutation disrupted the transactivity, DNA-binding and cell growth inhibition activity of p53 protein. Two available tumor samples (medulloblastoma and choroid plexus papilloma) underwent large rearrangement in the chromosomes and loss of wild-type TP53. Our data warranted further studies on the prevalence of germline TP53 mutation in various tumor patients in China.