Germline TP53 Mutations Research Articles

In search of TP53 mutational hot spots for Li‐Fraumeni syndrome in Asian populations

Germline mutations of the TP53 tumour suppressor gene are the only known cause of the hereditary autosomal disorder called Li-Fraumeni syndrome (LFS). However, little information is available about TP53 pathogenic variants in Asian LFS patients, making it difficult to provide precise genetic counselling with regard to long-term cancer risk. We conducted a systematic review to gather relevant case-control studies exploring the association between TP53 polymorphisms and the incidence of cancer belonging to the LFS spectrum in Asian populations. Systematic review and meta-analysis. The odds ratio was used as a summary effect measure to quantify the strength of the association between TP53 polymorphisms and cancer risk by means of random-effects meta-analysis. In total, 16 studies were included in this systematic review, with 13 studies (involving 10,645 cases and 28,288 controls) that enabled meta-analysis. The majority of the studies focused on a single-nucleotide variation at codon 72 in exon 4 (c.215C>G, p.Arg72Pro, rs1042522). Therefore, we tested either dominant, co-dominant, recessive, or heterozygous models and found that the p.Arg72Pro was not significantly associated with increased cancer risk in any of the models. We found the number of studies on cancers belonging to the LFS spectrum in Asia is very small. Thus, at the present time a meta-analysis approach is somewhat useful to identify germline TP53 mutations as potential markers of hereditary cancer associated with LFS in Asian populations.

Choroid Plexus Carcinomas With TP53 Germline Mutations: Management and Outcome.

BackgroundChoroid plexus carcinomas (CPCs) are rare pediatric tumors commonly associated with Li-Fraumeni syndrome (LFS), which involves a germline mutation of the tumor suppressor gene TP53.Materials and MethodsWe retrospectively analyzed the corresponding information of 12 cases, including the effects of surgery and radiotherapy and TP53 germline mutations, to analyse the management strategies. Kaplan-Meier curves and the log-rank test were used to evaluate the progression-free survival (PFS).ResultsTwelve CPC patients were included, of which TP53 germline mutations were found in eight cases. All patients underwent surgical resection, and six patients received radiotherapy following with operation after initial diagnosis, one patient received radiotherapy following relapse. It was significantly different (P=0.012 and 0.028) that patients with TP53 germline mutation receiving the gross total resection (GTR) without radiotherapy showed survival advantages. Without TP53 germline mutations also showed survival advantages, but there is no statistical significance (P=0.063)ConclusionsThese findings provide evidence for the therapeutic strategy that radiotherapy should not be considered for patients with TP53 germline mutations.

1539P Sarcomas in the Dutch LFS population: Data from the national screening of TP53 germline mutation carriers at the Netherlands Cancer Institute

Li-Fraumeni syndrome (LFS) is a rare, autosomal dominant cancer predisposition syndrome, associated with germline mutations in the TP53 gene and a variety of histologically different tumours, of which early-onset breast cancer, sarcomas and brain tumours tend to occur most frequently. In this study, we report on sarcoma incidence in the LFS population in the Netherlands, based on data of the Netherlands Cancer Institute (NCI), the national referral centre for LFS.

Clinical utility of targeted next-generation sequencing for the diagnosis of myeloid neoplasms with germline predisposition.

Myeloid neoplasms (MN) with germline predisposition (MNGP) are likely to be more common than currently appreciated. Many of the genes involved in MNGP are also recurrently mutated in sporadic MN. Therefore, routine analysis of gene panels by next‐generation sequencing provides an effective approach to detect germline variants with clinical significance in patients with hematological malignancies. Gene panel sequencing was performed in 88 consecutive and five nonconsecutive patients with MN diagnosis. Disease‐causing germline mutations in CEBPα, ASXL1, TP53, MPL, GATA2, DDX41, and ETV6 genes were identified in nine patients. Six out of the nine patients with germline variants had a strong family history. These patients presented great heterogeneity in the age of diagnosis and phenotypic characteristics. In our study, there were families in which all the affected members presented the same subtype of disease, whereas members of other families presented various disease phenotypes. This intrafamiliar heterogeneity suggests that the acquisition of particular somatic variants may drive the evolution of the disease. This approach enabled high‐throughput detection of MNGP in patients with MN diagnosis, which is of great relevance for both the patients themselves and the asymptomatic mutation carriers within the family. It is crucial to make a proper diagnosis of these patients to provide them with the most suitable treatment, follow‐up, and genetic counseling.

Abstract 886: Prediction of outcome in Li-Fraumeni Syndrome: Development of an integrative function-based prognostic model

Abstract Li-Fraumeni Syndrome (LFS) is a highly penetrant familial cancer disorder caused by germline TP53 mutations. Hundreds of different germline TP53 mutations with a wide gradient of functional consequences have been found in association with LFS, which has a remarkably diverse clinical spectrum in terms of tumor type, age of onset, penetrance, and survival rates. Clinical tools for prognostication and risk stratification are needed to guide clinical decision making. We performed an integrated analysis combining five large-scale mutant p53 functional screens to identify three functionally distinct groups of mutations. Combined functional scores measuring multiple parameters (loss-of-function, dominant negative activity, growth inhibition, oligomeric status, and transcriptional activity) were used to classify mutations as high, intermediate, or low pathogenicity. Patients identified with germline TP53 mutations at The Hospital for Sick Children and other institutes (174 patients from 50 families) provided the discovery set. An external validation cohort included 1674 patients from 1522 families with germline TP53 mutations collected from the International Agency for Research on Cancer database. Our mutation classifications stratified carriers into three distinct risk groups with significantly different overall survival outcomes in the discovery (P=0.02) and validation cohorts (P<0.0001). In the discovery dataset, patients in the high-risk group had considerably shorter median life expectancy (28 years; n=21) compared to the intermediate-risk group (61 years; n=51) and low-risk group (median survival not reached; n=10). On average, 92% (24/26) of patients in the high-risk group developed tumors compared to only 63% (32/51) in the low-risk group (P=0.005). This model remained significant when applied to the validation cohort. In conclusion, patients at increased risk of cancer mortality can be identified to guide treatment and cancer surveillance strategies. Citation Format: Nicholas Fischer, David Malkin. Prediction of outcome in Li-Fraumeni Syndrome: Development of an integrative function-based prognostic model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 886.

Abstract 2689: Investigating the molecular mechanisms linking disrupted growth homeostasis to tumourigenesis in Li-Fraumeni Syndrome

Abstract Li-Fraumeni Syndrome (LFS) is a highly penetrant cancer predisposition syndrome caused by germline TP53 mutations. Patients face an increased lifetime risk to develop a broad spectrum of cancers. Implementation of comprehensive cancer screening protocols has led to improvements in survival for LFS patients. However, these interventions pose a significant burden to both patient quality of life and health resource utilization. While these interventions will always be important, recent evidence has suggested an additional approach which may improve patient outcomes: pharmacological prevention of cancer onset. mTORC1 inhibition selectively targets tumor initiation. While rapamycin, an mTORC1 inhibitor, has not shown efficacy in treatment of established cancers, it is reported to prevent tumor onset in mice that are genetically predisposed to cancer, including mouse models of LFS. mTORC1 is associated with protein synthesis and cellular growth. Hyperactivated cellular growth is associated with gain-of-function (GOF) TP53 mutations that underlie many cases of LFS. Wild-type p53 (wtp53) inhibits mTORC1 and, as a consequence, biosynthesis. We have shown that mutant p53 with oncogenic GOF (mutp53) may promote the opposite effect. Under conditions of inappropriately elevated protein synthesis, as is seen in cancer, stress responses, such as the unfolded protein response (UPR), are activated. UPR activation contributes to the secretion of pro-tumorigenic cytokines. We hypothesized that under conditions of elevated protein synthesis, mutp53 engages in a feedforward activation of biosynthesis which hyperactivates UPR-mediated secretion of pro-tumorigenic cytokines. In order to harness the cancer risk reduction potential of mTORC1 inhibition, we undertook investigation of the stress responses which may underlie tumorigenesis in LFS. We sought to establish whether mTORC1 ablation in the tumor microenvironment could influence growth of tumor xenografts formed from the co-injection of LFS patient-derived mutp53 fibroblasts and RH4 rhabdomyosarcoma cells, a representative LFS spectrum cancer cell line. While both wtp53 fibroblasts and mutp53 fibroblasts supported tumor growth, only the tumor growth reinforced by mutp53 fibroblasts was suppressed by rapamycin. Additionally, we utilized protein arrays to profile conditioned media collected from mutp53 and wtp53 fibroblast cultures. Mutp53 fibroblasts secreted higher levels of various pro-tumorigenic cytokines compared to wtp53 fibroblasts, which was partially negated by rapamycin. UPR target gene expression is elevated in fibroblasts expressing mutp53, and this effect is negated by rapamycin. Altogether, our work supports a role for mutp53-driven, mTORC1-mediated hyperactivated protein biosynthesis and subsequent engagement of the UPR, resulting in production of a pro-tumorigenic secretory milieu. Citation Format: Camilla Giovino, Frank Telfer, Nish Patel, Sangeetha Paramathas, Ran Kafri, David Malkin. Investigating the molecular mechanisms linking disrupted growth homeostasis to tumourigenesis in Li-Fraumeni Syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2689.

Abstract 810: Enrichment and screening of LFS patients by analyzing TP53 germline mutations of a Chinese cancer cohort

Abstract Background: Li-Fraumeni syndrome (LFS) is a rare autosomal dominant inherited cancer syndrome; clinical diagnosis of it is mainly based on familial and personal history of cancer. Currently, most clinicians are lack of knowledge and experience of this rare disease, resulting in a difficulty to identify it. Consider that this is a rare tumor-type syndrome and 60-80% of the patients have germline variants of TP53, herein, we analyzed germline pathogenic/likely pathogenic (P/LP) TP53 variants in a Chinese tumor cohort with unknown familial history, and successfully established an analysis process to better screen for LFS patients. Methods: We retrospectively analyzed the germline TP53 mutations of a total of 19,226 Chinese tumor patients with unknown familial history. The screening process of LFS patients was as follows: 1) Germline P/LP TP53 variants must satisfy P/LP in any of the three databases: UMD_TP53, ClinVar or HGMD. It also must be defined as “non-functional” mutations in IARC database which includes all TP53 germline mutations of clinically determined LFS patients; 2) Follow up the familial and personal histories of patients with germline P/LP TP53 variants. Results: After screening, 26 germline P/LP TP53 variants were obtained, which involved 54 patients, mainly in brain cancer (34 pts) and lung cancer (9 pts). The median age of these 34 brain cancer patients was younger than that of 5,845 brain cancer patients in the cohort (28 vs. 44 year-old). Yet no such phenomenon was observed in lung cancer. It is necessary for young brain cancer patients to detect germline TP53 mutations. We then analyzed the relationship between germline P/LP TP53 variants and LFS in the 54 patients. According to the Chompret criterion of LFS, two patients who respectively had adrenocortical carcinoma (R175H of TP53) and choroid plexus carcinoma (G245S) were both LFS patients regardless of whether they had a familial history. We finally obtained follow-up information of 17 patients. Among them, four brain cancer patients (R248Q/R158H/C238Y/M237I), one lung cancer patient (R175H) and one leiomyosarcoma patient (R213Q) had family members who had cancers before 46-year-old. Another brain cancer patient (G245S; 1/17) had more than one cancer before 46-years-old. Hence, these seven patients (7/17; 41.18%) were also defined as LFS patients by the Chompret criterion. In total, 9 patients had LFS. It shows a high positive detection rate in our cohort by our analysis process. Conclusions: We have established an analysis process based on germline P/LP TP53 variants, which can efficiently screen for LFS patients in clinic. Citation Format: Changyu Lu, Yu Fang, Fachen Zhou, Yuntong Liu, Hongchuan Niu, Kai Li, Tonghui Ma, Xiaoyan Zhang. Enrichment and screening of LFS patients by analyzing TP53 germline mutations of a Chinese cancer cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 810.

Abstract 92: Clonal evolution of proliferative lesions into breast cancers

Abstract Introduction: Proliferative lesions in the breast have been implicated in the development of invasive breast cancer. Previous studies showed that adjacent atypical proliferative lesions and breast cancers shared common genetic alterations, suggesting that these evolved from the same ancestral cell. However, the clonal structure of atypical proliferative lesions and their clonal dynamics during progression to cancer are poorly understood. In this study, we compared genetic profiles of proliferative lesions and cancers from the same patients to illustrate the clonal evolution of cancer from a non-malignant epithelial cell. Methods: Multiple samples were collected from various lesions with different disease-level located in the cancer-borne breast, using micro-dissection from formalin-fixed, paraffin-embedded surgical specimens. Somatic mutations and copy number alterations (CNAs) were evaluated by whole exome sequencing. Results: A total of 39 samples from 7 premenopausal females carrying estrogen receptor-positive cancers were analyzed, where the samples were obtained from proliferative lesions (without/with atypia) (N = 3 and 10, respectively), and non-invasive (N = 22) and invasive (N = 4) cancers. The number of somatic mutations per sample increased with disease progression (ranging from 7 to 311). Two cases with bilateral cancers had a pathogenic germline mutation of either BRCA2 or TP53, where no somatic mutations or CNAs were shared by individual proliferative lesions, suggesting multifocal independent cancerous evolutions. By contrast, in the remaining five unilateral cases, no pathogenic germline mutations were detected, but all proliferative lesions, which were separated by a distance of 7 - 70 mm, shared one or more driver alterations, such as an AKT1 mutation, a GATA3 mutation, a CBFB mutation, a PTEN mutation and concurrent 1q gain and 16q loss, while harboring private mutations/CNAs of their own. The analysis of phylogenic trees based on the number of shared mutations predicted an early origin of these founder mutations, which frequently predated decades before the onset of cancer. Conclusions: Our results suggest that early breast cancer development is shaped by the evolution of multiple precancerous clones. In hereditary cases, this process is thought to be substantially promoted multi-focally within the entire breasts, due to innate genomic instability in each mammary epithelial cell for pathogenic germline mutations. By contrast, in sporadic cases, the ancestral cell which has acquired a founder genetic alteration expands macroscopically long before the onset of cancer. These expanded clones work as the niche predisposed to additional mutations, in which branching evolution occurs multi-focally and raises up multiple proliferative lesions, from which invasive cancer finally evolves. Our findings provide unique insight into the early development of breast cancer. Citation Format: Tomomi Nishimura, Nobuyuki Kakiuchi, Kenichi Yoshida, Yasuhide Takeuchi, Hirona Maeda, Yusuke Shiozawa, Masahiro M. Nakagawa, Yotaro Ochi, Yukiko Kawata, Kosuke Aoki, Masahiro Hirata, Tatsuki R. Kataoka, Takaki Sakurai, Satoko Baba, Yuichi Shiraishi, Kenichi Chiba, Kengo Takeuchi, Hironori Haga, Satoru Miyano, Masakazu Toi, Seishi Ogawa. Clonal evolution of proliferative lesions into breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 92.

Exceptional Responses to Epigenetic Based Therapy in Pediatric and Young Adult Monosomy 7 MDS/AML Patients with and without TP53 Mutations

▪Background: Children and young adults with relapsed/refractory or secondary acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) may not be candidates for conventional cytotoxic chemotherapy salvage regimens due to chemotherapy refractory disease or comorbidities. Hypomethylating agents including decitabine and azacitidine have favorable toxicities profiles and have demonstrated activity in adult AML/MDS. Favorable responses to decitabine have been associated with TP53 mutations in adult patients with AML/MDS (Welch et al., New England Journal of Medicine 2016) as well as elderly patients with high risk MDS and multiple autosomal monosomies (Lübbert et al., Annals of Hematology 2016). Pediatric data with hypomethylating agents are scarce due to lack of large prospective clinical trials. Previously, in a cohort of eight patients, we reported that decitabine therapy resulted in a complete response (CR) or complete response with incomplete count recovery (CRi) in 38% of patients, and at least a partial response in 75% of patients(Phillips et al., British Journal of Hematology 2013). However, prognostic factors for response are lacking in children and young adults.Methods: Data was collected using an IRB-approved retrospective chart review of any patient with MDS or AML who received epigenetic therapy with azacitidine or decitabine between 2012 and 2017 at a single center. Patients included received at least one course of hypomethylating agent and had response assessed by bone marrow evaluation.Patients received either decitabine at 20 mg/m2 IV for 10 days or azacitidine at 75mg/m2 IV for 7 days. Courses in which a hypomethylating agent was given in combination with vorinostat or sorafenib were also included.Results: 14 patients were treated with hypomethylating agents, with a median age of 8.5 years [range 2-34]; 10 of whom received concurrent vorinostat therapy. Previous therapy included an average of two prior regimens [range 1-3], with 46% having undergone hematopoietic stem cell transplant (HSCT). Genetic alterations included monosomy 7 (5/14 patients), as well as mutations in TP53 (2/14 germline, 1/14 somatic) and PTPN11 (1 somatic).CR/CRi was achieved in 4/14 patients, with partial response (PR) in 2/14 and stable disease (SD) in 3/14. In CR/CRi and PR patients, the best response was observed after a median of 1.5 cycles [range 1-4]. CR/CRi was achieved in 3/5 patients with monosomy 7 (2 CR/1 CRi); 2 of these patients had a germline TP53 mutation and secondary MDS/AML with monosomy 7. The third responding monosomy 7 AML patient had a somatic PTPN11 mutation, and was refractory to cytarabine and anthracyclines. This patient achieved CRi with azacitidine and sorafenib and remains alive 4 years following HSCT. The remaining 2 patients with monosomy 7 had stable disease over an average of three cycles of hypomethylating therapy. In contrast, of the 9 patients without monosomy 7, one patient achieved CR (11%), 2 others had a partial response, and one had stable disease. The single patient without monosomy 7 who achieved a CR had a normal karyotype but FISH detected loss of one copy of 16q22 (CBFB) and trisomy of 9q22. In the 3/14 patients with TP53 mutations, there were 2 CR/CRi and 1 SD. Overall, 3/14 patients (1 with monosomy 7) remain in CR two to four years post HSCT, after receiving hypomethylating therapy.Conclusions: Hypomethylating agent therapy demonstrates activity in a subset of children and young adults with relapsed/refractory MDS/AML with responses noted in 3 of 5 patients with monosomy 7, consistent with the published experience in adults.However, a clear conclusion on response pattern in pediatric patients with somatic TP53 mutations cannot be drawn, given this small sample size. This data warrants further investigation of response and resistance patterns in pediatric patients with relapsed/refractory AML/MDS. DisclosuresO'Brien:Celgene: Research Funding; Incyte: Research Funding; Pfizer: Research Funding; Amgen: Research Funding. Phillips:Novartis Pharmaceuticals Corporation: Membership on an entity's Board of Directors or advisory committees.

TP53 Germline Variations Influence the Predisposition and Prognosis of Acute Lymphoblastic Leukemia in Children

Germline TP53 mutations is the genetic basis of Li-Fraumeni syndrome (LFS), a highly penetrant cancer predisposition condition. Recent reports of germline TP53 variants in children with hypodiploid acute lymphoblastic leukemia (ALL) suggest that childhood leukemia is another manifestation of LFS. However, the pattern, prevalence, and clinical relevance of pathogenic variants in TP53 in childhood ALL remain unknown.To comprehensively characterize genetic variants in TP53 in childhood ALL, we performed targeted sequencing of TP53 coding regions in 3858 children from the Children's Oncology Group front-line ALL clinical trials (COG AALL0232 and P9900). In total, 49 different non-silent coding rare TP53 variants were identifiedin 77 (2.0%) patients sequenced, including 40 missense, 1 nonsense, 6 frameshift, and 2 inframe deletion variants. To determine which TP53 variants are potentially pathogenic and related to ALL risk, we examined their experimentally-validated p53 transcriptional activity, bioinformatically-predicted damaging effects on TP53 function, and also the variant frequency in non-ALL populations. Twenty-two TP53 variants were classified as ALL risk-related (VAR), including 7 protein-truncating and 15 missense variants, all of which were either absent or exceedingly rare in non-ALL populations (i.e., allele frequency < 0.006% in the ExAC dataset). Fourteen missense VAR reside in the p53 core DNA-binding domain, with two affecting residues essential for DNA contact and seven located at residues that are important for the overall architecture of the DNA-binding surface. The 27 remaining TP53 variants were classified as “variants of unknown significance” (VUS). Together, of 3858 children in this ALL cohort, 26 (0.67%) patients had a predicted VAR and 51 (1.3%) had a VUS in the TP53 gene.We next evaluated the association of germline TP53 variants with patient demographics and ALL tumor genetic characteristics. Children with a TP53 VAR were significantly older at diagnosis (P < 0.0001), and had significantly lower leukocyte count at presentation than those with a VUS or wild-type (WT) genotype (P= 0.006). Of 26 patients carrying a germline TP53 VAR, 17 (65.4%) exhibited hypodiploidy in ALL blasts (mostly low hypoploidy or masked hypoploidy). In contrast, hypodiploid ALL was only present in 3.9% and 1.2% of children with TP53 VUS or WT genotype, respectively. The prevalence of TP53 VAR did not differ by genetic ancestry (P= 0.9). We also examined the relationship between germline TP53 variants and treatment outcomes of ALL therapy. In the COG AALL0232 cohort, the presence of a TP53 VAR was associated with a significantly lower event free survival (EFS) and overall survival (OS) compared to patients without a risk variant (hazard ratio [HR] of 2.84, P= 0.0007 for EFS; and HR of 3.13, P= 0.003 for OS). In multivariate analyses, TP53 VAR remained prognostic after adjusting for ancestry, age, leukocyte count at diagnosis, and minimal residual disease at the end of remission induction therapy (HR of 3.36, P= 0.0002 for EFS; HR of 2.88, P= 0.007 for OS). Importantly, there was a markedly higher risk of second cancers among patients with TP53 VARs compared to those with TP53 VUS or WT TP53: 5-year cumulative incidence of 25.1% vs. 0.7%, P= 5.4 × 10-11. In the COG P9900 cohort, only 4 patients harbored TP53 VAR, of whom 3 cases experienced adverse events (one patient each with ALL relapse, second cancer, or death in remission), and both EFS and OS were significantly worse than patients with TP53 VUS or WT genotype (HR of 7.14, P= 0.0008 for EFS; HR of 14.19, P= 1.1 x 10-5 for OS). Taken together, 14 of 26 patients with a TP53 VAR experienced adverse events, with 5 ALL relapses (36% of all events) and 5 second cancers (36%). This pattern of adverse events was dramatically different from those in patients with WT TP53 or VUS, for whom ALL relapse accounted for 75% of all events with only 4% as second cancers (P= 1.2 × 10-7). In fact, even within hypodiploid ALL patients who experienced adverse events, the frequency of second cancer was significantly higher in those with a TP53 VAR than those without (50% vs 5%, P= 0.01), further suggesting that germline TP53 variation was the underlying cause of second cancers in these cases.In conclusion, our findings identified germline TP53 variants as an important determinant of ALL predisposition and adverse treatment outcomes, particularly the risk of second malignant neoplasms. DisclosuresBorowitz:Beckman Coulter: Honoraria; Becton-Dickinson Biosciences: Research Funding; HTG Molecular: Honoraria. Mullighan:Loxo Oncology: Research Funding; Amgen: Consultancy. Hunger:Jazz Pharmaceuticals: Honoraria; Novartis: Consultancy; Erytech Pharmaceuticals: Consultancy; Amgen: Consultancy, Equity Ownership.

Presence of Rare Germline Variants in Fanconi Anaemia Pathway Genes Confers a Poor Prognosis Comparable to TP53 Mutations in Therapy-Related Myeloid Neoplasms

Introduction: T-MN inclusive of therapy related myelodysplastic syndrome (T-MDS) and acute myeloid leukemia (T-AML) are aggressive neoplasms occurring after exposure to chemo (CT) and/or radiotherapy (RT) and are characterized by high frequency of complex cytogenetics and poor prognosis. TP53 and other genes involved in DNA repair such as Fanconi Anaemia(FANC) pathway are critical in maintaining genomic stability. TP53 mutations are associated with complex karyotype and poor prognosis in myeloid malignancies. Further, variants in the FANC pathway are a risk factor for malignancies, but remain less well studied in T-MN. Churpek et al . (Cancer 2016) reported germline mutations in BRCA1, BRCA2, TP53, CHEK2 and PALB2 in 8/43 (19%) treated breast cancer patients who developed T-MN. However, their interaction with TP53 mutations and impact on survival is unknown. Here we investigate the genomic architecture of T-MN patients from the South Australian Myelodysplastic Syndrome (SA-MDS) registry.Methods: Demographic, clinical and laboratory data including cytogenetic profile of 147 T-MN patients were analysed. Targeted Massively Parallel Sequencing of a custom panel of 63 genes (43 myeloid neoplasms associated genes & 20 FANC; all coding regions) was performed on diagnosis bone marrow samples from 101 T-MN samples. Rare FANC variants were selected based ExAC MAF <0.2% and variants only with VAL ≥20% were selected for further analysis. FANC variants were called deleterious if predicted to be deleterious by atleast two in-silico prediction model (e.g. CADD, SIFT, POLYPHEN and Mutation taster) and/or reported in COSMIC, gene specific databases or in literature.Results: Median age of T-MN was 71 (20-91) years and the most frequent primary neoplasms were lymphoproliferative neoplasms (n=56, 38%) and prostate cancer (n=22, 15%). Sixty-three (43%), 34 (23%) and 48(33%) patients received CT, RT and CT plus RT respectively. The T-MN group consisted of 104 T-MDS (71%) and 43 T-AML (29%). Poor risk cytogenetics were more frequent in T-MN cases following CT than after RT alone.Somatic mutations in myeloid genes were detected in 95/101 (94%) of T-MN cases. Notably, all normal karyotype T-MN (29/29, 100%) were mutated. Mutations were most frequently seen in transcriptional factors (35%), TP53 (32%) and splicing factors (26%). Significantly higher proportion of TP53mut T-MN patients had complex karyotype (22/32, 84%) compared to TP53wt (5/69; 7%, p<0.0001).Examination of 20 FANC pathway genes identified 38 rare variants in 31(31%) T-MN at a variant allele frequency (VAF) of ≥20% and most of the variants were missense (35/38; 92%). These were mostly seen in BRCA1, FANCA, FANCM, BRCA2, FANCL and SLX4 genes. Of patients with FANC variants, 42% (13/31) had concomitant TP53 mutations. The median VAF was 49% (range 20-100%) with no significant difference between the deleterious (n=13; 34%) and non-deleterious variants (n=25). Out of 13 deleterious variants (including 2 BRCA1 variants previously reported pathogenic on BIC database), ten variants were seen in nine TP53wt patients. We compared the disease characteristics, prior chemotherapy and survival outcome in patients with TP53mut (n=32), TP53wt harbouring predicted deleterious FANC variants (TP53wt /FANCdel var; n=9), TP53wt harbouring predicted non-deleterious FANC variants (TP53wt /FANCnon-del var; n=9) and TP53wt /FANCwt (n=51). There was no difference in bone marrow blast %, type of prior malignancy, prior therapy (CT vs RT vs combination), proportion of T-AML and treatment for T-MN between the groups. Interestingly, median number of mutations were significantly lower in TP53mut group (1; range 0-11) compared to TP53wt /FANCdel var, TP53wt /FANCnon-del var (both groups - 3; range 0-6) and TP53wt /FANCwt (3; range 0-9) (p=0.0005). Importantly, median OS of TP53wt /FANCdel var and TP53wt /FANCnon-del var groups was identical and significantly shorter than TP53wt /FANCwt (9.7 vs. 9.9 vs. 19.1 months; p=0.00485), and similar to TP53mut group (8.9 months).Conclusions: In our cohort, somatic mutations were seen in 90% of T-MN patients, comparable to primary MDS, contrary to previously published literature. Somatic TP53 mutations and FANC variants are seen in 32% and 31% of cases respectively and 13% harboring both. This study demonstrating that rare FANC variants are associated with significantly poor survival comparable to TP53 mutated T-MN patients. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

A solitary case of gliosarcoma an indication for TP53 mutation analysis: a non-concordant finding

Background: Li-Fraumeni syndrome (LFS) is a hereditary, autosomal dominant malignancy predisposition induced by a mutant TP53. Here, we describe a gliosarcoma (GS) case with a clinical family history impressive for an LFS case in the absence of inherited germline TP53 mutations. Case description: We present a 44-year-old female with a right high parietal mass. The mass proved pathologically to be GS with an isocitrate dehydrogenase-1 (IDH1) mutation. Pedigree analysis identified five first-degree and second-degree relatives with LFS spectrum malignancies. The patient tested positive for TP53 mutation; however, her family tested negative. Conclusion: Of all the tumours, GSs are the least described entity with LFS. We are highlighting the need to do a genetic survey in family members of the patient who has been diagnosed to have gliosarcoma and other tumours consistent with LFS.

Carbon ion radiotherapy eradicates medulloblastomas with chromothripsis in an orthotopic Li-Fraumeni patient-derived mouse model.

BackgroundMedulloblastomas with chromothripsis developing in children with Li-Fraumeni Syndrome (germline TP53 mutations) are highly aggressive brain tumors with dismal prognosis. Conventional photon radiotherapy and DNA-damaging chemotherapy are not successful for these patients and raise the risk of secondary malignancies. We hypothesized that the pronounced homologous recombination deficiency in these tumors might offer vulnerabilities that can be therapeutically utilized in combination with high linear energy transfer carbon ion radiotherapy.MethodsWe tested high-precision particle therapy with carbon ions and protons as well as topotecan with or without PARP inhibitor in orthotopic primary and matched relapsed patient-derived xenograft models. Tumor and normal tissue underwent longitudinal morphological MRI, cellular (markers of neurogenesis and DNA damage-repair), and molecular characterization (whole-genome sequencing).ResultsIn the primary medulloblastoma model, carbon ions led to complete response in 79% of animals irrespective of PARP inhibitor within a follow-up period of 300 days postirradiation, as detected by MRI and histology. No sign of neurologic symptoms, impairment of neurogenesis or in-field carcinogenesis was detected in repair-deficient host mice. PARP inhibitors further enhanced the effect of proton irradiation. In the postradiotherapy relapsed tumor model, median survival was significantly increased after carbon ions (96 days) versus control (43 days, P < .0001). No major change in the clonal composition was detected in the relapsed model.ConclusionThe high efficacy and favorable toxicity profile of carbon ions warrants further investigation in primary medulloblastomas with chromothripsis. Postradiotherapy relapsed medulloblastomas exhibit relative resistance compared to treatment-naïve tumors, calling for exploration of multimodal strategies.

TP53 and CHEK2 germline mutations in malignant solid tumors.

3119 Background: Li-Fraumeni syndrome (LFS, OMIM #151623) is an autosomal dominant cancer predisposition syndrome. Typical LFS tumors comprise adrenocortical carcinomas, sarcoma, breast cancer and central nervous system tumors. LFS is also associated with an increased risk of a multitude of other common types of cancer, such as prostate cancer, lung cancer, gastric cancer, colorectal cancer, ovarian cancer, melanoma, etc. TP53 germline mutations are the most common gene with LFS. Germline mutations of CHEK2 have been identified as another predisposing gene and associated with a range of cancer types. However, the pattern of TP53 and CHEK2 germline mutations in malignant tumors remains unknown. Methods: We identified 8535 malignant solid tumors patients without selecting age or family history in a retrospective cohort. Germline mutations were categorized based on ACMG (American College of Medical Genetics and Genomics) guidelines in pathogenicity. The patients were divided into three groups, P group (with pathogenic mutations), LP group (with likely-pathogenic mutations) and Non_P group (neither pathogenic nor likely-pathogenic mutation). Statistical significance was defined as P-value less than 0.05. Results: A total of 461 (461/8535) patients carried TP53 or CHEK2 germline mutations were identified, in which 15 patients with pathogenic mutations and 17 patients with likely-pathogenic mutations. One patient with lung cancer in LP group carried TP53 homozygous mutation ( p. Ser215Ile), and the remaining 31 patients all carried heterozygous mutations. Among these 31 carriers, 16 (51.6%) carried nonsense or missense mutations (10 for nonsense and 6 for missense mutations). 3 patients in the P group carried CHEK2 p. Y139* (one liver cancer patient and two lung cancer patients) were identified. The median age of group P, LP and Non_P was 55 (39 for TP53, 61 for CHEK2), 63 (52 for TP53, 66 for CHEK2) and 59, respectively. Somatic mutation analysis found no significant difference in tumor mutation burden (TMB) among three groups. The SNV/INDEL mutation frequency of LRP1B in the P or LP group was significantly lower than the Non_P group. Conclusions: Our data showed that 0.375% (32/8535) malignant solid tumor patients carried TP53 (16/8535) or CHEK2 (16/8535) germline pathogenic or likely-pathogenic mutations. The relationship between germline mutations and cancer susceptibility will be studied in the future.[Table: see text]

Racial disparity in OncotypeDX score in early stage, hormone receptor positive, HER-2 negative, node negative breast cancers: A systemic review and meta-analysis.

e12555 Background: Oncotype DX Breast Recurrence Score (RS) is the currently used risk-assessment tool for early-stage, hormone receptor-positive, HER-2 negative, node-negative breast cancer in the US. Studies showed inconsistency in RS distribution and treatment among races. Causes may include variations in somatic mutations like Ki-67, which have been reported to express higher in African American (AA) and Asian populations than in Non-Hispanic White (NHW) population, germline mutations in BRCA and TP53, that are not in the RS algorithm, and financial burden of the testing. We analyzed data from different countries to investigate racial disparity in RS. Methods: We searched Medline, EMBASE, Web of Science, and Cochrane Central Register of Controlled Trials, indexed from January 2010 to January 2021. More than 85% of studies were conducted in the pre-TAILORx study phase. To include data that are available and better represent different races, we included studies that used the previous cutoff value, low-risk ( &lt; 18), intermediate-risk (18-30), high-risk ( &gt; 30). Retrospective studies using Surveillance, Epidemiology, and End Results or National Cancer Database were excluded to avoid overlap data. A total of 17 studies, 9789 patients from seven countries (US, Japan, China, Taiwan, Kuwait, UAE, Israel) were pooled. The Odds Ratio (OR) was extracted with a 95% confidence interval (CI) for RS distribution and post-RS treatment. Both fixed-effect and random-effect meta-analysis were performed. Results: Among AA and NHW, AA were 1.7 times more likely to have high recurrence score (OR = 1.75; 95% CI = 1.46 - 2.10; P &lt; 0.0001), with no heterogeneity among studies (I2 = 0%, heterogeneity P = 0.59). Asian were 1.59 more likely than NHW to be high-risk using a random effects model (OR = 1.59; 95% CI = 1.06 - 2.40; P = 0.0259). High-risk Asian were two times more likely to receive adjuvant chemotherapy post-RS comparing to NHW (OR: 2.31, CI: 1.07 - 4.98, fixed effect model; OR: 2.85, CI: 0.48, 17.05, random effects model), while high-risk AA were less likely to receive chemotherapy comparing to NHW (OR: 0.74, CI: 0.54-1.01, fixed effect model; OR: 0.73, CI: 0.54-0.99, random effects model). Intermediate-risk Asian and AA were more likely to receive chemotherapy compared to NHW (Asian to NHW; OR: 1.68, CI: 1.16-2.43, with fixed effect model, OR: 1.68, CI: 0.94-3.02, with random effects model; AA to NHW; OR: 1.16, CI: 0.93-1.46 with fixed effect model; OR: 1.06, CI: 0.62-1.79 with random effect model). Conclusions: We identified racial disparity in RS and post-RS treatment. Future research is required to elucidate the causes for AA and Asian receiving higher recurrence scores, a need for tailoring RS cutoffs for different races, and the utilization in adequate post-RS treatment.

Comprehensive Study of Germline Mutations and Double-Hit Events in Esophageal Squamous Cell Cancer.

Esophageal squamous cell cancer (ESCC) is the eighth most common cancer around the world. Several reports have focused on somatic mutations and common germline mutations in ESCC. However, the contributions of pathogenic germline alterations in cancer susceptibility genes (CSGs), highly frequently mutated CSGs, and pathogenically mutated CSG-related pathways in ESCC remain unclear. We obtained data on 571 ESCC cases from public databases and East Asian from the 1000 Genomes Project database and the China Metabolic Analytics Project database to characterize pathogenic mutations. We detected 157 mutations in 75 CSGs, accounting for 25.0% (143/571) of ESCC cases. Six genes had more than five mutations: TP53 (n = 15 mutations), GJB2 (n = 8), BRCA2 (n = 6), RECQL4 (n = 6), MUTYH (n = 6), and PMS2 (n = 5). Our results identified significant differences in pathogenic germline mutations of TP53, BRCA2, and RECQL4 between the ESCC and control cohorts. Moreover, we identified 84 double-hit events (16 germline/somatic double-hit events and 68 somatic/somatic double-hit events) occurring in 18 tumor suppressor genes from 83 patients. Patients who had ESCC with germline/somatic double-hit events were diagnosed at younger ages than patients with the somatic/somatic double-hit events, though the correlation was not significant. Fanconi anemia was the most enriched pathway of pathogenically mutated CSGs, and it appeared to be a primary pathway for ESCC predisposition. The results of this study identified the underlying roles that pathogenic germline mutations in CSGs play in ESCC pathogenesis, increased our awareness about the genetic basis of ESCC, and provided suggestions for using highly mutated CSGs and double-hit features in the early discovery, prevention, and genetic counseling of ESCC.

Liposarcoma in children and young adults: a clinicopathologic and molecular study of 23 cases in one of the largest institutions of China.

The incidence of pediatric liposarcoma is rare and most published cases lack systematic genetic analyses. We present clinicopathologic and genetic features of 23 liposarcomas aged <22 years. The study cohort comprised 10 males and 13 females (M:F=1:1.3) aged 11-21 years (median 17 years). The tumors predominantly occurred at the extremities (16/23; 69.6%), followed by the head/neck (2/23; 8.7%), chest (2/23; 8.7%), waist (2/23, 8.7%), and retroperitoneum (1/23; 4.3%). The tumor subtypes were sixteen myxoid liposarcoma (ML), one well-differentiated liposarcoma (WDL), two dedifferentiated liposarcoma (DDL), one pleomorphic liposarcoma (PL), and three myxoid pleomorphic liposarcoma (MPL) cases. Fluorescence in situ hybridization analysis identified MDM2/CDK4 amplification in all WDL/DDL cases (3/3; 100%) and DDIT3 rearrangement in all ML cases (13/13; 100%). Whole-exome sequencing indicated that one PL case and one MPL case exhibited RB1 loss. The two tested MPL cases had TP53 mutation and one of them harbored a TP53 germline mutation. Follow-up information was available for 20 patients (20/23; 87.0%) with a median follow-up duration of 42.5 months (range, 13-120 months). Three patients exhibited tumor progression (3/20;15.0%). Seventeen patients (17/20; 85.0%) survived with no evidence of disease. One MPL case (1/20; 5.0%) died of the disease. In conclusion, despite some overlaps, the occurrence, distribution of subtype, and prognosis of liposarcoma are overall different in children and adults. Most MLs and ALT/WDL/DDLs showed similar genetic aberrations with adult counterparts. Molecular features of MPL overlapped with those of conventional PL. The genetic characteristics including Tp53 status of MPL need further investigation.

The Common Germline TP53-R337H Mutation Is Hypomorphic and Confers Incomplete Penetrance and Late Tumor Onset in a Mouse Model.

The TP53-R337H founder mutation exists at a high frequency throughout southern Brazil and represents one of the most common germline TP53 mutations reported to date. It was identified in pediatric adrenocortical tumors in families with a low incidence of cancer. The R337H mutation has since been found in association with early-onset breast cancers and Li-Fraumeni syndrome (LFS). To study this variability in tumor susceptibility, we generated a knockin mutant p53 mouse model (R334H). Endogenous murine p53-R334H protein was naturally expressed at high levels in multiple tissues and was functionally compromised in a tissue- and stress-specific manner. Mutant p53-R334H mice developed tumors with long latency and incomplete penetrance, consistent with many human carriers being at a low but elevated risk for cancer. These findings suggest the involvement of additional cooperating genetic alterations when TP53-R337H occurs in the context of LFS, which has important implications for genetic counseling and long-term clinical follow-up. SIGNIFICANCE: A p53-R334H knockin mouse serves as an important model for studying the most common inherited germline TP53 mutation (R337H) that is associated with variable tumor susceptibility.

First person profile: Lori J. Pierce, MD: First African American, first female radiation oncologist to serve as American Society of Clinical Oncology president makes equity her theme.

First person profile: Lori J. Pierce, MD: First African American, first female radiation oncologist to serve as American Society of Clinical Oncology president makes equity her theme.

Abstract PS8-04: Clinical and pathological characteristics and screening outcome for secondary cancers in breast cancer patients with li-fraumeni syndrome attending the MD anderson li-fraumeni education and early detection program clinic

Abstract Background: Germline TP53 mutations predispose to early onset breast cancer (BC) and are associated with Li-Fraumeni syndrome (LFS) Published data on the clinical and pathological characteristics and screening outcome for secondary cancers among women with BC and TP53 mutations is limited. The UTMD Anderson's Li-Fraumeni Education and Early Detection (LEAD) program conducts comprehensive cancer screening for patients with LFS. Here we report characteristics and screening outcome of patients with BC and LFS who were referred to the LEAD program. Methods: Patients with BC and LFS were identified from a prospective BC database between 2001 to 2018. Patients had genetic testing at The University of Texas MD Anderson Cancer Center (MDACC) Clinical Cancer Genetics (CCG) program and confirmed to have germline TP53 mutations. Data reviewed included clinical and pathological characteristics of their BC, the pattern of referral to the LEAD program, adherence to screening recommendation and rate of secondary cancer detection in the LEAD program. Results: A total of 78 female patients with positive germline TP53 mutation and BC diagnosis were identified. The clinical and pathological characteristics of these patients are provided in table 1. Out of the 78 patients, 62 patients were referred and followed at the LEAD clinic. 50 were referred after BC diagnosis and 12 were referred to LEAD clinic before BC diagnosis. A total of 137 cancers were diagnosed in the total population. The cancers were further grouped into diagnosed before or after BC diagnosis. (table 2). 24 cancers were diagnosed in LEAD clinic including 12 breast cancers, 2 soft tissue tumors, 2 thyroid cancers, 2 acute myeloid leukemia, 1 brain tumor, 1 lung cancer, 1 pancreatic cancer, 1 melanoma, 1 parotid cancer and 1 Merkel cell cancer. Adherence to follow up and recommended screening in the first year was 77%, second year 75% and third year 65%. 6 patients, who were diagnosed with leukemia, had received adjuvant chemotherapy with anthracycline and/or cyclophosphamide-based therapy for breast cancer with median time from chemotherapy to leukemia diagnosis of 9 years (5-10yrs). 8 patients developed chest wall sarcoma in the same location of prior radiation therapy for breast cancer with median time from radiation therapy to chest wall sarcoma diagnosis of 7 years (3-11yrs). Conclusion: Patients with LFS associated breast cancer are at significant increased risk to develop secondary cancers. Increased surveillance for secondary cancers in a dedicated program can increase adherence to screening, lead to early detection that could potentially lead to improved outcomes. Patient outcome of this cohort will be presented at the meeting. Table 1: Clinical and Pathological Characteristics of Women with Breast cancer and LFSN(%)N(%)Median Age (Range)33 (20, 63)——Hormonal receptor/HER-2 status+/+22(31.4%)RaceAsian/Pacific islander7(9%)+/-27(38.6%)Black8(10.3%)-/+14(20%)Hispanic12(15.4%)-/-7(10%)White51(65.4%)Menopausal status at the time of BC diagnosis.Pre-menopausal(72%)Stage013(16.9%)Post-menopausal(28%)I21(27.3%)HistologyDCIS12(15.6%)II31(40.3%)IDC49(63.6%)III9(11.7%)ILC3(3.9%)IV3(3.9%)LCIS1(1.3%)Breast cancer diagnosisMRI4(5.2%)Mixed8(10.4%)Palpated lesion51(66.2%)Mucinous2(2.6%)Screening mammogram22(28.6%)Phyllodes2(2.6%) Table 2: Cancer diagnosed in the total population N=78 grouped into before and after to BC diagnosisCancer diagnosed before BC diagnosisNCancer diagnosed after BC diagnosisNSoft tissue sarcoma13Soft tissue sarcoma18CNS1Lung2Thyroid3Thyroid3leukemia2Merkel cell1Adrenal2Leukemia6Uterus1CNS3Renal1pancreas1Melanoma1Parotid1 Citation Format: Aydah Al-Awadhi, Nour Abuhadra, Diane D Liu, Angelica M Gutierrez Barrera, Jessica Corredor, Louise C Strong, Banu K Arun. Clinical and pathological characteristics and screening outcome for secondary cancers in breast cancer patients with li-fraumeni syndrome attending the MD anderson li-fraumeni education and early detection program clinic [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-04.