TP53 Variants Research Articles

SAT-155 High Prevalence Alterations on DNA Mismatch Repair Genes Related to Lynch Syndrome in Pediatric Patients with Adrenocortical Tumor Carried of the Germline Mutation on TP53

Background: Adrenocortical cancer (ACC) is a rare malignant neoplasia associated with a variable clinical presentation. Pediatric patients generally have a better prognosis when compared to adults. In addition, unlike in adults where ACC which is usually sporadic, 50-80% of pediatric ACC is associated with genetic disorders such as Beckwith-Wiedemann and Li-Fraumeni syndromes. Recently, was showed that 3-5% of adult patients with ACC presented germline variants in DNA mismatch repair genes such as MSH2 and MSH6, the cause of Lynch syndrome (LS). The prevalence of these alterations in pediatric ACC is unknown. We aimed to investigate the prevalence of germline alterations in DNA mismatch repair genes among pediatric and adult patients with adrenocortical tumors (benign and malignant) carriers of the germline TP53 p.R337H mutation. Methods: 35 patients selected (30 pediatric and 5 adult) with functional tumors. ACC was diagnosed in 4 pediatric and in all adult patients. NGS was performed in 35 DNA blood samples by HNPCC MASTR Plus for the identification of SNV in 4 genes (MLH1, MSH2, MSH6, and PMS2) and 3’ UTR of EPCAM. Copy number variation (CNV) analyses were done by Copy Number Targeted Resequencing Analysis (CONTRA) and MLPA. The variants were classified, according to ACMG (American College Medical Genome) by Varsome platform. The protein expression was evaluated by Immunohistochemistry (IHC): MLH1 (clone ES05), MSH2 (FE11), MSH6 (EP49), and PMS2 (EP51). All patients were evaluated for variants in TP53. Results: NGS: 2 children presented 2 pathogenic allelic variants associated with LS (2/30, 6.6%), both patients with benign outcome and follow up of 4 years: 1 deletion in MLH1 (c.1500_1502del) and 1 nonsense in the MSH6 gene (c.328C>T p.Arg110X. CNV: MLPA specific for MLH1/MSH2 showed a normal copy number. ICH: the loss of expression in MLH1/PMS2 was identified in only one case without allelic variants. Discussion: Although our cohort is small, we observed 2 allelic pathogenic variants associated with LS among pediatric with adrenocortical tumors. It is higher than the prevalence of colorectal and endometrial cancer (3.2%) in LS. A personal and family history of LS tumors should be strongly considered for genetic risk assessment in pediatric patients with ACT. If the association with TP53 alteration can influence the tumor’s behavior with early clinical presentation, as seen in hereditary nonpolyposis colorectal cancer, it needs to be investigated. The patients with both alterations must be followed with surveillance, according to the US Multi-Society task force guideline for Lynch syndrome and for Li-Fraumeni syndrome.

Li-Fraumeni Exploration Consortium Data Coordinating Center: Building an Interactive Web-Based Resource for Collaborative International Cancer Epidemiology Research for a Rare Condition.

The success of multisite collaborative research relies on effective data collection, harmonization, and aggregation strategies. Data Coordination Centers (DCC) serve to facilitate the implementation of these strategies. The utility of a DCC can be particularly relevant for research on rare diseases where collaboration from multiple sites to amass large aggregate datasets is essential. However, approaches to building a DCC have been scarcely documented. The Li-Fraumeni Exploration (LiFE) Consortium's DCC was created using multiple open source packages, including LAM/G Application (Linux, Apache, MySQL, Grails), Extraction-Transformation-Loading (ETL) Pentaho Data Integration Tool, and the Saiku-Mondrian client. This document serves as a resource for building a rare disease DCC for multi-institutional collaborative research. The primary scientific and technological objective to create an online central repository into which data from all participating sites could be deposited, harmonized, aggregated, disseminated, and analyzed was completed. The cohort now include 2,193 participants from six contributing sites, including 1,354 individuals from families with a pathogenic or likely variant in TP53. Data on cancer diagnoses are also available. Challenges and lessons learned are summarized. The methods leveraged mitigate challenges associated with successfully developing a DCC's technical infrastructure, data harmonization efforts, communications, and software development and applications. These methods can serve as a framework in establishing other collaborative research efforts. Data from the consortium will serve as a great resource for collaborative research to improve knowledge on, and the ability to care for, individuals and families with Li-Fraumeni syndrome.

CCNB2 and AURKA overexpression may cause atypical mitosis in Japanese cortisol-producing adrenocortical carcinoma with TP53 somatic variant.

Many genomic analyses of cortisol-producing adrenocortical carcinoma (ACC) have been reported, but very few have come from East Asia. The first objective of this study is to verify the genetic difference with the previous reports by analyzing targeted deep sequencing of 7 Japanese ACC cases using next-generation sequencing (NGS). The second objective is to compare the somatic variant findings identified by NGS analysis with clinical and pathological findings, aiming to acquire new knowledge about the factors that contribute to the poor prognosis of ACC and to find new targets for the treatment of ACC. DNA was extracted from ACC tissue of seven patients and two reference blood samples. Targeted deep sequencing was performed using the MiSeq system for 12 genes, and the obtained results were analyzed using MuTect2. The hypothesis was obtained by integrating the somatic variant findings with clinical and pathological data, and it was further verified using The Cancer Genome Atlas (TCGA) dataset for ACC. Six possible pathogenic and one uncertain significance somatic variants including a novel PRKAR1A (NM_002734.4):c.545C>A (p.T182K) variant were found in five of seven cases. By integrating these data with pathological findings, we hypothesized that cases with TP53 variants were more likely to show atypical mitotic figures. Using TCGA dataset, we found that atypical mitotic figures were associated with TP53 somatic variant, and mRNA expression of CCNB2 and AURKA was significantly high in TP53 mutated cases and atypical mitotic figure cases. We believe this is the first report that discusses the relationship between atypical mitotic figures and TP53 somatic variant in ACC. We presumed that overexpression of CCNB2 and AURKA mRNA may cause atypical mitosis in TP53 somatic mutated cases. Because AURKA is highly expressed in atypical mitotic cases, it may be an appropriate indicator for AURKA inhibitors.

Loss of lenalidomide-induced megakaryocytic differentiation leads to therapy resistance in del(5q) myelodysplastic syndrome.

Interstitial deletion of the long arm of chromosome 5 (del(5q)) is the most common structural genomic variant in myelodysplastic syndromes (MDS)1. Lenalidomide (LEN) is the treatment of choice for patients with del(5q) MDS, but half of the responding patients become resistant2 within 2 years. TP53 mutations are detected in ~20% of LEN-resistant patients3. Here we show that patients who become resistant to LEN harbour recurrent variants of TP53 or RUNX1. LEN upregulated RUNX1 protein and function in a CRBN- and TP53-dependent manner in del(5q) cells, and mutation or downregulation of RUNX1 rendered cells resistant to LEN. LEN induced megakaryocytic differentiation of del(5q) cells followed by cell death that was dependent on calpain activation and CSNK1A1 degradation4,5. We also identified GATA2 as a LEN-responsive gene that is required for LEN-induced megakaryocyte differentiation. Megakaryocytic gene-promoter analyses suggested that LEN-induced degradation of IKZF1 enables a RUNX1-GATA2 complex to drive megakaryocytic differentiation. Overexpression of GATA2 restored LEN sensitivity in the context of RUNX1 or TP53 mutations by enhancing LEN-induced megakaryocytic differentiation. Screening for mutations that block LEN-induced megakaryocytic differentiation should identify patients who are resistant to LEN.

Targeted next generation sequencing identifies somatic mutations in a cohort of Egyptian breast cancer patients

Breast cancer (BC) incidence is progressively increasing in Egypt. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of its progression. To the best of our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients. Four hundred and nine cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies.TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in Tp53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, one drug response variant (p.P72R) in TP53 was detected in 8 samples. Furthermore, four novel variants were identified in JAK2, MTOR, KIT and EPHB. Further analysis, by Ingenuity Variant Analysis software (IVA), showed that PI3K/AKT signaling is altered in greater than 50% of Egyptian BC patients which implicates PI3K/AKT signaling as a therapeutic target. In this cohort, we shed the light on the most frequently detected somatic mutations and the most altered pathway in Egyptian BC patients.

The first pancreatic neuroendocrine tumor in Li-Fraumeni syndrome: a case report

BackgroundLi-Fraumeni syndrome is a cancer predisposition syndrome caused by germline TP53 tumor suppressor gene mutations, with no previous association with pancreatic neuroendocrine tumors (PNETs). Here we present the first case of PNET associated with Li-Fraumeni syndrome.Case presentationThis is a 43-year-old female who underwent laparoscopic distal pancreatectomy at age 39 for a well-differentiated grade 2 cystic PNET. When the patient was 41 years old, her seven-year-old daughter was found to have an astrocytoma and a germline TP53 mutation. While undergoing surveillance with 68Gallium-DOTATATE positron emission tomography/computed tomography for her PNET, the patient was found to have a large choroid plexus papilloma in her right temporal lobe. She underwent genetic counseling and testing that identified a germline pathogenic variant in TP53, leading to the diagnosis of Li-Fraumeni syndrome. Her PNET had a hemizygous pathogenic TP53 mutation with loss of the wild-type alternate allele, consistent with loss of heterozygosity and the two-hit hypothesis. She was enrolled in a Li-Fraumeni syndrome protocol and continues surveillance screening with our service.ConclusionsThis is the first PNET reported in association with Li-Fraumeni syndrome. Pancreatic cancer risk is elevated in this syndrome, and our case highlights the need for vigilance in screening for pancreatic neoplasms in these patients.

The prognostic significance of immune microenvironment in breast ductal carcinoma in situ

BackgroundThe role of different subtypes of tumour infiltrating lymphocytes (TILs) in breast ductal carcinoma in situ (DCIS) is still poorly defined. This study aimed to assess the prognostic significance of B and T lymphocytes and immune checkpoint proteins expression in DCIS.MethodsA well characterised DCIS cohort (n = 700) with long-term follow-up comprising pure DCIS (n = 508) and DCIS mixed with invasive carcinoma (IBC; n = 192) were stained immunohistochemically for CD20, CD3, CD4, CD8, FOXP3, PD1 and PDL1. Copy number variation and TP53 mutation status were assessed in a subset of cases (n = 58).ResultsCD3+ lymphocytes were the predominant cell subtype in the pure DCIS cohort, while FOXP3 showed the lowest levels. PDL1 expression was mainly seen in the stromal TILs. Higher abundance of TILs subtypes was associated with higher tumour grade, hormone receptor negativity and HER2 positivity. Mutant TP53 variants were associated with higher levels of stromal CD3+, CD4+ and FOXP3+ cells. DCIS coexisting with invasive carcinoma harboured denser stromal infiltrates of all immune cells and checkpoint proteins apart from CD4+ cells. Stromal PD1 was the most differentially expressed protein between DCIS and invasive carcinoma (Z = 5.8, p < 0.0001). Dense TILs, stromal FOXP3 and PDL1 were poor prognostic factors for DCIS recurrence, while dense TILs were independently associated with poor outcome for all recurrences (HR = 7.0; p = 0.024), and invasive recurrence (HR = 2.1; p = 0.029).ConclusionsImmunosuppressive proteins are potential markers for high risk DCIS and disease progression. Different stromal and intratumoural lymphocyte composition between pure DCIS, DCIS associated with IBC and invasive carcinoma play a potential role in their prognostic significance and related to the underlying genomic instability. Assessment of overall TILs provides a promising tool for evaluation of the DCIS immune microenvironment.

High Prevalence of Somatic Oncogenic Driver Alterations in Patients With NSCLC and Li-Fraumeni Syndrome.

Actionable somatic molecular alterations are found in 15% to 20% of NSCLC in Europe. NSCLC is a tumor observed in patients with germline TP53 variants causing Li-Fraumeni syndrome (LFS), but its somatic molecular profile is unknown. Retrospective study of clinical and molecular profiles of patients with NSCLC and germline TP53 variants. Among 22 patients with NSCLC and LFS (n= 23 lung tumors), 64% were women, median age was 51 years, 84% were nonsmokers, 73% had adenocarcinoma histological subtype, and 84% were diagnosed with advanced-stage disease. These patients harbored 16 distinct germline TP53 variants; the most common was p.R158H (5/22; three in the same family). Personal and family histories of cancer were reported in 71% and 90% of patients, respectively. In most cases (87%, 13/15), lung cancer was diagnosed with a late onset. Of the21 tumors analyzed, somatic oncogenic driver mutations were found in 19 of 21 (90%), EGFR mutations in 18 (exon 19 deletion in 12 cases, L858R in three cases, and G719A, exon 20 insertion, and missing mutation subtype, each with one case), and ROS1 fusion in one case. A PI3KCA mutation was concurrently detected at diagnosis in three EGFR exon 19-deleted tumors (3/12). The median overall survival was 37.3 months in 14 patients treated with EGFR inhibitors; seven developed resistance, five (71%) acquired EGFR-T790M mutation, and one had SCLC transformation. Driver oncogenic alterations were observed in 90% of the LFS tumors, mainly EGFR mutations; one ROS1 fusion was also observed. The germline TP53 variants and lung cancer carcinogenesis driven by oncogenic processes need further evaluation.

Functional Classification of TP53 Mutations in Acute Myeloid Leukemia.

Mutations of the TP53 gene occur in a subset of patients with acute myeloid leukemia (AML) and confer an exceedingly adverse prognosis. However, whether different types of TP53 mutations exert a uniformly poor outcome has not been investigated yet. Here, we addressed this issue by analyzing data of 1537 patients intensively treated within protocols of the German-Austrian AML study group. We classified TP53 mutations depending on their impact on protein structure and according to the evolutionary action (EAp53) score and the relative fitness score (RFS). In 98/1537 (6.4%) patients, 108 TP53 mutations were detected. While the discrimination depending on the protein structure and the EAp53 score did not show a survival difference, patients with low-risk and high-risk AML-specific RFS showed a different overall survival (OS; median, 12.9 versus 5.5 months, p = 0.017) and event-free survival (EFS; median, 7.3 versus 5.2 months, p = 0.054). In multivariable analyses adjusting for age, gender, white blood cell count, cytogenetic risk, type of AML, and TP53 variant allele frequency, these differences were statistically significant for both OS (HR, 2.14; 95% CI, 1.15–4.0; p = 0.017) and EFS (HR, 1.97; 95% CI, 1.06–3.69; p = 0.033). We conclude that the AML-specific RFS is of prognostic value in patients with TP53-mutated AML and a useful tool for therapeutic decision-making.

Abstract P2-09-08: Breast cancer tumor sequencing coupled with germline genetic testing aids the identification of at-risk individuals for hereditary breast cancer disorders

Abstract Background: With the rise of precision medicine, hereditary cancer germline testing and tumor genetic testing have been increasingly used to inform the management of patients with cancer. Recent studies report that approximately 10% of patient’s tumors have clinically significant variants in genes known to predispose to a hereditary cancer syndrome. Here we report the concordance rate between tumor genetic testing and germline genetic testing in patients with breast cancer and review its impact on the patients’ management and implications for their relatives. Methods: In this study, we used de-identified data from 101 consecutive patients with breast cancer who underwent tumor genetic testing followed by germline testing with NGS-based hereditary cancer gene panels. Results: Tumor genetic testing results included likely pathogenic or pathogenic (LP/P) variants in BRCA2 (21%), BRCA1 (20%), TP53 (10%), CDH1 (7%), ATM (4.3%), PALB2,CHEK2, and PTEN (3.7% each), and PIK3CA (2.5%) among 22 other genes. In 33/101 cases (33%) the P/LP variant was also detected in the germline. Genes in which disease-causing variants were most frequently confirmed to be in the germline included: BRCA2 (36%), BRCA1(21%), PALB2 (12%), and CHEK2 (12%). Variants in ATM, FH, FANCA, and MSH6 were confirmed in the germline in &amp;lt;10% of patients with variants in these genes. Variants in the TP53, CDH1, and PIK3CA genes were detected in the tumor but not in the germline. In 1 case a pathogenic germline variant was detected in the BRIP1 gene but not reported in the tumor, because the gene was not included in the tumor testing panel. Conclusions: A significant proportion (33%) of patients with clinically significant variants in tumors were identified to carry the same variant in the germline, uncovering a previously unknown risk of hereditary breast cancer disorder. Notably, some genes had a high probability of variants occurring in the germline, while others were primarily seen in tumors. Performing simultaneous germline and tumor testing may inform susceptibility to a hereditary cancer disorder, identify targets for precision therapy, early detection of secondary malignancies, and guide genetic counseling for relatives. Citation Format: Daniel E Pineda-Alvarez, Scott T Michalski, Meaghan Russell, Shan Yang, Ihn Young Song, Robert L Nussbaum, Edward D. Esplin. Breast cancer tumor sequencing coupled with germline genetic testing aids the identification of at-risk individuals for hereditary breast cancer disorders [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-09-08.

Abstract P2-16-03: Neoadjuvant treatment of triple negative breast cancer patients with docetaxel and carboplatin to assess anti-tumor activity

Abstract Background: Anthracycline- and taxane-based neoadjuvant chemotherapy (NAT) in triple negative breast cancer (TNBC) patients yields a pathological complete response (pCR) rate of approximately 45%. Anthracyclines can lead to long-term toxicities including congestive heart failure and leukemia. TNBC patients achieving pCR have excellent long-term outcomes irrespective of NAT regimen. This study was designed to evaluate the efficacy of a non-anthracycline NAT regimen with carboplatin and docetaxel in TNBC. Correlative studies include detecting and tracking plasma circulating tumor DNA (ctDNA) to determine if it will predict clinical outcomes, and whole exome sequencing (WES) on tissue samples to decipher the genomic architecture of those who achieve pCR versus those who do not. Methods: This is a joint analysis of two identical multicenter trials. Eligible patients with AJCC 7 clinical stages II and III TNBC received docetaxel 75mg/m2 and carboplatin AUC 6 every 3 weeks X 6 cycles. Following NAT, all patients underwent definitive surgery. The primary endpoint is pCR (no invasive tumor in the breast and axilla). Secondary objectives include evaluating ctDNA as a prognostic biomarker that may be used in identifying TNBC patients at a high risk of disease relapse, and evaluating differences in the genomic architecture between pCR and non-pCR patients. Patients have a research biopsy at baseline, cycle 1 day 3 (optional), and at definitive surgery for those with residual disease. Plasma for ctDNA is collected at baseline, cycle 1 day 3, at definitive surgery, and every 6 months for 5 years. Results: Between 2014 and 2019, 103 patients have been registered. Median age is 53 years (range 25-74), 27.2%: African-American, 77.7%: clinical stage II. Ninety-nine have completed NAT and have had surgery. In the intent to treat population, the preliminary pCR rate is 46.5% (95% CI 36.9% - 56.2%). Nine (8.7%) have developed recurrent disease, and 7 (6.8%) have died. Preliminary ctDNA results from 6 patients (4 non-pCR, 2 pCR) show that ctDNA is detectable in 67%. We identified 627 somatic variants by exome analysis. Of these, 10 variants overlapped with the Swift panel (Accel-Amplicon™ 56G Oncology Panel v2) used for ctDNA sequencing and variant detection. TP53 variants were identified in all 6 patients’ tumor tissue samples. At least one TP53 variant was identified in 4 patients’ baseline pre-chemotherapy ctDNA. Both pCR patients had either no detectable ctDNA TP53 mutations, or clearance of ctDNA following chemotherapy. Three non-PCR patients had persistent TP53 mutations in ctDNA during the treatment course. WES and ctDNA analysis on all patients is currently ongoing. Conclusions: We report a very encouraging pCR rate of 46.5% in TNBC patients with carboplatin and docetaxel NAT. This rate is similar to observed rates with anthracycline- and taxane-based NAT and may represent an option for treatment for TNBC patients. Correlative genomic and ctDNA studies are ongoing. Clinical trial information: NCT02124902 &amp; NCT02547987. Citation Format: FOLUSO O ADEMUYIWA, Mothaffar F Rimawi, Tracy Summa, Jingqin Luo, Tao Wang, Rama Suresh, Lindsay Peterson, Michael Naughton, Ashley Frith, Leonel Hernandez-Aya, Katherine Weilbaecher, Cynthia Ma, Aadel A Chaudhuri, Yang-Yang Feng, Zachary L Skidmore, Obi L Griffith, Malachi Griffith, Matthew Ellis. Neoadjuvant treatment of triple negative breast cancer patients with docetaxel and carboplatin to assess anti-tumor activity [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-16-03.

Abstract P6-10-21: Evaluation of genomic changes in ductal carcinoma in situ as potential biomarkers of recurrence risk

Abstract Routine breast cancer screening has increased detection of pre-invasive lesions such as ductal carcinoma in situ (DCIS). Currently, DCIS cases are mostly treated with wide local excision combined with adjuvant radiotherapy and/or hormonal therapy, even though only 25% of DCIS treated with surgery alone recur with 50% of recurrences being invasive. At present, prediction of recurrence risk is based on histopathological features and patient characteristics but reliable identification of individual recurrence risk is still challenging. Certain genetic aberrations (i.e. copy number variation, somatic mutations) are associated with breast cancer progression. While most recurrences are assumed to be genetically related to the primary tumour (“clonal recurrence”), the prevalence of ipsilateral independent primary events (“non-clonal recurrence”) after treatment for DCIS is uncertain. If this is a substantial proportion of cases, their presence would compromise attempts to find tumour intrinsic biomarkers of recurrence. To enable the discovery of better recurrence biomarkers, this project initially aims to identify cases with primary DCIS and later clonal ipsilateral recurrence. Sections from formalin-fixed paraffin-embedded blocks from primary DCIS cases and their subsequent recurrences were obtained from Nottingham City Hospital (UK). Two pathologists reviewed representative sections to identify areas for microdissection. Tumour epithelial cells were needle-microdissected and DNA was isolated. Sequencing libraries were prepared using a) a custom capture panel of 110 breast cancer-related genes or b) NEBNext Ultra II for low-coverage whole-genome sequencing (LC-WGS) depending on DNA quality and quantity. Sequencing was then performed on Illumina NextSeq 500 system with an average coverage of a) 400x and b) 1.3x, respectively. Data was processed by an in-house bioinformatics pipeline to detect and filter for high confidence somatic variants. Copy number profiles were obtained using CopywriteR (panel off-target reads), PureCN (panel on-target reads) and Control-FREEC (LC-WGS). Of 33 patients initially ascertained on the basis of a recurrent breast event, 30 had an ipsilateral recurrent tumour after 4.7 years on average, and 24 primary/recurrence pairs had sufficient data available to determine clonality. Eighteen pairs (75%) were classified as clonal by the following criteria: occurring in similar locations, showing a similar or higher tumour grade, and sharing ≥ 3 copy number breakpoints or likely somatic variants in the genes included in the panel. Six pairs (25%) did not meet this criteria and were classified as non-clonal. Preliminary data analysis shows that invasive recurrences (n = 12) were detected on average 3 years later than DCIS recurrences (n = 6), despite constant surveillance. The most commonly observed somatic mutations occurred in the TP53 and PIK3CA genes. Genetic variants in TP53 and PIK3CA were equally common in primary tumours with clonal and non-clonal recurrence. Frequent copy number alterations involved losses on 16q as well as gains on 1q, 8q and 17q, whereat the 8q gain was less profound. The presence of 25% non-clonal recurrences shows that differentiating between clonal and non-clonal recurrences might be crucial for further recurrence risk biomarker discovery. Thus, this project will proceed with comparing genetic variation in primary DCIS with clonal recurrence to DCIS cases without later recurrence. These samples are currently being obtained and analysed. Citation Format: Dorothea Lesche, Hugo Saunders, Sakshi Mahale, Magnus Zenthoven, Siobhan Huges, Tanjina Kader, Niko Thio, Islam M Miligy, Jia-Min Pang, Andrew R Green, Emad A Rakha, Ian G Campbell, Stephen B Fox, Kylie Gorringe. Evaluation of genomic changes in ductal carcinoma in situ as potential biomarkers of recurrence risk [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-10-21.

Abstract P5-01-10: Next generation sequencing-based gene variant-oriented characterization in metastatic breast cancer: An innovative analysis using ctDNA

Abstract Introduction: Novel high throughput genomic technologies are enhancing the ability to dynamically characterize cancer on a granular level. Although Next Generation Sequencing (NGS) is becoming part of the common practice, little is known on the role of a characterization on a gene variant level. Large heterochromatic regions or blocks are a characteristic feature in the autosomes 1, 9, 16 and the blocks contain about 10% of the human genome. The heterochromatic regions consist of highly repetitive DNA of the classes Sat I to IV. Thus, these specific regions are preferential positions for genome instability. The aim of this study was to explore the feasibility of a gene variant-oriented characterization for variants interplay discovery and to explore the role of chromosome stability in gene variants incidence. Methods: This study analyzed a pilot cohort of 35 metastatic breast cancer (MBC) patients (pts) treated and characterized for CTCs and circulating tumor DNA (ctDNA) at Northwestern University (Chicago, IL). ctDNA was analyzed using the PredicinePLUS™ NGS 180-gene panel (Predicine Inc, CA). Associations between gene variants and clinico-molecular characteristics were tested through Fisher’s exact test. Chromosomes 1, 9, 16 where defined as instable (instable_chr) based on the presence of highly repeated sequences. Results: An overall set of 35 samples was analyzed, and the main variants were detected in the ARID1A (40%), ATM (20%), DNMT3A (37%), ESR1 (20%), PIK3CA (26%), and TP53 (49%) genes. A total of 448 gene variants were detected through the NGS panel and across them, ARID1A accounted for 5.13%, ATM 2.23%, DNMT3A 4.91%, ESR1 4.02%, PIK3CA 2.23%, and TP53 for 6.03%. Among the genes mutated, the DNMT3A:c.2644C&amp;gt;T, DNMT3A:c.2645G&amp;gt;A, ESR1:c.1138G&amp;gt;C,ESR1:c.1609T&amp;gt;A, ESR1:c.1610A&amp;gt;C, ESR1:c.1613A&amp;gt;G, PIK3CA:c.1624G&amp;gt;A were the most detected. Thirty-eight copy number variations (CNV) and 3 splicing variants were observed. Notably, 55.6% of detected variants were found in instable_chr. No significant differences were observed between instable_chr variants and MBC subtype. Interestingly, ARID1Aaberrations were significantly linked to ATM, ESR1 (P=0.006) and PIK3CA with ESR1 (P= 0.019). Consistently with literature, ATM and TP53 variants were mutually exclusive (P&amp;lt;0.0001). Intriguingly, both ATM and TP53 were associated with a higher incidence of variants affecting genes in instable_chr. Conclusions: MBC is often described as a non-gene-addicted disease, rendering the onset of gene variants a multi-factor phenomenon. The present results suggest a role for both chromosomal intrinsic instability and DNA repair impairment in this process, with a potential down-stream selection mediated by treatment resistance. Future studies are warranted to further validate this proof of concept approach. Citation Format: Lorenzo Gerratana, Qiang Zhang, Ami N Shah, Alessandra Franzoni, Jianjun Yu, Shidong Jia, Andrew A Davis, Youbin Zhang, Firas Wehbe, Amir Behdad, Leonidas C Platanias, William J Gradishar, Massimo Cristofanilli. Next generation sequencing-based gene variant-oriented characterization in metastatic breast cancer: An innovative analysis using ctDNA [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-01-10.

Germline variants in DNA repair genes associated with hereditary breast and ovarian cancer syndrome: analysis of a 21 gene panel in the Brazilian population

BackgroundThe Hereditary Breast and Ovarian Cancer Syndrome (HBOC) occurs in families with a history of breast/ovarian cancer, presenting an autosomal dominant inheritance pattern. BRCA1 and BRCA2 are high penetrance genes associated with an increased risk of up to 20-fold for breast and ovarian cancer. However, only 20–30% of HBOC cases present pathogenic variants in those genes, and other DNA repair genes have emerged as increasing the risk for HBOC. In Brazil, variants in ATM, ATR, CHEK2, MLH1, MSH2, MSH6, POLQ, PTEN, and TP53 genes have been reported in up to 7.35% of the studied cases. Here we screened and characterized variants in 21 DNA repair genes in HBOC patients.MethodsWe systematically analyzed 708 amplicons encompassing the coding and flanking regions of 21 genes related to DNA repair pathways (ABRAXAS1, ATM, ATR, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MRE11, MSH2, MSH6, NBN, PALB2, PMS2, PTEN, RAD50, RAD51, TP53 and UIMC1). A total of 95 individuals with HBOC syndrome clinical suspicion in Southeast Brazil were sequenced, and 25 samples were evaluated for insertions/deletions in BRCA1/BRCA2 genes. Identified variants were assessed in terms of population allele frequency and their functional effects were predicted through in silico algorithms.ResultsWe identified 80 variants in 19 genes. About 23.4% of the patients presented pathogenic variants in BRCA1, BRCA2 and TP53, a frequency higher than that identified among previous studies in Brazil. We identified a novel variant in ATR, which was predicted as pathogenic by in silico tools. The association analysis revealed 13 missense variants in ABRAXAS1, BARD1, BRCA2, CHEK2, CDH1, MLH1, PALB2, and PMS2 genes, as significantly associated with increased risk to HBOC, and the patients carrying those variants did not present large insertions or deletions in BRCA1/BRCA2 genes.ConclusionsThis study embodies the third report of a multi-gene analysis in the Brazilian population, and addresses the first report of many germline variants associated with HBOC in Brazil. Although further functional analyses are necessary to better characterize the contribution of those variants to the phenotype, these findings would improve the risk estimation and clinical follow-up of patients with HBOC clinical suspicion.

Improving cascade genetic testing for families with inherited pancreatic cancer (PDAC) risk: The GENetic Education, Risk Assessment and TEsting (GENERATE) study.

TPS779 Background: 4-10% of PDAC patients harbor pathogenic germline variants in cancer susceptibility genes, including APC, ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, and TP53. For families with such pathogenic variants, the greatest potential impact of germline testing is to identify relatives with the same variant (cascade testing), thereby providing the opportunity for early detection and interception of PDAC and other associated cancers. Numerous factors limit cascade testing in real-world practice, including family dynamics, widespread geographic distribution of relatives, access to genetic services, and misconceptions about the importance of germline testing, such that the preventive benefits of cascade testing are often not fully realized. The primary aim of this study is to analyze two alternative strategies for cascade testing in families with inherited PDAC risk. Methods: 1000 individuals with a confirmed pathogenic germline variant in any of the above genes in a 1st/2nd degree relative and a 1st/2nd degree relative with PDAC will be remotely enrolled through the study website (www.GENERATEstudy.org) and randomized between two methods of cascade testing (individuals with prior genetic testing will be ineligible): Arm 1 will undergo pre-test genetic education with a pre-recorded video and live interactive session with a genetic counselor via a web-based telemedicine platform (Doxy.me), followed by germline testing through Color Genomics; Arm 2 will undergo germline testing through Color Genomics without dedicated pre-test genetic education. Color Genomics will disclose results to study personnel and directly to participants in both arms. All participants will have the option of pursuing additional telephone-based genetic counseling through Color Genomics. The primary outcome will be uptake of cascade testing. Secondary outcomes will include self-reported genetic knowledge, cancer worry, distress, decisional preparedness, familial communication, and screening uptake, which will be measured via longitudinal surveys. Enrollment is underway nationwide as of May, 2019. Clinical trial information: NCT03762590.

Pattern of nucleotide variants of TP53 and their correlation with the expression of p53 and its downstream proteins in a Sri Lankan cohort of breast and colorectal cancer patients

BackgroundBreast cancer (BC) is known to be the most common malignancy in females whereas colorectal cancer (CRC) incidence also higher in both genders in Sri Lanka. TP53 is an important tumour suppressor gene and its somatic mutations are reported in approximately 27% of BC and 43% of CRC cases. Analysis of TP53 gene variants not only provides clues for the aetiology of the tumour formation, but also has an impact on treatment efficacy. The current study was conducted to investigate the pattern of TP53 variants in patients with BC and CRC from Sri Lanka.Methods30 patients with BC, 21 patients with CRC and an equal number of healthy controls were screened for mutational status of TP53 by polymerase chain reaction (PCR) followed by direct sequencing. In addition, a subset of these samples were analysed for the protein expression of p53 and comparison made with the mutational status of TP53. We also analysed the protein expression of p21 and MDM2 as potential indicators of p53 functional status and compared it with the protein expression of p53. Additionally, hotspot codons of the KRAS, BRAF and PIK3CA genes were also analysed in a subset of CRC patients.ResultsTwenty seven sequence variants, including several novel variants in the TP53 gene were found. Nine BC and seven CRC tumour samples carried pathogenic TP53 variants. Pathogenic point missense variants were associated with strong and diffuse positive staining for p53 by immunohistochemistry (IHC), whereas, wild type TP53 showed complete absence of positive IHC staining or rare positive cells, regardless of the type of cancer. There was no direct correlation between p21 or MDM2 expression and p53 expression in either BCs or CRCs. Four of the CRC patients had pathogenic hotspot variants in KRAS; three of them were on codon 12 and one was on codon 61.ConclusionThe prevalence of pathogenic somatic TP53 variants was 31 and 33.33% in the studied BC and CRC cohorts respectively. All of them were located in exons 5–8 and the pathogenic missense variants were associated with strong immuno-positive staining for p53.

African-centric TP53 variant increases iron accumulation and bacterial pathogenesis but improves response to malaria toxin

A variant at amino acid 47 in human TP53 exists predominantly in individuals of African descent. P47S human and mouse cells show increased cancer risk due to defective ferroptosis. Here, we show that this ferroptotic defect causes iron accumulation in P47S macrophages. This high iron content alters macrophage cytokine profiles, leads to higher arginase level and activity, and decreased nitric oxide synthase activity. This leads to more productive intracellular bacterial infections but is protective against malarial toxin hemozoin. Proteomics of macrophages reveal decreased liver X receptor (LXR) activation, inflammation and antibacterial defense in P47S macrophages. Both iron chelators and LXR agonists improve the response of P47S mice to bacterial infection. African Americans with elevated saturated transferrin and serum ferritin show higher prevalence of the P47S variant (OR = 1.68 (95%CI 1.07–2.65) p = 0.023), suggestive of its role in iron accumulation in humans. This altered macrophage phenotype may confer an advantage in malaria-endemic sub-Saharan Africa.

Whole-body MRI within a surveillance program for carriers with clinically actionable germline TP53 variants - the Swedish constitutional TP53 study SWEP53

BackgroundThe current guidelines in Sweden regarding individuals with a clinically actionable (i.e. pathogenic or likely pathogenic) germline TP53 variant recommend patients to take part of the national Swedish P53 Study (SWEP53).MethodsThe study comprises a patient registry (mandatory for all participants) and three optional parts: a biobank, a surveillance program and a psychosocial evaluation of the surveillance. All known adult eligible carriers regardless of age are offered to take part of the surveillance program offering MRI yearly of the whole-body, breast, and brain as well as breast ultrasound. A special surveillance program is offered for individuals 15–18 years old with a 50% risk of being a mutation carrier or with a verified TP53 variation, includes ultrasound of the abdomen and urine corticosteroid profiles. Clinically motivated further examinations are performed upon need. The national inclusion is performed through the six clinical genetic units in Sweden at Umeå, Uppsala, Stockholm, Gothenburg, Linköping and Lund, and the surveillance is mainly performed through the oncology clinics.ResultsTo date, a total of 41 adults and 11 children have been included in the study.ConclusionsThe SWEP53 is the first structured national surveillance program including radiological and clinical routines for TP53 mutation carriers in the Scandinavian setting. The aim of this publication is to present and describe the ongoing Swedish surveillance study to encourage the initiation of similar studies and to contribute to the knowledge of adequate clinical handling of these cancer prone families.Trial registrationTrial registration number: ISRCTN13103571, retrospectively registered on 14/10/2019.

Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model

The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural stability of their affected proteins, information from structural change caused by genetic variants can be used to identify the variants with deleterious effects. In order to measure the structural change for proteins with large size, we designed a method named RP-MDS composed of Ramachandran plot (RP) and Molecular Dynamics Simulation (MDS). Ramachandran plot captures the variant-caused secondary structural change, whereas MDS provides a quantitative measure for the variant-caused globular structural change. We tested the method using variants in TP53 DNA binding domain of 219 residues as the model. In total, RP-MDS identified 23 of 38 (60.5%) TP53 known Pathogenic variants and 17 of 42 (41%) TP53 VUS that caused significant changes of P53 structure. Our study demonstrates that RP-MDS method provides a powerful protein structure-based tool to screen deleterious genetic variants affecting large-size proteins.

Health professionals' practice for young people with, or at risk of, Li-Fraumeni syndrome: An Australasian survey.

Li-Fraumeni syndrome (LFS), a rare cancer syndrome caused by pathogenic germline variants in TP53, has serious implications for adolescents and young adults (AYAs; aged 15-39years). The early-onset and multi-organ cancer risk associated with LFS means health professionals must concurrently contend with the developmental needs of individuals who are diagnosed from a young age, and recent changes in practice due to advances in whole-body cancer surveillance. To help understand how current practice meets the developmental needs of AYAs with, or at risk of, LFS, we conducted a national online survey to explore the experiences of health professionals who care for this population in Australia and New Zealand. Forty-three respondents completed the survey (56% genetic counselors), one-third of whom had facilitated predictive TP53 testing for minors (n=14/43, 33%). In hypothetical scenarios describing 15-year-olds eligible for predictive TP53 testing, respondents were more supportive of testing for emotionally mature compared to immature minors (p=.009); and more supportive of adolescent wishes compared to parental wishes for testing (p=.020) when families held discordant views on testing. Genetic health professionals were more likely than oncology health professionals to address psychological (p=.017) and information needs about reproductive options for LFS during consultations than to refer them on (p=.004). All respondents supported comprehensive risk management for LFS, but noted important medical, logistical, and psychosocial limitations for AYAs. This study offers valuable insight into developmentally appropriate practices of Australasian health professionals who care for AYAs with, or at risk of, LFS. These findings suggest they may foster the autonomy of minors undergoing predictive TP53 genetic testing and be supportive of new whole-body risk management guidelines.