scholarly journals ­­Differences in Somatic TP53 Mutation Type in Breast Tumors by Race and Receptor Status

2021 ◽  
Author(s):  
Nijole C Pollock ◽  
Johnny Ramroop ◽  
Heather Hampel ◽  
Melissa A. Troester ◽  
Kathleen Conway ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tp53 Mutation ◽  
African Ancestry ◽  
Dominant Negative ◽  
Driver Mutations ◽  
Published Data ◽  
Functional Impact ◽  
Receptor Status ◽  
Tp53 Mutations ◽  
Mutation Type

Abstract Purpose: Somatic driver mutations in TP53 are associated with triple negative breast cancer (TNBC) and poorer outcomes. Breast cancers in women of African ancestry (AA) are more likely to be TNBC and have somatic TP53 mutations than cancers in non-Hispanic White (NHW) women. Missense driver mutations in TP53 have varied functional impact including loss-of-function (LOF) or gain-of-function (GOF) activity, and dominant negative (DNE) effects. We aimed to determine if there were differences in somatic TP53 mutation types by patient ancestry or TNBC status. Methods: We identified breast cancer datasets with somatic TP53 mutation data, ancestry, age, and hormone receptor status. Mutations were classified for functional impact using published data and type of mutation. We assessed differences using Fisher’s exact test. Results: From 96 breast cancer studies, we identified 2964 women with somatic TP53 mutations: 715 (24.1%) Asian, 258 (8.7%) AA, 1931 (65.2%) NHW, and 60 (2%) Latina. The distribution of TP53 mutation type was similar by ancestry. However, 35.8% of tumors from NHW individuals had GOF mutations compared to 29% from AA individuals (p=0.04). Mutations with DNE activity were positively associated with TNBC (OR=1.37, p=0.03) and estrogen receptor (ER) negative status (OR=1.38; p=0.005).Conclusions: Somatic TP53 mutation types did not differ by ancestry overall, but GOF mutations were more common in NHW women than AA women. ER negative and TNBC tumors are less likely to have DNE+ TP53 mutations which could reflect biological processes. Larger cohorts and functional studies are needed to further elucidate these findings.

scholarly journals ­­Differences in somatic TP53 Mutation Type in Breast Tumors by Race and Receptor Status

2021 ◽  
Author(s):  
Nijole C Pollock ◽  
Johnny R Ramroop ◽  
Heather Hampel ◽  
Melissa A Troester ◽  
Kathleen Conway ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tp53 Mutation ◽  
Cpg Island ◽  
African Ancestry ◽  
Breast Tumors ◽  
Dominant Negative ◽  
Driver Mutations ◽  
Loss Of Function ◽  
Receptor Status ◽  
Mutation Type

Abstract Background: Somatic driver mutations in TP53 are associated with triple negative breast cancer (TNBC) and poorer outcomes. Breast cancers arising in women of African ancestry (AA) are more likely to be TNBC and have somatic TP53 mutations than non-Hispanic White (NHW) women. Missense driver mutations in TP53 are known to have different functional effects including loss-of function (LOF) or gain-of-function (GOF) activity. A subset of variants exhibit dominant negative (DNE) activity over wildtype TP53 or other TP53 family members. Methods: To determine if there were differences in TP53 mutation type by race or TNBC status we identified published and unpublished datasets with somatic mutation data, race, age, and hormone receptor status. Mutations were classified as LOF, GOF or CpG Island hotspot by published literature or type of mutation (e.g. frameshift and nonsense mutations were considered to be LOF). We used Fisher’s Exact test to assess for significant differences.Results: We identified 96 independent breast cancer studies with race and somatic TP53 mutation status available. The study comprised data from a total of 2964 women with somatic TP53 mutations: 715 (24.1%) Asian, 258 (8.7%) AA, 1931 (65.2%) NHW, and 60 (2%) Latina. Of the total TP53 mutations, 939 (31.7%) were GOF, 1739 (58.7%) were LOF, and the remaining 286 (9.6%) were not able to be classified. With respect to DNE activity, 1246 (42%) showed activity, 1190 (40.1%) showed no activity, and 528 (17.8%) were unknown status. The distribution of TP53 mutation type was similar by race and ethnicity. However, 35.8% of tumors from NHW individuals had GOF mutations compared to 29% in AA individuals (p=0.04). Mutations lacking DNE activity were positively associated with TNBC (OR=1.37, p=0.03) and estrogen receptor (ER) negative status (OR=1.38; p=0.005). Conclusions: In summary, ER negative and TNBC breast tumors are less likely to have DNE+ TP53 mutations which could reflect biological processes. Larger cohorts are needed to further elucidate some of these findings.

Disruption of TP53 function by Point Mutations and Deletions Is Associated with An Increased Risk of Disease Progression within Previously Treated, Relapsed Chronic Lymphocytic Leukemia Patients

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2445-2445
Author(s):  
Annika Dufour ◽  
Stefan K Bohlander ◽  
Evelyn Zellmeier ◽  
Gudrun Mellert ◽  
Karsten Spiekermann ◽  
...  
Keyword(s):  
Disease Progression ◽  
Research Funding ◽  
Tp53 Mutation ◽  
Lymphocytic Leukemia ◽  
Dominant Negative ◽  
Tp53 Mutations ◽  
Mutational Status ◽  
Igvh Mutational Status ◽  
Binet Stage ◽  
Previously Treated

Abstract Abstract 2445 Chronic lymphocytic leukemia (CLL) patients with a deletion of the TP53 tumor supressor gene located at 17p13 have a poor prognosis in first line chemotherapy regimens. Recent studies indicated somatic TP53 mutations as a prognostic factor in CLL independent of 17p13 deletion status. We aimed to further characterize the prognostic value and the impact of TP53 mutations on progression-free survival (PFS) in the presence and absence of a 17p13 deletion in previously treated and relapsed CLL patients within an international phase III clinical study comparing Fludarabine and Cyclophosphamide with or without Rituximab (FC versus R-FC: REACH trial). We analyzed 457 patients at diagnosis for mutations in the TP53 gene using a combination of a microarray-based resequencing assay (AmpliChip p53 Test, Roche Molecular Systems, USA.) and Sanger sequencing of TP53 exons 2–10. The data were correlated with clinical and biologic markers as well as with interphase fluorescence in situ hybridization (FISH) and with PFS. Association of the clinical data with PFS was assessed by Cox proportional hazard models. To estimate the functional significance of the individual TP53 mutations we used the IARC TP53 database. TP53 mutations (n=60) were detected in 52 of 457 patients (11.4%) and included 42 missense, 4 nonsense, 8 frameshift mutations, 2 in-frame deletions and 4 mutations in splice sites. Among other clinical variables, only 17p13 deletion was associated with TP53 mutations: 27 of 52 TP53 mutated patients had a 17p13 deletion (concordance rate: 52%, Fisher's test p<0.001). Median PFS for patients with TP53 mutations (n=52, 13 months, HR=1.9 (1.4–2.7), p<0.001) was significantly shorter as compared to patients without TP53 mutations (n=480, 27 months). In a sub-group analysis, chemoimmunotherapy including Rituximab did not significantly improve the PFS of patients with TP53 mutations. Multivariate analysis including treatment arm, Binet stage, age, IGVH mutational status, 17p13 deletion and TP53 mutation status confirmed TP53 mutation status (HR-TP53=1.7 (1.1–2.6), p=0.009) as a prognostic factor for PFS independent of 17p13 deletion status (HR-17p=1.7 (1.1–2.7), p=0.024) and with a similar effect size. The other independent prognostic factors were treatment (HR=0.61 (0.48–0.76), p<0.001), Binet stage (HR=1.64 (1.3–2.1), p<0.001) and IGVH mutational status (HR=2.4 (1.85–3.1), p<0.001). To further dissect the contribution of TP53 mutation and 17p13 deletion on PFS, we considered a multivariate analysis comparing patients with both TP53 mutation and 17p13 deletion (n=28), with only 17p13 deletion (n=9), with a dominant negative TP53 mutation or multiple TP53 mutations (n=8) or with a single TP53 mutation (n=16) against patients without TP53 abnormalities (n=271), adjusted for treatment, Binet stage, age and IGVH mutational status. Patients with a predicted biallelic disruption of TP53 either by a TP53 mutation in combination with a 17p13 deletion (HR: 2.8 (1.8,4.2), p=<0.001) or patients with a dominant negative TP53 mutation as predicted by the IARC TP53 database or multiple TP53 mutations (HR=3.26 (1.5,7.1), p=0.003) had a risk similar in size and which was quite high for disease progression (the reference to calculate the risk, here and in the following, is always the group of patients without TP53 abnormalities). The risk slightly decreased for patients with only a deletion 17p13 (HR=2.2, (1.1–4.3), p=0.021). Very interestingly, single TP53 mutations showed a much lower risk for disease progression (in this case not even significant) (HR=1.61 (0.9–2.8), p=0.084) especially compared to the risk conferred by a biallelic disruption. In this large cohort of previously treated CLL patients, complete disruption of TP53 function (by a combination of a 17p13 deletion and a TP53 mutation, through dominant negative TP53 mutations or through multiple TP53 mutations) was associated with a higher risk for disease progression. Prognosis of patients with a single TP53 mutation was not significantly different from patients without TP53 aberrations. It remains to be shown whether CLL patients with a single TP53 mutation are at a higher risk of acquiring additional mutations of TP53 during disease progression. Prognostic stratification of previously treated CLL patients should include a routine molecular TP53 mutational analysis in addition to deletion analysis of the TP53 locus by FISH. Disclosures: Dufour: Roche: Research Funding. Bohlander:Roche: Research Funding. Spiekermann:Roche: Research Funding. Schneider:Roche: Research Funding. Hiddemann:Roche: Research Funding. Truong:Roche: Employment. Patten:Roche: Employment. Wu:Roche: Employment. Dmoszynska:Mundipharma:; Roche: Honoraria. Robak:Centocor Ortho Biotech Research & Development: Research Funding. Geisler:Roche: Speakers Bureau. Dornan:Genentech: Employment. Lin:Genentech: Employment. Yeh:Genentech: Employment. Weisser:Roche: Employment. Duchateau-Nguyen:Roche: Employment. Palermo:Roche: Employment.

A meta-analysis of receptor status discordance between primary breast cancer and metastases.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 546-546 ◽  
Author(s):  
Gaetano Aurilio ◽  
Davide Disalvatore ◽  
Vincenzo Bagnardi ◽  
Elisabetta Munzone ◽  
Laura Adamoli ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Primary Breast Cancer ◽  
Meta Analysis ◽  
Receptor Expression ◽  
Her2 Status ◽  
Published Data ◽  
Her2 Receptor ◽  
Random Effects Models ◽  
Receptor Status ◽  
History Of

546 Background: There is an increasing awareness that biology of breast cancer may evolve over time. The discordance in estrogen (ER), progesterone (PgR) and HER2 receptor status between primary breast cancer and metastases is being intensively investigated and a large amount of data has been produced. However, results from different studies seem to be conflicting and heterogeneous. To highlight this issue, a meta-analysis of published data was performed. Methods: A literature search was performed with Medline. All studies published from 1983 to 2011 comparing changes inER, PgR and/or HER2 status in patients with matched breast primary and recurrent tumors were included. We used random-effects models to estimate pooled discordance proportions. Results: We selected 42 articles, mostly reporting retrospective studies. Twenty-eight, 20 and 27 articles were focused on ER, PgR and HER2 changes, respectively. A total of 2806 tumors were evaluated for ER discordance, 1809 for PgR discordance and 2801 for HER2 discordance. The heterogeneity between study-specific discordance proportions was high (I2 >75%, p<0.0001) for ER, PgR and HER2. Pooled discordance proportions were 20% (95% CI: 16-25%) for ER, 33% (95% CI: 28-38%) for PgR and 9% (95% CI: 6-12%) for HER2. Pooled proportions of tumors shifting from positive to negative and from negative to positive were 24% and 12% for ER (p=0.0115), respectively. The same figures were 44% and 15% for PgR (p<0.0001), and 14% and 6% for HER2 (p=0.04). Conclusions: To our knowledge, this is the first meta-analysis addressing this topic. The findings strengthen the concept that changes in receptor expression may occur during the natural history of breast cancer and therefore clinical implications with possible impact on treatment choice cannot be excluded. However, the high heterogeneity observed in our analysis may explain the disagreement among oncologists on performing a reassessment of the biological features. In our opinion, only high-powered prospective and randomized trials could clarify the controversies in this field.

Prevalence of germline TP53 p.R337H mutation in Brazilian young breast cancer patients.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e13101-e13101
Author(s):  
Fernanda Paschoal Fortes ◽  
Renata Tonhosolo ◽  
Rima Jbili ◽  
Karina Miranda Santiago ◽  
Kelvin Andrade ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Early Onset ◽  
Tp53 Mutation ◽  
Southeastern Brazil ◽  
Cancer Center ◽  
Breast Cancer Patients ◽  
Tp53 Mutations ◽  
Li Fraumeni Syndrome ◽  
Exon 10

e13101 Background: Germline TP53 mutations are associated with Li-Fraumeni syndrome (LFS), a disease that predisposes carriers to a wide variety of early onset tumors. Pre-menopausal breast cancer is the most frequent tumor found in carriers. In Southern and Southeastern Brazil, a germline TP53 mutation in exon 10, p.R337H, was diagnosed in 0,3% of the population due to a founder effect, a prevalence that is substantially higher than other LFS mutations. Methods: In this study we investigated the prevalence of the p.R337H TP53 germline mutation in 287 young female breast cancer patients (diagnosed before the age of 40) at A. C. Camargo Cancer Center, Sao Paulo, Brazil. DNA was extracted from saliva and Sanger sequencing of exon 10 was performed. All patients were consented. Results: The p.R337H TP53 mutation was present in 1.74% (5/287). Family history of cancer was present in three cases although it did not fulfill LFS clinical criteria. Conclusions: The identification of germline p.R337H mutation in this cohort strengthen the role of TP53 mutations in the early onset of breast cancer in pre-menopausal cancer in Brazil.

scholarly journals TP53 Mutations Negatively Impact Survival of Acute Myeloid Leukemia Patients Treated with Standard Doses of Azacitidine

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2745-2745
Author(s):  
Pierre Bories ◽  
Naïs Prade ◽  
Stéphanie Lagarde ◽  
Bastien Cabarrou ◽  
Julien Plenecassagnes ◽  
...  
Keyword(s):  
Missense Mutation ◽  
Tp53 Mutation ◽  
Response Rates ◽  
Classification Systems ◽  
Mutant P53 ◽  
Median Score ◽  
Functional Impact ◽  
Tp53 Mutations

Abstract Validated therapies for older pts with AML could rely on intensive or low-intensity strategies. Patient selection for these options remains controversial. There is currently no validated biomarker which can been used to guide therapeutic decision. TP53 mutations which are known to negatively impact AML pts outcome when treated with ICT, have been recently described as a positive prognosis factor for blast clearance with a 10-days regimen of decitabine (Welch, NEJM 2016). To date, it remains unclear whether AML pts with TP53 mutation represent a clinically homogeneous group. Several classification systems of p53 mutant, derived from in vitro or in vivo data, have been validated in solid tumors and aggressive lymphomas as predictors of p53 mutant functional impact or patient outcome. We retrospectively evaluated the impact of TP53 mutational status on the outcome of a real-world cohort of pts, treated frontline with standard doses of azacitidine (AZA). We further hypothesized that functional characterization of TP53 mutations could define a subgroup of pts with specific outcome with AZA From Jan 2007 to Dec 2016, we identified 279 AML pts enrolled in the regional cancer network ONCOMIP registry, treated frontline with AZA. Median age was 76 yrs (45-93), karyotype was adverse in 135 pts (49.1%), including 54 pts with -17 or del17p (19.4%). AML was secondary to MDS in 71 pts (25.4%), to MPN in 24 (8.6%) and therapy related in 46 pts (16.5%). Pts received a median of 6 cycles (1-67). Overall, 54 pts obtained CR/CRi (19.4%) and median OS was 10.6 months (95%CI ,9.7-12.1). For 224 pts with an available bone marrow baseline DNA sample, TP53 mutations were screened with next-generation sequencing on an Illumina® MiSeq sequencer. Sequencing results were filtered with the IARC TP53 mutations database and a variant allele frequency (VAF) >10%, strengthening the specificity of the data of this cohort. Of the 224 analyzed cases, 55 cases (24.6%) contained TP53 mutations. Response rates did not significantly differ between TP53mut (21.8% CR/CRi) and TP53wt (17.8% CR/CRi, p=.50) nor between pts with TP53mut and/or -17/del17p (19.1% CR/CRi) and pts without TP53 abnormality (18.6%CR/CRi, p=.93). Median OS was 7.9 months in pts with TP53mut and 12.6 months in TP53wt (p<.0001). With regards to the group of 109 pts with adverse karyotype, response rates did not significantly differ between TP53mut pts (20.8% CR/CRi) and TP53wt (14.3%, p=.37) and median OS was 7.9 months for TP53mut pts versus 9.6 for TP53wt pts (p=.02) Among the 55 pts with TP53mut, 53pts had adverse cytogenetics (96.4%), 16 pts had secondary AML to MDS or MPN (29.1%) and 13 had t-AML (23.6%). This subgroup included 49 cases (89%) with single TP53 mutation (missense n=42, nonsense n= 3, frameshift n=4) and 6 cases (11%) with 2 mutations (2 pts with missense and frameshift mutations and 4 pts with 2 missense mutation). We further characterized TP53mut pts with 3 validated classification systems. Due to dominant negative effect of TP53 mutation, for pts with >1 TP53 mutation, we selected the mutation with the predicted highest impact: 15 pts had disruptive mutations (i.e. missense mutation in L2/L3 helix of the DNA binding domain or truncating mutation) versus 40 pts with non-disruptive mutations (Poeta M, NEJM 2007), which was not associated with clinical response (25% in CR/CRi vs 27.9% in failure; p=1.00) nor with 6mOS (46.7% vs 55%, respectively; p=.79)Mutant p53 transactivation activity assessed with a 0-100 evolutionary score (Neskey D, Cancer Research 2015), was not associated with response (median score of 79.3[28-90] in CR/CRi vs 73.3 [49-96] in failure, p=1.00) nor with OS (HR 1.01; 95% CI, 0.99-1.03, p=.51).Relative fitness score (on a log2 scale) which was recently reported as a proxy of p53 mutant in vitro and in vivo cell proliferation advantage (Kotler E, Molecular cell 2018) was not associated with response (median score in CR/CRi of 0.094 [-0.79-0.58] vs 0.094 [-2.52-0.84] in failure, p=.68) nor with OS (HR 0.75; 95% CI, 0.45-1.22, p=.24) Overall, the response rate was not influenced by the TP53mut status, but median OS was negatively impacted by the TP53mut status in the entire cohort and in the sub-group of pts with adverse karyotype. None of the mutant p53 classification systems validated in other neoplasms succeed in identifying a subset of AML pts who specifically benefit from AZA suggesting a rather homogenous functional impact of TP53 mutations in this setting Disclosures Fornecker: Takeda: Honoraria; Servier: Honoraria.

TP53 Mutation Profile and New Mutations in Chronic Lymphocytic Leukemia in Normandy

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4593-4593
Author(s):  
Nordine Lahyane ◽  
Julien Alani ◽  
Xavier Troussard ◽  
Stephane Cheze ◽  
Jean-Pierre Vilque ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Tp53 Mutation ◽  
Lymphocytic Leukemia ◽  
Silent Mutation ◽  
Positive Pressure ◽  
Published Data ◽  
New Mutation ◽  
Tp53 Mutations ◽  
Poor Outcome ◽  
Mutation Databases

Abstract Abstract 4593 Introduction: As deletion of 17p13 (del 17p13) in Chronic lymphocytic leukemia (CLL) patients is associated with poor outcome and chemorefractoriness to alkylating agents and purine analogues, current diagnostic guidelines recommend its screening at diagnosis and prior to treatment initiation. TP53 is a tumor suppressor gene, maps to 17p13 and is inactivated through somatic mutations or by 17p13 deletion. Recent studies show that TP53 mutation is of clinical relevance in CLL patients and has practical implication for therapeutic stratification. The purpose of this study is to characterize the TP53 mutation pattern and its incorporation into treatment algorithms in CLL patients treated in our center. Materials and methods: A retrospective study was performed on a cohort of 42 patients with CLL for whom clinical, biological and fluorescent in situ hybridization (FISH) data were available. Ages ranged from 31 to 88 (median, 63 years), 17 patients were in Binet stage A, 12 in B and 13 in stage C. Treatment was not in controlled trials, and standard clinical criteria were used for the initiation of therapy. DNA was extracted from 52 available samples and TP53 exons 2 to 11 were screened for mutations by high resolution melting (HRM) (Roche LC480). Mutations were confirmed by sequencing both strands using different primer sets (Beckman, Ceq 8000) then validated by the IARC and UMD TP53 Mutation Databases. Results: Out of 42 patients, del 17p13 was observed in 11 (26%), del 11q22 in 8 (19%), del 13q14 in 13 (31%), trisomy 12 in 2 (5%) and normal FISH in 20 (47.6%). We found an overall incidence of TP53 mutations of 19% (8 of 42 patients), 1 new mutation was identified and 5 mutations were not previously reported in CLL but in other cancers according to the IARC and UMD TP53 mutation Databases (table 1). A total of 65 polymorphisms were detected with a prevalence for the g.11446C>G polymorphism of 0.9 compared to 0.49 in published data. Amongst the 8 patients with TP53 mutations, 7 (87%) presented a 17p deletion and mutations were mainly located in the DNA binding domain (62%). 7 of 11 patients (63%) with 17p13 deletion harbored a TP53 mutation. In the absence of del 17p13 only 3% of patients (1 of 31) had a TP53 mutation (table 2). 5 of 8 patients with mutations (62%) presented with an advanced clinical stage and a median age of 56 years. Clonal evolution leading to acquisition of the TP53 mutation was not necessary related to therapy; 3 sequential samples were available for a patient with no abnormalities at diagnosis and who developed a TP53 mutation after 2 years and before therapy initiation. Another patient who was initially devoid of TP53 mutations and responded to treatment with standard chemotherapy, developed chemorefractoriness concomitant with a TP53 mutation acquisition. An interesting case was that of a patient who had been in complete remission after treatment with rituximab, fludarabin and cyclophosphamid (RFC) despite the presence of a TP53 mutation without del 17p13 at diagnosis. Sequencing demonstrated that this patient harbored a silent mutation in exon 4 g.12441C>G. In Conclusion: This study shows similar findings to published data except for a higher incidence of patients with TP53 mutations probably due to bias selection and a low cohort of patients. We identified a new mutation and 5 other mutations not previously detected in CLL patients. As TP53 is associated with poor outcome and chemorefractoriness, and its acquisition might be a result of positive pressure selection following treatment, we think it is of utmost importance to look for TP53 mutations in parallel to FISH at diagnosis and in case of chemorefractoriness using the HRM a cheap and sensitive method followed by sequencing positive cases. Disclosures: No relevant conflicts of interest to declare.

Correlation of tumor mutational burden (TMB) with CDKN2A and TP53 mutation in HPV-negative head and neck squamous cell carcinoma (HNSCC).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 6552-6552 ◽  
Author(s):  
Barbara Burtness ◽  
Alexander Deneka ◽  
Yasmine Baca ◽  
Ilya Serebriiskii ◽  
Mitchell I. Parker ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Tp53 Mutation ◽  
Predictive Biomarker ◽  
Dominant Negative ◽  
Alternative Methods ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Tp53 Mutations ◽  
Cdkn2a Mutation ◽  
Mutational Status

6552 Background: The tumor suppressors TP53 and CDKN2A are commonly mutated or lost in HNSCC, impairing G1 checkpoints. This reduces ability to repair DNA damage arising from hypoxia, replication stress, and mutagen exposure, thus increasing TMB, a potential predictive biomarker for immunotherapy benefit. TP53 mutations can be classified as loss-of-function (LOF) with or without dominant negative (DNE) activity, gain-of-function (GOF) and benign. We investigated whether specific categories of TP53 mutation were associated with increased TMB, and whether these cooperated with CDKN2A mutation to elevate TMB. Methods: We analyzed 1010 HPV- HNSCC tumor samples (246 female) profiled with a 592-gene panel by Caris Life Sciences from 2015 to 2019. Predominant subsites were oral cavity (285), oropharynx (225) and larynx (153). TMB reflected all somatic nonsynonymous missense mutations detected. We report mean TMB per megabase (MB). Pathogenicity of TP53 and CDKN2A mutations was determined according to American College of Medical Genetics (ACMG) guidelines. We also used four alternative methods of characterizing TP53 mutations based on analysis of protein structure, public databases (IARC, ClinVar, InterVar), and publications (PMID: 25108461 and others) assessing structure-function relations. Results: 60% of cases had TP53 mutations ( TP53mut) designated pathogenic by ACMG guidelines. Estimates of frequency of LOF/DNE mutations ranged from 30-42.8% of cases among the alternative classification methods. Damaging CDKN2A mutations were present in 20%. Average TMB per MB varied from 8.2/8.6 (females/males) in oral cavity cancers to 26.5/27.7 (females/males) in cancer of the lip. Mean TMB was typically higher in the presence of damaging LOF/DNE TP53 mutations or CDKN2A mutations, but not TP53 GOF mutations. Based on ACMG, for tumors with TP53 and CDKN2A wild type (WT) TMB was 8.03, for those with CDKN2Amut-only 9.82, for TP53mut-only 10.56, and TP53 mut/CDKN2A mut 17.6 (p < 0.001). For disruptive TP53mut (Poeta algorithm), mean TMB for WT/WT was 8.67, for TP53mut 11.31, CDKN2Amut 17.9 and TP53mut/CDKN2A mut 15.83 (p < 0.001). Conclusions: Mutation of TP53 and/or CDKN2A is associated with increased mean TMB relative to WT; mean TMB was highest for tumors bearing damaging mutations in both genes. GOF TP53 mutation was not clearly associated with increased TMB. As TMB is evaluated as a predictive biomarker in the immunotherapy of HNSCC, specific TP53/CDKN2A mutational status should also be evaluated.

Sign in / Sign up

Export Citation Format

Share Document