Fanconi anemia caused by biallelic inactivation of BRCA2 can present with an atypical cancer phenotype in adulthood

Inherited biallelic pathogenic variants (PVs) in BRCA2 cause Fanconi Anemia complementation group D1 (FA-D1), a severe pediatric bone marrow failure and high-risk cancer syndrome. We identified biallelic BRCA2 PVs in a young adult with multiple basal cell carcinomas, adult-onset colorectal cancer and small cell neuroendocrine carcinoma, without bone marrow failure. No PVs were identified in any other known cancer susceptibility gene, and there was no evidence of reversion mosaicism. The proband's deceased sister had a classic FA-D1 presentation and was shown to carry the same biallelic BRCA2 PVs. A lymphoblastoid cell line derived from the proband demonstrated hypersensitivity to DNA damaging agents, and bone marrow showed aberrant RAD51 staining. Family expansion demonstrated the presence of BRCA2 related cancers in heterozygous family members. Our data highlight the striking phenotypic differences which can be observed within FA-D1 families and expands the clinical spectrum of FA-D1 to include adult presentation with a constellation of solid tumors not previously thought of as characteristic of Fanconi Anemia. Early recognition of this syndrome in a family could prevent further morbidity and mortality by implementation of hereditary breast and ovarian cancer screening and treatment strategies for heterozygous family members.

Cetuximab-Based vs Carboplatin-Based Chemoradiotherapy for Patients With Head and Neck Cancer

Importance

Cetuximab-based and carboplatin-based chemoradiotherapy (CRT) are often used for patients with locally advanced head and neck cancer who are ineligible for cisplatin. There are no prospective head-to-head data comparing cetuximab-based and carboplatin-based regimens for radiosensitization.

Objective

To compare survival with cetuximab-based and carboplatin-based CRT in locally advanced head and neck squamous cell carcinoma (HNSCC).

Design, Setting, and Participants

This cohort study included US veterans who received a diagnosis of HNSCC between January 2006 and December 2020 and were treated with systemic therapy and radiation. Data cutoff was March 1, 2022 and data analysis was conducted from April-May 2022.

Exposures

Cisplatin, cetuximab, or carboplatin-based systemic therapy as captured in VA medication data and cancer registry.

Main Outcomes and Measures

Overall survival by systemic therapy was estimated using Kaplan-Meier methods. We used propensity score and inverse probability weighting to achieve covariate balance between cetuximab-treated and carboplatin-treated patients and used Cox regression to estimate cause-specific hazard ratios of death associated with carboplatin vs cetuximab. We also performed subgroup analyses of patients with oropharynx vs nonoropharynx primary sites.

Results

A total of 8290 patients (median [IQR] age, 63 [58-68] years; 8201 men [98.9%]; 1225 [15.8%] Black or African American and 6424 [82.6%] White individuals) with nonmetastatic HNSCC were treated with CRT with cisplatin (5566 [67%]), carboplatin (1231 [15%]), or cetuximab (1493 [18%]). Compared with cisplatin-treated patients, patients treated with carboplatin and cetuximab were older with worse performance status scores and higher comorbidity burden. Median (IQR) overall survival was 74.4 (22.3-162.2) months in patients treated with cisplatin radiotherapy (RT), 43.4 (15.3-123.8) months in patients treated with carboplatin RT, and 31.1 (12.4-87.8) months in patients treated with cetuximab RT. After propensity score and inverse probability weighting, carboplatin was associated with improved overall survival compared with cetuximab (cause-specific hazard ratio, 0.85; 95% CI, 0.78-0.93; P = .001). This difference was prominent in the oropharynx subgroup.

Conclusions and Relevance

In this cohort study of a US veteran population with HNSCC undergoing treatment with CRT, almost a third of patients were ineligible to receive treatment with cisplatin and received cetuximab-based or carboplatin-based radiosensitization. After propensity score matching, carboplatin-based systemic therapy was associated with 15% improvement in overall survival compared with cetuximab, suggesting that carboplatin may be the preferred radiosensitizer, particularly in oropharynx cancers.

Association Between Up-front Surgery and Risk of Stroke in US Veterans With Oropharyngeal Carcinoma

Importance

Cardiovascular events are an important cause of morbidity in patients with oropharyngeal squamous cell carcinoma (OPSCC). Radiation and chemotherapy have been associated with increased risk of stroke; up-front surgery allows the opportunity for (chemo)radiotherapy de-escalation.

Objective

To evaluate whether up-front surgery was associated with decreased stroke risk compared to nonsurgical treatment for OPSCC.

Design, Setting, and Participants

This cohort study was conducted at the US Veterans Health Administration and examined US veterans diagnosed with nonmetastatic OPSCC from 2000 to 2020. Data cutoff was September 17, 2021, and data analysis was performed from October 2021 to February 2022.

Exposures

Up-front surgical treatment or definitive (chemo)radiotherapy as captured in cancer registry.

Main Outcomes and Measures

Cumulative incidence of stroke, accounting for death as a competing risk; and association between up-front surgery and stroke risk. After generating propensity scores for the probability of receiving surgical treatment and using inverse probability weighting (IPW) to construct balanced pseudo-populations, Cox regression was used to estimate a cause-specific hazard ratio (csHR) of stroke associated with surgical vs nonsurgical treatment.

Results

Of 10 436 patients, median (IQR) age was 61 (56-67) years; 10 329 (99%) were male; 1319 (13%) were Black, and 7823 (75%) were White; 2717 received up-front surgery, and 7719 received nonsurgical therapy with definitive (chemo)radiotherapy. The 10-year cumulative incidence of stroke was 12.5% (95% CI, 11.8%-13.3%) and death was 57.3% (95% CI, 56.2%-58.4%). Surgical patients who also received (chemo)radiotherapy had shorter radiation and chemotherapy courses than nonsurgical patients. After propensity score and IPW, the csHR of stroke for surgical treatment was 0.77 (95% CI, 0.66-0.91). This association was consistent across subgroups defined by age and baseline cardiovascular risk factors.

Conclusions and Relevance

In this cohort study, up-front surgical treatment was associated with a 23% reduced risk of stroke compared with definitive (chemo)radiotherapy. These findings present an important additional risk-benefit consideration to factor into treatment decisions and patient counseling and should motivate future studies to examine cardiovascular events in this high-risk population.

Abstract 2237: Rates of intervention after initial versus subsequent whole-body MRI screening in Li-Fraumeni Syndrome

Background: Yearly whole-body MRI is recommended for cancer screening in patients with the rare high risk cancer predisposition syndrome, Li-Fraumeni syndrome (LFS). This is based on data from multiple studies demonstrating an approximately 7% cancer detection rate on baseline screening. However, the rate of actionable findings and malignancies on initial versus subsequent screenings has yet to be compared in a patient cohort.

Patients and Methods: We identified 68 adult LFS patients in a single institutional cohort that received more than one full body MRI (including brain MRI). For each screening instance, findings and subsequent recommended interventions (immediate and short-term imaging, biopsy, and/or surgery) were recorded. Invasive interventions (biopsy and/or surgery) were denoted with free text describing pathology results. We analyzed findings on initial versus subsequent scans.

Results: There were 258 instances of whole-body MRI screenings performed in 68 patients (28% male, 72% female) in the cohort. The mean number of screenings per patient analyzed was 3.8±1.9 over 3.3±2.4 years. Among 68 initial screenings, 26 (38.2%) required follow-up imaging or invasive intervention. Among 190 subsequent screenings, the follow-up intervention rate was significantly lower (n=36, 18.9%, p=0.0026). Eleven screenings (5.8%) required invasive follow-up (biopsy or surgery); two (3% of patients) were from an initial screening and nine (13% of patients) were from a subsequent screening. From these interventions, we identified six total cancers in five patients amongst the cohort (7% of patients), with two cancers (3% of patients) being identified on the first screening and four (6% of patients) being identified on a subsequent screening.

Conclusion: Cancer detection rates were similar between initial and subsequent whole-body MRI screenings in LFS patients. Follow-up interventions decreased significantly on subsequent screenings compared to the initial screen. These findings may be useful in counseling of LFS patients initiating a screening program. Limitations of this study include lack of inclusion of other screening modalities in the analysis, short follow-up duration, and loss to follow-up. Further studies involving a larger cohort with longer-term follow-up are needed to fully determine the impact of long-term whole-body MRI screening in LFS.

Citation Format: Yun K. Du, Conrad Fernandes, Anh N. Le, Madeline Good, Miche Duvall, Sarah Jennings, Jacquelyn Powers, Kristen Zelley, Bryson W. Katona, Suzanne P. MacFarland, Kara N. Maxwell. Rates of intervention after initial versus subsequent whole-body MRI screening in Li-Fraumeni Syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2237.

Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank

PURPOSE

Genome-wide association studies have identified hundreds of single nucleotide variations (formerly single nucleotide polymorphisms) associated with several cancers, but the predictive ability of polygenic risk scores (PRSs) is unclear, especially among non-Whites.

METHODS

PRSs were derived from genome-wide significant single-nucleotide variations for 15 cancers in 20,079 individuals in an academic biobank. We evaluated the improvement in discriminatory accuracy by including cancer-specific PRS in patients of genetically-determined African and European ancestry.

RESULTS

Among the individuals of European genetic ancestry, PRSs for breast, colon, melanoma, and prostate were significantly associated with their respective cancers. Among the individuals of African genetic ancestry, PRSs for breast, colon, prostate, and thyroid were significantly associated with their respective cancers. The area under the curve of the model consisting of age, sex, and principal components was 0.621 to 0.710, and it increased by 1% to 4% with the inclusion of PRS in individuals of European genetic ancestry. In individuals of African genetic ancestry, area under the curve was overall higher in the model without the PRS (0.723-0.810) but increased by <1% with the inclusion of PRS for most cancers.

CONCLUSION

PRS moderately increased the ability to discriminate the cancer status in individuals of European but not African ancestry. Further large-scale studies are needed to identify ancestry-specific genetic factors in non-White populations to incorporate PRS into cancer risk assessment.

Inherited TP53 Variants and Risk of Prostate Cancer

BACKGROUND

Inherited germline TP53 pathogenic and likely pathogenic variants (gTP53) cause autosomal dominant multicancer predisposition including Li-Fraumeni syndrome (LFS). However, there is no known association of prostate cancer with gTP53.

OBJECTIVE

To determine whether gTP53 predisposes to prostate cancer.

DESIGN, SETTING, AND PARTICIPANTS

This multi-institutional retrospective study characterizes prostate cancer incidence in a cohort of LFS males and gTP53 prevalence in a prostate cancer cohort.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We evaluated the spectrum of gTP53 variants and clinical features associated with prostate cancer.

RESULTS AND LIMITATIONS

We identified 31 prostate cancer cases among 163 adult LFS males, including 26 of 54 aged ≥50 yr. Among 117 LFS males without prostate cancer at the time of genetic testing, six were diagnosed with prostate cancer over a median (interquartile range [IQR]) of 3.0 (1.3-7.2) yr of follow-up, a 25-fold increased risk (95% confidence interval [CI] 9.2-55; p < 0.0001). We identified gTP53 in 38 of 6850 males (0.6%) in the prostate cancer cohort, a relative risk 9.1-fold higher than that of population controls (95% CI 6.2-14; p < 0.0001; gnomAD). We observed hotspots at the sites of attenuated variants not associated with classic LFS. Two-thirds of available gTP53 prostate tumors had somatic inactivation of the second TP53 allele. Among gTP53 prostate cancer cases in this study, the median age at diagnosis was 56 (IQR: 51-62) yr, 44% had Gleason ≥8 tumors, and 29% had advanced disease at diagnosis.

CONCLUSIONS

Complementary analyses of prostate cancer incidence in LFS males and gTP53 prevalence in prostate cancer cohorts suggest that gTP53 predisposes to aggressive prostate cancer. Prostate cancer should be considered as part of LFS screening protocols and TP53 considered in germline prostate cancer susceptibility testing.

PATIENT SUMMARY

Inherited pathogenic variants in the TP53 gene are likely to predispose men to aggressive prostate cancer.

PTEN Loss and BRCA1 Promoter Hypermethylation Negatively Predict for Immunogenicity in BRCA-Deficient Ovarian Cancer

PURPOSE

Ovarian cancers can exhibit a prominent immune infiltrate, but clinical trials have not demonstrated substantive response rates to immune checkpoint blockade monotherapy. We aimed to understand genomic features associated with immunogenicity in BRCA1/2 mutation-associated cancers.

MATERIALS AND METHODS

Using the Cancer Genome Atlas whole-exome sequencing, methylation, and expression data, we analyzed 66 ovarian cancers with either germline or somatic loss of BRCA1/2 and whole-exome sequencing, immunohistochemistry, and CyTOF in 20 ovarian cancers with germline BRCA1/2 pathogenic variants from Penn.

RESULTS

We found two groups of BRCA1/2 ovarian cancers differing in their immunogenicity: (1) 37 tumors significantly enriched for PTEN loss (11, 30%) and BRCA1 promoter-hypermethylated (10, 27%; P = .0016) and (2) PTEN wild-type (28 of 29 tumors) cancers, with the latter group having longer overall survival (OS; P = .0186, median OS not reached v median OS = 66.1 months). BRCA1/2-mutant PTEN loss and BRCA1 promoter-hypermethylated cancers were characterized by the decreased composition of lymphocytes estimated by gene expression (P = .0030), cytolytic index (P = .034), and cytokine expression but higher homologous recombination deficiency scores (P = .00013). Large-scale state transitions were the primary discriminating feature (P = .001); neither mutational burden nor neoantigen burden could explain differences in immunogenicity. In Penn tumors, PTEN loss and high homologous recombination deficiency cancers exhibited fewer CD3+ (P = .05), CD8+ (P = .012), and FOXP3+ (P = .0087) T cells; decreased PRF1 expression (P = .041); and lower immune costimulatory and inhibitory molecule expression.

CONCLUSION

Our study suggests that within ovarian cancers with genetic loss of BRCA1/2 are two subsets exhibiting differential immunogenicity, with lower levels associated with PTEN loss and BRCA hypermethylation. These genomic features of BRCA1/2-associated ovarian cancers may inform considerations around how to optimally deploy immune checkpoint inhibitors in the clinic.

Breast and Prostate Cancer Risks for Male BRCA1 and BRCA2 Pathogenic Variant Carriers Using Polygenic Risk Scores

BACKGROUND

Recent population-based female breast cancer and prostate cancer polygenic risk scores (PRS) have been developed. We assessed the associations of these PRS with breast and prostate cancer risks for male BRCA1 and BRCA2 pathogenic variant carriers.

METHODS

483 BRCA1 and 1318 BRCA2 European ancestry male carriers were available from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). A 147-single nucleotide polymorphism (SNP) prostate cancer PRS (PRSPC) and a 313-SNP breast cancer PRS were evaluated. There were 3 versions of the breast cancer PRS, optimized to predict overall (PRSBC), estrogen receptor (ER)-negative (PRSER-), or ER-positive (PRSER+) breast cancer risk.

RESULTS

PRSER+ yielded the strongest association with breast cancer risk. The odds ratios (ORs) per PRSER+ standard deviation estimates were 1.40 (95% confidence interval [CI] =1.07 to 1.83) for BRCA1 and 1.33 (95% CI = 1.16 to 1.52) for BRCA2 carriers. PRSPC was associated with prostate cancer risk for BRCA1 (OR = 1.73, 95% CI = 1.28 to 2.33) and BRCA2 (OR = 1.60, 95% CI = 1.34 to 1.91) carriers. The estimated breast cancer odds ratios were larger after adjusting for female relative breast cancer family history. By age 85 years, for BRCA2 carriers, the breast cancer risk varied from 7.7% to 18.4% and prostate cancer risk from 34.1% to 87.6% between the 5th and 95th percentiles of the PRS distributions.

CONCLUSIONS

Population-based prostate and female breast cancer PRS are associated with a wide range of absolute breast and prostate cancer risks for male BRCA1 and BRCA2 carriers. These findings warrant further investigation aimed at providing personalized cancer risks for male carriers and informing clinical management.

A randomized study of genetic education versus usual care in tumor profiling for advanced cancer in the ECOG-ACRIN Cancer Research Group (EAQ152)

Background

Enthusiasm for precision oncology may obscure the psychosocial and ethical considerations associated with the implementation of tumor genetic sequencing.

Methods

Patients with advanced cancer undergoing tumor‐only genetic sequencing in the National Cancer Institute Molecular Analysis for Therapy Choice (MATCH) trial were randomized to a web‐based genetic education intervention or usual care. The primary outcomes were knowledge, anxiety, depression, and cancer‐specific distress collected at baseline (T0), posteducation (T1) and after results (T2). Two‐sided, 2‐sample t tests and univariate and multivariable generalized linear models were used.

Results

Five hundred ninety‐four patients (80% from NCI Community Oncology Research Program sites) were randomized to the web intervention (n = 293) or usual care (n = 301) before the receipt of results. Patients in the intervention arm had greater increases in knowledge (P for T1‐T0 < .0001; P for T2‐T0 = .003), but there were no significant differences in distress outcomes. In unadjusted moderator analyses, there was a decrease in cancer‐specific distress among women (T0‐T1) in the intervention arm but not among men. Patients with lower health literacy in the intervention arm had greater increases in cancer‐specific distress and less decline in general anxiety (T0‐T1) and greater increases in depression (T0‐T2) in comparison with those receiving usual care.

Conclusions

Web‐based genetic education before tumor‐only sequencing results increases patient understanding and reduces distress in women. Refinements to the intervention could benefit low‐literacy groups and men.

In the Communication and Education in Tumor Profiling (COMET) study, patients with advanced cancer undergoing tumor genetic sequencing in the National Cancer Institute Molecular Analysis for Therapy Choice (MATCH) trial have been randomized to a web‐based genetic education intervention or usual care. Web‐based genetic education has resulted in increased patient understanding and reduced distress in female patients with cancer.

SARS-CoV-2 Seropositivity and Seroconversion in Patients Undergoing Active Cancer-Directed Therapy

PURPOSE

Multiple studies have demonstrated the negative impact of cancer care delays during the COVID-19 pandemic, and transmission mitigation techniques are imperative for continued cancer care delivery. We aimed to gauge the effectiveness of these measures at the University of Pennsylvania.

METHODS

We conducted a longitudinal study of SARS-CoV-2 antibody seropositivity and seroconversion in patients presenting to infusion centers for cancer-directed therapy between May 21, 2020, and October 8, 2020. Participants completed questionnaires and had up to five serial blood collections.

RESULTS

Of 124 enrolled patients, only two (1.6%) had detectable SARS-CoV-2 antibodies on initial blood draw, and no initially seronegative patients developed newly detectable antibodies on subsequent blood draw(s), corresponding to a seroconversion rate of 0% (95% CI, 0.0 TO 4.1%) over 14.8 person-years of follow up, with a median of 13 health care visits per patient.

CONCLUSION

These results suggest that patients with cancer receiving in-person care at a facility with aggressive mitigation efforts have an extremely low likelihood of COVID-19 infection.

Analysis of the Li-Fraumeni Spectrum Based on an International Germline TP53 Variant Data Set: An International Agency for Research on Cancer TP53 Database Analysis

Questions

What is the phenotypic spectrum associated with variants in TP53, the gene variant in persons with Li-Fraumeni syndrome, and what mechanisms underlie phenotypic differences?

Findings

In this cohort study, the phenotypes within the classification Li-Fraumeni spectrum were defined, and data from 3034 persons from 1282 families with data available in the International Agency for Research on Cancer TP53 Database were analyzed and classified to reveal meaningful differences in the TP53 variant distribution between patients who met vs those who did not meet Li-Fraumeni syndrome testing criteria.

Meaning

The study results suggest that this classification is a potential step toward understanding the factors that lead to phenotypic differences in the Li-Fraumeni spectrum and may serve as a model for the reclassification of other hereditary conditions with an increased cancer risk.

Importance

Li-Fraumeni syndrome is a cancer predisposition syndrome that is associated with a high, lifelong risk of a broad spectrum of cancers that is caused by pathogenic TP53 germline variants. A definition that reflects the broad phenotypic spectrum that has evolved since the gene discovery is lacking, and mechanisms leading to phenotypic differences remain largely unknown.

Objective

To define the phenotypic spectrum of Li-Fraumeni syndrome and conduct phenotype-genotype associations across the phenotypic spectrum.

Design, Setting, and Participants

We analyzed and classified the germline variant data set of the International Agency for Research on Cancer TP53 database that contains data on a cohort of 3034 persons from 1282 families reported in the scientific literature since 1990. We defined the term Li-Fraumeni spectrum to encompass (1) phenotypic Li-Fraumeni syndrome, defined by the absence of a pathogenic/likely pathogenic TP53 variant in persons/families meeting clinical Li-Fraumeni syndrome criteria; (2) Li-Fraumeni syndrome, defined by the presence of a pathogenic/likely pathogenic TP53 variant in persons/families meeting Li-Fraumeni syndrome testing criteria; (3) attenuated Li-Fraumeni syndrome, defined by the presence of a pathogenic/likely pathogenic TP53 variant in a person/family with cancer who does not meet Li-Fraumeni syndrome testing criteria; and (4) incidental Li-Fraumeni syndrome, defined by the presence of a pathogenic/likely pathogenic TP53 variant in a person/family without a history of cancer. Data analysis occurred from November 2020 to March 2021.

Main Outcomes and Measures

Differences in variant distribution and cancer characteristics in patients with a germline TP53 variant who met vs did not meet Li-Fraumeni syndrome testing criteria.

Results

Tumor spectra showed significant differences, with more early adrenal (n = 166, 6.5% vs n = 0), brain (n = 360, 14.17% vs n = 57, 7.46%), connective tissue (n = 303, 11.92% vs n = 56, 7.33%), and bone tumors (n = 279, 10.98% vs n = 3, 0.39%) in patients who met Li-Fraumeni syndrome genetic testing criteria (n = 2139). Carriers who did not meet Li-Fraumeni syndrome genetic testing criteria (n = 678) had more breast (n = 292, 38.22% vs n = 700, 27.55%) and other cancers, 45% of them occurring after age 45 years. Hotspot variants were present in both groups. Several variants were exclusively found in patients with Li-Fraumeni syndrome, while others where exclusively found in patients with attenuated Li-Fraumeni syndrome. In patients who met Li-Fraumeni syndrome genetic testing criteria, most TP53 variants were classified as pathogenic/likely pathogenic (1757 of 2139, 82.2%), whereas 40.4% (404 of 678) of TP53 variants identified in patients who did not meet the Li-Fraumeni syndrome genetic testing criteria were classified as variants of uncertain significance, conflicting results, likely benign, benign, or unknown.

Conclusions and Relevance

The findings of this cohort study suggest that this new classification, Li-Fraumeni spectrum, is a step toward understanding the factors that lead to phenotypic differences and may serve as a model for other cancer predisposition syndromes.

Association of Inherited Mutations in DNA Repair Genes with Localized Prostate Cancer

Background:

Identification of germline mutations in DNA repair genes has significant implications for the personalized treatment of individuals with prostate cancer (PrCa).

Objective:

To determine DNA repair genes associated with localized PrCa in a diverse academic biobank and to determine genetic testing burden.

Design, setting, and participants:

A cross-sectional study of 2391 localized PrCa patients was carried out.

Outcome measurements and statistical analysis:

Genetic ancestry and mutation rates (excluding somatic interference) in 17 DNA repair genes were determined in 1588 localized PrCa patients and 3273 cancer-free males. Burden testing within individuals of genetically determined European (EUR) and African (AFR) ancestry was performed between biobank PrCa cases and cancer-free biobank and gnomAD males.

Results and limitations:

AFR individuals with localized PrCa had lower DNA repair gene mutation rates than EUR individuals (1.4% vs 4.0%, p = 0.02). Mutation rates in localized PrCa patients were similar to those in biobank and gnomAD controls (EUR: 4.0% vs 2.8%, p = 0.15, vs 3.1%, p = 0.04; AFR: 1.4% vs 1.8%, p = 0.8, vs 2.1%, p = 0.5). Gene-based rare variant association testing revealed that only BRCA2 mutations were significantly enriched compared with gnomAD controls of EUR ancestry (1.0% vs 0.28%, p = 0.03). Of the participants, 21% and 11% met high-risk and very-high-risk criteria; of them, 3.7% and 6.2% had any germline genetic mutation and 1.0% and 2.5% had a BRCA2 mutation, respectively. Limitations of this study include an analysis of a relatively small, single-institution cohort.

Conclusions:

DNA repair gene germline mutation rates are low in an academic biobank cohort of localized PrCa patients, particularly among individuals of AFR genetic ancestry. Mutation rates in genes with published evidence of association with PrCa exceed 2.5% only in high-risk, very-high-risk localized, and node-positive PrCa patients. These findings highlight the importance of risk stratification in localized PrCa patients to identify appropriate patients for germline genetic testing.

Patient summary:

In the majority of patients who develop localized prostate cancer, germline genetic testing is unlikely to reveal an inherited DNA repair mutation, regardless of race. High-risk features increase the possibility of a germline DNA repair mutation.

Clinical and Functional Significance of TP53 Exon 4-Intron 4 Splice Junction Variants

Germline TP53 splicing variants are uncommon, and their clinical relevance is unknown. However, splice-altering variants at exon 4-intron 4 junctions are relatively enriched in pediatric adrenocortical tumors (ACT). Nevertheless, family histories of cancer compatible with classic Li-Fraumeni syndrome are rarely seen in these patients. We used conventional and in silico assays to determine protein stability, splicing, and transcriptional activity of 10 TP53 variants at exon 4-intron 4 junctions and analyzed their clinical correlates. We reviewed public databases that report the impact of TP53 variants in human cancer and examined individual reports, focusing on family history of cancer. TP53 exon 4-intron 4 junction germline variants were identified in 9 of 75 pediatric ACTs enrolled in the International Pediatric Adrenocortical Tumor Registry and Children's Oncology Group ARAR0332 study. An additional eight independent TP53 variants involving exon 4 splicing were identified in the Pediatric Cancer Genome Project (n = 5,213). These variants resulted in improper expression due to ineffective splicing, protein instability, altered subcellular localization, and loss of function. Clinical case review of carriers of TP53 exon 4-intron 4 junction variants revealed a high incidence of pediatric ACTs and atypical tumor types not consistent with classic Li-Fraumeni syndrome. Germline variants involving TP53 exon 4-intron 4 junctions are frequent in ACT and rare in other pediatric tumors. The collective impact of these germline TP53 variants on the fidelity of splicing, protein structure, and function must be considered in evaluating cancer susceptibility. IMPLICATIONS: Taken together, the data indicate that splice variants at TP53 codon 125 and surrounding bases differentially impacted p53 gene expression and function.

EUS-based Pancreatic Cancer Surveillance in BRCA1/BRCA2/PALB2/ATM Carriers Without a Family History of Pancreatic Cancer

Carriers of a pathogenic/likely pathogenic (P/LP) BRCA1/BRCA2/ATM/PALB2 variant are at increased risk of pancreatic ductal adenocarcinoma (PDAC), yet current guidelines recommend surveillance only for those with a family history of PDAC. We aimed to investigate outcomes of endoscopic ultrasound (EUS)-based PDAC surveillance in BRCA1/BRCA2/ATM/PALB2 carriers without a family history of PDAC. We performed a retrospective analysis of all P/LP BRCA1/BRCA2/ATM/PALB2 carriers who underwent EUS at a tertiary care center. Of 194 P/LP BRCA1/BRCA2/ATM/PALB2 carriers who underwent EUS, 64 (33%) had no family history of PDAC and had at least 1 EUS for PDAC surveillance. These individuals underwent 143 total EUSs, were predominantly female (72%), and BRCA2 carriers (73%), with the majority having a personal history of cancer other than PDAC (67%). The median age at time of first EUS was 62 years [interquartile range (IQR), 53-67 years] and a median of 2 EUSs (IQR 1-3) were performed per patient, with a median of 3 years (IQR 2-4.5 years) between the first and last EUS for those with more than 1 EUS. Pancreatic abnormalities were detected in 44%, including cysts in 27%, and incidental luminal abnormalities in 41%. Eight percent developed a new pancreatic mass or cyst during surveillance, 2 individuals developed PDAC, and no serious complications resulted from surveillance. After discussion of the risks, limitations, and potential benefits, PDAC surveillance can be considered in BRCA1/BRCA2/ATM/PALB2 carriers without a family history of PDAC; however, the effectiveness of PDAC surveillance in this population requires further study. PREVENTION RELEVANCE: BRCA1/BRCA2/ATM/PALB2 carriers have increased pancreatic ductal adenocarcinoma (PDAC) risk, yet are typically not eligible for PDAC surveillance in the absence of PDAC family history. Herein we describe outcomes of PDAC surveillance in BRCA1/BRCA2/ATM/PALB2 carriers without a family history of PDAC, showing that PDAC surveillance can be considered in this high-risk group.

CD8+ T cells contribute to survival in patients with COVID-19 and hematologic cancer

Patients with cancer have high mortality from coronavirus disease 2019 (COVID-19), and the immune parameters that dictate clinical outcomes remain unknown. In a cohort of 100 patients with cancer who were hospitalized for COVID-19, patients with hematologic cancer had higher mortality relative to patients with solid cancer. In two additional cohorts, flow cytometric and serologic analyses demonstrated that patients with solid cancer and patients without cancer had a similar immune phenotype during acute COVID-19, whereas patients with hematologic cancer had impairment of B cells and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibody responses. Despite the impaired humoral immunity and high mortality in patients with hematologic cancer who also have COVID-19, those with a greater number of CD8 T cells had improved survival, including those treated with anti-CD20 therapy. Furthermore, 77% of patients with hematologic cancer had detectable SARS-CoV-2-specific T cell responses. Thus, CD8 T cells might influence recovery from COVID-19 when humoral immunity is deficient. These observations suggest that CD8 T cell responses to vaccination might provide protection in patients with hematologic cancer even in the setting of limited humoral responses.

Abstract 2723: How BRCA1/2 mutations in TNBC affect TME and subsequently immune cell functions

Breast cancer type 1 and 2 susceptibility proteins (BRCA1/BRCA2) are well known breast cancer genes, mutations in which lead to defective homologous recombination repair (HRR). HR-based DNA repair deficiency (HRD) scores can be used to indicate DNA damage, genomic instability and may predict response to DNA damaging agents in BRCA1/2 mutated tumors. Tumors with a high HRD score caused by complete loss of BRCA1 or BRCA2 function locus-specific LOH are sensitive to DNA damage agents including platinum-based chemotherapy and poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi). To understand the relationship between BRCA1/2 mutations and DNA damage in the tumor microenvironment (TME), we have characterized 107 BRCA1/2 tumors to determine HRD score using whole exome sequencing (WES) and simultaneously measured markers of DNA damage, PARP expression, tumor-infiltrating lymphocytes (TILs) and immune checkpoints to identify potential treatment targets on matching samples (n=47) using highly multiplexed fluorescence microscopy CO-Detection by indEXing (CODEX). We have established and validated a 40-plex breast cancer specific antibody panel consisting of markers to detect DNA damage, TILs and immune checkpoints to deeply profile how the TME is affected by BRCA1/2 mutations using CODEX. Computational image processing of CODEX data was performed to interrogate changes in number, size, morphology, and marker expression in tumor and immune cells. We have characterized BRCA1/2 tumors (n=47) on Tissue Microarrays (TMAs), and we have detected cytotoxic CD8+T and CD107a+NK cells in HRD low (&lt;42) and HRD high groups. Interestingly, their frequency and cytolytic function (measured by Granzyme A and perforin transcript level) appear to be associated with HRD scores. For instance, HRD low groups showed increased cytotoxic CD8+T and CD107a+NK cells whereas HRD high groups revealed decreased cell numbers as well as cytolytic function. We observed that HRD high, LOH positive was associated with increased DNA damage marker expression in tumor cells (H3pSer28, pATM, yH2AX) as well as NK cells (pATM) whereas immune checkpoint protein levels were decreased. We have planned quantitative analysis which allow us to determine the percentage of cell subtypes as well as the spatial compartmentalization of cells to interrogate the tumor microenvironment associated with BRCA1/2 mutations. In conclusion, BRCA1/2 mutated tumors with high HRD score revealed upregulated DNA damage expression in immune cells suggesting that BRCA1/2 mutations can impact HRR in CD8+T cells and CD107a+ NK cells and subsequently affect their ability to produce Granzyme A and Perforin. Our findings will decipher the role of DNA damage in BRCA1/2 mutated tumor cells and immune cell types. Outcomes can potentially predict treatment responses such as DNA damage, PARPi and checkpoint inhibitor therapies in TNBC BRCA1/2 breast cancer.

Citation Format: Dana Pueschl, Derek A. Oldrige, Jonathan Belman, Jake S. Shilan, Anupma Nayak, Bradley Wubbenhorst, John Pluta, Robert H. Vonderheide, Michael Feldman, Kara N. Maxwell, E. John Wherry, Susan M. Domchek, Katherine L. Nathanson. How BRCA1/2 mutations in TNBC affect TME and subsequently immune cell functions [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 2723.

Abstract PD9-10: Investigating the clinical utility of tumor mutational burden in predicting rapid progression and death in patients with metastatic breast cancer

Background Up to 30% of breast cancer patients will eventually relapse with metastatic disease. With an increasing array of therapeutic options, there is an ongoing need for predictive biomarkers to help guide treatment strategies including sequencing of therapies in the metastatic setting. We sought to evaluate the prognostic and predictive potential of a panel-specific tumor mutational burden (TMB) in metastatic breast cancer patients.

Methods METAMORPH is a prospective, longitudinal cohort study. Eligible patients (pts) had newly diagnosed or progressive metastatic breast cancer and enrolled prior to starting a new line of therapy (physician’s choice) at the University of Pennsylvania. Pts underwent tissue biopsy of a suspected metastatic site. Tumor samples were analyzed for mutations and copy number alterations (CNA’s) using our institution’s CLIA-certified Center for Personalized Diagnostics (CPD) targeted gene panel, which evolved over the course of the study from 20 genes to 152 genes. TMB-high (TMB-H) was defined as ≥3 mutations and/or copy-number gains (CNG) among 18 genes shared across all panel versions. Pts were followed for time to progression (TTP), progression-free survival (PFS), and overall survival (OS). The frequency of rapid progressors and rapid death (defined as having progressed or died within 3 months of enrollment, respectively) was assessed.

Results Three hundred pts enrolled from 2013-2020, of whom 200 pts had CPD reports generated. Of these, 12 pts were excluded due to either no treatment change on enrollment (n=11) or different primary cancer on biopsy (n=1). Thus 188 pts were included in this analysis. The median age was 55 years (range 28-79). 77% of pts identified as white, 18% as Black or African American, and 3.2% as Asian. Pts had a median of 1 line (range 0-12) of prior systemic therapy in the metastatic setting. 46.8% had no prior therapies for MBC, while 31% had ≥3 prior lines of therapy. 74.4% were HR+, 22.8% TNBC, and 2.7% HR-/HER2+. 6.9% of the cohort were classified as TMB-H. The average mutation/CNG rate was 2.2/sample, and 22.5% had no mutations or CNA’s. The most common mutations were TP53 (35%) and PIK3CA (26%).

While TMB-H patients showed a statistically non-significant trend towards shorter median TTP and PFS compared with TMB-L, they comprised a significantly greater proportion of rapid progressors (54.5% vs 24.1%, p=0.027), with an odds ratio for rapid progression of 3.8 (95% CI 1.08-13.2). In a multivariate logistic regression analysis, TMB-H remained independently associated with rapid progression when adjusted for receptor subtype and next line of therapy. Receptor subtype analysis revealed that ER- (including ER-/PR+) patients with TMB-H had a shorter median TTP compared to ER- TMB-L (147 vs 68 days, p=0.03). TMB-H was also associated with significantly shorter OS compared with TMB-L (587 vs 648 days, p=0.02; HR 2.2 [95% CI 1.11-4.41]). 44.4% of TMB-H pts died within 3 months of enrollment, as compared to 11.0% of TMB-L pts (p=0.005), with an odds ratio for rapid death, adjusted for number of previous lines of therapy and receptor subtype, of 6.7 (95% CI 1.5-31.0).

Conclusion MBC pts who are TMB-H represent a population who are highly resistant to standard therapies, progress rapidly, and have significantly shorter overall survival with more rapid time to death. Our data support further studies investigating the utility of TMB as a predictive biomarker in directing patients away from standard treatment options and towards novel approaches e.g. immunotherapy.

Citation Format: Igor Makhlin, Amy S Clark, Paul Wileyto, Noah Goodman, John Ndicu, Shannon DeLuca, Candace Clark, S. William Stavropoulos, Natalie Shih, Michael D Feldman, Susan M Domchek, Jennifer M Matro, Payal D Shah, Hayley M Knollman, Kevin R Fox, Kara N Maxwell, Lewis A Chodosh, Angela DeMichele. Investigating the clinical utility of tumor mutational burden in predicting rapid progression and death in patients with metastatic breast cancer [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 PD9-10.

CD8 T cells compensate for impaired humoral immunity in COVID-19 patients with hematologic cancer

Cancer patients have increased morbidity and mortality from Coronavirus Disease 2019 (COVID-19), but the underlying immune mechanisms are unknown. In a cohort of 100 cancer patients hospitalized for COVID-19 at the University of Pennsylvania Health System, we found that patients with hematologic cancers had a significantly higher mortality relative to patients with solid cancers after accounting for confounders including ECOG performance status and active cancer status. We performed flow cytometric and serologic analyses of 106 cancer patients and 113 non-cancer controls from two additional cohorts at Penn and Memorial Sloan Kettering Cancer Center. Patients with solid cancers exhibited an immune phenotype similar to non-cancer patients during acute COVID-19 whereas patients with hematologic cancers had significant impairment of B cells and SARS-CoV-2-specific antibody responses. High dimensional analysis of flow cytometric data revealed 5 distinct immune phenotypes. An immune phenotype characterized by CD8 T cell depletion was associated with a high viral load and the highest mortality of 71%, among all cancer patients. In contrast, despite impaired B cell responses, patients with hematologic cancers and preserved CD8 T cells had a lower viral load and mortality. These data highlight the importance of CD8 T cells in acute COVID-19, particularly in the setting of impaired humoral immunity. Further, depletion of B cells with anti-CD20 therapy resulted in almost complete abrogation of SARS-CoV-2-specific IgG and IgM antibodies, but was not associated with increased mortality compared to other hematologic cancers, when adequate CD8 T cells were present. Finally, higher CD8 T cell counts were associated with improved overall survival in patients with hematologic cancers. Thus, CD8 T cells likely compensate for deficient humoral immunity and influence clinical recovery of COVID-19. These observations have important implications for cancer and COVID-19-directed treatments, immunosuppressive therapies, and for understanding the role of B and T cells in acute COVID-19.

Rates of COVID-19-Related Outcomes in Cancer Compared With Noncancer Patients

Cancer patients are a vulnerable population postulated to be at higher risk for severe coronavirus disease 2019 (COVID-19) infection. Increased COVID-19 morbidity and mortality in cancer patients may be attributable to age, comorbidities, smoking, health care exposure, and cancer treatments, and partially to the cancer itself. Most studies to date have focused on hospitalized patients with severe COVID-19, thereby limiting the generalizability and interpretability of the association between cancer and COVID-19 severity. We compared outcomes of SARS-CoV-2 infection in 323 patients enrolled in a population-based study before the pandemic (n = 67 cancer patients; n = 256 noncancer patients). After adjusting for demographics, smoking status, and comorbidities, a diagnosis of cancer was independently associated with higher odds of hospitalization (odds ratio = 2.16, 95% confidence interval = 1.12 to 4.18) and 30-day mortality (odds ratio = 5.67, 95% confidence interval = 1.49 to 21.59). These associations were primarily driven by patients with active cancer. These results emphasize the critical importance of preventing SARS-CoV-2 exposure and mitigating infection in cancer patients.

SARS-CoV-2 seropositivity and seroconversion in patients undergoing active cancer-directed therapy

Multiple studies have demonstrated the negative impact of cancer care delays during the COVID-19 pandemic, and transmission mitigation techniques are imperative for continued cancer care delivery. To gauge the effectiveness of these measures at the University of Pennsylvania, we conducted a longitudinal study of SARS-CoV-2 antibody seropositivity and seroconversion in patients presenting to infusion centers for cancer-directed therapy between 5/21/2020 and 10/8/2020. Participants completed questionnaires and had up to five serial blood collections. Of 124 enrolled patients, only two (1.6%) had detectable SARS-CoV-2 antibodies on initial blood draw, and no initially seronegative patients developed newly detectable antibodies on subsequent blood draw(s), corresponding to a seroconversion rate of 0% (95%CI 0.0-4.1%) over 14.8 person-years of follow up, with a median of 13 healthcare visits per patient. These results suggest that cancer patients receiving in-person care at a facility with aggressive mitigation efforts have an extremely low likelihood of COVID-19 infection.

Upper Gastrointestinal Cancer Risk and Surveillance Outcomes in Li-Fraumeni Syndrome

INTRODUCTION

To assess the upper gastrointestinal (UGI) cancer risk and surveillance outcomes in Li-Fraumeni syndrome (LFS).

METHODS

Analysis of the International Agency for Research on Cancer database and a single-center adult LFS cohort.

RESULTS

UGI cancer was present in 7.2% of families and 3.9% of individuals with a pathogenic/likely pathogenic TP53 mutation in International Agency for Research on Cancer; 29% occurred before age 30. Our institutional cohort had 35 individuals (31% of the LFS cohort) with 48 cumulative upper endoscopies; 3 (8.5%) individuals had concerning UGI findings.

DISCUSSION

UGI cancer is observed in LFS. Upper endoscopy should be part of a comprehensive LFS surveillance program.