Partner And Localizer Of BRCA2 Mutations Research Articles

Diagnosis, Management, and Surveillance for Patients With PALB2, CHEK2, and ATM Gene Mutations

BackgroundThis study aims to capture clinical and surgical practice patterns of patients with deleterious mutations in partner and localizer of BRCA2 (PALB2), checkpoint kinase 2 (CHEK2) and ataxia telangiesctasia mutated (ATM) genes. Materials and MethodsThis study is a retrospective chart review of patients with PALB2, CHEK2 or ATM mutations. Patient demographics, testing indications, management decisions, and surveillance strategies were recorded. ResultsSixty-two patients were found to have deleterious mutations: 14 (23%) with a PALB2 mutation, 30 (48%) with a CHEK2 mutation, and 18 (29%) patients with an ATM mutation.Thirty-one (50%) patients have a history of breast cancer. Twenty-three patients were diagnosed and treated prior to genetic testing while 8 patients learned of their mutation status and breast cancer diagnosis simultaneously. Of these 8 patients, 4 sought treatment at our institution, 3 underwent bilateral mastectomy, and 1 patient opted for lumpectomy and surveillance.Thirty-one patients had no history of breast cancer. After genetic diagnosis, 3 of the 9 patients who continued clinical follow-up proceeded with bilateral prophylactic mastectomy within 2 years. Clinical surveillance continued for 23 months on average. ConclusionMost patients who learned of their genetic and breast cancer diagnoses simultaneously underwent bilateral mastectomy, whereas only a third of patients without cancer opted for bilateral prophylactic mastectomy.

A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes

Talazoparib, a PARP inhibitor, is active in germline BRCA1 and BRCA2 (gBRCA1/2)-mutant advanced breast cancer, but its activity beyond gBRCA1/2 is poorly understood. We conducted Talazoparib Beyond BRCA (NCT02401347), an open-label phase II trial, to evaluate talazoparib in patients with pretreated advanced HER2-negative breast cancer (n = 13) or other solid tumors (n = 7) with mutations in homologous recombination (HR) pathway genes other than BRCA1 and BRCA2. In patients with breast cancer, four patients had a Response Evaluation Criteria in Solid Tumors (RECIST) partial response (overall response rate, 31%), and three additional patients had stable disease of ≥6 months (clinical benefit rate, 54%). All patients with germline mutations in PALB2(gPALB2; encoding partner and localizer of BRCA2) had treatment-associated tumor regression. Tumor or plasma circulating tumor DNA (ctDNA) HR deficiency (HRD) scores were correlated with treatment outcomes and were increased in all gPALB2 tumors. In addition, a gPALB2-associated mutational signature was associated with tumor response. Thus, talazoparib has been demonstrated to have efficacy in patients with advanced breast cancer who have gPALB2 mutations, showing activity in the context of HR pathway gene mutations beyond gBRCA1/2.

1707P The landscape of PALB2 alteration in Chinese solid tumor patients

Partner and localizer of BRCA2 (PALB2) is a nuclear protein that localizes to sites of DNA double-strand breaks and interacts with BRCA1 and BRCA2 to promote DNA repair. The differences in mutation profiles of PALB2 gene in pan-cancer can help understand pathogenesis, prognosis, and identify targets for therapy. Using commercial NGS assays, we retrospectively analyzed genomic DNA alterations in normal-paired samples from 3880 patients with malignancies between 2019 to 2021, and alterations including single base substitution, short and long insertion/deletions, copy number variations, gene fusions and rearrangements. PALB2 gene was altered in 2.0% (78 of 3880) of all solid tumors, comparable to 1.5% (158 of 10336) of PALB2 alterations in the MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017). The frequency of PALB2 variations was assessed in multiple cancer types, including bladder cancer 6.1% (2/33), thyroid cancer 4.9% (2/41), colorectal cancer 4.0% (19/478), prostatic cancer 3.8% (1/26), small cell lung cancer 3.4% (1/29), pancreatic cancer 2.5% (4/160), gastrointestinal stromal tumor 2.3% (1/44), liver cancer 2.2% (5/230), biliary tract tumor 2.1% (3/141) and non-small cell lung cancer 2.0% (28/1402). A total 93 genetic alterations were identified in 78 patients, including 58 missense mutations (63%), 18 nonsense (12%), 12 frameshift (10%), 3 splicing (8%), 5 copy number loss (5%), 1 in-frame insertion (2%), 1 in-frame deletion (2%). Among these patients, 14 had pathogenic or likely pathogenic germline PALB2 heterozygous mutations, including prostatic cancer 3.8% (1/26), biliary tract tumor 2.1% (3/141), pancreas tic cancer 1.3% (2/160), colorectal cancer 0.8% (4/478), liver cancer 0.4% (1/230) and non-small cell lung cancer 0.2% (3/1821). Furthermore, in our cohort, PALB2 mutation carriers also owned other actionable, the most frequent one was TP53 (65%), followed by LRP1B (28%), KRAS (27%) and PIK3CA (24%). PALB2 deleterious mutations are highly diverse and present at low to moderate frequencies across many cancers. PALB2 alterations warrant further investigation as predictive biomarkers of response to PARP inhibitors or platinum-based therapy.

Partner and localizer of BRCA2 (PALB2) pathogenic variants and ovarian cancer: A systematic review and meta-analysis.

e17597 Background: Approximately 20% of ovarian cancers are due to an underlying germline pathogenic variant. While several genes have been well-established in the development of hereditary ovarian cancer (e.g. BRCA1/2, RAD51C, RAD51D, BRIP1, mismatch repair genes), there are other genes for which the cancer risk is less certain and management recommendations remain controversial, including partner and localizer of BRCA 2 (PALB2). We sought to evaluate the association between PALB2 germline pathogenic mutations and ovarian cancer in the first meta-analysis on this topic. Methods: We conducted a systematic review and meta-analysis in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PROSPERO no.: CRD42021281325). We searched key electronic databases to identify studies evaluating multigene panel testing in patients with ovarian cancer. Eligible trials were subjected to meta-analysis. Results: Thirty-seven studies met inclusion criteria. We found 55,137 cases of ovarian cancer with information available on germline PALB2 pathogenic variant status. Reported histological subtypes included serous adenocarcinoma (74.8%), endometroid (6.5%), clear cell (2.1%), mucinous (3.1%), and other (13.5%). Most ovarian cancers were stages III (73.5%) and IV (22.3%), followed by II (6.0%), and I (4.1%). Among ovarian cancer cases with PALB2 sequencing data available, 0.4% demonstrated a germline pathogenic variant in the PALB2 gene and the pooled odds ratio (OR) for having a PALB2 mutation was 2.31 (95% CI 0.89- 5.98). Among 94 patients with a germline PALB2 pathogenic variant, the pooled odds ratio (OR) for developing ovarian cancer was 2.85 (95% CI 1.58-5.15) relative to 33,855 patients without PALB2 mutations. Conclusions: Our meta-analysis demonstrates that the pooled OR for developing ovarian cancer with an underlying PALB2 germline pathogenic variant was 2.85 (95% CI 1.58-5.15). While this risk is lower than many of the well-established hereditary ovarian cancer genes, it does exceed the baseline population risk of 1-2%. Whether this meets the threshold to consider risk-reducing salpingo-oophorectomy is up for debate. Large population-based studies and evaluation of the combination of PALB2 mutations and cancer family history are needed to improve management recommendations for patients harboring pathogenic mutations in this gene.

Germline PALB2 Mutation in High-Risk Chinese Breast and/or Ovarian Cancer Patients.

Simple SummaryBreast cancer is the most commonly diagnosed cancer in women globally. BRCA1 and BRCA2 mutations are most prevalent in hereditary breast cancer and are associated with increased risk of breast and ovarian cancer. The PALB2 (partner and localizer of BRCA2) mutation was found to be associated with an increased risk of breast cancer and one of the most common mutations, after BRCA1 and BRCA2, in non-BRCA1/2 breast cancer patients. The prevalence of the PALB2 mutation in breast cancer varies across different ethnic groups; hence, it is of intense interest to evaluate the cancer risk and clinical association of PALB2 mutation in Chinese breast and/or ovarian cancer patients. The prevalence of the PALB2 mutation in breast cancer varies across different ethnic groups; hence, it is of intense interest to evaluate the cancer risk and clinical association of the PALB2 mutation in Chinese breast and/or ovarian cancer patients. We performed sequencing with a 6-gene test panel (BRCA1, BRCA2, TP53, PTEN, PALB2, and CDH1) to identify the prevalence of the PALB2 germline mutation among 2631 patients with breast and/or ovarian cancer. In this cohort, 39 mutations were identified with 24 types of mutation variants, where the majority of the mutations were frame-shift mutations and resulted in early termination. We also identified seven novel PALB2 mutations. Most of the PALB2 mutation carriers had breast cancer (36, 92.3%) and were more likely to have family history of breast cancer (19, 48.7%). The majority of the breast tumors were invasive ductal carcinoma (NOS type) (34, 81.0%) and hormonal positive (ER: 32, 84.2%; PR: 23, 60.5%). Pathogenic mutations of PALB2 were found in 39 probands with a mutation frequency of 1.6% and 1% in breast cancer and ovarian cancer patients, respectively. PALB2 mutation carriers were more likely have hormonal positive tumors and were likely to have familial aggregation of breast cancer.

A phase II clinical trial of talazoparib monotherapy for PALB2 mutation-associated advanced breast cancer.

TPS1109 Background: PALB2 (Partner and Localizer of BRCA2) plays a critical role in the maintenance of genomic integrity through its role in the Fanconi anemia and homologous recombination DNA repair pathways. Our recently reported phase II clinical trial (Gruber, et al. JCO 2019) showed that talazoparib monotherapy was associated with single agent activity in germline PALB2 (gPALB2) mutation-associated advanced breast cancers. Of 5 patients with a germline PALB2 mutation, all 5 had reduction in target lesions > 20% with 3 of 5 achieving a RECIST 1.1 response. All patients had visceral metastases and were heavily pretreated; one response occurred in a patient with 8 prior lines of therapy for metastatic breast cancer. Clinical activity of the PARP inhibitor olaparib was also demonstrated in breast cancer patients with gPALB2 mutations in the Olaparib Expanded trial (TBCRC 048). Thus, we believe there is significant value in generating additional PARP inhibitor monotherapy data in subjects with advanced PALB2 mutation-associated breast cancer. We propose this phase II trial to better estimate the rate of RECIST 1.1 objective response in this patient population. Methods: This is a single-arm, two-stage, non-randomized study to assess the objective response rate (ORR) of talazoparib monotherapy in patients with PALB2 mutation-associated advanced breast cancer. Eligible subjects will be adults with inoperable locally advanced or metastatic breast cancer with a germline or somatic PALB2 mutation with 0-3 prior therapies for advanced disease. Eligible patients must have a deleterious or suspected deleterious mutation in PALB2 on a CLIA approved commercial germline or next generation sequencing tumor assay. Study treatment is talazoparib 1 mg PO daily. In stage 1, ORR will be assessed after 15 patients; if at least 2 responses are observed then an additional 15 patients will be enrolled; if less than 2 responses are observed the study will be terminated. The primary objective is to evaluate whether talazoparib monotherapy can induce a 30% ORR in subjects with advanced breast cancer associated with a PALB2 mutation. Response will be assessed by RECIST 1.1. Secondary objectives include safety, PFS, clinical benefit rate, and patient-reported quality-of-life. Exploratory endpoints will assess for the presence of PALB2 loss-of-heterozygosity, biallelic mutations, correlation of ctDNA profile with treatment response and the correlation of germline versus somatic mutations with response rate. This trial is currently activated and enrolling at Stanford Cancer Center and it is expected that 4 additional sites will be added. Conclusion: This trial will evaluate gPALB2 as a biomarker for PARP inhibitor monotherapy in advanced or metastatic HER2- breast cancer. Clinical trial information: pending .

PALB2 upregulation is associated with a poor prognosis in pancreatic ductal adenocarcinoma.

During DNA repair, BRCA1 and BRCA2 interact with the tumor suppressor partner and localizer of BRCA2 (PALB2). PALB2 mutations are associated with an increased risk of breast and ovarian carcinoma, and upregulated PALB2 expression is associated with poor clinical outcomes. The present study investigated the role and prognostic value of PALB2 in pancreatic ductal adenocarcinoma (PDAC). PALB2 expression was inhibited using a small interfering RNA in PDAC cell lines, and the subsequent effects on cell proliferation and migration were investigated. Tissue microarrays from 157 patients undergoing a pancreaticoduodenectomy for PDAC were analyzed via immunohistochemistry, and PALB2 expression was compared with patient outcomes using Kaplan-Meier curves and the multivariate Cox regression model. PALB2-knockdown in PDAC cells had little effect on cell proliferation, but significantly decreased cell migration. Relatively high PALB2 expression was observed in PDAC tissues compared with in peritumoral tissues. Overall survival (OS) was negatively associated with PALB2 expression. TNM stage and PALB2 expression were identified as independent prognostic factors associated with OS via multivariate analysis. Overall, the present study demonstrated that PDAC cell migration was dependent on PALB2, which was further supported by the finding that elevated PALB2 expression in PDAC tissues was associated with poor survival in patients with PDAC. Therefore, PALB2 may serve as a novel prognostic marker in PDAC, which may aid with the development of therapeutic strategies for the disease.

Abstract P2-09-03: Spectrum, prevalence and clinical outcomes of germline mutations in PALB2 genes in 16501 unselected BRCA1/2-negative breast cancer patients: A multi-center analysis

Abstract Background: PALB2 (Partner and Localizer of BRCA2) is a breast cancer predisposition gene, which plays a critical role in homologous recombination via interacting with BRCA1/2 and RAD51 when DNA break. However, the clinical relevance of PALB2 germline mutations in Chinese breast cancer patients remains unknown. We attempted to illustrate the full prevalence and spectrum of PALB2 germline mutations in Chinese breast cancer population, and to investigate the clinical outcomes of PALB2 germline mutations. Patients and methods: A total of 21216 unselected breast cancer patients were enrolled from multiple clinical centers in China. After evaluation of the DNA quality and clinical information, 16501 eligible BRCA1/2-negative breast cancer patients were analyzed. A group of 5890 Chinese women without cancer was enrolled as healthy controls. PALB2 screening was based on next-generation sequencing, by screening complete coding sequence and intron-exon boundaries of PALB2. Clinical information was synchronously collected. Results: The 79 PALB2 deleterious germline mutations included 25 nonsense mutations, 47 frameshift mutations, and 7 splicing mutations. The hotspot region for PALB2 mutations was exon4. A total of 41 novel mutations were identified in PALB2. Among the 16501 BRCA1/2-negative breast cancer patients and 5890 healthy women, PALB2 deleterious mutation carriers account for 0.97% (n=160) and 0.19% (n=11) separately. PALB2 mutations were significantly associated with increased breast cancer risk (OR: 5.23, 95% CI 2.89-9.49; P<0.0001), and especially in women aged 30 or younger (OR: 11.97, 95% CI 3.76-34.39; P<0.0001). PALB2 mutation carriers were significantly more likely to be triple negative breast cancers and have bigger tumors, positive axillary lymph nodes, bilateral breast cancers, family history of breast and/or ovarian cancer and family history of any other cancer, than noncarriers. Conclusions: The PALB2 mutations confer a moderately increased breast cancer risk in women, but relatively highly increased breast cancer risk in those aged 30 or younger. PALB2 mutation status is associated with distinct clinical characteristics in breast cancer. Key words:PALB2, breast cancer, germline mutations, next-generation sequencing Citation Format: Jiaojiao Zhou, Honglian Wang, Fangmeng Fu, Zhanwen Li, Yun Liu, Qingjian Feng, Weizhu Wu, Hongxia Wang, Chuan Wang, Yiding Chen. Spectrum, prevalence and clinical outcomes of germline mutations in PALB2 genes in 16501 unselected BRCA1/2-negative breast cancer patients: A multi-center analysis [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 P2-09-03.

Novel PALB2 deleterious mutations in breast cancer patients from South Indian population

Breast cancer is the most common cancer in women across the world. Partner and localizer of BRCA2 (PALB2) were recently identified as a breast cancer predisposition gene. The ultimate goal of this study is to understand the status of PALB2 mutations among the breast cancer subjects from the Indian population. We have evaluated the PALB2 gene mutation in 200 breast cancer patients and 200 controls that tested negative for BRCA1/2. Single Stranded Conformation Polymorphism (SSCP) assay was performed for screening the variants on amplified regions followed by direct sequencing for conforming mutations. Among the analyzed subjects, 128 patients were of inherited familial history and the rest 72 patients were of sporadic cases. Two novel deleterious mutations and one novel missense mutation were identified from this study, with the prevalence of about 3.5% (7/200). Among the deleterious mutations in familial breast cancer, PALB2 c.780delG and c.725delT was identified. One missense mutation of PALB2 c.404C > T was found in our study subjects. In this study, the prevalence of PALB2 gene mutation in familial breast cancer is about 4.6% (6/128). Our study demonstrates that the PALB2 gene mutations prevail among familial breast cancer patients.Clinically, these data may be helpful in the genetic counseling for breast cancer patients with PALB2 germline mutation.

Higher Expression of PALB2 Predict Poor Prognosis in AML Patients and Identifies Potential Targets of Synthetic Lethal Therapies

Background - Partner and localizer of BRCA2 (PALB2) plays a key role in the DNA damage repair (DDR). Genomic alterations of DDR genes rarely occur in AML, while their deregulation at transcriptional level is a known mechanism exploited by leukemic cells in order to sustain the high genetic instability and to continue proliferation.Aim - We aimed to characterize the role of PALB2 in AML by investigating its expression levels and its prognostic value, in order to evaluate its potential as target of therapies based on a synthetic lethality approaches.Methods - Gene expression profiling (GEP, Affymetrix) was performed on bone marrow cells of 7 healthy donors (HD) and 60 AML patients with more than 80% blast cells. K-means clustering of patients according to the expression of PALB2 was performed and differences in survival were assessed d by Kaplan-Meier survival analysis.Results - Our cohort was characterized by a median age at diagnosis of 60 years-old. Twelve out of 43 patients harbored a mutation in FLT3 (27.9%, 17 patients not tested); 8 patients were NPM1 mutated (27.6%, 31 patients not tested); 2 patients were TP53 mutated (3%, all patients tested). According to ELN2017 guidelines, 17 cases were high-risk AML, 38 cases were intermediate, 3 cases had low-risk classification and 2 cases were not classified due to the lack of prognostic markers. We detected variable levels of PALB2 mRNA (range 52.90-244.37) in AML patients and its median expression was higher compared to HD (129.26 vs 67.85, respectively; p=.019). We clustered our patients according to PALB2 expression and we defined 2 groups of patients: cluster H and L with higher and lower expression levels of PALB2, respectively (cluster centers 158.86 and 105.41, respectively; figure A). Notably, HD revealed PALB2 expression values comparable with the cluster L (range 52.90-99.60). No differences were detected in term of incidence mutations in FLT3 and NPM1, white blood cell count at diagnosis, age at diagnosis and prevalence of karyotype alterations. Patients were treated with best supportive therapy (n=11/58, therapy data missing for 2 patients), hypomethylating agents (n=2/58) and intensive chemotherapy ( n=45/58). Within patients treated with intensive chemotherapy, we compared complete remission rate after induction and we found no differences between H and L. However, patients with higher expression of PALB2 had worst overall survival than patients in cluster L (median survival group H=397 days; CI 95%=288.9-505.0, L=not reached; p=.045; figure B). Notably, we confirmed worst prognosis in patients in cluster H when considering 33 out of 45 patients with intermediate/low risk karyotype (i.e. normal karyotype, t(8;21) or less than 3 aberrations according to ELN2017; p=.026).Conclusion - We identified a subgroup of AML patients with higher expression of PALB2, which predicted poorer prognosis in patients treated with curative intent and it associated with poorer prognosis in patients with low/intermediate risk. While patients carrying mutations in PALB2 (and BRCA1/2) are candidate for PARP inhibitors (PARPi) therapies in breast cancers, few clinical trials with PARPi are available in AML and the frequency of mutations is very low. Our data opens a new scenario in which PALB2 may be a target of therapies in AML based on synthetic lethal approaches targeting the DDR pathway. However, a better understanding of the biological role of PALB2 in AML and its interaction with other alterations is needed.Supported by Fondazione Del Monte [Display omitted] DisclosuresCavo:Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive Biotechnologies: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; GlaxoSmithKline: Honoraria, Membership on an entity's Board of Directors or advisory committees. Soverini:Novartis: Consultancy; Bristol Myers Squibb: Consultancy; Incyte Biosciences: Consultancy. Martinelli:Roche: Consultancy; Celgene: Consultancy, Speakers Bureau; Janssen: Consultancy; Ariad/Incyte: Consultancy; Amgen: Consultancy; Pfizer: Consultancy, Speakers Bureau; Abbvie: Consultancy; Jazz Pharmaceuticals: Consultancy; Novartis: Speakers Bureau.

Prevalence of PALB2 Germline Mutations in Early-onset and Familial Breast/Ovarian Cancer Patients from Pakistan.

PurposePartner and localizer of BRCA2 (PALB2) is a breast cancer susceptibility gene that plays an important role in DNA repair. This is the first study assessing the prevalence of PALB2 mutations in early-onset and familial breast/ovarian cancer patients from Pakistan.Materials and MethodsPALB2 mutation screening was performed in 370 Pakistani patients with early-onset and familial breast/ovarian cancer, who were negative for BRCA1, BRCA2, TP53, CHEK2, and RAD51C mutations, using denaturing high-performance liquid chromatography analysis. Mutations were confirmed by DNA sequencing. Novel PALB2 alterations were analyzed for their potential effect on protein function or splicing using various in silico prediction tools. Three-hundred and seventy-two healthy controls were screened for the presence of the identified (potentially) functional mutations.ResultsA novel nonsense mutation, p.Y743*, was identified in one familial breast cancer patient (1/127, 0.8%). Besides, four in silico-predicted potentially functional mutations including three missense mutations and one 5' untranslated region mutation were identified: p.D498Y, novel p.G644R, novel p.E744K, and novel c.-134_-133delTCinsGGGT. The mutations p.Y743* and p.D498Y were identified in two familial patients diagnosed with unilateral or synchronous bilateral breast cancer at the ages of 29 and 39, respectively. The other mutations were identified in an early-onset (≤ 30 years of age) breast cancer patient each. All five mutations were absent in 372 healthy controls suggesting that they are disease associated.ConclusionOur findings show that PALB2 mutations account for a small proportion of early-onset and hereditary breast/ovarian cancer cases in Pakistan.

PALB2 (partner and localizer of BRCA2).

PALB2 (Partner and Localizer of BRCA2) was first identified as a BRCA2-interacting protein. Subsequently, PALB2 has been recognized as a cog in the cellular machinery for DNA repair by homologous recombination (HR). PALB2 also mediates S and G2 DNA damage checkpoints, and has an apparent function in protecting transcriptionally active genes from genotoxic stress. PALB2 also interacts with, is localized by, and functions downstream of BRCA1. Further, PALB2 interacts with other essential effectors of HR, including RAD51 and RAD51C, as well as BRCA2. Consistent with its function in HR and its interaction with key HR proteins, PALB2-deficient cells are hypersensitive to ionizing radiation and DNA interstrand crosslinking agents such as mitomycin C and cisplatin. Mechanistically, PALB2 is required for HR by mediating the recruitment of BRCA2 and the RAD51 recombinase to sites of DNA damage. Similar to bi-allelic loss-of-function mutations of BRCA1, BRCA2, RAD51 and RAD51C, bi-allelic mutations in PALB2 cause Fanconi anemia (FA), a rare childhood disorder which is associated with progressive bone marrow failure, congenital anomalies, and a predisposition to leukemia and solid tumors. Due to their close functional relationship, bi-allelic mutations of PALB2 and BRCA2 cause particularly severe forms of FA, called FANCN and FANCD1, both characterized by severe congenital abnormalities and very early onset of various cancers. This includes acute leukemias, Wilms tumor, medulloblastoma and neuroblastomas. Also, heterozygous germ-line mutations of PALB2, like mutations in several other essential HR genes listed above, yield an increased susceptibility to breast and pancreatic cancer.

Germline mutations of PALB2 gene in a sequential series of Chinese patients with breast cancer.

PALB2 (Partner and Localizer of BRCA2) is recently recognized as a breast cancer predisposition gene. Germline loss-of-function mutations in PALB2 lead to increased breast cancer risk. Since the germline mutation frequency of PALB2 is much less than BRCA1/2, the distinct mutation spectrum of PALB2 is still obscure. To verify the utility of PALB2 genetic testing in Chinese population, we assessed the mutational frequency, spectrum, and predictors of the PALB2 gene in a sequential series of Chinese breast cancer patients from our Research DNA Bank. We examined breast cancer samples (n = 2279) collected from 2000 through 2016 from Chinese patients who agreed to participate in research DNA banking. To identify the mutations, complete coding sequence and intron-exon boundaries of PALB2 were screened with Next-Generation Sequencing. Personal and family histories were synchronously collected for mutation identification. Among the 2279 breast cancer patients, 305 patients were familial breast cancer cases and the rest 1967 patients were sporadic breast cancer cases. PALB2 loss-of-function mutation carriers accounted for 1.31% (n = 4) and 0.56% (n = 11) in familial and sporadic breast cancer cohort separately. In total, 30 missenses, four nonsenses, three frameshifts, three splicings, and one inframe deletions of PALB2 were identified in this study. Among the deleterious mutations, PALB2 c.1744C>T, c.2748+1G>A, c.2749-1G>C, c.3114-1G>A were newly identified in sporadic breast cancer, and c.3271delC newly found in familial breast cancer. Based on in silico analysis, we found two potentially damaging missense variants with high frequency: c.1213C>G, c.3054G>C, and classified six new potentially damaging missense variants. Our data presented the germline mutation status of PALB2 in Chinese breast cancer patients, suggesting that loss-of-function germline mutations of PALB2 are important in both familial and sporadic breast cancer. Clinically, these data may be helpful in genetic counseling of breast cancer patients with PALB2 germline mutation.

Structural basis for recruitment of BRCA2 by PALB2.

The breast cancer 2, early onset protein (BRCA2) is central to the repair of DNA damage by homologous recombination. BRCA2 recruits the recombinase RAD51 to sites of damage, regulates its assembly into nucleoprotein filaments and thereby promotes homologous recombination. Localization of BRCA2 to nuclear foci requires its association with the partner and localizer of BRCA2 (PALB2), mutations in which are associated with cancer predisposition, as well as subtype N of Fanconi anaemia. We have determined the structure of the PALB2 carboxy-terminal β-propeller domain in complex with a BRCA2 peptide. The structure shows the molecular determinants of this important protein–protein interaction and explains the effects of both cancer-associated truncating mutants in PALB2 and missense mutations in the amino-terminal region of BRCA2.

Abstract 2470: Compromised BRCA1-PALB2 interaction is associated with breast cancer risk

Abstract The major breast cancer suppressor proteins BRCA1 and BRCA2 play essential roles in homologous recombination (HR)-mediated DNA repair, which is thought to be critical for tumor suppression. The two BRCA proteins are physically and functionally linked by a third tumor suppressor, PALB2 (partner and localizer of BRCA2), in the HR pathway. Heterozygous PALB2 mutation carriers have increased risk of breast, ovarian and pancreatic cancer. While truncating mutations in BRCA genes are generally pathogenic, interpretations of missense variants remains a challenge. To date, patient-derived missense variants that disrupt PALB2 binding have been identified in BRCA1 and BRCA2; however, there has not been sufficient evidence to establish their pathogenicity in humans. Variants in PALB2 that disrupt either its BRCA1 or BRCA2 binding have not been reported. Here, we report on the identification of a novel PALB2 variant, c.104T>C [p.L35P], that segregated in a family with a strong history of breast cancer. Functional analyses showed that L35P abrogates the PALB2-BRCA1 interaction, resulting in impaired HR and sensitivity to platinum salts and PARP inhibitors. Whole-exome sequencing of breast tumor from a c.104T>C carrier revealed a somatic, truncating mutation in the second allele of PALB2, with the tumor displays hallmark genomic features of tumors with BRCA mutations and HR defects. Using a combination of traditional clinical genetics, tumor whole-exome sequencing and in-depth functional analyses, we have provided direct evidence to cement the pathogenicity of L35P. Parallel analyses of other germline variants in the PALB2 N-terminal BRCA1-binding domain also identified multiple variants that affect HR function to varying degrees, suggesting their possible contribution to cancer development. Our findings establish p.L35P as the first pathogenic missense mutation in PALB2 identified to date and directly demonstrate the requirement of the PALB2-BRCA1 interaction for breast cancer suppression. Citation Format: Tzeh Keong Foo, Marc Tischkowitz, Srilatha Simhadri, Talia Boshari, Kathleen A. Burke, Samuel H. Berman, Nadia Zayed, Yuan Chun Ding, Susan L. Neuhausen, Britta Weigelt, Jorge S. Reis-Filho, William D. Foulkes, Bing Xia. Compromised BRCA1-PALB2 interaction is associated with breast cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2470. doi:10.1158/1538-7445.AM2017-2470

Germline mutations of PALB2 gene in a sequential series of Chinese patients with breast cancer.

1530 Background: PALB2 (Partner and Localizer of BRCA2) is recently recognized as a breast cancer predisposition gene, which plays a critical role in genome maintenance via interacting with BRCA1/2 and RAD51 when DNA break. Germline loss-of-function mutations in PALB2 lead to increased breast cancer risk. Since the germline mutation frequency of PALB2 is much less than BRCA1/2, the distinct mutation spectrum of PALB2 is still obscure. Therefore, we assessed the mutational frequency, spectrum and predictors of the PALB2 gene in a sequential series of Chinese breast cancer patients from our Research DNA Bank, to verify the utility of PALB2 genetic testing in Chinese population. Methods: We examined Chinese breast cancer cases (n = 2279) who agreed to participate in research DNA banking, recruited from 1990 through 2016. To identify the mutations, complete coding sequence and intron–exon boundaries of PALB2 were screened with Next Generation Sequencing. Personal and family histories were synchronously collected for mutation identification. Results: Among the 2279 breast cancer patients, 307 patients were familial breast cancer cases and the rest 1972 patients were sporadic breast cancer cases. PALB2 mutation carriers accounted for 7.8% (n = 24) and 4.8% (n = 95) in familial and sporadic breast cancer cohort separately. In total, 31 missense, 4 nonsense, 3 frameshift, 3 splicing and 1 codon mutations of PALB2 were identified in this study. Among the pathologic variants, PALB2 c.1744C > T, c.2748+1G > A, c.2749-1G > C, c.3114-1G > A were newly identified in sporadic breast cancer, and c.3271delC newly found in familial breast cancer. Based on in silico analysis, a total of 6 potential damaging missense variants were novelly found in this study, among which the PALB2 c.3035C > T was detected in both sporadic and familial breast cancer. Conclusions: Our data presents the germline mutation status of PALB2 in Chinese patients with breast cancer, suggesting that loss-of-function germline mutations of PALB2 are important in both familial and sporadic breast cancer. Clinically, this information may be helpful in genetic counseling of breast cancer patients with PALB2 germline mutation.

Frequency of germline PALB2 mutations among women with epithelial ovarian cancer.

Recent studies suggest that mutations in the partner and localizer of BRCA2 (PALB2) gene may predispose to ovarian cancer. It is of importance to clarify the prevalence and penetrance of PALB2 mutations in an unselected population so that clinical recommendations for prevention can be implemented. We evaluated the prevalence of germline mutations in PALB2 among 1421 epithelial ovarian cancer patients and 4300 European controls from the National Heart, Lung, and Blood Institute's Exome Sequencing Project dataset. Clinical information was obtained from medical records and survival status was determined by linkage. PALB2 coding exons were sequenced using next generation sequencing technology. Of the 1421 patients, three (0.21%) had a germline PALB2 mutation compared to two of the 4300 control subjects (0.05%). The mean age at diagnosis was 59years (range 55-62) and all three women died within 2years of diagnosis. A PALB2 mutation was associated with a four-fold, albeit not significant, increased risk of ovarian cancer (OR=4.55; 95% CI 0.76-27.24; P=0.10). These results suggest that germline PALB2 mutations are rare. The true effect of such mutations on ovarian cancer risk require further study before the clinical relevance of inherited PALB2 mutations is established.

Mutation analysis of the PALB2 gene in unselected pancreatic cancer patients in the Czech Republic

Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis among common solid cancer diagnoses. It has been shown that up to 10% of PDAC cases have a familial component. Characterization of PDAC-susceptibility genes could reveal high-risk individuals and patients that may benefit from tailored therapy. Hereditary mutations in PALB2 (Partner and Localizer of BRCA2) gene has been shown to predispose, namely to PDAC and breast cancers; however, frequencies of mutations vary among distinct geographical populations. Using the combination of sequencing, high-resolution melting and multiplex ligation-dependent probe amplification analyses, we screened the entire PALB2 gene in 152 unselected Czech PDAC patients. Truncating mutations were identified in three (2.0%) patients. Genotyping of found PALB2 variants in 1226 control samples revealed one carrier of PALB2 truncating variant (0.08%; P = 0.005). The mean age at PDAC diagnosis was significantly lower among PALB2 mutation carriers (51 years) than in non-carriers (63 years; P = 0.016). Only one patient carrying germline PALB2 mutation had a positive family breast cancer history. Our results indicate that hereditary PALB2 mutation represents clinically considerable genetic factor increasing PDAC susceptibility in our population and that analysis of PALB2 should be considered not only in PDAC patients with familial history of breast or pancreatic cancers but also in younger PDAC patients without family cancer history.

Heterozygous PALB2 c.1592delT mutation channels DNA double-strand break repair into error-prone pathways in breast cancer patients.

Hereditary heterozygous mutations in a variety of DNA double-strand break (DSB) repair genes have been associated with increased breast cancer risk. In the Finnish population, PALB2 (partner and localizer of BRCA2) represents a major susceptibility gene for female breast cancer, and so far, only one mutation has been described, c.1592delT, which leads to a sixfold increased disease risk. PALB2 is thought to participate in homologous recombination (HR). However, the effect of the Finnish founder mutation on DSB repair has not been investigated. In the current study, we used a panel of lymphoblastoid cell lines (LCLs) derived from seven heterozygous female PALB2 c.1592delT mutation carriers with variable health status and six wild-type matched controls. The results of our DSB repair analysis showed that the PALB2 mutation causes specific changes in pathway usage, namely increases in error-prone single-strand annealing (SSA) and microhomology-mediated end-joining (MMEJ) compared with wild-type LCLs. These data indicated haploinsufficiency regarding the suppression of error-prone DSB repair in PALB2 mutation carriers. To the contrary, neither reduced HR activities, nor impaired RAD51 filament assembly, nor sensitization to PARP inhibition were consistently observed. Expression of truncated mutant versus wild-type PALB2 verified a causal role of PALB2 c.1592delT in the shift to error-prone repair. Discrimination between healthy and malignancy-presenting PALB2 mutation carriers revealed a pathway shift particularly in the breast cancer patients, suggesting interaction of PALB2 c.1592delT with additional genomic lesions. Interestingly, the studied PALB2 mutation was associated with 53BP1 accumulation in the healthy mutation carriers but not the patients, and 53BP1 was limiting for error-prone MMEJ in patients but not in healthy carriers. Our study identified a rise in error-prone DSB repair as a potential threat to genomic integrity in heterozygous PALB2 mutation carriers. The used phenotypic marker system has the capacity to capture dysfunction caused by polygenic mechanisms and therefore offers new strategies of cancer risk prediction.

Development of a novel PTT assay for mutation detection in PALB2 large exons and PALB2 screening in medullary breast cancer.

Beyond BRCA1 and BRCA2 genes, PALB2 (Partner and localizer of BRCA2) emerges as the third breast cancer susceptibility gene due to its role in the same DNA repair pathway: homologous recombination. In most populations studied so far, PALB2 mutations are detected in 1-2% of BRCA negative female patients. PALB2 gene contains 13 exons; exons 4 and 5 consist 65% of the coding area. We developed a protein truncation test (PTT) for quick screening of truncating pathogenic mutations of these two large exons. Specific primers were de novo, in silico designed and the PTT-PCR products were translated in the presence of biotinylated lysine and detected colorimetrically. The assay was initially tested in 30 patients with hereditary breast cancer, negative for BRCA mutations and then, in 17 patients with the rare medullary breast cancer subtype. Small PALB2 exons were screened with high-resolution melting curve analysis (HRMA) and the large DNA rearrangements with multiplex ligation-dependent probe amplification (MLPA). Any alterations detected were verified by Sanger DNA Sequencing. The developed PTT methodology is highly specific for clinical significant mutations; positive control samples that produce truncated PALB2 peptides were correctly identified and the method was accurate when compared to DNA sequencing. We did not detect any deleterious PALB2 mutation in both groups of patients. HRMA and MLPA were also negative for all tested samples. However, our novel, fast and cost-effective PTT method for pathogenic mutation detection of the two large PALB2 exons can be applied in screening of a large number of breast cancer patients.