PALB2 Research Articles

"You Always Have It in the Back of Your Mind"-Feelings, Coping, and Support Needs of Women with Pathogenic Variants in Moderate-Risk Genes for Hereditary Breast Cancer Attending Genetic Counseling in Germany: A Qualitative Interview Study.

Hereditary breast cancer accounts for approximately 30% of newly diagnosed breast cancer (BC) cases. Pathogenic variants in moderate-risk BC genes (MBCG) differ from those in high-risk genes in terms of associated cancer risks, affected organs, and available preventive options. Little is known about how MBCG pathogenic variant carriers who have attended post-test genetic counseling perceive their situation, how they cope with their situation, and which support needs they might have. Problem-centered, guided, individual interviews were conducted with twelve women carrying pathogenic variants in MBCG. The interview analysis was based on Mayring’s qualitative content analysis. The women were between 29 and 59 years old and carried pathogenic variants in the risk genes CHEK2 (n = 8), ATM (n = 1), or PALB2 (n = 3). Women reported a wide range of feelings, both positive (relief, calmness) and negative (overwhelm, fear, grief, guilt). All women applied strategies of emotion-focused coping to deal with this lifelong situation. Appraisal and evaluation of the affected mother’s coping might influence the patient’s own behavior and coping style. These results could be used during and after post-test genetic counseling to provide more needs-oriented counseling, and to help women in adjusting to and coping with being a pathogenic variant carrier.

Detection of a pathogenic Alu element insertion in PALB2 gene from targeted NGS diagnostic data.

Despite routine analysis of a large panel of genes, pathogenic variants are only detected in approximately 20% of families with hereditary breast and/or ovarian cancer. Mobile element insertions (MEI) are known to cause genetic diseases in humans, but remain challenging to detect. Retrospective analysis of targeted next-generation sequencing (NGS) data from 359 patients was performed using a dedicated MEI detection pipeline. We detected one MEI in exon 9 of the PALB2 gene in a woman with a family history of breast cancer. The pathogenic variant, c.2872_2888delins114AluL2, disrupts the PALB2 coding sequence and leads to the production of a truncated protein, p.(Gln958Valfs*38). This is the first report of a pathogenic MEI in PALB2. This study illustrates that MEI analysis may help to improve molecular diagnostic yield and can be performed from targeted NGS data used for routine diagnosis.

Prevalence of Fanconi anemia gene mutations among men undergoing multigene germline testing for prostate cancer: Interim results from the EMPOWeR study.

188 Background: Germline testing for prostate cancer (PCA) is now central to treatment, screening, and hereditary cancer management. The Fanconi anemia (FA) pathway is a key DNA repair pathway involved in PCA biology and treatment. Prevalence of FA genes BRCA2, PALB2, and BRIP1 is well-described; however, multiple other FA genes are not routinely tested, with limited prevalence data. Here we report mutation prevalence of a spectrum of FA genes among men undergoing PCA multigene testing on the Evaluation and Management for Prostate Oncology, Wellness, and Risk (EMPOWeR) study. Methods: Eligibility includes any male with PCA or at-risk for PCA. Multigene testing includes 51 genes; FA pathway genes include BRCA2, PALB2, BRIP1, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, and FANCM. Multiple additional cancer risk genes were tested. Fisher’s exact tests were conducted to compare the prevalence of FA gene mutations between participants in the EMPOWeR study vs population prevalence reported in the literature. Statistical significance level of all tests was set a priori to 0.05. Results: The current cohort includes 235 participants. Characteristics are White (83.3%), Black (13.7%), PCA diagnosis (83.4%), mean age of PCA diagnosis 61.7 + 7.69 years, Gleason score >=7 (66.2%), and T3 or higher (29.4%). Genetic results were available for 179 participants. Overall, 11.1% of participants (n=20) had a pathogenic/likely pathogenic mutation identified. Among mutation carriers, 45% (n=9) had mutations in FA genes, including FANCA (n=3), BRCA2 (n=2), FANCM (n=1), FANCD2 (n=1), PALB2 (n=1), and BRIP1 (n=1). Table shows clinical characteristics of participants with mutations in FANCA, FANCM, and FANCD2. Further mutation spectrum included: CHEK2 (n=3), NBN (n=2), MUTYH (n=2), BRCA (n=1), ATM (n=1), HOXB13 (n=1), APC (n=1). Compared to population prevalence, FA mutation prevalence was significantly higher overall (5.0% vs. 0.6%, p = 0.010) and among mutation carriers (45% vs. 0.6%, p<0.001). Conclusions: While prevalence of FA genes BRCA2, PALB2, and BRIP1 is well-described, our study supports testing a broader range of FA genes given the prevalence rates, potential implications for clinical trials, targeted therapy, inherited syndromes, and reproductive implications.[Table: see text]

Differential efficacy of PARP inhibitors in metastatic castration-resistant prostate cancer with DNA repair defects: A systematic review and meta-analysis.

134 Background: Recent trials have suggested poly ADP-ribose polymerase inhibitors (PARPi) sensitivity in patients with treatment-refractory metastatic castration-resistant prostate cancer (mCRPC) harboring mutations in DNA damage and response repair genes (DDR). However, the efficacy profile might differ with different genes and is still being explored in multiple studies. Methods: We systematically searched several electronic databases (MEDLINE, EMBASE), and conference proceedings to include abstracts and full-text publications of phase II/III trials evaluating PARPi in treatment-refractory mCRPC with DDR gene alterations. Outcomes of interest included objective response rate (ORR), complete response (CR), prostate specific antigen (PSA) 50% response, circulating tumor cells conversion (CTCc) from ≥ 5 to < 5 cells, composite response (CoR) and risk of progression. Data was pooled using Inverse-variance approach. A DerSimonian and Laird random-effect meta-analysis was conducted to estimate pooled proportion (PP) of events using the Freeman-Tukey transformation in each gene. Clopper-Pearson method was used to estimate the associated 95% confidence intervals (CI). Results: This systematic review and meta-analysis included five unique trials with 648 patients and four PARPi (niraparib, olaparib, rucaparib, talazoparib). Objective response to PARPi was observed in 44.7% of patients with mutations in either BRCA1 or 2 or both (95% CI: 36.0%-53.6%; I2: 0%), 23.5% with ATM (95% CI: 3.91%-51.0%; I2: 65%), 25.0% with CDK12 (95% CI: 8.66%-49.1%), and 45.3% with PALB2 alterations (95% CI: 14.8%-77.5%; I2: 0%). Consistent results were observed for CR outcome. PSA50% response to PARPi was observed in 60.3% of patients with BRCA1/2 mutations (95% CI: 50.3%-70.0%; I2: 57%), 5.54% (95% CI: 0.01-16.6; I2: 0%) with ATM, and 70.1% (95% CI: 35.6%-96.6%; I2: 0%) with PALB2 mutations while no PSA 50% response was observed in patients with CDK12 mutations (PP: 0.00%; 95% CI: 0%-16.84%). Moreover, CTCc was observed in 68.3% of patients with BRCA1/2 mutations (95% CI: 45.0%-87.8%; I2: 77), 34.2% (95% CI: 11.2-61.3%; I2: 45%) with ATM, 41.7% (95% CI: 15.2%-72.3%) with CDK12, and 48.5% (95% CI: 6.39%-92.9%; I2: 49%) with PALB2. CoR was observed in 76.5% patients with BRCA1/2 mutations (95% CI: 65.4%-86.1%; I2: 22%), 30.4% (95% CI: 16.0%-46.9%) with ATM, 25% (95% CI: 8.66%-49.1%) with CDK12, and 63.9% (95% CI: 31.0%-91.8%; I2: 0%) with PALB2 mutations. Similarly, the risk of progression was 50.9% in patients with BRCA1/2 mutations (95% CI: 37.7%-63.9%), 70.9% (95% CI: 60.0%-80.40%; I2: 0%) with ATM, and 75% (95% CI: 19.4-99.3%) with PALB2. Conclusions: Current evidence is sparse regarding efficacy by specific genes. Limited data favors the use of PARPi in mCRPC patients harboring mutations in BRCA1/2 and PALB2 genes.

Psychosocial outcome and health behaviour intent of breast cancer patients with BRCA1/2 and PALB2 pathogenic variants unselected by a priori risk.

There is an increasing number of cancer patients undertaking treatment-focused genetic testing despite not having a strong family history or high a priori risk of being carriers because of the decreasing cost of genetic testing and development of new therapies. There are limited studies on the psychosocial outcome of a positive result among breast cancer patients who are at low a priori risk, particularly in women of Asian descent. Breast cancer patients enrolled under the Malaysian Breast Cancer Genetic Study between October 2002 and February 2018 were tested for BRCA1, BRCA2 and PALB2 genes. All 104 carriers identified were invited by a research genetic counsellor for result disclosure. Of the 104 carriers, 64% (N = 66) had low a priori risk as determined by PENN II scores. Psychosocial, risk perception and health behaviour measures survey were conducted at baseline (pre-result disclosure), and at two to six weeks after result disclosure. At baseline, younger carriers with high a priori risk had higher Cancer Worry Scale scores than those with low a priori risk but all scores were within acceptable range. Around 75% and 55% of high a priori risk carriers as well as 80% and 67% of low a priori risk carriers had problems in the “living with cancer” and “children” psychosocial domains respectively. All carriers regardless of their a priori risk demonstrated an improved risk perception that also positively influenced their intent to undergo risk management procedures. This study has shown that with sufficient counselling and support, low a priori risk carriers are able to cope psychologically, have improved perceived risk and increased intent for positive health behaviour despite having less anticipation from a family history prior to knowing their germline carrier status.

Abstract P3-07-07: Prevalence of BRCA 1/2 germinal mutation among young women with breast cancer: Experience in a third level private center

Abstract BACKGROUND: Breast cancer (BC) in young women has a behavior and biology associated with an increased risk of recurrence and death. The diagnosis of MC in young women is strongly associated with the presence of genetic mutations, mainly in the BRCA gene. However, an association between the presence of inherited genetic mutations and prognosis has not been observed. OBJECTIVE: To describe the prevalence and analyze the clinical-pathological characteristics of women, <50 years with BC, with and without BRCA germline mutation. MATERIAL AND METHODS: A descriptive, observational, cross-sectional study of women <50 years with BC with and without BRCA germline mutation who received treatment at a private third level Medical Center. RESULTS: During the period from January 1, 2015 to June 1, 2020, 807 women with a diagnosis of breast cancer were identified who received systemic treatment under adjuvant, neoadjuvant or palliative indication. Of these, 360 (44.6%) were 50 years old or younger. 53 women with BC <50 years had the result of a genetic panel and are the ones that were included for the analysis. Median age was 40 years (27-50), 55% <40 years old. The immunophenotype, according to the evaluation by immunohistochemistry of the hormonal receptors, Ki-67 and HER2/neu status, was luminal A like in 13 (24.5%) women, luminal B like in 18 (34%), luminal B like with overexpression of HER2/neu in 7 (13.2%), HER2/neu in 3 (5.7%) and in 12 (22.6%) cases it was triple negative. 30/53 women (56.6%), presented some mutation in the genetic panel. BRCA1 and/or BRCA2 9/30 (30%) mutation, all of them were pathogenic variants. Mutations other than BRCA in 21/30 (70%), of these 7/21 (33.3%) pathogenic (P) mutations in the ATM (2), MUTYH (2), TP53 (2) and PALB2 (1) genes. In 14/21 (66.7%) variants of uncertain significance (VUS) were identified. We did not observe an association between the clinicopathological characteristics and the BRCA mutational status or other genetic mutations, except for the high degree of differentiation (p = 0.04), being more frequent in the mutated group. There were no differences in disease-free time between BRCA mutated and non-mutated patients (p = 0.12). CONCLUSIONS: The prevalence of the BRCA germline mutation in women with BC <50 years in our population was 30%. The clinical and biological characteristics and the disease-free time were not different among the group with and without BRCA germline mutation, or other genes. BRCA GENETIC VARIANTS (n:9)IDGenProtein changeNCBI 1000Clinical risk4BRCA1c.1960A>Tp.Lys654*rs80357355P16BRCA1c.815_824dupAGCCATGTGGp.Thr276Alafs*14rs387906563P38BRCA1c.211 A>Gp.Arg71Glyrs80357382P8BRCA2c.658_659delp.Val220llefs*4rs80359604P25BRCA2c.6024dupGp.Gln2009Alafs*9rs80359554P24BRCA1ex9-12del c.548?PBRCA2c.6413T>Ap.Val2138Asprs80358877VUS40BRCA2c.8988_8990delATAinsTTp.Leu2996Phefsrs397508027P42BRCA2c.5146_5149dep.Tyr1716LysFs*8rs276174854P49BRCA2c.6244delp.Leu2082fsrs1131691125PNO BRCA GENETIC VARIANTS (n:21)IDGENProtein changeNCBI 1000Clinical risk45ATMc.7502A>Gp.Asn2501Serrs531617441VUS48ATMc.3663G>Ap.Trp1221rs864622490P52ATMc.2839-3_2839delinsGATACTArs786202148PAPCc.1895T>Cp.Ile632Thrrs587781360VUS3ATMc.6919C>Tp.Leu2307Phers56009889VUSSMAD4c746_747delinsCCp.Gln249delinsPrors587782209VUS23BAP1c.623G>Ap.Arg208Glnrs867416499VUS32BRIP1c.3088_3096dupp.Ala1030_Ser1032duprs1187782159VUS36CDKN2Ac.146T>Cp.Ile49Thrrs199907548VUS5CHEK2c.1567C>Tp.Arg523Cysrs149501505VUS30DICER1c.1798G>Cp.D600HVUS22FANCMc.5832G>Tp.Leu1944Phers201017015VUS41FHc.1481C>Tp.Ala494Valrs752369363VUSTSC1c.2432G>Ap.Arg811Glnrs761281095VUS11MLH1c.2219T>Cp.Ile740Thrrs1044486319VUS12MUTYHc.1227_1228dupp.Glu4110Glyfs*43rs587780078P16MUTYHc.1227_1228dupp.Glu4110Glyfs*43rs587780078P20PALB2c.509_510delp.Arg17Ilefs*14rs515726123P14PMS2c.865T>Ap.Phe2891lers771787834VUS47POLEc.4150C>TVUS6RAD51Cc.492T>Gp.Phe164Leurs573992101VUS17TP53c.604C>Tp.Arg202Cysrs587780072VUS50TP53c.587G>Cp.Arg196Prors483352697P43TP53c.587G>Cp.Arg196Prors483352697PKDRc.1416A>Tp.Gln472Hisrs1870377VUS Citation Format: Daniela Vazquez-Juarez, Juan A Serrano-Olvera, Alejandro Noguez-Ramos, Gabriela O Regalado-Porras, Jesus M Lazaro-León, Guillermo Olivares-Beltran, Raquel Gerson-Cwilich. Prevalence of BRCA 1/2 germinal mutation among young women with breast cancer: Experience in a third level private center [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-07-07.

Abstract P3-07-02: Identification of potential germline variants (GV) on tumor comprehensive genomic profiling (CGP) in patients with advanced breast cancer (BC): BRCA1/2 and beyond

Abstract Background Detection of pathogenic GVs in patients with BC has implications for both patients and their family members. Management options such as increased surveillance, chemoprevention, and surgical prophylaxis are available to GV carriers. Beyond BRCA1/2, GVs in the cancer susceptibility genes (CSGs) PALB2, ATM, and CHEK2 confer a 2-11-fold lifetime risk of BC. One opportunity CGP assays present is the potential to detect clinically-relevant GVs in addition to targetable somatic variants. While the Breast Cancer Association Consortium found that 5.2% of women with BC carried a GV in one of these five CSGs, we sought to describe the frequency of these potential GVs detected by CGP in a cohort of patients with advanced disease. Methods We reviewed an internal database of patients with advanced BC who underwent testing with a CGP panel using tissue (n= 20,109, FoundationOne® CDx) or plasma (n= 4,182, FoundationOne®Liquid CDx or FoundationOne®Liquid). Cases with a potential GV were identified by filtering base substitutions and short indels for inclusion in ClinVar as pathogenic or likely pathogenic and by variant allele frequency (VAF) based on an optimized assay-specific threshold, focusing on the select CSGs of BRCA1/2, PALB2, ATM and CHEK2. To enable follow-up of potential GVs, we implemented a new reporting “banner” to highlight select short variants in these CSGs. Predominant patient ancestry was inferred using a SNP-based classifier and Fisher’s exact test was utilized for comparison between groups. Results A total of 24,291 unique patients with primarily advanced BC had CGP results available for study, with common actionable findings including PIK3CA mutations (8,572, 35.3%), ESR1 mutations (3,289, 13.5%), and HER2 amplification (1,602, 6.6%). Focusing on the 5 CSGs, 16.4% of patients (3,986) had at least one pathogenic alteration detected in BRCA2 (1,153, 4.7%), ATM (969, 4.0%), CHEK2 (982, 4.0%) BRCA1 (849, 3.5%) or PALB2 (308, 1.3%); 1.1% of patients (263) harbored alterations in multiple CSGs. 50.7% (2,020/3,986) of patients with pathogenic alterations in these CSGs - 8.3% (2,020/24,291) of total patients with advanced BC - had an alteration meeting criterion as a potential GV. Variants in BRCA1 (511/919, 55.6%), BRCA2 (786/1,425, 55.2%), and PALB2 (201/376, 53.5%), more frequently met criteria as potential GVs than variants in CHEK2 (328/1,046, 31.4%) or ATM (265/1,100, 24.1%). In these five CSGs, 1,796/3,195 alterations detected on tissue CGP (56.2%) and 295/1,671 detected in plasma (17.7%) met criteria as a potential GVs. Ancestry analysis of 20,108 assessable BC patients tested using tissue CGP showed potential GVs in CHEK2 were more common in European vs non-European (1.7% vs 0.4%, p<0.01) and potential GVs in PALB2 were more common in African vs non-African (1.4% vs 0.7%, p<0.01) ancestries. Of 1,961 patients with BC tested over a 2-month period, 9.7% of reports (191) included a germline banner reporting a potential GV in one of these 5 CSGs and recommending consideration of referral for germline testing. Conclusion Potential pathogenic GVs in BRCA1/2, PALB2, ATM and CHEK2 were identified in 8.3% of patients with advanced BC tested utilizing CGP when filtering by VAF and ClinVar annotation. Highlighting these potential GVs with a report banner provides the opportunity for follow-up germline testing and genetic counseling for patients who otherwise may not have been referred for additional testing. These alterations were detected in both tissue and plasma CGP and in patients of varying ancestries. The potential for detection of potential GVs plus the detection of actionable driver and resistance mechanisms may add to the clinical value of CGP for patients with breast cancer. Citation Format: Marni B Tierno, Kali C Dougherty, Erica Gornstein, Dean C Pavlick, Alexa Schrock, Geoff R Oxnard. Identification of potential germline variants (GV) on tumor comprehensive genomic profiling (CGP) in patients with advanced breast cancer (BC): BRCA1/2 and beyond [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-07-02.

Molecular Features and Clinical Management of Hereditary Pancreatic Cancer Syndromes and Familial Pancreatic Cancer.

Hereditary pancreatic cancers are caused by several inherited genes. Familial pancreatic cancer is defined as pancreatic cancer arising in a patient with at least two first-degree relatives with pancreatic cancer in the absence of an identified genetic cause. Hereditary pancreatic cancer syndromes and familial pancreatic cancers account for about 10% of pancreatic cancer cases. Germline mutations in BRCA1, BRCA2, ATM, PALB2, CDKN2A, STK11, and TP53 and mismatch repair genes (MLH1, MSH2, MSH6, PMS2, and EPCAM) are among the well-known inherited susceptibility genes. Currently available targeted medications include poly (ADP-ribose) polymerase inhibitors (PARP) for cases with mutant BRCA and immune checkpoint inhibitors for cases with mismatch repair deficiency. Loss of heterozygosity of hereditary pancreatic cancer susceptibility genes such as BRCA1/2 plays a key role in carcinogenesis and sensitivity to PARP inhibitors. Signature 3 identified by whole genome sequencing is also associated with homologous recombination deficiency and sensitivity to targeted therapies. In this review, we summarize molecular features and treatments of hereditary pancreatic cancer syndromes and surveillance procedures for unaffected high-risk cases. We also review transgenic murine models to gain a better understanding of carcinogenesis in hereditary pancreatic cancer.

Increased incidence of pathogenic variants in ATM in the context of testing for breast and ovarian cancer predisposition.

Pathogenic Variants (PV) in major cancer predisposition genes are only identified in approximately 10% of patients with Hereditary Breast and Ovarian Cancer (HBOC) syndrome. Next Generation Sequencing (NGS) leads to the characterization of incidental variants in genes other than those known to be associated with HBOC syndrome. The aim of this study was to determine if such incidental PV were specific to a phenotype. The detection rates of HBOC-associated and incidental PV in 1812 patients who underwent genetic testing were compared with rates in control groups FLOSSIES and ExAC. The rates of incidental PV in the PALB2, ATM and CHEK2 genes were significantly increased in the HBOC group compared to controls with, respective odds ratios of 15.2 (95% CI = 5.6-47.6), 9.6 (95% CI = 4.8-19.6) and 2.7 (95% CI = 1.3-5.5). Unsupervised Hierarchical Clustering on Principle Components characterized 3 clusters: by HBOC (P = 0.01); by ExAC and FLOSSIES (P = 0.01 and 0.02 respectively); and by HBOC, ExAC and FLOSSIES (P = 0.01, 0.04 and 0.04 respectively). Interestingly, PALB2 and ATM were grouped in the same statistical cluster defined by the HBOC group, whereas CHEK2 was in a different cluster. We identified co-occurrences of PV in ATM and BRCA genes and confirmed the Manchester Scoring System as a reliable PV predictor tool for BRCA genes but not for ATM or PALB2. This study demonstrates that ATM PV, and to a lesser extent CHEK2 PV, are associated with HBOC syndrome. The co-occurrence of ATM PV with BRCA PV suggests that such ATM variants are not sufficient alone to induce cancer, supporting a multigenism hypothesis.

Clinical Significance of Gene Mutations and Polymorphic Variants and their Association with Prostate Cancer Risk in Polish Men.

Objectives: We tested the association of germline variants in BRCA1, BRCA2, CHEK2, CDKN2A, CYP1B1, HOXB13, MLH1, NBS1, NOD2 and PALB2 genes, as well as in 8q24 region, with prostate cancer (PC) risk and estimated their impact on disease clinical course, including overall survival time in Polish men with localized PC qualified for radical treatment.Materials and Methods: DNA of 110 patients with localized prostate cancer treated with radical prostatectomy (RP), from each age group and with different stages of the disease. DNA samples of the control group consisted of 111 men, volunteers, without PC (age-matched to study group). Sanger sequencing, AS-PCR, RFLP-PCR, and multiplex-PCR were used for variants detection.Results: The percentage of men with ≥1 germline variant was higher in PC group (52.7%) than in healthy men (37.8%) (P = .03). The presence of ≥2 variants was associated with shorter survival than the presence of one or no variant in the PC group (P = .14, trend). The HOXB13 G84E was detected in 2.9% of PC men and in no healthy men (P = .19, trend, OR = 7.21). A CHEK2 truncating mutation (1100delC or IVS2+1G>A) was detected in 2/110 (1.8%) PC patients and in no healthy men (P = .29, OR=5.14). The NBS1 I171V was detected in 2/110 (1.8%) PC patients and in no men from the control group (OR=5.14, P = .29, NS).Conclusions: We conclude that the presence of more than 2 germline variants was probably associated with shorter survival of patients with localized prostate cancer qualified for radical treatment. The HOXB13 (G84E), CHEK2 (1100delC or IVS2+1G>A) truncating variants and NBS1 (I171V) are associated with PC and hereditary form of the disease. The HOXB13 (G84E) and NOD2 (3020insC) single variants are associated with shorter and CYP1B1 (48CC, 119GG) single genotypes with longer overall survival.

EARS2 significantly coexpresses with PALB2 in breast and pancreatic cancer

BackgroundPALB2 (BRCA2 partner and localizer) is a BRCA2-interacting protein that is required for BRCA2 genome caretaker tasks and interacts with BRCA1. Women with PALB2 mutation have a 40% to 60% higher risk of breast cancer, almost equivalent to women who have BRCA mutations. PALB2 mutation may also increase the risk of pancreatic cancer. New guidelines for PALB2 mutation in breast cancer advise pancreatic cancer screening, which includes M.R.I.s of the pancreas as well as endoscopic ultrasonography, for women who have a family history of pancreatic cancer. Using the Cancer Genome Atlas (TCGA) and The Human Protein Atlas we examined genes that co-express with PALB2 in breast and pancreatic cancer. MethodsWe used cBioPortal for Cancer Genomics to analyze data in TCGA. cBioPortal provides visualization, analysis and download of large-scale cancer genomics data sets. We used the UCSC Xena Browser to additionally analyze gene expression in TCGA. ResultsSix genes, EARS2, ARL6IP1, DNAJA3, KNOP1, RPUSD1, and TMEM186, significantly coexpressed with PALB2 in both breast and pancreatic cancer. Glutamyl-tRNA synthetase 2 (EARS2) was the only gene coexpressing with PALB2 in the breast and pancreatic cancer subjects that was significantly related to pancreatic cancer survival. Elevated PALB2 and EARS2 gene expression are both significantly associated with the PAM50 Luminal B subtype and high risk of recurrence, suggesting why these women may need active intervention, such as prophylactic mastectomy. ConclusionsEARS2 expression might be a risk factor for pancreatic cancer in breast cancer patients with PALB2 mutations. By assessing EARS2 expression in breast tumors, the clinician might obtain a second piece of information that, with family history of pancreatic cancer, could inform the decision to perform pancreatic cancer screening.

Estrogen and DNA damage modulate mRNA levels of genes involved in homologous recombination repair in estrogen-deprived cells

Aims: Breast and ovarian cancers are frequently associated with mutations in genes involved in DNA double-strand break (DSB) repair by homologous recombination (HR). Risk factors for breast cancer are often linked to estrogen-related pathways. Here, we studied the crosslink between estrogen and the HR pathway. Methods: We analyzed, using online annotation tolls, the enrichment of candidate estrogen-upregulated genes among DNA repair pathways. We analyzed how estrogen modulates mRNA levels of HR repair (HRR) genes in estrogen-receptor (ER)-positive cells. The cells were deprived of estrogen, and the mRNA levels of HRR genes were determined using real-time polymerase chain reaction, following estrogen addition as well as DNA damage induction. In addition, we examined the effect of estrogen on DNA repair, by immuno-fluorescence analysis, using the DSB marker phospho-histone H2AX, as an indicator for DSB repair. Finally, we performed a clonogenic survival assay to determine the effect of estrogen on cell survival. Results: We discovered that genes whose mRNA levels are upregulated by estrogen are strongly associated with the HR pathway. We validated that estrogen upregulates mRNA levels of the HRR genes MRE11, RAD50, and PALB2, which have not been previously shown to be regulated by estrogen. Additionally, we revealed that DNA damage induces an upsurge in mRNAs encoding BRCA1, MRE11, RAD50, PALB2, and CtIP, in ER-positive cells deprived of estrogen. Notably, DSB repair was impaired in ER-positive cells deprived of estrogen, compared to cells exposed to the hormone. We also established that ER-positive cells deprived of estrogen are hypersensitive to DSBs. Conclusion: These results suggest that exposure of ER-positive cells to estrogen triggers the expression of HRR genes, which is required to meet the increased repair demands due to the proliferating effect induced by estrogen. This may explain the higher chances of developing estrogen-dependent cancers due to mutations in HRR genes.

Platinum-based chemotherapy for pancreatic cancer: impact of mutations in the homologous recombination repair and Fanconi anemia genes.

Background:Mutations in homologous recombination (HR) and Fanconi anemia (FA) genes may predispose to pancreatic cancer (PC) and enable the prediction of sensitivity to platinum-based chemotherapy. FOLFIRINOX is a standard treatment option for non-selected PC patients and could be effective due to undiagnosed DNA repair deficiency. Here, we aimed to determine the frequency of mutations in genes involved in the HR and FA pathways, evaluate their clinical implications, and determine the objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) of PC patients treated with platinum.Methods:We performed targeted DNA sequencing of 30 genes (ABRAXAS1, ATM, ATR, BARD1, BLM, BRCA1, BRCA2, BRIP1, CDKN2A, CHEK1, CHEK2, FANCC, FANCF, FANCG, FANCI, FANCL, FANCM, MRE11A, NBN, PALB2, PTEN, RAD50, RAD51C, RAD51D, RAD52, RAD54B, RBBP8, RINT1, SLX4, and XRCC2) for 543 PC patients.Results:In BRCA/PALB2-mutated patients with advanced PC (33 patients, 6.1%), the PFS and OS were higher for first-line platinum therapy than for non-platinum therapy [PFS: HR = 0.28, 95% confidence interval (CI) = 0.10–0.81, p = 0.02; OS: HR = 0.31, 95% CI = 0.08–1.16, p = 0.08]. Among 93 patients (17.1%) with mutations in other HR/FA genes, no statistically significant difference in PFS and OS was observed between first-line platinum therapy and non-platinum therapy (PFS: HR = 0.83, 95% CI = 0.43–1.62, p = 0.59; OS: HR = 0.58, 95% CI = 0.28–1.22, p = 0.15). For patients with early PC, no prognostic value was observed for BRCA1/2, PALB2, or other HR/FA genes mutations. Moreover, a personal history of breast, ovarian, pancreatic, or prostate cancer was identified as the only independent predictor of the risk of BRCA/PALB2 mutations (HR = 5.83, 95% CI = 2.16–15.73, p < 0.01).Conclusion:Mutations in the BRCA1/2 and PALB2 genes increase the sensitivity of PC to platinum agents. Thus, alterations in these genes in PC patients must be determined prior to anticancer therapy.

The Effect of Gene Mutations on Metastasis and Overall Survival in Metastatic and Nonmetastatic Colon Cancers.

Objective:It is known that many genes are associated with colon cancer. We aimed to investigate the effect of gene mutations on metastasis and overall survival in metastatic and non metastatic colon cancers. Methods:A total of 50 patients with metastatic (n=25) and non metastatic (n=25) diagnosed with colon cancer between 2010 and 2018 were included in the study. APC, MUTYH, RAD50, MEN1, ATM, PALB2, NSH2, BRCA1, BRCA2, MLH1, BRIP1, TP53, PTEN, BARD1, MSH6, PMS2, NBN, and FAM175A gene mutations were evaluated using the next generation sequencing method. The effect of gene mutations on metastasis and overall survival were evaluated. Results:The mean age of patients with colon cancer without distant metastasis was 48.64±14.72 years and for patients with distance metases was 56.68±11.65. The mean survival time of colon cancer patients with distant organ metastasis after the metastasis date was 104.36±58.59 weeks. The presence of APC, MUTYH, and TP53 genetic mutations was observed with a higher rate in metastatic colon cancer (p<0.05). Conclusion:We showed that APC, MUTYH, and TP53 mutations are associated with distant organ metastasis.

Medical knowledge and information needs among women with pathogenic variants in moderate-risk genes for hereditary breast cancer attending genetic counseling at an academic hospital in Germany-A qualitative approach.

With 69,000 newly diagnosed cases every year, breast cancer (BC) is the most frequent cancer disease among women in Germany. Familial clustering is seen in about 30% of newly diagnosed cases. Besides the high-risk genes BRCA1/2, there are also moderate-risk BC genes (MBCG) that are associated with a 20%-50% risk of BC, such as CHEK2, ATM, and PALB2. In Germany, carriers of pathogenic variants in MBCG receive specific information on their test results, individual risks, and preventive options during genetic counseling for the disclosure of the results in a specialized center. Little is known about the medical knowledge that women have after attending counseling. This study aims to identify the medical knowledge, further information needs, and the possible impact of a lack of information on dealing with everyday life for women with pathogenic variants in MBCG who have attended genetic counseling at an academic hospital in Germany. Problem-centered, guided, individual interviews were conducted with twelve women carrying pathogenic variants in MBCG. The interview guide was developed based on the methods of the problem-centered interview according to Witzel. The interview analysis was based on Mayring's qualitative content analysis. The women were between 29 and 59years old and carried pathogenic variants in the risk genes CHEK2 (n=8), ATM (n=1), or PALB2 (n=3). Several medical uncertainties and information needs emerged from the data, concerning (a) medical terms, (b) risk perception, (c) BC therapy for hereditary BC, (d) lifestyle advice and risk factors, and (e) family planning and risk-reducing mastectomy. Women with pathogenic variants in MBCG might develop their own conceptions regarding the onset of disease and inheritance. In order to meet the need for information and address the uncertainties that may still exist after genetic counseling, structured, evidence-based and comprehensible written information in German should be developed for this group.

Exonic sequencing and MLH3 gene expression analysis of breast cancer patients.

Breast cancer is the most common cancer in women worldwide. Detection of breast cancer susceptibility genes is an important issue. Also, MLH3 is a DNA mismatch repair gene and mutation in this gene is harmful in different cancers. This study aimed to use exome sequencing to uncover previously undetected breast cancer-predisposing variants. Also, we investigated the MLH3 gene expression of breast cancer patients which can be a breast cancer susceptibility gene. A total of 80 samples including 40 paired normal and cancer tissue samples were collected at Zheen International Hospital, Erbil, Iraq. Exome sequencing was used to identify mutations. Different in silico tools were used to predict the effect of mutation on the structural features or protein function. Real-time PCR was used for assessing the expression of MLH3 in breast cancer patients. We identified 26 variants in breast cancer patients, 22 inherited variants were found in MLH3, CHECK2, BRCA1, BRCA2, BLM, TP53, MSH6, NBN and PTEN genes and 4 somatic variants were found in PALB2, RAD50 and RBM10 genes. It was found that the expression of the MLH3 gene in tumor samples was significantly down-regulated compared with normal tissues. Statistically, high significance was found. The decreased expression of MLH3 was significant in all ranges of ages and all breast cancer types. Also, the expression of MLH3 decreased significantly in patients with breast cancer grades of II and III. In conclusion, MLH3 can be used as a susceptibility gene especially in grades II and III of breast cancer.

Abstract PO-011: The spectrum of pathogenic germline variants in pancreatic cancer patients with multiple primary tumors

Abstract Introduction: Approximately 10% of pancreatic ductal adenocarcinomas (PDAC) are considered hereditary due to pathogenic germline variants in cancer predisposition genes. It is crucial to recognize hereditary PDAC to ensure surveillance of affected individuals and their relatives, and to identify the underlying molecular defects for application of targeted therapies. Methods: The study cohort includes 207 patients with PDAC and additional primary tumors in personal history selected from the Dutch Pathology Archive. Germline DNA was analyzed using two customized targeted next-generation sequencing panels including 26 cancer predisposition genes. Identified variants were checked for pathogenicity. Results: The study includes 207 patients diagnosed with PDAC in combination with two other primary tumors (n = 51), breast (n = 51), colorectal (n = 41), prostate (n = 18), ovarian (n = 8), gastric (n = 5), endometrial (n = 4) carcinomas, and melanoma (n = 29). Germline sequencing identified pathogenic or likely pathogenic variants (PV/LPV) in 43/207 (20.8%) of the patients. Per combination, PV/LPV were detected in PDAC patients with ovarian (4/8), gastric (2/5), melanoma (9/29), breast (12/51), prostate (3/18), colorectal (6/41), and two other primary (7/51) cancers. The most frequently affected genes were ATM (14/43), BRCA2 (7/43; one patient with a concurrent PMS2 LPV), CDKN2A (7/43; 5/7 with Dutch founder p16-Leiden PV), and TP53 (3/43). Eight patients carried PV/LPV in BRCA1 (2/43), MSH6 (2/43), biallelic NTHL1 (2/43), and PALB2 (2/43) genes. Four patients each had a single PV/LPV in BRIP1 (1/43), CDH1 (1/43), CHEK2 (1/43), and RAD51C (1/43). Importantly, more than a half of identified PV/LPV (28/43) occurred in double-strand DNA damage repair genes (14 ATM, 7 BRCA2, 2 BRCA1, 2 PALB2, 1 BRIP1, 1 CHEK2, and 1 RAD51C), potentially conferring a sensitivity to PARP inhibitors and platinum-based chemotherapies. Two patients (2/43) had MSH6 PV, predisposing to Lynch syndrome, potentially responsive to immunotherapies. Overall, almost 70% of PV/LPV carriers and about 14.5% of all cases have potentially targetable germline defects. The median age at PDAC in PV/LPV carriers was only slightly younger (64 years, range: 36 – 82) than in non-carriers (66 years, range: 42 – 84), however, the difference was not significant. Conclusions: Up to 20% of patients with PDAC and multiple primary tumors have a hereditary predisposition to cancer onset; the majority harbor PV/LPV in double-strand DNA damage repair genes. Up to 15% of PDAC patients with multiple primaries and up to 70% of PV/LPV carriers have potentially targetable germline defects. Age-based preselection has limited utility to identify hereditary PDAC, however, the presence of specific other malignancies in personal history strongly indicates on underlying genetic predisposition, and should warrant further investigation and genetic screening. Citation Format: Valentyna Kryklyva, Lodewijk A. A. Brosens, Marjolijn J. L. Ligtenberg, Iris D. Nagtegaal. The spectrum of pathogenic germline variants in pancreatic cancer patients with multiple primary tumors [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-011.

Risk-Reducing Salpingo-Oophorectomy and the Use of Hormone Replacement Therapy Below the Age of Natural Menopause: Scientific Impact Paper No. 66 October 2021: Scientific Impact Paper No. 66.

This paper deals with the use of hormone replacement therapy (HRT) after the removal of fallopian tubes and ovaries to prevent ovarian cancer in premenopausal high risk women. Some women have an alteration in their genetic code, which makes them more likely to develop ovarian cancer. Two well-known genes which can carry an alteration are the BRCA1 and BRCA2 genes. Examples of other genes associated with an increased risk of ovarian cancer include RAD51C, RAD51D, BRIP1, PALB2 and Lynch syndrome genes. Women with a strong family history of ovarian cancer and/or breast cancer, may also be at increased risk of developing ovarian cancer. Women at increased risk can choose to have an operation to remove the fallopian tubes and ovaries, which is the most effective way to prevent ovarian cancer. This is done after a woman has completed her family. However, removal of ovaries causes early menopause and leads to hot flushes, sweats, mood changes and bone thinning. It can also cause memory problems and increases the risk of heart disease. It may reduce libido or impair sexual function. Guidance on how to care for women following preventative surgery who are experiencing early menopause is needed. HRT is usually advisable for women up to 51 years of age (average age of menopause for women in the UK) who are undergoing early menopause and have not had breast cancer, to minimise the health risks linked to early menopause. For women with a womb, HRT should include estrogen coupled with progestogen to protect against thickening of the lining of the womb (called endometrial hyperplasia). For women without a womb, only estrogen is given. Research suggests that, unlike in older women, HRT for women in early menopause does not increase breast cancer risk, including in those who are BRCA1 and BRCA2 carriers and have preventative surgery. For women with a history of receptor-negative breast cancer, the gynaecologist will liaise with an oncology doctor on a case-by-case basis to help to decide if HRT is safe to use. Women with a history of estrogen receptor-positive breast cancer are not normally offered HRT. A range of other therapies can be used if a woman is unable to take HRT. These include behavioural therapy and non-hormonal medicines. However, these are less effective than HRT. Regular exercise, healthy lifestyle and avoiding symptom triggers are also advised. Whether to undergo surgery to reduce risk or not and its timing can be a complex decision-making process. Women need to be carefully counselled on the pros and cons of both preventative surgery and HRT use so they can make informed decisions and choices.

Precision Oncology of High-Grade Ovarian Cancer Defined through Targeted Sequencing.

Simple SummaryOvarian cancer is a rare and deadly gynaecologic cancer, with a relatively large hereditary component. Genomic analysis of tumour material can potentially provide information regarding therapy and identify hereditary carriers and their families. The aim of our prospective study was to apply genomic characterization to tumour material from women with ovarian cancer to identify women that might benefit from PARP inhibitor therapy, as well as to detect and triage women to genetic counselling. We used next generation sequencing using a targeted panel to prospectively analyse 274 tumours and identified 50 with a BRCA1/2 pathogenic variant. Twenty patients received olaparib based on these results, and 16 previously unknown hereditary carriers were identified. In addition, in a subset examined by an extended sequencing panel, actionable mutations were found in 84/88 tumours. This study demonstrates that personalized medicine approaches can be useful for women with ovarian cancer and can help with therapy selection and identification of at risk families. Background: We examined whether molecular characterization of high-grade epithelial ovarian cancer can inform the diagnosis and/or identify potential actionable targets. Methods: All of the consecutively sequenced high-grade ovarian tumours with consent between 2014 until 2019 were included. A total of 274 tumours underwent next generation sequencing using a targeted panel. Results: Patients with high-grade ovarian epithelial cancer were consented to prospective molecular characterization. Clinical information was extracted from their medical record. Tumour DNA was subjected to sequencing, and selected patients received PARP inhibitor therapy. Conclusions: Tumours from 274 women were sequenced, including high-grade serous carcinoma (n = 252), clear cell carcinoma (n = 4), carcinosarcoma (n = 9), endometrioid carcinoma (n = 3), undifferentiated carcinoma (n = 1), and mixed tumours (n = 5). Genomic profiling did not influence histologic diagnosis. Mutations were identified in TP53, BRCA1, BRCA2, as well as additional homologous recombination repair pathway genes BARD1, ATR, CHEK2, PALB2, RAD51D, RAD50, SLX4, FANCA, RAD51C, and RAD54L. In addition, mutations in PTEN and CDKN2A were identified. Several somatic mutations with implications for germline testing were identified, including RMI1, STK11, and CDH1. Germline testing identified 16 previously unknown BRCA1/2 carriers. Finally, 20 patients were treated with the PARP inhibitor olaparib based on the sequencing results.

Genetic Susceptibility to Breast Cancer in Sub-Saharan African Populations.

Breast cancer (BC) is the most common cancer among African women and is the second most common cause of cancer deaths in Africa as estimated by GLOBOCAN 2018.1 Cancer incidence is increasing in Africa1 and is associated largely with lifestyle changes, resulting from increased urbanization.2 Ferlay et al3 predicted a 49% increase in BC incidence across Africa between 2018 and 2040, an increase faster than any other region in the world. The International Association of Cancer Registries cancer incidence report includes data for only 20 of 46 sub-Saharan African (SSA) countries,4 and it is likely that the incidence of BC is under-reported owing to lack of infrastructure for cancer diagnosis in resource-constrained countries in SSA.5 Also, owing to the large burden of communicable and other noncommunicable diseases in SSA, most resources are directed at controlling these diseases.6,7 Cancer research, especially molecular research, in SSA is often deprioritized against other pressing public health concerns.8 CONTEXT Key Objective Both rare and common genetic variants contribute to the risk of breast cancer (BC). Much is known about the genetics of BC in populations of European origin. Our objective was to review studies of genetic susceptibility to BC in the populations of sub-Saharan Africa to identify knowledge gaps and propose study designs to address these. Knowledge Generated A total of 22 studies were identified in 10 of 46 countries in sub-Saharan Africa. Rare variants predicted to be pathogenic were detected most commonly in the BRCA1, BRCA2, and PALB2 genes. There were few studies of common genetic variants, none of which provided strong evidence for association with BC risk. Relevance Knowledge of genetic factors contributing to BC risk has important implications for patients and their families both for genetic counseling and for potential access to new therapies, which improve survival and reduce side effects.