FANCC Mutations Research Articles

PD46-11 ASSESSING THE ROLE OF NEOADJUVANT CHEMOTHERAPY IN UPPER TRACT UROTHELIAL CARCINOMA EVOLUTION

You have accessJournal of UrologyCME1 Apr 2023PD46-11 ASSESSING THE ROLE OF NEOADJUVANT CHEMOTHERAPY IN UPPER TRACT UROTHELIAL CARCINOMA EVOLUTION Neeta D'Souza, Andrew B. Katims, Ali Mouzannar, Eugene J. Pietzak, David Solit, Kwanghee Kim, and Jonathan A. Coleman Neeta D'SouzaNeeta D'Souza More articles by this author , Andrew B. KatimsAndrew B. Katims More articles by this author , Ali MouzannarAli Mouzannar More articles by this author , Eugene J. PietzakEugene J. Pietzak More articles by this author , David SolitDavid Solit More articles by this author , Kwanghee KimKwanghee Kim More articles by this author , and Jonathan A. ColemanJonathan A. Coleman More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003359.11AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Systemic neoadjuvant chemotherapy (NAC) may apply selective pressure on tumors and shape cancer evolution. In bladder cancer, intratumor genetic heterogeneity can help predict response to NAC, with RB1, ERCC2, ATM, and FANCC mutations significantly associated with a positive response to NAC. Molecular studies have shown upper tract urothelial carcinoma (UTUC) to be genetically distinct from bladder cancer with a significantly worse response to NAC, yet still harboring significant intratumor heterogeneity. This study aims to assess the effect of NAC in selecting chemotherapy-resistant mutations among the intratumor heterogeneity in UTUC. METHODS: We identified patients with UTUC who underwent platinum-based NAC followed by nephroureterectomy treated at Memorial Sloan Kettering Cancer Center. Patients with complete response to NAC were excluded. Pre-NAC biopsy and post-NAC nephroureterectomy samples underwent next generation targeted gene sequencing through MSK-IMPACT. Mutational frequency among the 505 tested genes was compared in the pre-and post- treatment cohorts to assess for significant changes (p<0.05). RESULTS: We identified 15 patients with UTUC that had an incomplete response/progression of disease after NAC with gemcitabine/cisplatin as determined by final pathology at radical nephroureterectomy. The median age at the time of NAC was 60 (IQR 55-70). The most common mutations are seen in Figure 1. The most common mutated genes in pre-NAC UTUC biopsy were TERT (53.3%), KMT2D (40.0%), and ARID1A (33.3%). Post-chemotherapy, the most common mutations were TERT (56.3%), FGFR3 (31.3%), and KMT2D (31.3%). There were no significant differences between the frequency of mutations pre- and post-NAC. There was no decrease in the frequency of RB1, ERCC2, ATM, and FANCC post-NAC. CONCLUSIONS: Administration of NAC did not select for specific resistant mutations in the global tumor landscape. It is possible that changes to the tumor microenvironment, sub-clonal expansion, or differences in expression may be identified through RNA based studies. Source of Funding: N/A © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e1174 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Neeta D'Souza More articles by this author Andrew B. Katims More articles by this author Ali Mouzannar More articles by this author Eugene J. Pietzak More articles by this author David Solit More articles by this author Kwanghee Kim More articles by this author Jonathan A. Coleman More articles by this author Expand All Advertisement PDF downloadLoading ...

A phase II trial of risk-enabled therapy after initiating neoadjuvant chemotherapy for bladder cancer (RETAIN).

438 Background: Cisplatin-based neoadjuvant chemotherapy (NAC) followed by cystectomy or chemoradiation is the standard of care for urothelial carcinoma (UC) patients with MIBC. Both cystectomy and chemoradiation have short and long-term toxicity and QOL implications. Mutations in DNA damage repair/response genes are associated with pathologic downstaging after NAC. We hypothesized that a combination of biomarker selection and clinical staging would identify patients prospectively for a cystectomy or chemoradiation avoidance algorithm. Methods: We conducted a single-arm, phase II, non-inferiority trial (NCT02710734) to evaluate a risk-adapted approach for MIBC. Patients with cT2-T3N0M0 UC underwent NAC with accelerated MVAC. Pre-NAC TURBT specimens were sequenced (Caris) for mutations in ATM, ERCC2, FANCC or RB1. Patients with ≥ 1 mutations and no clinical evidence of disease by restaging TUR, urine cytology and imaging post-NAC began pre-defined active surveillance (AS). Remaining patients underwent bladder-directed therapy. The primary endpoint was metastasis-free survival (MFS) at 2 years for the entire cohort. The risk-adapted approach would be declared non-inferior to the standard of care if the lower bound of an exact 1-sided 95% CI for MFS was &gt; 64%. The study required 70 patients with a 4.5% type I error and 81.6% power. Results: 71 (ITT) patients were enrolled over 33 months at four academic centers. Median age was 70 years (47-83), 74% were male, 92% Caucasian, 81% ECOG PS 0 and 79% cT2. 90% completed 3 cycles of MVAC with 17% grade 3-4 TRAEs. In the ITT population, 33 (46%) had a relevant mutation and 26 (37%) began AS. With a median follow-up of 41 months, 47 patients (66%) are metastasis-free (CI 54%-77%). The 2-year MFS for the ITT patients (primary endpoint) was 72% (lower bound exact 1-sided 95% CI=62%). On post hoc analysis, the 2-year MFS was 65% in the AS group (CI 44%-83%) and 76% (CI 60%-87%) in the remaining patients (P=0.42). In the AS group, 18 patients (69%) had some UC recurrence, 8 had a cystectomy, 2 chemoradiation, and 13 (50%) are metastasis-free with an intact bladder. Of the 10 patients (38%) on AS who developed metastatic disease, 9 recurred with localized disease first. The 2-year OS is 83% (CI 72%-90%) and 89% (CI 68%-96%) in the ITT and AS groups, respectively. Associations between mutation presence and MFS or UC recurrence were not observed. Conclusions: The 72% 2-year MFS rate in this MIBC cohort treated with a risk-adapted approach did not satisfy the pre-specified non-inferiority condition. 38% of AS patients developed metastatic disease, with most patients first recurring locally in the bladder. With a median follow-up of 41 months, although 50% of AS patients have been able to avoid cystectomy without metastatic disease, further refinement of this approach is necessary. Clinical trial information: NCT02710734 .

Investigation of mutations in Fanconi anemia genes and malignancy predisposition in Brazilian patients.

This study proposed to identify Fanconi anemia (FA) mutations in Brazilian patients and to investigate their impact on clinical manifestations and malignancies onset. A total of 116 patients were screened for nine mutations in FANCA, FANCC, FANCG. Those with no mutations were investigated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing for FANCA, FANCC, FANCE, FANCF, FANCG, FANCD1/BRCA2. Genetic subtype was identified in 107/116 (78 FA-A, 8 FA-C, 13 FA-G, 8 FA-E), with only one mutation in 1/116, and no mutations in 9/116 patients. Before hematopoietic cell transplantation (HCT), malignancies were detected in 16/116 patients (14/78 FA-A, 01/08 FA-C, 01/08 FA-E), and 12 of them were hematological. Observed to expected ratio (O/E) of hematologic malignancy was 303.7 (95% CI=148.6-458.7). This study allowed the identification of biallelic mutations in 91.4% of patients. FANCG and FANCC mutations had significantly earlier bone marrow failure onset, and FANCG severe cytopenia at diagnosis. Despite the inherent limitations of the small number of malignancy events in each genetic subtype, the hematologic malignancies O/E ratio was very high. Cumulative incidence of malignancy before HCT was higher in the third and fourth decades of life, considering HCT and death as competing risks. The cumulative incidence of HCT increased during the first decade, competing with malignancy development.

S1314 correlative analysis of ATM, RB1, ERCC2, and FANCC mutations and pathologic complete response (pT0) at cystectomy after neoadjuvant chemotherapy (NAC) in patients with muscle invasive bladder cancer (MIBC): Implications for bladder preservation.

4581 Background: SWOG S1314 (NCT02177695) was designed to validate the CoXEN classifier as a predictive biomarker in pts undergoing cystectomy after NAC. We repurposed banked DNA samples and prospective trial data from S1314 to further validate the predictive ability of the Philadelphia 4 gene signature (P4GS: any mutation in ATM, RB1, FANCC, ERCC2) to predict pT0 as previously reported (PMID: 26238431) and used in the RETAIN trial (NCT02710734). The RETAIN trial prospectively enrolled pts to receive NAC (DDMVAC) followed by allocation to bladder observation vs. intervention (cystectomy or RT) based on clinical evaluation and presence vs absence of P4GS. The primary objective of this correlative investigation was to determine whether presence of P4GS is predictive of pT0 at surgery. Methods: Eligibility for S1314 included cT2-T4a N0 M0 MIBC, cisplatin eligible, with plan for cystectomy; 237 pts were randomized between ddMVAC and gem/cis (GC) using standard dose/schedule. Of 167 pts who were evaluable for the original COXEN analysis (received 3+ cycles of chemo and evaluable for path response) adequate banked DNA was available for 105. Next-generation sequencing using the CARIS 592 Gene Panel (Caris Life Sciences, Phoenix, AZ) was performed. Pathogenic mutation or VUS of ATM, RB1, FANCC or ERCC2 was noted as present or absent for each pt and correlated with pT0 using logistic regression, adjusting for clinical stage. Results: Among the 105 pts, 51% ddMVAC, 49% GC. 15% female, 95% white, 15% clinical stage T3/T4a Prevalence of mutations: ATM (24%), ERCC2 (17%), FANCC (4%), RB1 (24%) and any variant 53%. Presence of any mutation correlated with pT0 (p = 0.0006), sensitivity 79%, specificity 59%. This association did not vary by treatment arm (MVAC vs. GC). The table below shows the contributions of each of the 4 genes with the greatest contribution from ATM and ERCC2. FANCC was non-contributory due to low prevalence. Conclusions: Patients with a mutation in ATM, RB1, FANCC or ERCC2 (P4GS) have a statistically significantly higher odds of a pT0 with GC or MVAC compared to those who do not have any variant. This signature was used to prospectively allocate patients to bladder observation as part of the RETAIN trial previously reported (ASCO GU 2021). RETAIN completed enrollment, final analysis of the primary endpoint – 2-year metastasis free survival – is expected later in 2022. Clinical trial information: NCT02177695.

Optimization of Robust Diagnostic Strategy for Patients with Fanconi Anaemia (FA)- an Indian Perspective

Objective:Fanconi anaemia is a genotypically heterogeneous disease. A fast and reliable genetic diagnosis method helps is important for the clinical care of these patients. The objective of this study was to establish a strategy for expeditious molecular diagnosis for the Indian FA patients.Methods:Exome sequencing was performed for 119 FA patients on Illumina HiSeq X system and the data was analysed by Sentieon (v201808.01) to identify germline variants. Single nucleotide variants (SNVs) with an allele frequency of <3% in various population databases including the Indian population database were analysed and annotated using an in-house pipeline. Copy number variants (CNVs) were detected using ExomeDepth (v1.1.10). Long amplicon next-generation sequencing was performed for FANCA and FANCG genes. Gene dosage analysis was performed for the deletions identified by WES in the FANCT/UBE2T gene. Sanger sequencing was performed for the selected variants identified by WES.Results:SNVs associated with FA were identified in heterozygous states in 93 (78%) patients. Of the remaining 20 patients, 8 had homozygous deletions, and twelve were compound heterozygous with deletions and SNVs. We detected deletions in 20 patients: 7 with heterozygous and 12 with homozygous deletions in FANCA, and one with a homozygous deletion in FANCT (UBE2T). MLPA confirmed the deletions in the FANCA gene. The homozygous deletion in the FANCT gene was confirmed by the lack of amplification by PCR using the primers binding to the deleted region.By combining the SNVs and deletions, disease-causing genotypes were identified in 113 of 119 (95%) patients. A large number of our patients (81.5 %) were homozygous (Figure) due to the high rate of consanguinity in the population. FANCA was found to be the most frequently mutated gene in (57.5%) while mutations in FANCG gene accounted for 14.2% of our patients. FANCC mutations were found at a very low frequency (1.8%) in our patients.Although mutations in FANCL are rare in all the populations, 24 (21.2%) patients with FANCL mutations were identified in our study. A previously reported synonymous splicing mutationFANCL c.1092G>A;p.K364= was found in homozygous state in 22 (19.5%) patients. Two other FANCL mutations identified includes a missense mutation c.827C>T; p.Pro281Leu in the homozygous state in one patient and a nonsense mutation c.997C>T; p.Gln333Ter in the compound heterozygous state with the common FANCL c.1092G>A;p.K364= mutation in another patient. Mutations in rarely mutated FA genes included 1 patient each in FANCT/UBE2T and FANCI and two each in FANCJ/BRIP1 and FANCF gene. Based on the comprehensive genotype analysis, we could design an algorithm for FA in the Indian population. ~20% of the FA patients who have FANCL c.1092G>A;p.K364= mutation can be diagnosed by Sanger sequencing. MLPA can detect FANCA deletions (16.5% of the overall mutations). The results from these two tests can be obtained in 48 hours. For those who are negative for the mutations by these two methods, LA-NGS can detect SNVs in the FANCA and FANCG genes, which constitute >55% of the FA mutations in the population. We have tested this algorithm for expedited molecular diagnosis in 27 FA patients and found that the disease genotypes could be established in 94% of the patients in less than two weeks.Conclusion/Clinical applicability:Exome sequencing identified several novel mutations in the FA pathway genes in the FA patients. A cost-effective and time-saving algorithm was explicitly established for molecular diagnosis of FA in the Indian population. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Next generation sequencing identifies potential PARP inhibitor sensitive mutations

Abstract Introduction/Objective Poly ADP-ribose polymerase (PARP) inhibitors are a novel and important drug class targeting homologous recombination DNA repair defects (HRD) and have been approved for use in breast, pancreatic and ovarian cancers. Originally targeted for loss of function mutations in BRCA1 and BRCA2, many other genes are involved in the HRD pathway; Rimar et al detailed 19 DNA repair genes associated with homologous recombination and PARP inhibitor sensitivity. Our 214 gene NGS panel, Iowa Cancer Mutation Profile, includes BRCA1, BRCA2 and 15 other HRD pathway genes. We reviewed cases from the prior 12 months to determine the frequency of HRD7 pathway gene variants in various tumor types with potential PARP inhibitor sensitivity. Methods/Case Report Iowa Cancer Mutation Profile NGS test results from June 4, 2020 through May 7, 2021 were reviewed for variants involving ATM, ATR, BAP1, BLM, BRCA1, BRCA2, CDK12, CHEK1, CHEK2, FANCA, FANCC, FANCD2, MRE11A, NBN, PALB2, RAD51c and RAD51d, categorized as pathogenic, likely pathogenic or of unknown significance and had the tumor type identified. Additional chart review for PARP inhibitor therapy was performed in cases of breast, pancreatic, and ovarian cancer. Results (if a Case Study enter NA) A total of 599 cases were reviewed with 234 found to have variants in genes with possible PARP inhibitor sensitivity. Of these 2% (n=8) and 11% (n=43) of variants were categorized as pathogenic or likely pathogenic while most (n=334) were categorized as variants of unknown significance. The pathogenic and likely pathogenic variants included mutations in ATM (n=13), BRCA2 (n=12), BAP1 (n=8), FANCA (n=5), BRCA1 (n=4), NBM (n=3), FANCD2 (n=2), ATR (n=1), CDK12 (n=1), FANCC (n=1), and RAD51d (n=1), and frameshift (n=19) and nonsense (n=19) alterations were most common. Non-small cell lung cancer was the most frequent tumor type identified (n=78). At this time no PARP inhibitors were identified for use in cases of breast (n=9), pancreatic (n=3) and ovarian cancer (n=33). Conclusion Review of our institutional results for mutations in HRD pathway genes identified possible PARP inhibitor sensitivity in 8% (46 of 599) of cases during the period of review in a wide variety of tumor types. Our results suggest that variants with possible sensitivity to PARP inhibitor therapy are frequently identified from many tumor types and should be a component of solid tumor mutation profiling.

A phase II trial of risk enabled therapy after initiating neoadjuvant chemotherapy for bladder cancer (RETAIN BLADDER): Interim analysis.

397 Background: Cisplatin-based neoadjuvant chemotherapy (NAC) followed by cystectomy (Cx) or chemoradiation (CRT) is the standard of care for urothelial carcinoma (UC) pts with muscle invasive bladder cancer (MIBC). Both Cx and CRT have potential short and long-term toxicity and QOL implications. Mutations in DNA damage repair/response genes are associated with pathologic downstaging after NAC. Methods: We conducted a phase II, multi-institutional clinical trial (NCT02710734) to evaluate a risk-adapted approach to treatment of MIBC. Pts with cT2-T3N0M0 UC of the bladder, ECOG PS 0-1 and CrCl≥50 mL/min, underwent NAC with accelerated methotrexate, vinblastine, doxorubicin, and cisplatin (AMVAC). Pre-NAC TURBT specimens were sequenced (Caris Life Sciences) for mutations (pathogenic or VUS) in ATM, ERCC2, FANCC or RB1. Pts with at least one mutation and no clinical evidence of disease by restaging TUR and imaging post-NAC began pre-defined active surveillance (AS). Remaining pts underwent bladder-directed therapy: intravesical therapy ( &lt; cT2 post-NAC), CRT or Cx. The primary endpoint was metastasis-free survival (MFS) at 2 years which is not mature. We herein report key interim results of clinically-meaningful intermediate endpoints. Results: Seventy-one (ITT) pts were enrolled over 33 months at four academic centers. Median age was 70 years (47-83), 74% were male, 92% Caucasian, 81% ECOG PS 0 and 79% cT2. 90% completed 3 cycles of NAC and with 17% grade 3-4 TRAEs and one death during AMVAC. At the time of data cut-off (September 11, 2020), for the ITT pts, 32 pts have had a Cx, 5 underwent CRT and 7 underwent intravesical therapy, at some point during the trial. Thirty-three pts (46%) had a mutation of interest and 28 pts (39%) started AS (2 of the 28 pts on AS did not have a mutation but elected to start AS after achieving cT0 post AMVAC). 76% of those with a mutation were cT0 at post-NAC TURBT. With a median follow-up of 14.9 mo (range: 3.1-35.3 mo), 14 AS pts recurred (50%). Of the 14 recurrences, 2 recurred with locally advanced or metastatic disease and have died, 5 had MIBC with one eventual metastatic recurrence, and 7 had NMIBC. Six (14%) non-AS pts have died. Out of the 40 pts who did not go to upfront Cx [AS (N = 28), CRT (N = 5), intravesical tx (N = 7)], 3 (7.5%) (all in the AS group) went on to Cx later. The bladder preservation rate is 55% for ITT pts and 89% for the AS group. In the AS cohort, mutations were seen in RB1 (50%), ATM (42%), ERCC2 (31%), FANCC (4%) with lowest rate for recurrence in ERCC2 (25% recurrence) vs RB1 (62% recurrence). Conclusions: Interim results of a phase II trial of risk enabled therapy utilizing a selection of clinical and genomic factors in pts with cT2-T3 MIBC demonstrates a 50% rate of any UC recurrence and a 11% rate of locally advanced/metastatic disease in the AS group. 89% of AS pts have retained their bladder. Follow-up continues for the primary endpoint of 2-year MFS. Clinical trial information: NCT02710734.

Contribution of Germline Predisposition Gene Mutations to Breast Cancer Risk in African American Women.

The risks of breast cancer in African American (AA) women associated with inherited mutations in breast cancer predisposition genes are not well defined. Thus, whether multigene germline hereditary cancer testing panels are applicable to this population is unknown. We assessed associations between mutations in panel-based genes and breast cancer risk in 5054 AA women with breast cancer and 4993 unaffected AA women drawn from 10 epidemiologic studies. Germline DNA samples were sequenced for mutations in 23 cancer predisposition genes using a QIAseq multiplex amplicon panel. Prevalence of mutations and odds ratios (ORs) for associations with breast cancer risk were estimated with adjustment for study design, age, and family history of breast cancer. Pathogenic mutations were identified in 10.3% of women with estrogen receptor (ER)-negative breast cancer, 5.2% of women with ER-positive breast cancer, and 2.3% of unaffected women. Mutations inBRCA1,BRCA2, andPALB2were associated with high risks of breast cancer (OR = 47.55, 95% confidence interval [CI] = 10.43 to >100; OR = 7.25, 95% CI = 4.07 to 14.12; OR = 8.54, 95% CI = 3.67 to 24.95, respectively). RAD51D mutations were associated with high risk of ER-negative disease (OR = 7.82, 95% CI = 1.61 to 57.42). Moderate risks were observed for CHEK2, ATM, ERCC3, and FANCC mutations with ER-positive cancer, and RECQL mutations with all breast cancer. The study identifies genes that predispose to breast cancer in the AA population, demonstrates the validity of current breast cancer testing panels for use in AA women, and provides a basis for increased referral of AA patients for cancer genetic testing.

Defects in DNA Repair Genes Confer Improved Long-term Survival after Cisplatin-based Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer

Cisplatin-based neoadjuvant chemotherapy (NAC) has demonstrated an overall survival (OS) benefit in muscle-invasive bladder cancer (MIBC). However, only a subset of patients (25–50%) have a pathologic complete response at cystectomy. Using a cohort of 58 patients from two phase 2 trials, our group previously reported that mutations in the ATM, RB1, and FANCC genes correlate with complete response to cisplatin-based NAC, and consequently improve OS and disease-specific survival (DSS). These trials enrolled patients with T2–4 (N0 or N1) MIBC and treated them with accelerated/dose-dense NAC with methotrexate, vinblastine, adriamycin, and cisplatin, or gemcitabine and cisplatin, with a plan for curative cystectomy. Updated long-term follow-up (median 74 mo) shows that significantly greater OS and DSS was maintained for patients with ATM, RB1, or FANCC mutations. The 5-yr survival rate for patients with at least one mutation was 85%, compared to 45% for patients without a mutation. On the basis of the associations with response and long-term OS and DSS, we propose that these alterations may be useful as predictive biomarkers to allow clinicians to prioritize patients who are most likely to benefit from NAC before radical cystectomy. Patient summaryIn this report we looked at outcomes for patients with muscle-invasive bladder cancer treated with cisplatin-based chemotherapy before surgery (neoadjuvant) who had mutations in a set of DNA damage repair genes (ATM, RB1, FANCC) compared to those who did not. We found that patients who had at least one mutation in one of these genes survived longer after receiving cisplatin chemotherapy before surgery than patients who did not.

SMC5/6 acts jointly with Fanconi anemia factors to support DNA repair and genome stability

SMC5/6 function in genome integrity remains elusive. Here, we show that SMC5 dysfunction in avian DT40 B cells causes mitotic delay and hypersensitivity toward DNA intra‐ and inter‐strand crosslinkers (ICLs), with smc5 mutants being epistatic to FANCC and FANCM mutations affecting the Fanconi anemia (FA) pathway. Mutations in the checkpoint clamp loader RAD17 and the DNA helicase DDX11, acting in an FA‐like pathway, do not aggravate the damage sensitivity caused by SMC5 dysfunction in DT40 cells. SMC5/6 knockdown in HeLa cells causes MMC sensitivity, increases nuclear bridges, micronuclei, and mitotic catastrophes in a manner similar and non‐additive to FANCD2 knockdown. In both DT40 and HeLa systems, SMC5/6 deficiency does not affect FANCD2 ubiquitylation and, unlike FANCD2 depletion, RAD51 focus formation. SMC5/6 components further physically interact with FANCD2‐I in human cells. Altogether, our data suggest that SMC5/6 functions jointly with the FA pathway to support genome integrity and DNA repair and may be implicated in FA or FA‐related human disorders.

314P - Next-generation DNA sequencing (NGS) results for tumours from phase II ABRAZO study of talazoparib after platinum or cytotoxic non-platinum regimens in patients (pts) with advanced breast cancer (ABC) and germline BRCA1/2 (gBRCA) mutations

314P - Next-generation DNA sequencing (NGS) results for tumours from phase II ABRAZO study of talazoparib after platinum or cytotoxic non-platinum regimens in patients (pts) with advanced breast cancer (ABC) and germline BRCA1/2 (gBRCA) mutations

1957P - Comparative molecular analyses between microsatellite stable BRAFV600E mutant colorectal cancers and BRAFV600E mutant melanomas

BackgroundSeveral studies in BRAFV600E colorectal cancers (CRC) have failed to replicate the efficacy of BRAF inhibitors in treatment of BRAFV600E melanomas (Mel), suggesting the existence of different resistance mechanisms as well as molecular and biological differences between the 2 tumor types. Herein, we examine these differences. MethodsTumor samples submitted to Caris Life Sciences for NGS DNA sequencing (592 gene panel) and RNA sequencing (54 gene panel) between the years 2015 and 2019 were retrospectively studied. Only microsatellite stable (MSS) tumors with either BRAFV600E mutation or wild type (WT) BRAF status were included in this initial analysis. Chi-square tests determined differences. ResultsA total of 8409 tumor samples were analyzed: CRC (N=7453: BRAFV600E=373; WT=7080) and Mel samples (N=956: BRAFV600E=274; WT=682). The most frequently mutated genes in BRAFV600E CRC were TP53 (81%), APC (26%), and SMAD4 (22.4%), compared to CDKN2A (22%), PTEN (13%), and TP53 (13%) in BRAFV600E Mel. Molecular alterations that are significantly more frequent in BRAFV600E CRC vs BRAFV600E Mel but not significantly different between BRAF WT CRC vs BRAF WT Mel included RSPO3 fusions (CRC=22.6% vs Mel=0%, P=0.027); RNF43 deletions (2.0% vs 0%, p=0.019); and mutations in RNF43 (18.8% vs 0%, P<0.001), AKT1 (3.5% vs 0.4%, p=0.008), and MTOR (2.4% vs 0.4%, p=0.037). RSPO3 fusions and RNF43 mutations/deletions are mutually exclusive. Significantly more frequent alterations in BRAFV600E Mel compared to BRAFV600E CRC (but not in either WT) included deletions in PTEN (7% vs 3%, p=0.005) and mutations in PTEN (12.9% vs 5.4%), MITF (1.9% vs 0%), STK11 (1.5% vs 0%), ERCC2 (1.1% vs 0%), FANCC (1.2% vs 0%), and CDK4 (1.5% vs 0%) (p<0.05 for all). ConclusionsBRAFV600E CRC carry molecular alterations that are distinct from BRAFV600E Mel. RSPO3 fusions and RNF43 alterations are prevalent in BRAFV600E CRC tumors in a mutually exclusive manner, suggesting that Wnt pathway activation via genetic alterations in upstream Wnt pathway regulators may play an important role in BRAFV600E CRC tumorigenesis and resistance to BRAF inhibitors. Drug combinations that target both the MAPK and Wnt pathways may warrant further investigation. Legal entity responsible for the studyThe authors. FundingHas not received any funding. DisclosureM.E. Salem: Travel / Accommodation / Expenses: Caris Life Sciences. J. Xiu: Full / Part-time employment: Caris Life Sciences. A. Grothey: Travel / Accommodation / Expenses: Caris Life Sciences. R.M. Goldberg: Research grant / Funding (self), Travel / Accommodation / Expenses: Caris Life Sciences. Z. Gatalica: Full / Part-time employment: Caris Life Sciences. R. Feldman: Full / Part-time employment: Caris Life Sciences. M. Saul: Full / Part-time employment: Caris Life Sciences. W..M. Korn: Full / Part-time employment: Caris Life Sciences. A.F. Shields: Research grant / Funding (institution), Travel / Accommodation / Expenses: Caris Life Sciences. J.L. Marshall: Advisory / Consultancy: Caris Life Sciences. H.J. Lenz: Travel / Accommodation / Expenses: Caris Life Sciences. All other authors have declared no conflicts of interest.

679PD - Large-scale analysis of CDH1 mutations define a distinctive molecular subset in gastric cancer (GC)

BackgroundThough molecular classifications have been well studied, targeted therapies for GC are still limited. CDH1 mutations are characteristics of genomically stable GC and associated with poor prognosis. Herein, to understand the specific mutation profile and enriched pathways in CDH1-mutated (MT) GC could help to discover novel drug targets. MethodsGC (N=1596) were analyzed by next-generation sequencing (NGS) and immunohistochemistry (Caris Life Sciences, Phoenix, AZ). Tumor mutational burden (TMB) was calculated based on somatic nonsynonymous mutation, and microsatellite instability (MSI) was evaluated by NGS of known MSI loci. Gene fusions were evaluated using Archer (N=253) or Whole Transcriptome Sequencing (WTS, N=96). ResultsThe overall mutation frequency of CDH1 was 9.7%. A significant association of CDH1 mutations with cancer types (GC, 12% vs gastroesophageal junction adenocarcinoma, 2%), sex (female, 13% vs male, 8%), Lauren subtypes (diffuse, 27% vs intestinal, 1%) and younger age (58 vs 62) were observed (p<0.05). The most frequently mutated genes in CDH1-MT GC were ARID1A (55%), TP53 (44%), KMT2D (8%), RNF43 (7%), PIK3CA (6%). Compared to CDH1-wild type (WT) GC, mutations in ARID1A (55% vs 39%), WRN (3% vs 1%), POT1 (2% vs 0.1%), CDK12 (2% vs 0.6%) and FANCC (1.4% vs 0.2%) were significantly higher, while TP53 (44% vs 64%) and APC (2% vs 6%) were significantly lower in CDH1-MT GC (p<0.05); Amplifications of KRAS and HER2 were significantly lower, while CRKL and IGF1R amplifications were significantly higher in CDH1-MT GC, compared to CDH1-WT GC (p<0.05). For immune-related markers, CDH1-MT GC showed significantly lower rates of PD-L1 positivity (CPS score>0) (57% vs. 73%, p<0.05). No significant difference of TMB and MSI-H were overserved between CDH1-MT/WT GC. RNA sequencing showed similar frequency of ARHGAP26 fusion (6% vs 7%) in CDH1-MT vs WT tumors. ConclusionsThis is the largest study to explore the distinct genomic landscape in CDH1-MT GC. It indicates CDH1-MT GC patients could potentially benefit from agents targeting WRN, POT1, CDK12 and IGF1R, while immunotherapy may be of lower efficacy in this cohort based on lower CPS score. Efficiency of these therapeutic targets and enriched pathways in CDH1-MT GC warrant further investigation. Legal entity responsible for the studyNorris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California. FundingHas not received any funding. DisclosureAll authors have declared no conflicts of interest.

Two truncating variants in FANCC and breast cancer risk

Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Defects in DNA repair genes and long-term survival in cisplatin-based neoadjuvant chemotherapy for muscle invasive bladder cancer (MIBC).

4536 Background: Although cisplatin-based neoadjuvant chemotherapy (NAC) has demonstrated an overall survival (OS) benefit in MIBC, only a subset of patients have pathologic complete response (pT0) at cystectomy. ATM, RB1 and FANCC mutations have shown correlation with pT0 to cisplatin-based NAC, as previously published. We now report updated OS and disease specific survival (DSS) from two phase II trials using these gene alterations as biomarkers. Methods: Patients with stage T2-T4 (N0 or N1) MIBC were enrolled in phase II trials of dose-dense NAC with MVAC (methotrexate, vinblastine, adriamycin, and cisplatin; NCT01031420) or GC (gemcitabine and cisplatin; NCT01611662). Patients were treated with NAC with plan for curative cystectomy. DNA from pretreatment tumor tissue was sequenced for coding exons of 287 cancer-related genes and analyzed for mutations. Survival in patients with one or more mutations in ATM, RB1, or FANCC genes was compared to those without mutations. Results: Of 58 pts treated, 38% (22/58 pts) had relevant mutations in the combined group of MVAC (13/34 pts) and GC (9/24 pts) trials. At a median follow-up of 56 months and minimum follow up of 16 months, patients with mutations had statistically significantly greater OS (p = 0.0043) and DSS (p = 0.0015). Median OS/DSS was not reached for patients with a mutation in any group. At 5 years post treatment, OS/DSS were greater in mutated vs non-mutated patients in all groups (see table). Conclusions: Long-term follow up reveals that previously reported improved responses to cisplatin-based NAC associated with mutations in ATM, RB1 and FANCC also confer a clinically meaningful and statistically significant survival benefit in these patients. These alterations may be useful as predictive biomarkers to allow clinicians to prioritize patients most likely to benefit from NAC prior to radical cystectomy. [Table: see text]

Deleterious Mutations in DNA Repair Gene FANCC Exist in BRCA1/2-Negative Chinese Familial Breast and/or Ovarian Cancer Patients.

Introduction: FANCC is reported as a novel susceptibility gene for breast cancer, however, its mutation remains unclear in Chinese population. We aimed to identify the germline mutations of FANCC in high-risk breast cancer patients in China.Methods: 255 BRCA1/2-negative Chinese familial breast and/or ovarian cancer (FBOC) patients were recruited for FANCC germline mutations screen. For whom 90 patients were detected by PCR-sequencing assay, and another 165 patients were detected by a 98-gene panel sequencing assay. The 98-gene panel sequencing assay was also used to screen other possible gene mutations for the patients with FANCC mutations detected by PCR-sequencing assay. Two hundred and fifty sporadic breast cancer (SBC) patients and 248 female non-cancer controls (FNCCs) were recruited for the genotyping analysis. Immunohistochemistry (IHC) analysis was used to evaluate the FANCC expression in patients with FANCC mutation.Results: We found one rare FANCC deleterious mutation (c.339G>A, p.W113X, 0.4%) and two novel non-synonymous variants (c.51G>C, p.Q17H, 0.4% and c.758C>A, p.A253E, 0.4%) in FBOC patients, whereas none of above mutations was identified in SBC patients or FNCCs. We also found that one novel synonymous variant (c.903A>G, p.A301A) existed in one FBOC patient. Additionally, two non-synonymous SNPs rs201407189 (c.973G>A, p.A325T) and rs1800367 (c.1345G>A, p.V449M), and two synonymous SNPs rs55719336 (c.816C>T, p.I272I) and rs79722116 (c.1407G>A, p.T469T) were identified in FBOC patients.Conclusion: FANCC deleterious mutations exist in Chinese FBOC patients and investigations on the penetrance and spectrum of FANCC mutations need to be further conducted.

Abstract A096: Phase II study of the PARP inhibitor talazoparib in advanced cancer patients with somatic alterations in BRCA1/2, mutations/deletions in PTEN or PTEN loss, aberrations in other BRCA pathway genes, and germline mutations in BRCA1/2 (not breast or ovarian cancer)

Abstract Background: Cancer cells deficient in BRCA1/2 are selectively sensitive to the double-stranded DNA breaks induced by poly (ADP-ribose) polymerase (PARP) inhibitors. Multiple ongoing trials are evaluating PARP inhibitors in patients with breast, ovarian, and prostate cancers and germline or somatic BRCA1/2 mutations. There is, however, a great need to determine if the benefit of PARP inhibition can be extended to other tumor types. We sought to assess the efficacy of talazoparib, a potent oral PARP1/2 inhibitor, in patients with germline BRCA mutations in cancer types other than breast and ovarian cancer, and in patients with somatic BRCA alterations or aberrations in other homologous repair genes or PTEN. Methods: This was a single-center, phase II trial in patients with measurable advanced solid tumors. Patients were enrolled on one of four cohorts: 1) somatic alterations of BRCA1/2, 2) mutations/deletions in other BRCA pathway genes, 3) mutations/deletions in PTEN and/or PTEN loss by IHC, and 4) germline BRCA1/2 mutations (not breast/ovarian cancer). Patients were treated with talazoparib at 1 mg PO daily. Response was assessed per RECIST v1.1. Primary end point was clinical benefit rate (CBR; complete response [CR], partial response [PR] or stable disease [SD]&amp;gt;6m). Patients were enrolled based on standard of practice molecular testing. Patients underwent pretreatment biopsies with whole exome sequencing (WES) of tumor and normal DNA. Results: 35 patients (pts) (30 evaluable) were enrolled. Pts had a median of 4 prior lines of treatment. Grade 3-4 treatment-related AEs occurred in 37% of pts, and the most common was thrombocytopenia (23%). The median follow-up was 15.8 mo. CBR was 0%, 44%, 8%, and 29% for cohorts 1-4, respectively. In cohort 1, one patient with a somatic BRCA2 mutation enrolled and did not respond. In cohort 2, two of 9 evaluable pts had a PR: cholangiocarcinoma [CCA] with ATM mutation and bladder cancer with PALB2 mutation, and 2 of 9 pts had prolonged SD (one pt with ovarian cancer and BRIP1 mutation, and one pt with sarcoma and FANCC mutation). Among 13 evaluable pts in the PTEN mutation/loss cohort (cohort 3), one patient with PTEN mutation had prolonged SD. Among 7 evaluable pts with germline BRCA1/2 mutations (cohort 4), one pt with carcinoma of ampulla of Vater had a durable CR, and one pt with CCA had SD for 8 months. WES was performed on 28 evaluable patients. Alterations in two genes, POLQ and PTEN, were significantly associated with progressive disease. PTEN mutations were associated with shorter time to progression (p=0.004) and lower overall survival (p=0.02). Conclusion: Talazoparib demonstrated clinical benefit in selected patients with germline as well as somatic alterations in BRCA pathway genes. Patients with PTEN mutations/loss did not derive significant clinical benefit from PARP inhibition. Further study is needed to confirm these findings and determine implications for patient selection and combination therapy. Clinical trial information: NCT 02286687. Citation Format: Sarina A. Piha-Paul, Wendy Wen Xiong, Tyler Moss, Rosa M. Mostorino, Shelby Sedelmeier, Kenneth Hess, Siqing Fu, David Hong, Filip Janku, Daniel Karp, Aung Naing, Shubham Pant, Jordi Rodon, Vivek Subbiah, A M. Tsimberidou, Timothy Yap, Milind Javle, Coya Tapia, Kenna R. Shaw, Karina Eterovic, Gordon B. Mills, Funda Meric-Bernstam. Phase II study of the PARP inhibitor talazoparib in advanced cancer patients with somatic alterations in BRCA1/2, mutations/deletions in PTEN or PTEN loss, aberrations in other BRCA pathway genes, and germline mutations in BRCA1/2 (not breast or ovarian cancer) [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A096.

A strategy for molecular diagnostics of Fanconi anemia in Brazilian patients.

BackgroundFanconi anemia (FA) is a predominantly autosomal recessive disease with wide genetic heterogeneity resulting from mutations in several DNA repair pathway genes. To date, 21 genetic subtypes have been identified. We aimed to identify the FA genetic subtypes in the Brazilian population and to develop a strategy for molecular diagnosis applicable to routine clinical use.MethodsWe screened 255 patients from Hospital de Clínicas, Universidade Federal do Paraná for 11 common FA gene mutations. Further analysis by multiplex ligation‐dependent probe amplification (MLPA) for FANCA and Sanger sequencing of all coding exons of FANCA, ‐C, and –G was performed in cases who harbored a single gene mutation.ResultsWe identified biallelic mutations in 128/255 patients (50.2%): 89, 11, and 28 carried FANCA,FANCC, and FANCG mutations, respectively. Of these, 71 harbored homozygous mutations, whereas 57 had compound heterozygous mutations. In 4/57 heterozygous patients, both mutations were identified by the initial screening, in 51/57 additional analyses was required for classification, and in 2/57 the second mutation remained unidentified. We found 52 different mutations of which 22 were novel.ConclusionThe proposed method allowed genetic subtyping of 126/255 (49.4%) patients at a significantly reduced time and cost, which makes molecular diagnosis of FA Brazilian patients feasible.

WEE1 inhibition in pancreatic cancer cells is dependent on DNA repair status in a context dependent manner.

Pancreatic ductal adenocarcinoma (PDA) is a lethal disease, in part, because of the lack of effective targeted therapeutic options. MK-1775 (also known as AZD1775), a mitotic inhibitor, has been demonstrated to enhance the anti-tumor effects of DNA damaging agents such as gemcitabine. We evaluated the efficacy of MK-1775 alone or in combination with DNA damaging agents (MMC or oxaliplatin) in PDA cell lines that are either DNA repair proficient (DDR-P) or deficient (DDR-D). PDA cell lines PL11, Hs 766T and Capan-1 harboring naturally selected mutations in DNA repair genes FANCC, FANCG and BRCA2 respectively, were less sensitive to MK-1775 as compared to two out of four representative DDR-P (MIA PaCa2 and PANC-1) cell lines. Accordingly, DDR-P cells exhibit reduced sensitivity to MK-1775 upon siRNA silencing of DNA repair genes, BRCA2 or FANCD2, compared to control cells. Only DDR-P cells showed increased apoptosis as a result of early mitotic entry and catastrophe compared to DDR-D cells. Taken together with other recently published reports, our results add another level of evidence that the efficacy of WEE1 inhibition is influenced by the DNA repair status of a cell and may also be dependent on the tumor type and model evaluated.

Clinical characteristics and genetic subtypes of Fanconi anemia in Saudi patients

We reviewed our institutional experience from 2011 to 2015 on new cases of Fanconi anemia (FA). Ten unrelated cases were diagnosed during this period. Four patients with severe aplastic anemia (SAA) had c.2392C > T (p.Arg798*) BRIP1/FANCJ mutation. Another child with SAA had novel c.1475T > C (p.Leu492Pro) FANCC mutation. One individual with SAA and acute myeloid leukemia had c.637_643del (p.Tyr213Lysfs*6) FANCG mutation. Three patients presented with early onset of cancer, two had BRCA2 mutation c.7007G > A (p.Arg2336His) and one had a novel c.3425del (p.Leu1142Tyrfs*21) PALB2 mutation. Another infant with c.3425del PALB2 mutation had clonal aberration with partial trisomy of the long arm of chromosome 17. Mutations in FA downstream pathway genes are more frequent in our series than expected. Our preliminary observation will be confirmed in a large multi-institutional study.