Mutations In Cancer Predisposition Genes Research Articles

Abstract LB007: A systematic evaluation of the therapeutic potential of Endogenous-ADAR base editors in cancer prevention and treatment

Abstract Base editing encompasses techniques that efficiently alter specific nucleotides at the DNA or RNA level. Initially explored for inherited diseases, these techniques hold promise for addressing various genetically driven disorders caused by single nucleotide variants (SNVs). The precise programmability of base editors (BEs) for specific sequences allows customization for rare genetic variants, tailoring them to individual patients within affordability and delivery constraints. Cancer stems from the accumulation of mutations. However, the relevance of BEs in cancer therapy is doubted due to the limited types of mutations they can address within tumors. Yet, their untapped potential in the realm of cancer treatment invites exploration. BEs utilize a modified form of a deaminase enzyme to catalyze the conversion of one nucleotide to another by removing an amino group. A 'classic' BE consists of a deaminase, a Cas nuclease, and a guide RNA (gRNA) ensuring target specificity through Watson-Crick base pairing. An alternative RNA BE, known as Endogenous-ADAR, involves designing a gRNA to recruit native Adenosine Deaminases Acting on RNA (ADAR), responsible for extensive A-to-I(G) editing in mammals. Due to its reliance on ADAR capabilities, Endogenous-ADAR exclusively targets G>A SNVs at the RNA level. Notably, RNA editing, occurring before splicing, provides the flexibility to target all gene regions. Also, editing the RNA sequence is considered 'safer' in the event of an off-target error. Our objective is to systematically explore the potential of Endogenous-ADAR for cancer prevention and treatment. Our first approach evaluates Endogenous-ADAR's potential to revert germline mutations in cancer predisposition genes (CPGs) for cancer prevention. Focusing on CPGs recommended for pediatric genetic testing by NCBI, associated with cancer predisposition disorders, our findings indicate that among the 2,820 SNVs examined, 566 (20%) are suitable for Endogenous-ADAR. Remarkably, 88% of correctable variants show no off-target sites, indicating safe therapeutic targets. Further examining pathogenic high-penetrance germline variants in adults, 48 (20%) of the 239 SNVs examined are correctable using Endogenous-ADAR. Second, we estimate the potential to correct cancer driver mutations. Examining 5,913 driver mutations from 2,010 patients representing 36 cancer types, which underwent whole genome sequencing (WGS) in the PCWAG project, we find that 955 (16%) are suitable for Endogenous-ADAR. In 729 (36%) of patients, at least one driver mutation is correctable, and in 91 (5%), all known driver mutations are correctable. Aligned with the swift incorporation of WGS in oncology, our systematic exploration portrays a favorable landscape of correctable mutations in cancer. This points to the future possibility of leveraging the unique capabilities of base editing, particularly Endogenous-ADAR, for clinical cancer risk/prevention and treatment outcomes. Citation Format: Rona Merdler-Rabinowicz, Ariel Dadush, Sumeet Patiyal, Padma Sheila Rajagopal, Gulzar Daya, Alejandro Schäffer, Eli Eisenberg, Eytan Ruppin, Erez Y. Levanon. A systematic evaluation of the therapeutic potential of Endogenous-ADAR base editors in cancer prevention and treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB007.

Abstract 3346: JMJD6 as a novel tumorigenic factor and therapeutic target in group 3 (MYC-driven) medulloblastoma

Abstract Medulloblastoma (MB) is the most common type of childhood brain cancer worldwide. Although current treatment with surgery and extensive chemoradiation has led to increased survival rates, many MB patients still die from the disease. Moreover, surviving patients suffer severe long-term side effects as a consequence of treatment. It is therefore crucial to develop more effective and less toxic therapies. The most aggressive subtype of MB tumors often exhibits amplification or overexpression of the MYC oncogene. Patients with MYC-amplified MB exhibit a high frequency of cerebrospinal tumor dissemination, often experience treatment resistance and have extremely poor prognoses. While the MYC oncogene is established as the oncogenic driver in Group 3 MB, it has remained undruggable. Thus, targeting regulatory components of MYC and the signaling pathways regulated by it is of great potential therapeutic value. Studies have revealed that MB has very few germline mutations in cancer predisposition genes, suggesting that dysregulated epigenetic pathways might be critical in MB pathogenesis. Particularly, dysregulation of epigenetic modifiers, including histone methyltransferases and histone demethylases, is very common in Group 3 MB, compared to other MB subgroups. Therefore, it is important to identify such epigenetic modifiers that may have controls on MYC and its tumorigenic activities and explore these as the epigenetic drug-candidate targets in Group 3 (MYC-driven) MB. In this regard, we found that protein arginine demethylase Jumonji C domain-containing protein 6 (JMJD6), an emerging key epigenetic enzyme in cancers, is a novel regulator of MYC expression in MYC-driven MB. We observed high levels of JMJD6 that not only mirror MYC expression in the most aggressive MB but also correlate with poor outcomes in these patients. Knockdown of JMJD6 decreased MYC expression, cellular proliferation/survival and stemness in MYC-amplified MB cells. Mechanistically, our results revealed that JMJD6 forms complexes with proteins involved in maintaining and regulating the promoter-pause at super-enhancers, suggesting that JMJD6 can regulate MYC at the transcription level. Moreover, our in vivo analyses of JMJD6 inhibition, either with inducible gene knockdown or a pharmacologic small molecule inhibitor, demonstrated anti-MB potential with suppressed MYC expression. Based on this background and preliminary observations, we hypothesize that JMJD6 plays crucial roles in the most aggressive MB by regulating MYC expression and hence MYC-driven tumorigenesis. Accordingly, we hypothesize that targeting the JMJD6-MYC axis by JMJD6 inhibition can serve as a powerful therapeutic strategy for MYC-driven MB. Citation Format: Matthew Kling, Devendra Kumar, Sutapa Ray, Shantaram Joshi, Don Coulter, Nagendra K. Chaturvedi. JMJD6 as a novel tumorigenic factor and therapeutic target in group 3 (MYC-driven) medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3346.

Germline mutations in cancer predisposition genes among pediatric patients with cancer and congenital anomalies.

Childhood cancer has a poorly known etiology, and investigating the underlying genetic background may provide novel insights. A recognized association exists between non-chromosomal birth defects and childhood cancer susceptibility. We performed whole-exome sequencing and chromosomal microarray analysis in a cohort of childhood cancer (22 individuals, 50% with congenital anomalies) to unravel deleterious germline variants. A diagnostic yield of 14% was found, encompassing heterozygous variants in bona fide dominant Cancer Predisposition Genes (CPGs). Considering candidate and recessive CPGs harboring monoallelic variants, which were also deemed to play a role in the phenotype, the yield escalated to 45%. Most of the deleterious variants were mapped in genes not conventionally linked to the patient's tumor type. Relevant findings were detected in 55% of the syndromic individuals, mostly variants potentially underlying both phenotypes. We uncovered a remarkable prevalence of germline deleterious CPG variants, highlighting the significance of a comprehensive genetic analysis in pediatric cancer, especially when coupled with additional clinical signs. Moreover, our findings emphasized the potential for oligogenic inheritance, wherein multiple genes synergistically increase cancer risk. Lastly, our investigation unveiled potentially novel genotype-phenotype associations, such as SETD5 in neuroblastoma, KAT6A in gliomas, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. Novel gene-phenotype associations and candidate genes for pediatric cancer were unraveled, such as KAT6A in gliomas, SETD5 in neuroblastoma, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. Our analysis revealed a high frequency of deleterious germline variants, particularly in cases accompanied by additional clinical signs, highlighting the importance of a comprehensive genetic evaluation in childhood cancer. Our findings also underscored the potential for oligogenic inheritance in pediatric cancer risk. Understanding the cancer etiology is crucial for genetic counseling, often influencing therapeutic decisions and offering valuable insights into molecular targets for the development of oncological therapies.

Germline mutations in pediatric cancer cohort with mixed-ancestry Mexicans.

Childhood cancer is one of the primary causes of disease-related death in 5- to 14-year-old children and currently no prevention strategies exist to reduce the incidence of this disease. Childhood cancer has a larger hereditary component compared with cancer in adults. Few genetic studies have been conducted on children with cancer. Additionally, Latin American populations are underrepresented in genomic studies compared with other populations. Therefore, the aim of this study is to analyze germline mutations in a group of mixed-ancestry Mexican pediatric patients with solid and hematological cancers. We analyzed genetic variants from 40 Mexican childhood cancer patients and their relatives. DNA from saliva or blood samples was used for whole-exome sequencing. All variants were identified following GATK best practices. We found that six patients (15%) were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS cancer predisposition genes, and additional new variants predicted to be deleterious by in silico algorithms. A population genetics analysis detected five components consistent with the demographic models assumed for modern mixed-ancestry Mexicans. This report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population.

Abstract C105: A systematic evaluation of the therapeutic potential of base editing in cancer prevention and treatment

Abstract Base editing (BE) techniques offer efficient means to modify specific nucleotides in the genome. While current research mainly focuses on applying BE for treating genetic diseases caused by single-nucleotide variants (SNVs), its potential in cancer is worth exploring, as many tumors arise from an accumulation of various mutations. BE techniques primarily consist of a fusion between a Cas nuclease and a deaminase (Cas-BE), that enables A-to-G or C-to-T edits. This allows for the correction of G>A and T>C SNVs at the DNA or RNA level. Additionally, BE can correct C>T and A>G SNVs at the DNA level through the cellular DNA repair response. Precise targeting is aimed by a programmed guide RNA (gRNA), which engages in Watson-Crick base pairing with the desired region. However, a remaining concern is gRNA binding to additional locations in the genome, leading to unintended off-target edits. An alternative approach of RNA editing, involves utilizing the gRNA alone, harnessing the native Adenosine Deaminases Acting on RNA (ADAR) enzyme (Non-Cas-BE). This eliminates the need for a vector vehicle and acting on the RNA level its effects are transient, thus potentially reducing off target permanent damage. Our first objective was to evaluate BE potential to reverse germline mutations in cancer predisposition genes (CPGs) as a strategy for cancer prevention. We analyzed the 64 CPGs recommended for pediatric genetic testing by NCBI, which are associated with cancer predisposition disorders. We extracted the known pathogenic SNVs reported in ClinVar within these genes, filtering those classified as neoplastic according to MedGen. Our findings indicate that among the 2820 SNVs examined, 54% display a suitable match for BE (34% for Cas-BE and 20% for Non-Cas-BE). To identify off-target sites, we utilized BLAST to compare the 40 nucleotides surrounding each mutation, resembling the gRNA, to the genome. Remarkably, our findings revealed that in 87% of BE correctable sites no off-target sites are detected, indicating that they are safe therapeutic targets. We further examined a list of pathogenic high-penetrance germline variants in adult patients who developed cancer, finding that among 250 SNVs reported, 59% could be addressed using BE. Second, we estimated the potential of BE to correct cancer driver mutations. Detecting the small subset of driver mutations within a tumor is indeed an open challenge, but once detected, correcting them holds considerable promise. We examined 5,913 driver mutations from 2,010 patients representing 36 cancer types, which underwent whole genome sequencing (WGS) in the PCWAG project, and found that 43% are suitable for BE, 16% by Non-Cas-BE. In 1,051 (52%) of the tumors at least one driver mutation is BE correctable, and in 208 (10%) all known driver mutations were BE correctable. Aligning with the swift incorporation of WGS in the field of oncology, this systematic exploration highlights the potential of BE to correct driver mutations for cancer prevention and treatment. Citation Format: Rona Merdler-Rabinowicz, Ariel Dadush, Sumeet Patiyal, Gulzar Daya, Lipika Ray, Padma Sheila Rajagopal, Alejandro A. Schaffer, Eytan Ruppin, Erez Y. Levanon. A systematic evaluation of the therapeutic potential of base editing in cancer prevention and treatment [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C105.

Role and Prevalence of Risk Factors That Trigger Therapy Related Myeloid Neoplasms (TRMN) in Patients with Previous Treated Breast Cancer

INTRODUCTION: Cytotoxic treatment of a primary tumor (PT) is one of the main drivers for the development of a Therapy Related Myeloid Neoplasm (TRMN). However, other intrinsic factors associated with TRMN contribute to their heterogeneous etiology. It has been suggested that around 18.5% of TRMN patients have a germline cancer mutation. On the other hand, prevalence of pre-existing clonal hematopoiesis of indeterminate potential (CHIP) is estimated in around 30% at the time of PT diagnosis, which has been associated with a worse outcome and a higher incidence of TRMN. Thus, scenarios with different etiologies must be identified for TRMN classification, differential diagnosis, and management of patients at risk. AIM: To evaluate the relative risk factor contribution of CHIP and germline mutations to develop TRMN in patients with previous breast cancer (BC) treated with chemotherapy and/or radiotherapy. METHODOLOGY: Paired samples from bone marrow (BM) and peripheral blood (PB) of 19 TRMN patients with a previous BC have been studied by tNGS (N=7) and WES (N=12) at the time of TRMN diagnosis to describe the molecular alterations (including germline landscape and somatic drivers). BM samples were used as a source of tumoral DNA, while CD3+ T lymphocytes were isolated from PB and were used as germline sample. Variants with frequency (VAF)<30% found in BM but not in CD3+ sample were annotated as somatic. Variants with 2%>VAF<10% found in PB of BC patients were annotated as CHIP. Only pathogenic/likely pathogenic variants were considered. RESULTS: Germline mutations in cancer predisposition genes and myeloid genes were found in 31.3% and 62.5% of TRMN patients, respectively. Myeloid somatic mutations were found in 37.5.1% of TRMN patients (Table 1). On the other hand, CHIP prevalence in longitudinal samples of BC series was found in 27.3% and 45.5% of treatment-naïve and 6-12 months after the treatment samples, respectively. The somatic alterations found in TRMN patients were compared with CHIP in sequential blood samples of 25 BC patients. Three somatic profiles were observed (Fig.1): A) Drivers of TRMN not found in any of the BC samples might highlight that both neoplasms do not share risk factors but might involve independent germline predisposition instead. B) TRMN drivers not found in pretreatment samples but appearing in BC samples after cytotoxic therapy suggest a prominent role of treatment. C) TRMN drivers found at low frequency in the BC samples prior to the treatment might suggest that other factors different than cytotoxic therapy could be involved in TRMN development. Similar percentage of somatic drivers in TRMN patients was found in the three profiles; however, different gene frequencies were observed. Finally, CHIP and TRMN drivers were also evaluated regarding the germline predisposition landscape. The percentage of patients with CHIP was higher in patients with no germline cancer predisposition mutations. However, a higher increase after cytotoxic treatment was observed in patients with germline predisposition (Table 1). On the other hand, TRMN patients with no germline cancer predisposition showed an increased percentage of myeloid somatic drivers (25%) in comparison with germline mutation carriers (13%). Otherwise, 37.5% of TRMN patients were carrying germline mutations in cancer predisposition and myeloid genes, suggesting low relevance of treatment in these patients. CONCLUSION: Our results identified different etiologic scenarios in TRMN, highlighting the role of germline landscape instead of treatment. Otherwise, the percentage of somatic drivers in TRMN patients was found increased in patients with no germline cancer mutations. However, CHIP differences in pre and post treatment samples were found to be higher in BC patients with germline mutations. Deeper studies regarding the involved genes and somatic and germline associations comparing different treatment regimens are ongoing and will be further presented to discuss the contribution of different risk factors to the development of TRMN in BC patients. Understanding the risk factors contribution to TRMN development is needed for the adequate management of BC patients. Financial support: This work was supported by a grant from the Instituto de Salud Carlos III, Ministerio de Economia y Competitividad, Spain (PI 20/00531)(Co-funded by European Regional Development Fund. ERDF, a way to build Europe) and Fundació Adey.

Clinical and Molecular Characterization of Patients with Therapy Related Myeloid Neoplasms (TRMN)

Acknowledgements Chemotherapy and/or radiotherapy in cancer patients compose a future risk of developing a therapy related myeloid neoplasm (TRMN). However, the presence of a germline landscape might contribute and modify the overall risk. It has been suggested that around 18.5% of TRMN patients have a germline cancer mutation. In particular, cancer predisposing genes or syndromes involving alterations in the DNA repair mechanism such as CHEK2, BRCA1, BRCA2, MLH1, MSH2, MSH6 or PMS2 might be enriched in patients who develop a primary tumor (PT) and a subsequent secondary myeloid neoplasm. The role of the alterations in cancer susceptibility genes in association with the treatment for the PT in the development of TRMN is still unclear. To evaluate the clinical and genetic landscape of TRMN patients to understand the role of different risk factors and provide tools for differential diagnosis and clinical management. Clinical evaluation of 96 patients with TRMN and 12 patients with a secondary myeloid neoplasm after a non-treated with chemotherapy primary tumor (nTMN) was performed. In addition, germline landscape and somatic alterations were studied in the TRMN series by tNGS (N=49) and WES (N=47). Tumoral sample was obtained from bone marrow. CD3+ T lymphocytes from peripheral blood (PB) were enriched by immunomagnetic selection and used as germline/control sample. A minimum of 98% purity in CD3+ was selected to prevent myeloid contamination. Variant frequency (VAF) <30% found in tumor but not in CD3+ sample was annotated as somatic alteration. Only pathogenic/likely pathogenic variants were considered. The median age of onset was 62.3 and 71.1 years for the PT and the TRMN, respectively. 32.5% had complex karyotype. Similar positive correlation was found between the age of onset of the PT and the age of onset of the TRMN and nTNM. A negative correlation was found between the age of onset of the PT and the latency until the TRMN and nTMN diagnosis, which suggests that elderly age condition is more relevant than the cytotoxic treatment (Fig.1). No differences in latencies were found between MN subtypes, despite ring sideroblasts and del(5q) myeloid subtypes correlated with shorter and higher latencies, respectively. Different latencies were neither found when the PT was solid or hematologic, but interestingly, TRMN patients with previous colorectal cancer had shorter latencies. On the other hand, 91.3% of the TRMN patients presented a molecular alteration (considering both genetic or cytogenetic alterations), including 60.9% and 75% of patients with germline and acquired alterations, respectively. Germline mutations included 52.2% and 47.8% annotated in cancer predisposition genes of the DNA repair mechanisms and myeloid genes, respectively. Only 39.1% of TRMN patients were found with pathogenic somatic variants in myeloid genes while 68.75% were found with an abnormal karyotype. Finally, higher number of germline and somatic mutations was found in TRMN patients with an abnormal karyotype. However, a higher percentage of germline mutations in myeloid genes was found in TRMN with a normal karyotype (Fig.2). Higher percentage of molecular alterations (both germline and somatic) in myeloid genes was found in TRMN patients with a previous solid PT. However, higher percentage of mutations in cancer predisposition genes was found when the PT was hematologic. Our results highlight the role of mutations in cancer predisposition genes in the development of TRMN. Similar latency associations were found for TRMN and nTMN patients, which suggest that other risk factors different than treatment might contribute to the TRMN development. Altered karyotypes in TRMN patients are associated with acquired mutations in myeloid genes but not with germline mutations, which suggests two different entities with different prognosis. Molecular alterations in myeloid genes are more relevant in TRMN patients with solid PT, while molecular alterations in cancer predisposition genes are associated with TRMN patients with hematologic PT. This work was supported in part by a grant from the Instituto de Salud Carlos III, Ministerio de Economia y Competitividad, Spain (PI 20/00531)(Co-funded by European Regional Development Fund. ERDF, a way to build Europe). 2021 SGR 00560 (GRC) Generalitat de Catalunya; economical support from CERCA Programme and Fundació Adey.

Associations Between Cancer Predisposition Mutations and Clonal Hematopoiesis in Patients With Solid Tumors.

Clonal hematopoiesis (CH), the expansion of clones in the hematopoietic system, has been linked to different internal and external features such as aging, genetic ancestry, smoking, and oncologic treatment. However, the interplay between mutations in known cancer predisposition genes and CH has not been thoroughly examined in patients with solid tumors. We used prospective tumor-blood paired sequencing data from 46,906 patients who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing to interrogate the associations between CH and rare pathogenic or likely pathogenic (P/LP) germline variants. We observed an enrichment of CH-positive patients among those carrying P/LP germline mutations and identified a significant association between P/LP germline variants in ATM and CH. Germline and CH comutation patterns in ATM, TP53, and CHEK2 suggested biallelic inactivation as a potential mediator of clonal expansion. Moreover, we observed that CH-PPM1D mutations, similar to somatic tumor-associated PPM1D mutations, were depleted in patients with P/LP germline mutations in the DNA damage response (DDR) genes ATM, CHEK2, and TP53. Patients with solid tumors and harboring P/LP germline mutations, CH mutations, and mosaicism chromosomal alterations might be at an increased risk of developing secondary leukemia while germline variants in TP53 were identified as an independent risk factor (hazard ratio, 36; P < .001) for secondary leukemias. Our results suggest a close relationship between inherited variants and CH mutations within the DDR genes in patients with solid tumors. Associations identified in this study might translate into enhanced clinical surveillance for CH and associated comorbidities in patients with cancer harboring these germline mutations.

Somatic profiling guides germline genetic testing in patients with mutations in cancer predisposition genes.

10608 Background: 15% of patients with advanced cancer have an inherited predisposition to cancer. Over a third of patients carrying a pathogenic germline variant would not qualify for genetic testing based on current National Comprehensive Cancer Network genetic testing guidelines. Supplementing the current practice of somatic sequencing with germline testing would improve treatment decisions and be informative of the risk of developing subsequent cancers in the individual. It may also extend the benefits of high-risk screening programs to family members. Offering genetic testing to patients with the highest likelihood of carrying a germline mutation is preferable to unselected sequencing given the current environment. Methods: We developed a list of genes to help identify patients whose somatic mutations were more likely to be found in the germline as well. We classified these genes into 3 tiers based on the likelihood of germline pathogenicity. All somatic sequencing panel results were reviewed based on the IRB-approved protocol for our designated Tier One genes ( ATM, BAP1, BMPR1A, BRCA1, BRCA2, BRIP1, MSH2, MSH6, MUTYH, MYH11, PALB2, RUNX1, SDHAF2, SDHB, SDHC, and known founder mutations in additional genes). Treating physicians for patients whose tumors harbored a mutation in one of these genes were contacted and, if they agreed, patients were offered participation in this ongoing study. Enrolled patients had genetic counseling and testing for a multi-gene panel at no cost to them. Results: We reviewed 3621 somatic test results, and 339 (9.4%) patients were eligible for the study. 34 (10.03%) eligible patients were enrolled, and 33 (9.73%) completed testing. Of these, 16 had positive germline results (48.5%, though they may not all be in the originally identified genes), 8 had a variant of uncertain significance (24.2%), and 9 had negative testing (27.3%). Some patients were not referred by their treating physicians based on their own clinical assessment. Others were hesitant to enroll due to concerns about the privacy of genetic information. Other confounding factors may have affected our accrual, including the pandemic. Conclusions: Implementing a somatic profiling-based screening program to identify inherited cancer predisposition syndromes is feasible in patients who may not meet current germline genetic testing guidelines. Our study showed 9.73% of eligible patients underwent genetic counseling and testing, and an inherited predisposition to cancer was confirmed in almost 50% of these patients. In addition, family members were offered cascade testing. Germline genetic evaluation remains underutilized even when payor constraints are removed as a barrier. To increase the identification of patients with inherited predispositions to cancer other barriers such as a lack of referrals by treating oncologists need to be overcome.

Prevalence of Germline Mutations in Cancer Predisposition Genes in Patients with Pancreatic Cancer or Suspected Related Hereditary Syndromes: Historical Prospective Analysis

we enrolled for NGS with an Illumina TrueSight Cancer panel comprising 19 CPGs and 113 consecutive subjects referred to cancer genetic clinics for metastatic PDAC, early onset PDAC, suspected hereditary syndrome, or positive family history. Overall, 23 (20.1%) subjects were carriers of 24 pathogenetic variants (PVs). We found 9 variants in BRCA2 (37.5%), 6 in CDKN2A (25%), 3 in ATM (12.5%), 2 in BRCA1 (8.3%), 1 in CHEK2 (4.1%), 1 in PALB2 (4.1%), 1 in MITF (4.1%), and 1 in FANCM (4.1%). A double PV (BRCA1 plus BRCA2) was found in 1 subject. We observed a nearly 30% (16/55) mutational rate in the subgroup of subjects tested for the suspected syndromes (PDAC and other synchronous or metachronous tumors or an indicative family history), and the frequency was significantly higher than that in patients with only metastatic PDAC (p = 0.05). In our cohort, 39 variants of unknown significance (VUS) were identified, most of which (16/39, 41%) in genes belonging to the Lynch syndrome spectrum. A clinically relevant proportion of pancreatic cancer is associated with mutations in known predisposition genes. Guidelines instructing on an adequate selection for accessing genetic testing are eagerly needed. The heterogeneity of mutations identified in this study reinforces the value of using a multiple-gene panel in pancreatic cancer.

The Largest Chinese Cohort Study Indicates Homologous Recombination Pathway Gene Mutations as Another Major Genetic Risk Factor for Colorectal Cancer with Heterogeneous Clinical Phenotypes.

While genetic factors were associated with over 30% of colorectal cancer (CRC) patients, mutations in CRC-susceptibility genes were identified in only 5% to 10% of these patients. Besides, previous studies on hereditary CRC were largely designed to analyze germline mutations in patients with single genetic high-risk factor, which limited understanding of the association between genotype and phenotypes. From January 2015 to December 2018, we retrospectively enrolled 2,181 patients from 8,270 consecutive CRC cases, covering 5 categories of genetic high-risk factors. Leukocyte genomic DNA was analyzed for germline mutations in cancer predisposition genes. The germline mutations under each category were detected and analyzed in association with CRC susceptibility, clinical phenotypes, and prognoses. A total of 462 pathogenic variants were detected in 19.3% of enrolled CRC patients. Mismatch repair gene mutation was identified in 9.1% of patients, most prevalent across all high-risk groups. Homologous recombination (HR) gene mutations were detected in 6.5% of cases, penetrated in early-onset and extra-colonic cancer risk groups. Mutations in HR genes, including BARD1, RAD50, and ATM, were found to increase CRC risk with odds ratios of 2.8-, 3.1-, and 3.1-fold, respectively. CRC patients with distinct germline mutations manifested heterogeneous phenotypes in clinicopathology and long-term prognoses. Thus, germline mutation screenings should be performed for CRC patients with any of those genetic risk factors. This study also reveals that HR gene mutations may be another major driver for increased CRC risk.

Screening Programs for Breast Cancer: Toward Individualized, Risk-Adapted Strategies of Early Detection.

Early detection of breast cancer (BC) comprises two approaches: screening of asymptomatic women in a specified target population at risk (usually a target age range for women at average risk), and early diagnosis for women with BC signs and symptoms. Screening for BC is a key health intervention for early detection. While population-based screening programs have been implemented for age-selected women, the pivotal clinical trials have not addressed the global utility nor the improvement of screening performance by utilizing more refined parameters for patient eligibility, such as individualized risk stratification. In addition, with the exception of the subset of women known to carry germline pathogenetic mutations in (high- or moderately-penetrant) cancer predisposition genes, such as BRCA1 and BRCA2, there has been less success in outreach and service provision for the unaffected relatives of women found to carry a high-risk mutation (i.e., "cascade testing") as it is in these individuals for whom such actionable information can result in cancers (and/or cancer deaths) being averted. Moreover, even in the absence of clinical cancer genetics services, as is the case for the immediate and at least near-term in most countries globally, the capacity to stratify the risk of an individual to develop BC has existed for many years, is available for free online at various sites/platforms, and is increasingly being validated for non-Caucasian populations. Ultimately, a precision approach to BC screening is largely missing. In the present chapter, we aim to address the concept of risk-adapted screening of BC, in multiple facets, and understand if there is a value in the implementation of adapted screening strategies in selected women, outside the established screening prescriptions, in the terms of age-range, screening modality and schedules of imaging.

Whole-Exome Sequencing Study of Familial Nasopharyngeal Carcinoma and Its Implication for Identifying High-Risk Individuals.

Nasopharyngeal carcinoma (NPC) is closely associated with genetic factors and Epstein-Barr virus infection, showing strong familial aggregation. Individuals with a family history suffer elevated NPC risk, requiring effective genetic counseling for risk stratification and individualized prevention. We performed whole-exome sequencing on 502 familial NPC patients and 404 unaffected relatives and controls. We systematically evaluated the established cancer predisposition genes and investigated novel NPC susceptibility genes, making comparisons with 21 other familial cancers in the UK biobank (N = 5218). Rare pathogenic mutations in the established cancer predisposition genes were observed in familial NPC patients, including ERCC2 (1.39%), TP63 (1.00%), MUTYH (0.80%), and BRCA1 (0.80%). Additionally, 6 novel susceptibility genes were identified. RAD54L, involved in the DNA repair pathway together with ERCC2, MUTYH, and BRCA1, showed the highest frequency (4.18%) in familial NPC. Enrichment analysis found mutations in TP63 were enriched in familial NPC, and RAD54L and EML2 were enriched in both NPC and other Epstein-Barr virus-associated cancers. Besides rare variants, common variants reported in the studies of sporadic NPC were also associated with familial NPC risk. Individuals in the top quantile of common variant-derived genetic risk score while carrying rare variants exhibited increased NPC risk (odds ratio = 13.47, 95% confidence interval = 6.33 to 28.68, P = 1.48 × 10-11); men in this risk group showed a cumulative lifetime risk of 24.19%, much higher than those in the bottom common variant-derived genetic risk score quantile and without rare variants (2.04%). This study expands the catalog of NPC susceptibility genes and provides the potential for risk stratification of individuals with an NPC family history.

Spectrum and management of breast cancer patients with variant of uncertain significance mutations at a tertiary care centre in North India.

BackgroundThe spectrum and significance of Variants of Uncertain Significance (VUS) mutations in breast cancer predisposition genes is poorly defined in the Indian population.MethodsAll new female breast cancer patients from 1 March 2019 to 28 February 2020 were screened. Those providing informed consent and without previous genetic testing were recruited. Multigene panel testing (107 genes) by next-generation sequencing was performed for all patients. Descriptive statistics was used to describe the spectrum of VUS mutations.ResultsOut of 236 patients recruited in the study, a VUS was detected in 89 patients (37.71%). VUS pathogenic ratio was 2.02. A total of 121 different VUS mutations in 40 different genes were detected. Fourteen patients (15.7%) had a VUS in high penetrance genes and 36 VUS mutations (29.8%) were detected in one of the genes involved in homologous recombination repair pathway. No therapeutic interventions were done based on VUS.ConclusionsIn this large prospective study of genetic determinants of breast cancer from India, a high prevalence of VUS (37.71%) was detected with 15.7% patients having a VUS in high penetrance genes. More evidence needs to be generated from larger multicentric studies to better understand the implications of these genetic variants and enable their reclassification.

Multi-Gene Mutation Profiling by Targeted Next-Generation Sequencing in Premenopausal Breast Cancer.

Breast cancer has distinct etiology, prognoses, and clinical outcomes at premenopausal ages. Determination of the frequency of germline and somatic mutations will refine our understanding of the genetic contribution to premenopausal breast cancer susceptibility. We applied a comprehensive next generation sequencing-based approach to analyze blood and/or tissue samples of 54 premenopausal breast cancer patients treated in our clinic. Genetic testing results were descriptively analyzed in correlation with clinicopathological data. In the present study, 42.5% of premenopausal breast cancer patients tested carried pathogenic mutations in cancer predisposition genes (CHEK2, BRCA1, TP53, and MUTYH). Germline variants of unknown/uncertain significance (VUSs) in eight different cancer susceptibility genes, namely BRCA1, BRCA2, CHEK2, RAD51C, RAD51D, ATM, BRIP1, and PMS2, were also identified in 14 premenopausal patients (35%). Of the breast tumors tested, 61.8% harbored pathogenic somatic variants in tumor suppressor genes (TP53, NF1, RB), genes involved in DNA repair (BRCA1, BRCA2, ATM, RAD50), cell proliferation (PTEN, PIK3C FGFR3, AKT1, ROS1, ERBB2, NOTCH1), and cell adhesion (CTNNB1). This descriptive study employs the powerful NGS technology to highlight the high frequency of premenopausal cases attributable to genetic predisposition. Mutation identification in a larger cohort may further ensure that these patients receive tailored treatment according to their menopausal status.

Genetic Disorders with Predisposition to Paediatric Haematopoietic Malignancies-A Review.

Simple SummaryA significant progress in understanding the genetic basis of childhood cancers has been made over the past years. Genome sequencing has identified significant differences between paediatric and adult cancers. A higher prevalence of germline alterations in cancer predisposition genes is observed, in comparison to somatic mutations in paediatric cancers. Interestingly, pathogenic germline variants and somatic mutations can affect the same genes. The early recognition of genetic predispositions for childhood cancers may provide an opportunity of therapy adjustment and specific screening for different syndrome-related malignancies. Research on the biological function of gene variants with increased cancer predispositions is critical to the needs of adequate patient management. Genetic counselling with targeted therapy have become basis of integrated cancer care in paediatric oncology.The view of paediatric cancer as a genetic disease arises as genetic research develops. Germline mutations in cancer predisposition genes have been identified in about 10% of children. Paediatric cancers are characterized by heterogeneity in the types of genetic alterations that drive tumourigenesis. Interactions between germline and somatic mutations are a key determinant of cancer development. In 40% of patients, the family history does not predict the presence of inherited cancer predisposition syndromes and many cases go undetected. Paediatricians should be aware of specific symptoms, which highlight the need of evaluation for cancer syndromes. The quickest possible identification of such syndromes is of key importance, due to the possibility of early detection of neoplasms, followed by presymptomatic genetic testing of relatives, implementation of appropriate clinical procedures (e.g., avoiding radiotherapy), prophylactic surgical resection of organs at risk, or searching for donors of hematopoietic stem cells. Targetable driver mutations and corresponding signalling pathways provide a novel precision medicine strategy.Therefore, there is a need for multi-disciplinary cooperation between a paediatrician, an oncologist, a geneticist, and a psychologist during the surveillance of families with an increased cancer risk. This review aimed to emphasize the role of cancer-predisposition gene diagnostics in the genetic surveillance and medical care in paediatric oncology.

Abstract 5872: Investigation on the prevalence of germline and somatic mutations in gynecological malignancies: Implications for risk assessment and therapeutic decision-making

Abstract Introduction: Heritable mutations in cancer predisposition genes increase the relative risk of developing malignant gynecological tumors, whereas actionable somatic mutations could serve as biomarker for therapeutic decision-making. Our study explored the prevalence of germline pathogenic/likely-pathogenic (P/LP) mutations and actionable somatic mutations to understand the clinical utility of next-generation sequencing (NGS) in gynecological malignancies. Methods: Genomic data was retrospectively analyzed for 1,610 women with various stages of gynecological malignancies including ovarian (OC, n=945), cervical (CC, n=358), and endometrial cancers (EC, n=307). Genomic data were derived from targeted NGS of paired white blood cell and other biological samples using a 520-gene panel that included 62 cancer predisposition genes. Genomic signatures including tissue-based tumor mutation burden (tTMB) and microsatellite instability (MSI) were also estimated from somatic mutation profiles. Results: The prevalence of germline P/LP mutations in cancer predisposition genes was 20.6% for OC, 13.4% for EC, and 6.4% for CC. OC had the highest mutation rate in genes involved in the homologous recombination repair pathway (18.8%, 178/945), while EC had the highest mutation rate in genes involved in mismatch repair (MMR) pathway (5.5%, 17/307). The frequency of actionable germline P/LP mutations was 19.8% for OC, 11.7% for EC, and 5.0% for CC. The detection rate for actionable somatic mutations were comparable between carrier and non-carrier of germline mutations (OC, 80.5% vs 76.3%, p=0.2; EC, 73.2% vs 80.5%, p=0.4; and CC, 56.5% vs 63.0%, p=0.7). tTMB was also comparable and generally low among carrier and non-carrier of germline mutations (OC, 3.0 [range: 2.0-5.0] vs 3.0 [2.0-5.0], p=0.9; EC, 6.2 [4.8-45.1] vs. 4.8 [2.8-13.2], p=0.1; and CC, 4.8 [2.4-6.0] vs 4.0 [2.4-7.9], p=0.8). The proportion of MSI-H was comparable for OC patients with or without germline mutations (2.6% vs 1.2%, p=0.2); however, the proportion of MSI-H was significantly higher for EC (29.3% vs 11.7%, p=0.019) and CC (13.0% vs 1.2%, p&amp;lt;0.001) who were carriers of germline mutations than non-carriers. The proportion of MSI-H was comparable between EC patients with germline (n=5) and somatic (n=29) MMR gene mutations (40.0%, 2/5 vs 48.3%, 14/29; p=1). EC patients with MSI-H were more likely to have high tTMB (cut-off ≥7 mutations/Mb) (p&amp;lt;0.001). Conclusions: The comparable frequency of actionable somatic mutations in women with or without germline mutations indicates that both populations could benefit from NGS testing. Our findings raise the importance of NGS-based genetic testing with a large gene panel as part of gynecological cancer screening and diagnosis to explore heritable and acquired mutation status for risk assessment and therapeutic decision-making. Citation Format: Hao Wen, Qin Xu, Xiujie Sheng, Huawen Li, Xipeng Wang, Xiaohua Wu. Investigation on the prevalence of germline and somatic mutations in gynecological malignancies: Implications for risk assessment and therapeutic decision-making [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5872.

Abstract 5219: Frequency of germline mutations in Mexican children with cancer

Abstract Childhood cancer is a leading cause of death by disease in children from 5 -14 ages, for whom there are no prevention strategies. Due to early-age of diagnosis and short-time environmental factors exposition, increasing evidence suggests childhood cancer could have stronger association with germline alterations in predisposition cancer genes. It has been estimated that up to 30% all childhood cancer diagnosis may be caused by germline variants, but their frequency and distribution remain unclear. Elucidating the prevalence and role of germline mutations in the development of childhood cancer is crucial for understanding its bases, causes, cancer-risk reduction plan, surveillance, and treatment. Here, we present a pilot study on cancer children’s patients and their relatives. A total of 40 Mexican-mestizo children with any cancer diagnosis were recruited from several Institutions of Health in Mexico and a sample of saliva or blood was obtained. Whole Exome Sequencing was performed and bioinformatic analysis was carried out following GATK best practices for germline genetic variants. Additionally, we evaluated a risk selection tool for recognition of genetic predisposition in pediatric cancer patients. Pathogenic or likely-pathogenic genetic variants (mutations) were identified from the application of a filtering chain based on ACMG guidelines, and they were subsequently validated by Sanger sequencing. Germline mutations in MSH6, NF1, MUTYH, CDKN2A, CHEK2, DICER1, FANCA and SBDS genes were identified in 5/40 (12.5%) patients with cancer, only 3 of 5 index cases (60%) reported family history of cancer and all patients meet at least one criterion of the risk selection tool. Two patients were carriers of one mutation, while in three patients were identified 2 pathogenic variants. Additionally, we identified four nonsense candidate genetic variants on EWSR1, FANCL, EPCAM and HRAS genes and two pathogenic variants in non-cancer predisposition gene, ABCA4. Our results show for the first time a higher frequency (12.5%) of germline mutations in cancer predisposition genes in Mexican-mestizo children with cancer. The lack of family history in two carriers showed the need to establish standardized suspicion criteria for identification of children with higher risk of cancer who can benefitfrom genetic testing. Further characterization of additional genetic variants identified without clinical classification will be important to evaluate their real contribution, as well as the influence of environmental factors on de novo mutation promotion. Citation Format: Oscar Alonso Luna, Jorge Meléndez Zajgla, Marta Zapata Tarres, Luis Enrique Juárez Villegas, Elvia Cristina Mendoza Caamal, Elianeth Rey Helo, Socorro Aida Borges Yanez, Gabriela Elisa Mercado Celis, Rodrigo Barquera Lozano. Frequency of germline mutations in Mexican children with cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5219.

Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution

The mechanisms underlying T-ALL relapse remain essentially unknown. Multilevel-omics in 38 matched pairs of initial and relapsed T-ALL revealed 18 (47%) type-1 (defined by being derived from the major ancestral clone) and 20 (53%) type-2 relapses (derived from a minor ancestral clone). In both types of relapse, we observed known and novel drivers of multidrug resistance including MDR1 and MVP, NT5C2 and JAK-STAT activators. Patients with type-1 relapses were specifically characterized by IL7R upregulation. In remarkable contrast, type-2 relapses demonstrated (1) enrichment of constitutional cancer predisposition gene mutations, (2) divergent genetic and epigenetic remodeling, and (3) enrichment of somatic hypermutator phenotypes, related to BLM, BUB1B/PMS2 and TP53 mutations. T-ALLs that later progressed to type-2 relapses exhibited a complex subclonal architecture, unexpectedly, already at the time of initial diagnosis. Deconvolution analysis of ATAC-Seq profiles showed that T-ALLs later developing into type-1 relapses resembled a predominant immature thymic T-cell population, whereas T-ALLs developing into type-2 relapses resembled a mixture of normal T-cell precursors. In sum, our analyses revealed fundamentally different mechanisms driving either type-1 or type-2 T-ALL relapse and indicate that differential capacities of disease evolution are already inherent to the molecular setup of the initial leukemia.

Utility of germline multi-gene panel testing in patients with endometrial cancer

ObjectivesPatients with germline mutations in mismatch repair genes (MLH1, MSH2, MSH6, PMS2) associated with Lynch syndrome (LS) have an increased lifetime risk of endometrial cancer (EC). Multi-gene panel testing (MGPT) is a recent hereditary cancer risk tool enabling next-generation sequencing of numerous genes in parallel. We determined the prevalence of actionable cancer predisposition gene mutations identified through MGPT in an EC patient cohort. MethodsA single center retrospective cohort study was conducted of patients with EC who had a clinical indication for genetic testing and who underwent MGPT as part of standard of care treatment between 2012 and 2021. Pathogenic mutations were identified and actionable mutations were defined as those with clinical management implications. Additionally, the number of individuals identified with LS was compared between MGPT and tumor-based screening. ResultsThe study included a total of 224 patients. Thirty-three patients [14.7%, 95% confidence interval (CI) = 10.4–20.1] had actionable mutations. Twenty-one patients (9.4%, 95% CI = 5.9–14.0) had mutations in LS genes (4 MLH1, 5 MSH2, 7 MSH6, 4 PMS2, 1 Epcam-MSH2). MGPT revealed two patients with LS (9.5% of LS cases) not identified through routine tumor-based screening. Thirteen patients (5.8%, 95% CI = 3.1–9.7) had at least one actionable mutation in a non-Lynch syndrome gene (6 CHEK2, 2 BRCA2, 2 ATM, 2 APC, 1 RAD51C, 1 BRCA1). ConclusionsGermline MGPT is both feasible and informative as it identifies LS cases not found on tumor testing as well as additional actionable mutations in patients with EC.