A paternal-specific methylation imprint marks the alleles of the mouse H19 gene

Imprinting, the differential expression of the two alleles of a gene based on their parental origin, requires that the alleles be distinguished or marked. A candidate for the differentiating mark is DNA methylation. The maternally expressed H19 gene is hypermethylated on the inactive paternal allele in somatic tissues and sperm, but to serve as the mark that designates the imprint, differential methylation must also be present in the gametes and the pre-implantation embryo. We now show that the pattern of differential methylation in the 5' portion of H19 is established in the gametes and a subset is maintained in the pre-implantation embryo. That subset is sufficient to confer monoallelic expression to the gene in blastocysts. We propose that paternal-specific methylation of the far 5' region is the mark that distinguishes the two alleles of H19.

An enhancer deletion affects both H19 and Igf2 expression

The distal end of mouse Chromosome 7 contains four tightly linked genes whose expression is dependent on their parental inheritance. Mash-2 and H19 are expressed exclusively from the maternal chromosome, whereas Insulin-2 (Ins-2) and Insulin-like growth factor 2 (Igf2) are paternally expressed. The identical expression during development of the 3'-most genes in the cluster, Igf2 and H19, led to the proposal that their imprinting was mechanistically linked through a common set of transcriptional regulatory elements. To test this hypothesis, a targeted deletion of two endoderm-specific enhancers that lie 3' of H19 was generated by homologous recombination in embryonic stem cells. Inheritance of the enhancer deletion through the maternal lineage led to a loss of H19 gene expression in cells of endodermal origin, including cells in the liver, gut, kidney, and lung. Paternal inheritance led to a very similar loss in the expression of Igf2 RNA in the same tissues. These results establish that H19 and Igf2 utilize the same endoderm enhancers, but on different parental chromosomes. Mice inheriting the enhancer deletion from fathers were 80% of normal size, reflecting a partial loss-of-function of Igf2. The reduction was uniformly observed in a number of internal organs, indicating that insulin-like growth factor II (IGFII), the product of Igf2, acts systemically in mice to affect prenatal growth. A modest decline in Ins-2 RNA was observed in the yolk sac. In contrast Mash-2, which is expressed in spongiotrophoblast cells of the placenta, was unaffected by the enhancer deletion.

Inducible gene knockouts in the small intestinal and colonic epithelium

We have developed two systems for performing Cre-mediated recombination of target genes in the rapidly self-renewing mouse small intestinal and colonic epithelium. When expression of Cre recombinase is placed directly under the control of transcriptional regulatory elements from a fatty acid-binding protein gene (Fabp), deletion of loxP flanked (floxed) DNA sequences is initiated as early as embryonic day 13.5, well before completion of intestinal morphogenesis. By embryonic day 16.5, Fabp-Cre also directs recombination in all cell layers of the transitional epithelium that lines the renal calyces and pelvis, ureters, and bladder. Fabp-Cre expression and recombination are maintained in both epithelia throughout adulthood. The second system allows recombination to be induced only in the gut and at any period during adulthood. This system uses Fabp regulatory elements to direct expression of a reverse tetracycline-regulated transactivator (rtTA). Another transgene encodes Cre under the control of tet operator sequences and a minimal promoter from human cytomegalovirus (tetO-P(hCMV)-Cre). In the absence of a doxycycline inducer, no basal recombination is detectable in the gut of adult tri-transgenic mice containing Fabp-rtTA, tetO-P(hCMV)-Cre, plus a floxed reporter gene. After 4 days of oral administration of doxycycline, recombination of the reporter is apparent in the small intestinal, cecal, and colonic epithelium. After doxycycline is withdrawn, the recombined locus persists for at least 60 days, indicating that recombination has occurred in epithelial cell progenitors that have long residency times in the proliferative units of the intestine (crypts of Lieberkühn). This inducible system should have a number of applications for examining gene function at selected times in postnatal life, under selected physiologic or pathophysiologic conditions.

A comprehensive laboratory-based program for classification of variants of uncertain significance in hereditary cancer genes

Genetic testing has the potential to guide the prevention and treatment of disease in a variety of settings, and recent technical advances have greatly increased our ability to acquire large amounts of genetic data. The interpretation of this data remains challenging, as the clinical significance of genetic variation detected in the laboratory is not always clear. Although regulatory agencies and professional societies provide some guidance regarding the classification, reporting, and long-term follow-up of variants, few protocols for the implementation of these guidelines have been described. Because the primary aim of clinical testing is to provide results to inform medical management, a variant classification program that offers timely, accurate, confident and cost-effective interpretation of variants should be an integral component of the laboratory process. Here we describe the components of our laboratory's current variant classification program (VCP), based on 20 years of experience and over one million samples tested, using the BRCA1/2 genes as a model. Our VCP has lowered the percentage of tests in which one or more BRCA1/2 variants of uncertain significance (VUSs) are detected to 2.1% in the absence of a pathogenic mutation, demonstrating how the coordinated application of resources toward classification and reclassification significantly impacts the clinical utility of testing.

Notes from some crypt watchers: regulation of renewal in the mouse intestinal epithelium

The mouse intestinal epithelium undergoes rapid renewal throughout life, thereby requiring continuous coordination of its cellular proliferation, differentiation, and death programs. Recent advances in our understanding of this process have highlighted some of the molecules that regulate renewal and their potential roles in gut neoplasia.

Genetic mosaic analysis based on Cre recombinase and navigated laser capture microdissection

Defining molecular interactions that occur at the interface between "normal" and "abnormal" cell populations represents an important but often underexplored aspect of the pathogenesis of diseases with focal origins. Here, we illustrate an approach for conducting such analyses based on mosaic patterns of Cre recombinase expression in the adult mouse intestinal epithelium. Transgenic mice were generated that express Cre in the stem cell niche of crypts located in specified regions of their intestine. Some of these mice were engineered to allow for doxycycline-inducible Cre expression. Recombination in all pedigrees was mosaic: Cre-expressing crypts that supported recombination in all of their active multipotent stem cells were located adjacent to "control" crypts that did not express Cre at detectable levels. Cre-mediated recombination of a floxed LacZ reporter provided direct evidence that adult small-intestinal crypts contain more than one active multipotent stem cell, and that these cells can be retained in both small-intestinal and colonic crypts for at least 80 d. A method was developed to recover epithelial cells from crypts with or without recombination for subsequent gene expression profiling. Stained sections of intestine were used to create electronic image templates to guide laser capture microdissection (LCM) of adjacent frozen sections. This navigated form of LCM overcomes problems with mRNA degradation encountered when cells are marked directly by immunohistochemical methods. Combining Cre-engineered genetic mosaic mice with navigated-LCM will allow biology and pathobiology to be explored at the junction between normal and perturbed cellular cohorts.

Loss of the maternal H19 gene induces changes in Igf2 methylation in both cis and trans

Recent investigations have shown that the maintenance of genomic imprinting of the murine insulin-like growth factor 2 (Igf2) gene involves at least two factors: the DNA (cytosine-5-)-methyltransferase activity, which is required to preserve the paternal specific expression of Igf2, and the H19 gene (lying 90 kb downstream of Igf2 gene), which upon inactivation leads to relaxation of the Igf2 imprint. It is not yet clear how these two factors are related to each other in the process of maintenance of Igf2 imprinting and, in particular, whether the latter is acting through cis elements or whether the H19 RNA itself is involved. By using Southern blots and the bisulfite genomic-sequencing technique, we have investigated the allelic methylation patterns (epigenotypes) of the Igf2 gene in two strains of mouse with distinct deletions of the H19 gene. The results show that maternal transmission of H19 gene deletions leads the maternal allele of Igf2 to adopt the epigenotype of the paternal allele and indicate that this phenomenon is influenced directly or indirectly by the H19 gene expression. More importantly, the bisulfite genomic-sequencing allowed us to show that the methylation pattern of the paternal allele of the Igf2 gene is affected in trans by deletions of the active maternal allele of the H19 gene. Selection during development for the appropriate expression of Igf2, dosage-dependent factors that bind to the Igf2 gene, or methylation transfer between the parental alleles could be involved in this trans effect.

Genomic imprinting in mice: its function and mechanism

Genomic imprinting is an epigenetic phenomenon by which the two parental alleles of a gene are differentially expressed. Although the function of genomic imprinting is not clear, it has been proposed that it evolved in mammals to regulate intrauterine growth. This proposal is consistent with experiments that were designed to reveal the mechanism and impact of genomic imprinting in a region of mouse chromosome 7 that contains four imprinted genes: Mash-2 (a transcription factor) and H19 (a noncoding RNA) are maternally expressed, whereas Insulin-2 (Ins-2) and Insulin-like growth factor 2 (Igf-2) are paternally expressed. Two targeted disruptions at the locus were generated in mice; these support the hypothesis that the function of the H19 gene is to set up the imprinting of both Igf-2 and Ins-2. H19 transcription on the maternal chromosome precludes transcription of the other two genes by a mechanism that involves competition for a common set of enhancers. On the paternal chromosome the H19 gene is silenced by DNA methylation, thus permitting the use of enhancers by the other genes.

Monoallelic expression of reactivated imprinted genes in embryonal carcinoma cell hybrids

Though DNA methylation is necessary to maintain monoallelic expression of imprinted genes, it is still unclear whether it represents the primary mark. Here we ask whether the imprinting mark is still present in terminally differentiated somatic cells in which the transcription of embryo-specific imprinted genes was shut off. For such analysis H19 and Igf2 genes were activated by inducing differentiation of (mouse embryonal carcinoma cell x mouse lymphocyte) hybrid cell clones. Although lymphocytes do not express H19 and Igf2, both genes are reactivated in a proper monoallelic manner in hybrid cells. Analysis of the upstream region of the H19 gene confirmed maintenance of differential methylation of the active and inactive H19 genes of lymphocyte origin, although a tendency toward in vitro induced hypermethylation was apparent. We conclude that the imprints of the H19, U2af1-rs1, and Igf2 genes are maintained in lymphocytes in adult mice.

Structure and expression of the mouse L23mrp gene downstream of the imprinted H19 gene: biallelic expression and lack of interaction with the H19 enhancers

The human L23 (mitochondrial)-related protein gene, located 40 kb downstream of the imprinted H19 gene, is biallelically expressed. We have cloned and characterized its mouse homolog, L23mrp, which maps to the conserved syntenic region on mouse chromosome 7. The promoter of L23mrp is a CpG island that is transcribed ubiquitously, but at different levels, in different fetal tissues. Allele-specific expression analysis revealed that both parental alleles are equally active. Since the enhancers located between H19 and L23mrp had been shown to be involved in the imprinted expression of Ins-2, Igf-2, and H19, we asked whether they also influence L23mrp. Analysis of mice with a targeted deletion of the enhancers demonstrated that they were not disrupted in the expression of L23mrp. These findings indicate that L23mrp is functionally insulated from the Ins-2/Igf-2/H19 domain in terms of both imprinting and enhancer action.

Abstract PD7-03: Characterization of Li-Fraumeni syndrome diagnosed using a 25-gene hereditary cancer panel

Background: Clinical diagnostic criteria for Li-Fraumeni syndrome (LFS) have evolved with increased utilization of TP53 germline testing and subsequent improved understanding of the diversity of the associated cancer phenotypes. However, data on LFS still suffer from ascertainment bias as patients are typically selected to undergo TP53 testing based on the presence of hallmark features of LFS. Analyzing TP53 mutation carriers identified from multi-gene panel testing, for which the diagnosis of LFS may not have been suspected or was included in a longer differential diagnosis, affords an opportunity to characterize additional TP53 carriers who might not otherwise have been ascertained.

Methods: Patients with a deleterious or suspected deleterious germline TP53 mutation were identified from 80,748 consecutive cases that underwent a 25-gene hereditary cancer panel test between September 2013 and March 2015 at a commercial diagnostic laboratory. Patient clinical data were obtained by healthcare provider report on test requisition forms. Each TP53 mutation carrier was evaluated to determine whether the National Comprehensive Cancer Network's (NCCN) guidelines were met for TP53 testing.

Results: Eighty-one TP53 mutation carriers were identified and had a total of 115 cancers (0.1% overall prevalence). Among the 76 carriers with at least one cancer, the average age at first diagnosis was 42 years (range 11-76 years) and 24% were first diagnosed older than age 50 years. The most common first cancers were of the breast (n=45), ovary (n=9), and gastrointestinal tract (n=8). Fifty-two of the 75 (69%) women had breast cancer, 44% of which were first diagnosed at 35 years or younger, and 21% were first diagnosed at 50 years or older. Only 27 TP53 carriers met NCCN criteria for TP53 testing, 14 of whom only met based on having early-onset breast cancer. An additional 8 did not meet criteria themselves but had a first- or second-degree relative who did. Among the 28 individuals with more than one primary cancer, 21 (75%) developed their second primary at a site for which increased surveillance is recommended in LFS, but only 4 would have met NCCN criteria for TP53 testing at their first cancer diagnosis. The most common second cancers were of the breast (n=16), gastrointestinal tract (n=4), or kidney (n=2) and occurred an average of 11 years after the first cancer (range 0-36 years).

Conclusion: In this analysis, a large proportion of carriers would not have been identified as TP53 testing candidates based on NCCN guidelines. Our data are consistent with other studies demonstrating high second primary cancer risks in LFS, and highlight the value of multigene panel testing in identifying individuals who may be candidates for increased surveillance and/or cancer risk-reducing management options.

Citation Format: Rich T, Lotito M, Kidd J, Saam J, Lancaster J. Characterization of Li-Fraumeni syndrome diagnosed using a 25-gene hereditary cancer panel. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD7-03.

Abstract P3-10-06: Genetic testing for HBOC among women with a personal diagnosis of breast cancer in patients with Medicaid as compared to patients with private insurance

Introduction: National guidelines recommend that women diagnosed with early-onset breast cancer and/or a strong family history receive BRCA1/2 testing to guide treatment decisions. Among newly diagnosed patients, a positive test result will often prompt more aggressive surgical treatment to minimize the risk of second primary cancers. Currently, coverage for genetic counseling and testing for Hereditary Breast and Ovarian Cancer (HBOC) under the Medicaid expansion program of the Affordable Care Act has varied by state, where some states require a copayment for this service. Similarly, there is no mandate to cover risk-reducing surgery for patients found to carry a genetic mutation despite research showing cost-effectiveness. This analysis sought to determine whether genetic testing for HBOC among patients with breast cancer is different for those with Medicaid compared to those with private insurance.

Methods: A commercial laboratory database was analyzed for patients with a personal history of breast cancer who underwent testing with a 25-gene hereditary cancer panel from September 2013-February 2016. Patients were eligible for inclusion if they were between ages 18 and 64 at the time of testing and had not undergone previous genetic testing. A total of 17,020 patients with either Medicaid (N=4,313) or one of 5 private payers (N=12,707) were tested during this period. Descriptive statistics, including means for continuous variables and proportions for categorical variables, were calculated. Chi-square tests were used to test associations and differences of positive rates between insurance provider category. Two-tailed p-values are reported, and any p-value less than 0.05 is considered statistically significant.

Results: Medicaid patients had a median age of breast cancer diagnosis of 45 compared to 47 for patient with private insurance. Among women with Medicaid insurance, a higher proportion were of African (13.3% vs 6.4%) and Latin American ancestry (16.4% vs 5.3%). The mutation positive rate among patients with Medicaid was 13.0%, which was statistically higher than patients with private insurance (9.5%) (p<0.001). The positive rate was higher among Medicaid patients of all ancestries suggesting that this discrepancy was not due to ancestry difference among the two testing populations.

Positive rate by ancestry MedicaidPrivateOverallAfrican80 (13.9%)72 (8.9%)152 (11.0%)Ashkenazi3 (17.6%)20 (15.3%)23 (15.5%)Asian26 (13.3%)40 (7.5%)66 (9.1%)Caucasian201 (12.9%)171 (9.9%)918 (10.4%)Latin American/Caribbean98 (13.8%)65 (9.6%)163 (11.8%)Native American7 (13.7%)9 (7.9%)16 (9.7%)Neareast/Mideast10 (17.9%)8 (9.3%)18 (12.7%)Multiple49 (12.3%)77 (9.0%)126 (10.0%)None Specified85 (11.3%)199 (8.8%)284 (9.4%)Total559 (13.0%)1207 (9.5%)1766 (10.4%)

Conclusions: Overall, the positive mutation rate among individuals with Medicaid insurance was higher than those with private insurance, suggesting the testing requirements applied to this population may be more stringent than those applied to the private insurance population. Consistent genetic testing insurance criteria are necessary for all patients to receive care in line with guidelines following a breast cancer diagnosis.

Citation Format: Baron P, Johnson-Isidore K, Miller L, Brown K, Kidd J, Saam J, Lancaster J. Genetic testing for HBOC among women with a personal diagnosis of breast cancer in patients with Medicaid as compared to patients with private insurance [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-10-06.

Abstract P1-10-01: Defining the spectrum of germline variants among African American patients with triple negative breast cancer

Background: African American (AA) women are more likely to have breast cancer at a younger age and be diagnosed with triple negative breast cancer (TNBC), which is as yet unexplained. We examined results of multi-gene panel testing in AA women with TNBC tested at a large commercial laboratory to assess the utility of gene panels and findings in this group.

Methods: We assessed individuals who had clinical hereditary cancer testing with a multi-gene panel between September 2013 and May 2018. Women were included for analysis if they had a personal history of TNBC and self-identified as having any AA ancestry (n=3,268) or only Caucasian (CA) ancestry (n=8,953). Clinical data was collected from provider-completed test request forms. Comparisons were performed using descriptive statistics, t-tests (continuous variables), and chi-square tests (categorical variables) adjusting for multiple testing when necessary.

Results: In this cohort, AA women were significantly more likely than CA women to meet NCCN guidelines (97.5% vs. 96.6%, p=0.010) and significantly less likely to have an additional personal (16.2% vs. 21.8%, p<0.001) or family (79.3% vs. 86.3%, p<0.001) history of cancer. Overall, 11.5% of AA women were found to carry a pathogenic variant (PV) compared to 13.4% of CA women (p=0.004; Table 1). Compared to CA women, AA women with a PV were significantly younger at diagnosis (46.7 vs. 49.5 years of age; p<0.001). The prevalence of PVs in BRCA1, CHEK2 and the Lynch syndrome genes was higher in CA women, whereas the prevalence of BRCA2 PVs was higher in AA women. While the prevalence of PVs in individual genes was not significantly different according to ancestry after adjusting for multiple comparisons, AA women were significantly less likely to have a PV in any breast cancer-related gene compared to CA women (p=0.048). AA women were significantly more likely to have a Variant of Uncertain Significance (VUS; 35.6% vs. 20.9%; p<0.001) and to have >1 VUS (8.6% vs. 2.6%, p<0.001). Regardless of ancestry, patients diagnosed before age 40 were more likely to carry a PV (19.7% AA, 22.2% CA). However, the prevalence of PVs among patients diagnosed after age 60 was still striking (8.9% AA, 10.9% CA) and was similar to the PV prevalence among patients diagnosed between 40-60 (10.1% AA, 12.3% CA).

Conclusions: In the era of multi-gene panel testing, this large cohort of patients with TNBC supports the use of panel testing in AA women with TNBC regardless of age or additional personal/family history of cancer. While additional research to the rate and pathogenicity of VUS in AA women is needed, genetic counseling is necessary to explain the possibility and meaning of a VUS in this group.

Table 1.Distribution of PVs in BC-related genes according to ancestry AA WomenCA WomenGeneN (%)N (%)Any Breast Cancer-Related Gene347 (10.6)1104 (12.3)BRCA1132 (4.0)496 (5.5)BRCA297 (3.0)236 (2.6)ATM6 (0.2)25 (0.3)BARD119 (0.6)67 (0.7)BRIP120 (0.6)46 (0.5)CDH11 (<0.1)1 (<0.1)CHEK22 (0.1)33 (0.4)NBN2 (0.1)10 (0.1)PALB244 (1.3)138 (1.5)PTEN2 (0.1)4 (<0.1)RAD51C20 (0.6)41 (0.5)STK1101 (<0.1)TP532 (0.1)6 (0.1)Lynch Syndrome Genes10 (0.3)46 (0.5)Other Genes12 (0.4)24 (0.3)Multiple PVs6 (0.2)28 (0.3)Total (Any Gene)375 (11.5)1202 (13.4)

Citation Format: Pederson HJ, Heald B, Budd GT, Bernhisel R, Cummings S, Saam JR, Lancaster JM, Grobmyer SR, Eng C. Defining the spectrum of germline variants among African American patients with triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-10-01.

Modeling 5-FU AUC-dose relationship to develop a PK dosing algorithm

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Background: 5-fluorouracil (5-FU) is an ideal candidate for pharmacokinetic (PK) dosing. 5-FU is administered based on standard BSA dosing. BSA administration results in highly variable PK and exposure, and potential underdosing in about 50% of patients. Patients with higher 5-FU AUC levels derive greater clinical benefit but with increased risk of toxicity. An immunoassay (OnDose) that measures 5-FU concentration in plasma and reports a computed AUC in mg·h/L has been developed to aid optimization of therapy using PK dosing. The results of an analysis to model the 5-FU AUC-dose change relationship from our clinical database are presented.

Methods: A set of 585 sequential patients from our database receiving FOLFOX6 regimen with 5-FU continuous infusion (CI) over 41-48 hours, with or without bevacizumab, for the adjuvant and metastatic treatment of CRC was used for the preliminary analyses. A subset restricted to include only patients that had at least two consecutive cycles tested, received 1,600-3,600 mg/m2 at the initial test cycle, and had blood sample collection times ≥ 18 hours was used to conduct regression modeling of change in AUC versus change in dose. Outliers such as AUC values < 5 mg·h/L and > 50 mg·h/L were excluded from the analysis.

Results: Our analysis corroborates previous findings that large variability in 5-FU PK measurements exists during the early part of the infusion cycle. The following simple regression model with an R2=0.51 developed over N=307 cycle-pair observations characterizes the AUC-dose relationship as: change in AUC (mg·h/L) = 0.02063 * dose change (mg/m2).

Conclusions: The above model suggests that dose changes ranging from 145 to 720 mg/m2 would be sufficient to adjust the AUC to a potential therapeutic threshold of >20 mg·h/L for most patients. Assuming a 2,400 mg/m2 baseline dose, a maximum 720 mg/m2 dose increase would correspond to a 30% increase, but would likely be needed only by 10% of the patient population with low AUC readings. Our data from the US clinical setting indicate that it is possible to optimize 5-FU therapy by adjusting the dose based on AUC measurement.

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