Racial Disparities in Family Variant Testing for Cancer Predisposition Genes

PURPOSE

Despite the substantial clinical impact of genetic testing, racial disparities exist in the delivery of this service. Here, we partnered with a commercial laboratory (Invitae) to establish whether there are racial disparities in the uptake of family variant testing (FVT). We also investigated if providing FVT at no cost impacts rates of cascade testing in Black and White families.

METHODS

This is a retrospective analysis comparing rates of FVT in self-reporting Black probands to self-reporting White probands who underwent germline genetic testing for genes associated with hereditary cancer through Invitae. All Black and White patients found to have a pathogenic/likely pathogenic variant P/LPV) in a hereditary cancer syndrome gene were identified up to one year before and up to one year after FVT became no-charge in 1/2017. The proportion of probands with at least one at- risk family member who underwent FVT was compared between Black and White probands using logistic regression, including the interaction between covariates of cost and race.

RESULTS

Between 1/2016 and 1/2018, 8,530 Black and 87,846 White probands underwent genetic testing. Of these, 9.3% (n =791) Black probands and 11.4% (n=9,998) White probands had a P/LPV identified. The uptake of FVT, defined by percentage of positive probands with at least one family member undergoing testing, was significantly lower in Black participants compared to White participants (11.9% versus 21.7%, odds ratio 0.5, 95% CI 0.4-0.6, p<0.001). Period of testing before or after FVT was no-charge did not impact this difference (p=0.23 for the interaction). FVT rates were significantly lower in Black patients compared to White patients both before (8.1% versus 18.7%, OR 0.4, 95% CI 0.2-0.6, p<0.001) and after (13.6% versus 23.1%, OR 0.5, 95% CI 0.4-0.7, p<0.001) testing became no-charge.

CONCLUSION

While FVT rates were low overall, they were significantly lower in Black families compared to White families. Cost of FVT did not have a significant impact on the racial disparity seen, suggesting additional barriers exist. Recognizing these disparities and determining the contributing factors are crucial to developing tailored interventions that would ultimately advance racial equity in cancer care.

Abstract PD01-08: Decoding the Transcriptional Landscape of Triple-Negative Breast Cancer Using Next-Generation Whole Transcriptome Sequencing

Background: Triple-negative breast cancer (TNBC) has been plagued by the absence of targeted therapies. Discovery of therapeutic targets in TNBC has in part, been hampered by an inadequate understanding of the transcriptional biology of the normal breast as an optimal comparator. Using next-generation sequencing, we embarked on a study to compare the transcriptomes of TNBC and normal breast to comprehensively identify novel targets by analyzing all full length transcripts expressed in these tissues.

Methods: Normal breast tissues from healthy pre-menopausal volunteers with no history of disease were procured from the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center. To eliminate bias from stromal tissue, normal tissues were laser capture microdissected for ductal epithelium. cDNA libraries from 10 TNBC tumors and 10 normal breast tissues were sequenced on an Applied Biosystems (AB) SOLiD3 sequencer using 50bp fragment runs. For gene expression, mapping of reads to the genome was performed using the AB BioScope 1.2 Pipeline and outputs imported into Partek Genomics Suite for analysis. In Partek, mapped reads were cross-referenced against known genes from the UCSC database followed by statistical comparison of RPKM values for each gene between TNBC and normal. Dimensionality reduction analyses (PCA & Hierarchical clustering) and identification of Novel Transcribed Regions were also performed in Partek, whereas construction of gene networks was performed using Ingenuity Pathway Analysis. To identify gene fusions, partially mapped reads were interrogated utilizing a novel algorithm that searched for reads spanning exons from two different genes. Fusions that were supported by at least 3 reads (of which 2 had to be unique) were considered candidates and were subsequently validated. Results/Discussion: Sequencing produced 1.1 billion reads equaling 57.3GB of data of which 36.0GB (63%) mapped to the human genome. In comparing RPKM values between TNBC and Normal, we report 7140 RefSeq Genes, 22 pre-miRNAs, 109 lincRNA exons, and 15 ultraconserved regions that were differentially expressed between these tissues (FDR&lt;0.01). Biological interpretation of these results reveals upregulation of genes and miRNAs involved in DNA repair, angiogenesis, and inhibitors of Estrogen Receptor-alpha. Some previous drug targets (e.g. EGFR and c-kit) were not found to be upregulated here which may explain lack of clinical success to date. Conversely, PARP was significantly upregulated and early trial results suggest a strong signal for efficacy with inhibition of PARP. We also surveyed the genome for Novel Transcribed Regions (NTRs), defined as areas of significant transcription where no annotated gene is present. When comparing between TNBC and Normal, we report 6408 NTRs to be differentially expressed (FDR&lt;0.01). Lastly, when analyzing the dataset for gene fusions, we identified several gene fusions in the TNBC samples, though no individual fusion was present in more than one sample.

Conclusion: We report an extensive comparison of the transcriptomes of TNBC and normal ductal epithelium. We identified numerous genes previously unknown to be dysregulated in TNBC that can be utilized for therapeutic discovery.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD01-08.

Resequencing of the Vascular Endothelial Growth Factor Promoter Reveals Haplotype Structure and Functional Diversity

Our group has previously reported that SNPs in the VEGF promoter are strongly associated with efficacy and toxicity to the anti-VEGF antibody bevacizumab in metastatic breast cancer. In order to better understand the biologic mechanism for our previously reported biomarkers, we embarked on a comprehensive evaluation of the genetic variation in the VEGF promoter coupled with a study of its intrinsic function. By resequencing 96 DNA samples (48 Caucasians, 48 African-Americans) for the VEGF promoter, we elucidated its complete haplotype structure and identified SNPs that were not previously reported in prior resequencing efforts. SNPs that were identified included twenty previously reported SNPs/insertions/deletions, one novel SNP, and one novel deletion. Among these variants, we identified five SNPs (VEGF-3818G/T, -2305G/T, -1210C/A, -1154G/A, & -7C/T) that tag six haplotypes capturing 74% of the genetic variation of the VEGF promoter. Subsequently, we cloned the six major haplotypes into reporter constructs in order to determine the effect of genetic variation on function. The reporter assays were performed in 5 breast cancer cell lines representing all ER and HER-2 statuses along with an inflammatory breast cancer cell line. We demonstrate that there is significant variation in promoter-induced expression among the haplotypes. More importantly, we show that the haplotypes containing the SNPs previously reported to be associated with increased survival with the use of bevacizumab are high-expressing haplotypes, thus lending putative functional evidence to the prior clinical finding. Further, we also report the presence of a low-expressing haplotype predominantly in African-Americans. Altogether, these results set the foundation for future studies elucidating the role of VEGF genetic variation with response to anti-angiogenic therapy and associations with angiogenesis-related diseases.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2122.

Antitumor activity of a new cholesterol derivative (24-ethyl-cholestane- 3β, 5α,6α-triol) in solid tumors

e13541

Oxysterols are oxygenated derivatives of cholesterol. They have nuclear receptors and have been shown to pass cell membranes and the blood-brain barrier at a faster rate than cholesterol itself. In addition, oxysterols have been ascribed a number of important roles in connection with cholesterol turnover, atherosclerosis, apoptosis, and necrosis. Oxysterols have been shown to have antitumor effects on experimental models. These compounds however may be toxic and to our knowledge, although some derivatives have been tested in animals, none have reached the clinical level. 24-ethyl-cholestane- 3β,5α,6α-triol is a new oxysterol developed in our lab. An oral form of this compound has been tested in mice and rats and has shown neither acute nor chronic toxicity. It has also been tested on animal tumor models and on human cancer xenografts. The results of these tests were very promising showing an anti-tumor activity on a panel of tumor cell lines. Our experiments on humans have shown no toxicity for this drug. Many patients with a variety of solid tumors all of whom have received many lines of chemotherapy and considered refractory to any conventional therapy have received this new drug. We observed in most of these patients a rapid and dramatic improvement in their quality of life and a fast pain control. Some patients could stop taking high doses of opioids within 1 or 2 days. A high rate of clinical benefit has also been observed in a variety of solid tumors including lung, breast, pancreatic, ovarian and uterine cancers, associated in some cases with a sharp decrease in tumor markers. Some patients with brain tumors (glioblastomas) have also responded to this therapy.

No significant financial relationships to disclose.

Clinical trial: dextofisopam in the treatment of patients with diarrhoea-predominant or alternating irritable bowel syndrome

BACKGROUND

Dextofisopam modulates stimulated activity in animal models of stress, altered bowel motility, and visceral hypersensitivity.

AIM

To evaluate the effects of dextofisopam in men and women with diarrhoea-predominant or alternating irritable bowel syndrome (IBS) (d-IBS or a-IBS).

METHODS

In this double-blind, placebo-controlled study, patients were randomly assigned to receive dextofisopam 200 mg b.d. or placebo for 12 weeks. The prospectively defined primary endpoint was number of months of adequate overall relief of IBS symptoms. Bowel function was assessed primarily via stool frequency and consistency.

RESULTS

Of 140 enrolled patients, 66 received dextofisopam and 74 placebo; 73% of the patients were women, and 78% had d-IBS. Dextofisopam was superior to placebo on the primary endpoint (P = 0.033). In d-IBS patients treated with dextofisopam, both men and women had improved stool consistency, but stool frequency was reduced only in women. Benefit diminished over time on the primary endpoint, but persisted on frequency and consistency. Dextofisopam and placebo had similar rates and types of adverse events, with more events of worsening abdominal pain with dextofisopam (12% vs. 4%) and more headaches with placebo (12% vs. 5%). Constipation was rare.

CONCLUSION

Dextofisopam should be further evaluated as a new treatment for men and women with d-IBS and a-IBS.

Long-term follow-up of premature infants treated with prophylactic, intratracheal recombinant human CuZn superoxide dismutase

OBJECTIVE

To examine the long-term effects of treatment with recombinant human CuZn superoxide dismutase (rhSOD) in infants enrolled previously in two placebo-controlled trials.

STUDY DESIGN

Records for 46 (88%) infants were examined, with 19 infants having received either single or multiple intratracheal (i.t.) doses of placebo, 12 having received a single i.t. dose of rhSOD, and 15 having received multiple i.t. doses of rhSOD. Mean age at follow-up was 28 months corrected age. Records were examined for neurologic dysfunction, developmental delay, and any significant medical disorders.

RESULTS

Four placebo infants (21%) had evidence of neurodevelopmental abnormalities and four infants developed asthma. Four single-dose rhSOD infants (33%) had neurodevelopmental abnormalities and two infants developed asthma. One multiple-dose rhSOD infant had evidence of neurodevelopmental abnormalities and one developed asthma. No other differences were found between the placebo and rhSOD groups.

CONCLUSION

Preliminary data suggest that rhSOD is safe and not associated with any long-term adverse effects. Further results will depend on the results of multicenter trials of rhSOD in preterm infants.

Intrathecal administration of recombinant human superoxide dismutase 1 in amyotrophic lateral sclerosis: a preliminary safety and pharmacokinetic study

We undertook a safety and pharmacokinetic study of intrathecal (i.t.) recombinant human superoxide dismutase (rhSOD1). We administered rhSOD1 as an acute bolus in three sheep and 16 human subjects with amyotrophic lateral sclerosis (ALS). Two sheep received chronic i.t. infusion of rhSOD1 (one at 17.7 mg per day, the second at 38.0 mg per day) for six months. Two of the 16 subjects had familial ALS and mutations in the gene for Cu/Zn SOD1. They both received i.t. infusion of rhSOD1 (5 to 10 mg per day) for 3 to 6 months. Intrathecal rhSOD1 administration was safe. Bolus i.t. administration of 0.25 mg rhSOD1 in sheep revealed a mean elimination half-life of 0.4 (SD +/- 0.06) hours, clearance of 12.2 +/- 3.2 ml per hour, and volume of distribution of 7.3 +/- 0.9 ml. After chronic i.t. infusion, the initial alpha-phase half-life was estimated as 1.2 hours and the extended beta-phase half-life was 15.0 hours. The mean clearance rate was 25.9 ml per hour and the steady-state volume of distribution was 920.6 ml. Bolus i.t. administration of 20 micrograms of rhSOD1 in ALS subjects revealed a mean elimination half-life of 2.2 +/- 0.8 hours, clearance of 1.2 +/- 0.6 ml per hour, and volume of distribution of 3.5 +/- 0.4 ml. With chronic i.t. infusion of 5 mg per day, cerebrospinal SOD1 levels increased approximately fortyfold. We detected no benefit of this treatment in the two patients with familial ALS.

Safety and pharmacokinetics of multiple doses of recombinant human CuZn superoxide dismutase administered intratracheally to premature neonates with respiratory distress syndrome

OBJECTIVES

To examine the safety and pharmacokinetics of multiple intratracheal (IT) doses of recombinant human CuZn superoxide dismutase (rhSOD) in premature infants with respiratory distress syndrome who are at risk for developing bronchopulmonary dysplasia (BPD). Methods. Thirty-three infants (700 to 1300 g) were randomized and blindly received saline, 2.5 mg/kg or 5 mg/kg rhSOD IT within 2 hours of surfactant administration. Infants were treated every 48 hours (as long as endotracheal intubation was required) up to 7 doses. Serial blood and urine studies, chest radiographs, neurosonograms, SOD concentration and activity measurements, and tracheal aspirate (TA) inflammatory markers were assessed throughout the 28-day study.

RESULTS

SOD concentrations in serum (0.1 [0.05/0.15] microg/mL-geometric mean with lower/upper confidence intervals), tracheal aspirates (TA) (0.2 [0.1/0.3] microg/mL) and urine (0.3 [0.2/0.4] microg/mL) were similar at baseline in all 3 groups and did not change significantly in the placebo group. In the rhSOD treatment groups, SOD concentrations were increased on day 3 and did not change significantly thereafter over the 14-day dosing period (also measured on days 5, 7, and 13). SOD concentrations averaged 0.4 [0.3/0.5] microg/mL in serum, 0.8 [0.6/1.2] microg/mL in TA and 1.1 [1.0/1.3] microg/mL in urine for the low-dose group and 0.6 [0.5/0.7] microg/mL in serum, 1.1 [0.9/1.5] microg/mL in TA, and 2.2 [1.6/2.9] microg/mL in urine for the high-dose group over the 14-day dosing period. Enzyme activity directly correlated with SOD concentration and rhSOD was active even when excreted in urine. TA markers of acute lung injury (neutrophil chemotactic activity, albumin concentration) were lower in the rhSOD agroups compared with placebo. No significant differences in any clinical outcome variable were noted between groups.

CONCLUSIONS

These data indicate that multiple IT doses of rhSOD increase the concentration and activity of the enzyme in serum, TA and urine, reduce TA lung injury markers and are well-tolerated. Further clinical trials examining the efficacy of rhSOD in the prevention of BPD are warranted.

Safety and pharmacokinetics of recombinant human superoxide dismutase administered intratracheally to premature neonates with respiratory distress syndrome

OBJECTIVE

As a first step in the evaluation of recombinant human CuZn superoxide dismutase (rhSOD) in the prevention of neonatal lung injury, safety and pharmacokinetics of intratracheally (IT) administered rhSOD were studied.

METHODS

Twenty-six preterm infants weighing 750 to 1250 g with respiratory distress syndrome were studied in three sequential groups (placebo, 0.5, and 5 mg/kg). Placebo or rhSOD was administered IT 30 minutes after the first surfactant dose. Serial blood and urine studies, rhSOD levels, tracheal aspirate fluid (TAF) markers of acute inflammation, radiographs, and ultrasounds were performed over the 28-day study period.

RESULTS

Serum SOD concentrations were similar at baseline for all three groups (geometric mean 0.2, upper-lower limit 0.1 to 0.2 microgram/mL). In the 0.5-mg/kg group, levels were highest at 12 hours (geometric mean 0.7, upper-lower limit 0.5 to 0.8 microgram/mL) and returned to baseline by day 3. In the 5-mg/kg group, levels were highest at 6 hours (geometric mean 3.0, upper-lower limit 2.3 to 4.0 micrograms/mL) and returned to baseline by day 4. Concentrations of SOD in TAF were also similar at baseline for all three groups (geometric mean 0.2, upper-lower limit 0.2 to 0.3 microgram/mL). There were no significant increases in the placebo group, but levels in the 0.5-mg/kg group were highest when first sampled at 24 hours (geometric mean 1.1, upper-lower limit 0.8 to 1.4 micrograms/mL) and returned to baseline by day 3. In the 5-mg/kg group, levels were also highest when sampled at 24 hours (geometric mean 1.4, upper-lower limit 0.9 to 2.1 micrograms/mL) and returned to baseline by day 4. Urine levels were highest at 12 hours in both the 0.5-mg/kg (geometric mean 1.3, upper-lower limit 1.0 to 1.7 micrograms/mL) and 5-mg/kg infants (geometric mean 6.4, upper-lower limit 3.9 to 10.4 micrograms/mL) and decreased significantly by day 2 to 3. rhSOD activity assays (serum, TAF, and urine) demonstrated that the enzyme still possessed significant activity. No adverse effects of rhSOD were found. TAF neutrophil chemotactic activity and albumin concentrations, important acute lung injury markers, were significantly lower in the high-dose rhSOD group compared with the other groups.

CONCLUSIONS

Data suggest that a single IT dose of rhSOD results in significant increases in both concentration and activity of the antioxidant in serum, TAF, and urine for 2 to 3 days. The enzyme appears to be well tolerated, and TAF inflammatory markers are reduced after administration. This has important implications in rhSOD trials to prevent acute and chronic lung injury in preterm neonates.

A clinically relevant modification to existing inhaler therapy

A modified formulation of inhaled salbutamol and a new inhaler device were studied in a group of 11 moderate-to-severe asthmatic patients. Changes in airway calibre (FEV1, Vmax30) were measured before and after inhalation of the new formulation, and compared with changes following inhalation of conventional salbutamol. A standard Rotahaler was used as a reference for the new inhaler. The study was conducted as a two-part randomized, double-blind cross-over trial. We found a significantly greater bronchodilatation of the larger airways using the modified drug in the Rotahaler. The new inhaler did not show any superiority over the Rotahaler, contrary to expectations from in vitro work. A slightly shorter model may better reflect the in vitro results. The study has implications for inhalation therapy in general.

Effects of loratadine (SCH 29851) in suppression of histamine-induced skin wheals

The efficacy and safety of single oral doses (10, 20, 40, and 80 mg) of loratadine (SCH 29851) in suppressing formation of histamine-induced wheals were assessed in a crossover study in 29 healthy male subjects. One hour prior to dosing and 1, 2, 3, 4, 6, 8, 12, 16, 24, 28, 32, 36, 40, and 48 hours after dosing, histamine and saline were injected intradermally into opposite arms. Measurements of resulting wheal areas showed loratadine suppressed wheal formation significantly better than placebo; suppression was dose related. The mean suppression over 48 hours was 16% in placebo-treated subjects and 35%, 45%, 51%, and 67% in the 10, 20, 40, and 80 mg loratadine-treated subjects, respectively. The onset of action occurred within the first hour. Duration of suppression was dose related, ranging from 12 hours with the lowest dose (10 mg) to 48 hours with the higher doses (40 and 80 mg). Incidence of sedation and other side effects were comparable among all doses of loratadine and placebo.

Suppression of histamine-induced wheal response by loratadine (SCH 29851) over 28 days in man

Five groups of 12 healthy volunteers each received in double-blind, randomized fashion oral b.i.d. doses of 10, 20, or 40 mg loratadine, 12 mg chlorpheniramine maleate (CTM), or placebo for 28 days. Histamine and saline were injected intradermally into opposite arms at baseline and at specified times following treatment on days 1, 3, 7, 14, 21, and 28. Notable suppression of adjusted wheal formation (histamine-induced minus saline-induced) occurred within two hours after the first dose of each active treatment on day 1. In general, throughout the treatment period, suppression of adjusted wheal formation by all doses of loratadine was significantly greater than by placebo. Suppression by 10 mg loratadine was comparable to CTM, and 20 and 40 mg loratadine were significantly greater than CTM. Suppression of wheal formation by loratadine during the treatment period and during five days posttreatment were dose related. The continued effectiveness of loratadine throughout the 28 days suggests that tolerance to loratadine did not develop in this study. Sedation occurred in 8 of 12 subjects receiving CTM, 1 of 12 receiving 10 mg loratadine, and 1 of 12 receiving placebo.

Pharmacodynamics of intravenous labetalol and follow-up therapy with oral labetalol

The effectiveness, safety, and pharmacodynamics of repeated doses of intravenous labetalol for rapid reduction of severe hypertension and of subsequent oral labetalol dosing were studied. Twelve patients with severe hypertension were admitted to the hospital after the withholding of antihypertensive therapy for 2 to 14 days. Thirty minutes after an injection of vehicle only, labetalol, 0.25 mg/kg body weight, was injected and followed by repeat injections of 0.5 mg/kg every 15 minutes until the supine diastolic blood pressure (BP) was reduced to less than 90 mm Hg or a total of 3.25 mg/kg had been administered. Twenty-four hours after the last injection, oral labetalol was started at an initial dosage of 100 or 200 mg b.i.d., then increased every 2 days until the standing diastolic BP was less than 90 mm Hg or a maximum daily dosage of 2400 mg was reached. The initial injection achieved mean falls in supine systolic/diastolic BPs of 11/7 mm Hg. Subsequent injections produced additional falls in a dose-related fashion; the mean falls after the last injection (total cumulative dose 2.7 mg/kg) were 40/20 mm Hg. The effect lasted for 12 hours or more in most patients and tended to be biphasic, with one peak at approximately 5 minutes and another much less pronounced peak at about 4 hours. There was no evidence of precipitous falls in BP. All patients were able to ambulate 6 hours after the last injection without symptoms of postural hypotension. Oral labetalol effectively and safely restored and maintained the BP reductions achieved with intravenous labetalol.