Abstract P3-04-02: Molecular analysis of breast cancers from individuals with hereditary cancer syndromes secondary to mutations in BRCA1, BRCA2, ATM, CHEK2, and PALB2

Background: Despite a growing understanding of the somatic landscape of breast tumors from BRCA1 and BRCA2 mutation carriers, less is known about breast tumors from carriers of germline mutations in other homologous recombination and DNA repair pathway genes such as ATM, CHEK2, and PALB2.

Methods: We identified 44 clinically annotated breast cancer cases that included carriers of germline mutations in BRCA1 (n=9), BRCA2 (n=9), ATM (n=5), CHEK2 (n=7), and PALB2 (n=6) from the Hereditary Cancer Risk Program at BUMC. Sporadic breast cancers cases (n=8) were also collected. Genomic DNA and RNA were extracted from macro-dissected FFPE tumor sections, adjacent normal FFPE tissue, along with constitutional genomic DNA from blood. Expanded whole exome sequencing (WES) was performed on normal/tumor pairs and RNA-seq from tumors for each case. Bioinformatics analysis was performed using industry standard methods for somatic characterization.

Results: All germline mutations were confirmed by WES. Somatic mutational analysis and copy number profiling from WES revealed the greatest similarities among BRCA1 and CHEK2 carriers. As expected, TP53 mutations were found in 8 of 9 BRCA1 carriers as all were triple negative subtype. We also detected somatic TP53 mutations in tumors from 4 of 7 CHEK2 carriers. Somatic TP53 mutations were found in only 1 of 7 BRCA2 tumors and 1 of 4 PALB2 tumors tested. Furthermore, BRCA1 and CHEK2 tumors showed trends of having higher mutation burden. Analysis of copy number BRCAness demonstrated stronger similarities between BRCA1, ATM, CHEK2, and PALB2 tumors. BRCA2 tumors were unique with fewer events and characterized by specific amplifications including 11q23 (CCND1) and 17q23 (BRIP1). Hierarchical clustering of RNA-seq data revealed strong clustering of BRCA1 tumors compared to all other tumors, predominantly attributed to breast cancer subtype. Furthermore, pathway analysis of genes that distinguish BRCA1 mutation positive versus non-BRCA mutated tumors showed strong correlation to pro-inflammatory and immune pathway signatures.

Conclusions: Molecular analysis of 44 breast cancers from individuals with inherited predisposition to breast cancer via BRCA1, BRCA2, ATM, CHEK2, and PALB2 germline mutations demonstrated strongest somatic similarities between BRCA1 and CHEK2 tumors although all BRCA1 were TNBC and all CHEK2 tumors were ER positive. Marked differential gene expression differences in RNA expression patterns were observed in BRCA1 mutation carriers compared with all other groups analyzed. Our study is among the first to interrogate the profile of non-BRCA mutated hereditary breast cancers.

Citation Format: Blum JL, Wong S, Pearson EJ, Nair A, Snipes GJ, Briones N, Baker A, Cropp CD, Carpten JD. Molecular analysis of breast cancers from individuals with hereditary cancer syndromes secondary to mutations in BRCA1, BRCA2, ATM, CHEK2, and PALB2 [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-04-02.

Isolation of bacteriophages from air using vacuum filtration technique: an improved and novel method

AIM

Development of a simple and economical air sampler for isolation and enrichment of bacteriophages from air samples.

METHODS AND RESULTS

A vacuum filtration unit with simple modifications was used for isolation of bacteriophages from air sampled in the lavatory. Air was sampled at the rate of 62 l min^-1 by bubbling into Mcllvaine buffer for 30 min, which was used as bacteriophage solution for enrichment and plaque assessment against individual hosts. Alternatively, the aforementioned phage solution was enriched using a host consortium before plaque assessment. Phages were isolated in the range of 1-12 PFU per ml by the first method, whereas enrichment with host consortium gave phages around 10- to 1000-folds higher in number. Combining with established enrichment method, an improvement of about 10 times in phage isolation efficiency was attained.

CONCLUSIONS

The method is very useful for studying the natural bacteriophages of air, requiring only a basic microbiological laboratory setup making it simple and economical.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study brings out a simple, economical air sampler for assessing air bacteriophages that can be employed by any microbial laboratory. Although various methods are available for studying bacteriophages in water and soil, very limited are available for air. To the best of our knowledge, the method developed in this study is unique in its design and concept for studying bacteriophages in air. The sampler is sterilizable by autoclaving and maintains a healthy rate of airflow provided by conventional vacuum pumps. The use of a nonspecific 'trapping solution' allows for the qualitative and quantitative study of air bacteriophages.

The influence of inspiratory effort and emphysema on pulmonary nodule volumetry reproducibility

AIM

To evaluate the impact of inspiratory effort and emphysema on reproducibility of pulmonary nodule volumetry.

MATERIALS AND METHODS

Eighty-eight nodules in 24 patients with emphysema were studied retrospectively. All patients had undergone volumetric inspiratory and end-expiratory thoracic computed tomography (CT) for consideration of bronchoscopic lung volume reduction. Inspiratory and expiratory nodule volumes were measured using commercially available software. Local emphysema extent was established by analysing a segmentation area extended circumferentially around each nodule (quantified as percent of lung with density of -950 HU or less). Lung volumes were established using the same software. Differences in inspiratory and expiratory nodule volumes were illustrated using the Bland-Altman test. The influences of percentage reduction in lung volume at expiration, local emphysema extent, and nodule size on nodule volume variability were tested with multiple linear regression.

RESULTS

The majority of nodules (59/88 [67%]) showed an increased volume at expiration. Mean difference in nodule volume between expiration and inspiration was +7.5% (95% confidence interval: -24.1, 39.1%). No relationships were demonstrated between nodule volume variability and emphysema extent, degree of expiration, or nodule size.

CONCLUSION

Expiration causes a modest increase in volumetry-derived nodule volumes; however, the effect is unpredictable. Local emphysema extent had no significant effect on volume variability in the present cohort.

Chronic Colovesical Fistula Leading to Chronic Urinary Tract Infection Resulting in End-Stage Renal Disease in a Chronic Granulomatous Disease Patient

A 46-year old man with X-linked chronic granulomatous disease (CGD) being followed at the National Institute of Health with uncontrolled CGD colitis who developed chronic colovesical fistula, and end-stage renal disease (ESRD). Despite aggressive medical management of symptoms with immunomodulators and antibiotic prophylaxis, the chronic colovesical fistula led to chronic pyelonephritis, recurrent urinary tract infections, persistent air in the collecting system and bladder, and post-renal obstruction resulting in renal failure. Patient is now hemodialysis dependent and required diverting loop ileostomy placement. This report highlights multiple potential etiologies of rising serum creatinine in patients with CGD.

Membrane filtration immobilization technique-a simple and novel method for primary isolation and enrichment of bacteriophages

AIM

To develop a method for the isolation and enrichment of bacteriophages selectively against specific bacteria coupled with a membrane filtration technique.

METHODS AND RESULTS

Rapid isolation and concentration of host-specific bacteriophages was achieved by exposure of the sample suspected to contain bacteriophages to a specific host immobilized on a 0·45 μm membrane in a membrane filtration unit. The principle behind this method is the exploitation of host-specific interaction of bacteriophages with their host and maximizing this interaction using a classic membrane filtration method. This provides a chance for each bacteriophage in the sample to interact with the specific host on the membrane filter fitted with a vacuum pump. Specific bacteriophages of the host are retained on the membrane along with its host cells due to the effect of adsorption and these adsorbed bacteriophages (along with their hosts) on the filter disc are then amplified and enriched in regular nutritive broth tryptose soya broth by incubation. With the help of the plaque assay method, host-specific phages of various bacterial species were isolated, segregated and enriched.

CONCLUSIONS

The phage concentration method coupled with membrane filtration immobilization of host bacteria was able to isolate and enrich the host-specific bacteriophages by several fold using a lower quantity of an environmental water sample, or other phage suspensions. Enrichment of phages from single plaques was also achieved.

SIGNIFICANCE AND IMPACT OF THE STUDY

The isolation and detection of host-specific bacteriophages from a low density bacteriophage water sample in a single step by the use of a simple and basic microbiological technique can be achieved. Enrichment of phages from low phage titre suspensions is also achieved very effectively.

Aldrin and Dieldrin Residues in Human Fat, Milk and Blood Serum Collected from Delhi

1 Aldrin and dieldrin residues were monitored in the fat, breast milk and blood serum from female residents of Delhi.

2 The average aldrin and dieldrin contents were 0.048 and 0.099 ppb in adipose tissue, 0.003 and 0.060 ppb in breast milk and 0.004 and 0.002 ppb in blood serum, respectively.

3 The older donors contained higher levels of aldrin and dieldrin in their adipose tissue.

4 Primagravidae contained more of these chemicals in their breast milk.

5 A positive correlation was observed between the aldrin concentration in adipose tissue and breast milk, and that in adipose tissue and blood serum. Similarly, a significant correlation was found between dieldrin in adipose tissue and blood serum.

6 The levels of aldrin and dieldrin were low in samples from residents of Delhi when compared to those in developed countries.

Factors predictive of patient outcome following total wrist arthrodesis

Aims

Total wrist arthrodesis (TWA) produces a spectrum of outcomes. We investigated this by reviewing 77 consecutive TWA performed for inflammatory and post-traumatic arthropathies, wrist instability and as a salvage procedure.

Patients and Methods

All operations were performed by a single surgeon using a specifically designed pre-contoured dorsally applied non-locking wrist arthrodesis plate at a single centre.

Results

Median post-operative Buck-Gramcko Lohman (BGL), Disabilities of the Arm, Shoulder and Hand and Patient Rated Wrist Evaluation scores at six years (interquartile range (IQR) 3 to 11) were 9 (IQR = 6 to 10), 19 (IQR = 7 to 45) and 13 (IQR = 1 to 31) respectively. Polyarticular inflammatory arthritis and female gender were associated with poorer patient-reported outcomes, although the effect of gender was partly explained by higher rates of inflammatory disease among women. Return to work was negatively influenced by workers’ compensation and non-inflammatory wrist pathology. There was no difference in complication rates for inflammatory and non-inflammatory indications. Take home message: Polyarticular inflammatory arthritis is a risk factor for adverse patient-reported outcomes in TWA. Furthermore, when compared with patients without inflammatory arthritis, dorsally applied pre-contoured plates can be used for wrist arthrodesis in patients with inflammatory arthritis without an increased risk of complications. Cite this article: Bone Joint J 2016;98-B:647–53.

UK Lung Cancer RCT Pilot Screening Trial: baseline findings from the screening arm provide evidence for the potential implementation of lung cancer screening

Background

Lung cancer screening using low-dose CT (LDCT) was shown to reduce lung cancer mortality by 20% in the National Lung Screening Trial.

Methods

The pilot UK Lung Cancer Screening (UKLS) is a randomised controlled trial of LDCT screening for lung cancer versus usual care. A population-based questionnaire was used to identify high-risk individuals. CT screen-detected nodules were managed by a pre-specified protocol. Cost effectiveness was modelled with reference to the National Lung Cancer Screening Trial mortality reduction.

Results

247 354 individuals aged 50–75 years were approached; 30.7% expressed an interest, 8729 (11.5%) were eligible and 4055 were randomised, 2028 into the CT arm (1994 underwent a CT). Forty-two participants (2.1%) had confirmed lung cancer, 34 (1.7%) at baseline and 8 (0.4%) at the 12-month scan. 28/42 (66.7%) had stage I disease, 36/42 (85.7%) had stage I or II disease. 35/42 (83.3%) had surgical resection. 536 subjects had nodules greater than 50 mm³ or 5 mm diameter and 41/536 were found to have lung cancer. One further cancer was detected by follow-up of nodules between 15 and 50 mm³ at 12 months. The baseline estimate for the incremental cost-effectiveness ratio of once-only CT screening, under the UKLS protocol, was £8466 per quality adjusted life year gained (CI £5542 to £12 569).

Conclusions

The UKLS pilot trial demonstrated that it is possible to detect lung cancer at an early stage and deliver potentially curative treatment in over 80% of cases. Health economic analysis suggests that the intervention would be cost effective—this needs to be confirmed using data on observed lung cancer mortality reduction.

Trial registration

ISRCTN 78513845.

Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set

Multiple studies have identified loci associated with the risk of developing prostate cancer but the associated genes are not well studied. Here we create a normal prostate tissue-specific eQTL data set and apply this data set to previously identified prostate cancer (PrCa)-risk SNPs in an effort to identify candidate target genes. The eQTL data set is constructed by the genotyping and RNA sequencing of 471 samples. We focus on 146 PrCa-risk SNPs, including all SNPs in linkage disequilibrium with each risk SNP, resulting in 100 unique risk intervals. We analyse cis-acting associations where the transcript is located within 2 Mb (±1 Mb) of the risk SNP interval. Of all SNP–gene combinations tested, 41.7% of SNPs demonstrate a significant eQTL signal after adjustment for sample histology and 14 expression principal component covariates. Of the 100 PrCa-risk intervals, 51 have a significant eQTL signal and these are associated with 88 genes. This study provides a rich resource to study biological mechanisms underlying genetic risk to PrCa.

Single nucleotide polymorphisms—SNPs—have been identified for prostate cancer but whether these SNPs alter the expression of genes is largely unknown. In this study, the authors search for genes located within 2 Mb of the SNPs and identify SNPs that influence gene expression, so called expression quantitative trait loci.

One-step continuous extrusion process for the manufacturing of solid dispersions

The purpose of this study was to evaluate the performance of synthetic magnesium aluminometasilicate (MAS) as a novel inorganic carrier in hot melt extrusion (HME) processing of indomethacin (IND) for the development of solid dispersions. A continuous extrusion process at various IND/excipient blend ratios (20%, 30% and 40%) was performed using a twin-screw extruder. Physicochemical characterization carried out by SEM, DSC, and XRPD demonstrated the presence of IND in amorphous nature within the porous network of the inorganic material for all extruded formulations. Further, AFM and FTIR studies revealed a single-phase amorphous system and intermolecular H-bonding formation. The IND/MAS extrudates showed enhanced INM dissolution rates within 100% been released within 1h. Stability studies under accelerated conditions (40°C, RH 75%) showed that MAS retained the physical stability of the amorphous solid dispersions even at high drug loadings for 12 months.

Custom Milled Zirconia Implant Supporting an Ceramic Zirconia Restoration: A Clinical Report

Dental implants constitute a well-established approach for replacement of lost teeth with titanium being the most favored material for implantation. However, titanium has its limitations in esthetically demanding cases and neither the form nor material of such implants has changed much over the past 40 years. Today, there is scientific evidence that zirconia dental implants osseointegrate well and offer many advantages over titanium implants. This report demonstrates the successful clinical use of a custom milled root analogue zirconia implant for single tooth replacement. A left maxillary first molar was removed, allowed to heal for four months and a custom-made, root-analogue, roughened zirconia was fabricated and placed. Subsequently it was restored with zirconia all ceramic crown. No complications occurred during the healing period. This successful case warrants further clinical research on zirconia custom milled implants in well controlled trials.Kathmandu Univ Med J 2013; 11(4): 328-331