Sentinel-lymph-node-based management or routine axillary clearance? Three-year outcomes of the RACS Sentinel Node Biopsy versus Axillary Clearance (SNAC) 1 trial

Purpose We sought to determine whether the benefits of sentinel-node-based management (SNBM) over routine axillary clearance (RAC) at 1 year persisted to 3 years of follow-up. Methods 1088 women with clinically node negative breast cancer were randomly assigned to SNBM versus RAC. Upper limb volume, symptoms and function were assessed at 1, 6, 12, 24 and 36 months after surgery objectively with upper limb measurements by clinicians, and subjectively by patients’ using validated self-rating scales. Results Upper limb volume increased in both groups over the first 2 years and differed between the two groups all time points beyond 1 month (P<0.02), but then plateaued. Upper limb swelling was no worse in women who had axillary clearance as two-stage procedure than in women assigned RAC as a one-stage procedure. Upper limb volume had increased 15% or more in 6.0% at 6 months and 17.6% at 3 years in those assigned RAC versus 4.2% and 11.9% in those assigned SNBM. Reductions in upper limb movement were also greater with RAC than SNBM over 6 months, but improved and were similar in the two groups from 1 to 3 years. Subjective ratings of upper limb swelling, symptoms, dysfunction, and disability over 3 years were worse in the RAC group. Upper limb swelling at 3 years was rated severe by few women (1.1%), but moderate by 9.4% in the RAC group and 2.5% in the SNBM group (P<0.001). Conclusions The benefits of SNBM over RAC persist 3 years after surgery.Royal Australasian College of Surgeon

Homologous recombination DNA repair defects in PALB2- associated breast cancers

Abstract: Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

The mechanism of action of antilymphocyte serum

162 leavesThesis (M.D.) -- University of Adelaide, Dept. of Surgery, 197

The clinical utility of assessment of the axilla in women with suspicious screen detected breast lesions in the post Z0011 era

Axillary ultrasound (AUS) and biopsy are now part of the preoperative assessment of breast cancer based on the assumption that any nodal disease is an indication for axillary clearance (AC). The Z0011 trial erodes this assumption. We applied Z0011 eligibility criteria to patients with screen detected cancers and positive axillary assessment to determine the relevance of AUS to contemporary practice. Women screened between 1/1/2012 and 30/6/2013 and assessed for lesions with highly suspicious imaging features are included. We analysed demographic and assessment data and ascertained the final histopathology with particular reference to axillary nodal status. Among 449 lesions, AUS was recorded in 303 lesions (67.5 %). 290 (96 %) were carcinomas, 30.3 % with nodal disease. AUS was abnormal in 46 (15.9 %). AUS had a sensitivity of 39.8 %, specificity 94.6 %, positive predictive value (PPV) 79.2 % and negative predictive value (NPV) 78.1 %. Axillary FNAB was positive in 27 women, suspicious in two, benign in 16 and not performed in one. In one FNA positive case, the lesion was a nodular breast primary in the axillary tail in a multifocal breast cancer. Combining AUS and FNAB, the sensitivity was 76.5 %, specificity 90.9 %, PPV 96.3 % and NPV 55.6 %. Applying the Z0011 inclusion criteria, 24 of the 27 (88.9 %) women with abnormal AUS and positive FNA were ineligible for Z0011-based management. Of three women eligible for Z0011, one proceeded to AC after SN biopsy, leaving only two women (7.4 %) who might have been considered for SN only management had it not been for the results of the axillary assessment. Among women with negative AUS, nodal metastasis was demonstrated in 21.7 %, 86.8 % of these women having only 1-2 positive nodes. Abnormal AUS and FNA preferentially identify candidates for AC. Negative AUS predicts negative or low nodal burden. Axillary assessment streamlines care.Gelareh Farshid, James Kollias, P. Grantley Gil

Silencing of the Major Salt-Dependent Isoform of Pectinesterase in Tomato Alters Fruit Softening1

Pectinesterase (PE; E.C. 3.1.1.11) is an enzyme responsible for the demethylation of galacturonyl residues in high-molecular-weight pectin and is believed to play an important role in cell wall metabolism. In this study, Pmeu1, a ubiquitously expressed PE gene, has been characterized by antisense suppression in tomato (Solanum lycopersicum). Transgenic tomato plants showed reduced PE activity levels in both green fruit and leaf tissue to around 65% and 25% of that found in wild-type plants, respectively. Pmeu1 was observed to encode a salt-dependent PE isoform that correlated with PE1 as previously described in fruit tissue. Silencing of Pmeu1 did not result in any detectable phenotype within the leaf tissue despite the gene product representing the major isoform in this tissue. In comparison, silencing in fruit resulted in an enhancement to the rate of softening during ripening. The role of PMEU1 in fruit ripening is discussed