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Author(s): Ann-Marie Patch; Elizabeth L. Christie; Dariush Etemadmoghadam; Dale W. Garsed; Joshy George; Sian Fereday; Katia Nones; Prue Cowin; Kathryn Alsop; Peter J. Bailey; Karin S. Kassahn; Felicity Newell; Michael [...]

Background Clinical specimens undergoing diagnostic molecular pathology testing are fixed in formalin due to the necessity for detailed morphological assessment. However, formalin fixation can cause major issues with molecular testing, as it causes DNA damage such as fragmentation and non-reproducible sequencing artefacts after PCR amplification. In the context of massively parallel sequencing (MPS), distinguishing true low frequency variants from sequencing artefacts remains challenging. The prevalence of formalin-induced DNA damage and its impact on molecular testing and clinical genomics remains poorly understood. Methods The Cancer 2015 study is a population-based cancer cohort used to assess the feasibility of mutational screening using massively parallel sequencing (MPS) in cancer patients from Victoria, Australia. While blocks were formalin-fixed and paraffin-embedded in different anatomical pathology laboratories, they were centrally extracted for DNA utilising the same protocol, and run through the same MPS platform (Illumina TruSeq Amplicon Cancer Panel). The sequencing artefacts in the 1-10% and the 10-25% allele frequency ranges were assessed in 488 formalin-fixed tumours from the pilot phase of the Cancer 2015 cohort. All blocks were less than 2.5 years of age (mean 93 days). Results Consistent with the signature of DNA damage due to formalin fixation, many formalin-fixed samples displayed disproportionate levels of C>T/G>A changes in the 1-10% allele frequency range. Artefacts were less apparent in the 10-25% allele frequency range. Significantly, changes were inversely correlated with coverage indicating high levels of sequencing artefacts were associated with samples with low amounts of available amplifiable template due to fragmentation. The degree of fragmentation and sequencing artefacts differed between blocks sourced from different anatomical pathology laboratories. In a limited validation of potentially actionable low frequency mutations, a NRAS G12D mutation in a melanoma was shown to be a false positive. Conclusions These findings indicate that DNA damage following formalin fixation remains a major challenge in laboratories working with MPS. Methodologies that assess, minimise or remove formalin-induced DNA damaged templates as part of MPS protocols will aid in the interpretation of genomic results leading to better patient outcomes. [ABSTRACT FROM AUTHOR]

The capacity of tumour cells to maintain continual overgrowth potential has been linked to the commandeering of normal self-renewal pathways. Using an epithelial cancer model in Drosophila melanogaster, we carried out an overexpression screen for oncogenes capable of cooperating with the loss of the epithelial apico-basal cell polarity regulator, scribbled (scrib), and identified the cell fate regulator, Abrupt, a BTB-zinc finger protein. Abrupt overexpression alone is insufficient to transform cells, but in cooperation with scrib loss of function, Abrupt promotes the formation of massive tumours in the eye/antennal disc. The steroid hormone receptor coactivator, Taiman (a homologue of SRC3/AIB1), is known to associate with Abrupt, and Taiman overexpression also drives tumour formation in cooperation with the loss of Scrib. Expression arrays and ChIP-Seq indicates that Abrupt overexpression represses a large number of genes, including steroid hormone-response genes and multiple cell fate regulators, thereby maintaining cells within an epithelial progenitor-like state. The progenitor-like state is characterised by the failure to express the conserved Eyes absent/Dachshund regulatory complex in the eye disc, and in the antennal disc by the failure to express cell fate regulators that define the temporal elaboration of the appendage along the proximo-distal axis downstream of Distalless. Loss of scrib promotes cooperation with Abrupt through impaired Hippo signalling, which is required and sufficient for cooperative overgrowth with Abrupt, and JNK (Jun kinase) signalling, which is required for tumour cell migration/invasion but not overgrowth. These results thus identify a novel cooperating oncogene, identify mammalian family members of which are also known oncogenes, and demonstrate that epithelial tumours in Drosophila can be characterised by the maintenance of a progenitor-like state. [ABSTRACT FROM AUTHOR]

Despite intensive efforts using linkage and candidate gene approaches, the genetic etiology for the majority of families with a multi-generational breast cancer predisposition is unknown. In this study, we used whole-exome sequencing of thirty-three individuals from 15 breast cancer families to identify potential predisposing genes. Our analysis identified families with heterozygous, deleterious mutations in the DNA repair genes FANCC and BLM, which are responsible for the autosomal recessive disorders Fanconi Anemia and Bloom syndrome. In total, screening of all exons in these genes in 438 breast cancer families identified three with truncating mutations in FANCC and two with truncating mutations in BLM. Additional screening of FANCC mutation hotspot exons identified one pathogenic mutation among an additional 957 breast cancer families. Importantly, none of the deleterious mutations were identified among 464 healthy controls and are not reported in the 1,000 Genomes data. Given the rarity of Fanconi Anemia and Bloom syndrome disorders among Caucasian populations, the finding of multiple deleterious mutations in these critical DNA repair genes among high-risk breast cancer families is intriguing and suggestive of a predisposing role. Our data demonstrate the utility of intra-family exome-sequencing approaches to uncover cancer predisposition genes, but highlight the major challenge of definitively validating candidates where the incidence of sporadic disease is high, germline mutations are not fully penetrant, and individual predisposition genes may only account for a tiny proportion of breast cancer families. [ABSTRACT FROM AUTHOR]

Purpose: Tubo-ovarian cancer (TOC) is a sentinel cancer for BRCA1 and BRCA2 pathogenic variants (PVs). Identification of a PV in the first member of a family at increased genetic risk (the proband) provides opportunities for cancer prevention in other at-risk family members. Although Australian testing rates are now high, PVs in patients with TOC whose diagnosis predated revised testing guidelines might have been missed. We assessed the feasibility of detecting PVs in this population to enable genetic risk reduction in relatives., Patients and Methods: In this pilot study, deceased probands were ascertained from research cohort studies, identification by a relative, and gynecologic oncology clinics. DNA was extracted from archival tissue or stored blood for panel sequencing of 10 risk-associated genes. Testing of deceased probands ascertained through clinic records was performed with a consent waiver., Results: We identified 85 PVs in 84 of 787 (11%) probands. Familial contacts of 39 of 60 (65%) deceased probands with an identified recipient (60 of 84; 71%) have received a written notification of results, with follow-up verbal contact made in 85% (33 of 39). A minority of families (n = 4) were already aware of the PV. For many (29 of 33; 88%), the genetic result provided new information and referral to a genetic service was accepted in most cases (66%; 19 of 29). Those who declined referral (4 of 29) were all male next of kin whose family member had died more than 10 years before., Conclusion: We overcame ethical and logistic challenges to demonstrate that retrospective genetic testing to identify PVs in previously untested deceased probands with TOC is feasible. Understanding reasons for a family member's decision to accept or decline a referral will be important for guiding future TRACEBACK projects., Competing Interests: Belinda CreightonEmployment: Cancer Specialists 1/84 Bridge Rd, Richmond VIC 3121 AustraliaConsulting or Advisory Role: Bristol Myers Squibb, Eisai Dinuka AriyaratneResearch Funding: AstraZeneca Elizabeth ChristieHonoraria: AstraZeneca Sian FeredayConsulting or Advisory Role: Geneseq Biosciences Pty LtdResearch Funding: AstraZeneca (Inst), AstraZeneca (Inst) Nadia TraficanteResearch Funding: AstraZeneca (Inst) Bryony ThompsonConsulting or Advisory Role: Genetic Technologies Kenneth DoigStock and Other Ownership Interests: CSL Limited Christopher LoveEmployment: Geneseq Biosciences Yeh Chen LeeConsulting or Advisory Role: GlaxoSmithKlineResearch Funding: AstraZeneca (Inst)Travel, Accommodations, Expenses: AstraZeneca Rachel WilliamsHonoraria: AstraZeneca Andrew N. StephensConsulting or Advisory Role: Invion Pty Ltd (Inst)Research Funding: Invion Pty Ltd (Inst) Adeline TanEmployment: Sonic HealthcareStock and Other Ownership Interests: Sonic Healthcare Stephen B. FoxConsulting or Advisory Role: Novartis (Inst), BMS (Inst), AstraZeneca (Inst), MSD (Inst), Pfizer (Inst), Roche (Inst)Research Funding: AstraZeneca (Inst), Amgen (Inst), Roche (Inst), BMS (Inst)Expert Testimony: AstraZeneca (Inst), MSD (Inst)Travel, Accommodations, Expenses: Ventana Medical Systems, AstraZeneca, MSD Mary-Anne YoungUncompensated Relationships: Illumina (Inst) Jane HillOther Relationship: Medicines Australia Paul A. CohenEmployment: St John of God HealthcareStock and Other Ownership Interests: Clinic IQHonoraria: AstraZenecaConsulting or Advisory Role: Clinic IQResearch Funding: ANZGOG, St John of God Foundation Penelope M. WebbResearch Funding: AstraZeneca (Inst) Michael FriedlanderHonoraria: AstraZeneca, MSD, Lilly, Takeda, Novartis, GlaxoSmithKlineConsulting or Advisory Role: AstraZeneca, MSD, AbbVie, Lilly, Takeda, Novartis, GlaxoSmithKlineSpeakers' Bureau: AstraZeneca, ACT GenomicsResearch Funding: BeiGene (Inst), AstraZeneca (Inst), Novartis (Inst)Travel, Accommodations, Expenses: AstraZeneca David BowtellHonoraria: AstraZenecaConsulting or Advisory Role: Exo TherapeuticsResearch Funding: Roche/Genentech, AstraZeneca, BeiGenePatents, Royalties, Other Intellectual Property: AstraZeneca Genentech Roche Kathryn AlsopResearch Funding: AstraZeneca (Inst)No other potential conflicts of interest were reported.

Loss of c-MYC is required for downregulation of ribosomal RNA (rRNA) gene (rDNA) transcription by RNA Polymerase I (Pol I) during granulocyte differentiation. Here, we demonstrate a robust reduction of Pol I loading onto rDNA that along with a depletion of the MYC target gene upstream binding factor (UBF) and a switch from epigenetically active to silent rDNA accompanies this MYC reduction. We hypothesized that MYC may coordinate these mechanisms via direct regulation of multiple components of the Pol I transcription apparatus. Using gene expression arrays we identified a 'regulon' of Pol I factors that are both downregulated during differentiation and reinduced in differentiated granulocytes upon activation of the MYC-ER transgene. This regulon includes the novel c-MYC target genes RRN3 and POLR1B. Although enforced MYC expression during granulocyte differentiation was sufficient to increase the number of active rRNA genes, its activation in terminally differentiated cells did not alter the active to inactive gene ratio despite increased rDNA transcription. Thus, c-MYC dynamically controls rDNA transcription during granulocytic differentiation through the orchestrated transcriptional regulation of core Pol I factors and epigenetic modulation of number of active rRNA genes.